bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonoperating room anaesthesia for elderly patients
Authors: Kim Duk Kyung
Published: June 2020

Purpose of review

The number of elderly patients receiving non-operating room anaesthesia (NORA) has substantially increased because of clinical, epidemiological, social and economic reasons. Considering the high risk of anaesthesia-related adverse events in this population, along with the limitations of NORA, more specific knowledge and skills are required.

Recent findings

Advanced age appears to be an independent risk factor for anaesthesia-related adverse events in a NORA setting, similar to the traditional operating room. As significant changes occur in the pharmacological effects of anaesthetic agents with aging, reducing dosage and carefully titrating drugs are essential. Because NORA-related injury is frequently related to airway obstruction/respiratory depression, non-invasive respiratory activity monitoring is more useful for sedation of elderly patients. Additionally, advanced age increases the risk of aspiration and cognitive complications, even during sedation.

Elderly patients may greatly benefit from the lower invasiveness and faster recovery offered by interventional procedures. However, as they represent a highly heterogeneous population with large variations in physiological reserves and comorbidities, anaesthesiologists should strive to maintain the same practice standards throughout all anaesthetizing locations. Knowledge of the unique hazards associated with NORA in elderly patients may further enhance patient safety.

Video abstract: NORA for elderly patients.mp4: http://links.lww.com/COAN/A66.
Maternal morbidity: how to reduce it
Authors: Chong Martin Shao Foong , Clayton Matthew , Lucas Nuala
Published: June 2020

Purpose of review

Internationally there has been increased interest in maternal morbidity; both as a strategy to reduce maternal deaths and also because of the significant impact on a woman's life as a result of suffering from maternal morbidity. The present review will evaluate the current knowledge of, and strategies to reduce maternal morbidity.

Recent findings

The study of maternal morbidity and how to reduce it has been hampered for many years by the lack of a standard approach to measurement and evaluation. The World Health Organization has attempted to standardize the approach to maternal morbidity with the development of a new definition that recognizes the multiple dimensions of maternal morbidity, including external factors such as socioeconomic factors. This approach will assist with a more accurate evaluation of maternal morbidity. Maternal morbidity arises from many and varied causes. Many of these are amenable to quality improvement with an associated reduction in maternal morbidity.

There have been significant advances in the understanding of maternal morbidity: incidence causes and management. Future research should aim to establish accurate rates for maternal morbidity and further develop ways for healthcare professionals, including anaesthesia care providers, to reduce it.
Expert Opinion Regarding Appropriately Timing Dermatological Surgeries in Patients With Recent Myocardial Infarctions
Authors: McLawhorn Justin M. , Imtiaz Rasheen , Jasterzbski Thomas , Stubblefield Alexander , Chen Sixia , Stasko Thomas , Collins Lindsey
Published: June 2020

BACKGROUND

There is limited data on the risk of perioperative myocardial infarctions (MIs) in patients with a recent MI who undergo dermatologic surgeries.

OBJECTIVE

Present the recommendations of dermatologic surgeons and cardiologists to determine the safety of dermatologic surgeries after a recent MI.

METHODS

An electronic survey was distributed to Mohs surgeons and cardiologists to infer the risk of major adverse cardiac events (MACE) inherent to dermatologic surgery and determine timing of dermatologic surgery in patients with a recent MI.

RESULTS

One hundred twenty Mohs surgeons and 30 cardiologists were surveyed. Ninety-seven percent of cardiologists and 87% of Mohs surgeons deemed cutaneous excisions and Mohs micrographic surgery as low-risk procedures with less than one-percent chance of MACE. Seventy-seven percent of cardiologists and 46% of Mohs surgeons stated dermatologic surgery should either not be delayed or be delayed up to 1 month after an MI. Responses between cardiologists and Mohs surgeons did not significantly differ.

CONCLUSION

A preponderance of surveyed experts believe that most dermatologic surgeries may be safely performed in patients with a history of an MI within 1 month. The decision to implement urgent dermatologic surgery in patients with a recent MI should account for all clinically significant factors.
Limits and Applications of Genomic Analysis of Circulating Tumor DNA as a Liquid Biopsy in Asymptomatic Forms of Multiple Myeloma
Authors: Manzoni Martina , Pompa Alessandra , Fabris Sonia , Pelizzoni Francesca , Ciceri Gabriella , Seia Manuela , Ziccheddu Bachisio , Bolli Niccolò , Corradini Paolo , Baldini Luca , Neri Antonino , Lionetti Marta
Published: June 2020

Supplemental Digital Content is available in the text
Severe Postmenopausal Genital Pain Treated Successfully With Prolonged Estrogen Therapy: A Case Series and Narrative Review
Authors: Goetsch Martha F.
Published: June 2020

Objective

The aim of the study was to describe a debilitating postmenopausal condition of continuous burning genital pain that remitted with prolonged estrogen focused on the vulvar vestibule.

Materials and Methods

Postmenopausal patients with constant genital pain seen by the author in a specialty vulvar health clinic comprised an institutional review board–approved descriptive case series. Examinations to localize pain used 4% lidocaine topical solution. Each patient received estradiol nightly as vestibule crème or constantly by transdermal route and was followed by serial examinations and follow-up telephone contact. Statistical tests included Student t test, Fisher exact test, and Pearson correlation coefficient.

Results

Between 2008 and 2016, 16 women presented with constant genital pain that was partly or fully extinguishable with topical vestibular lidocaine, and their pain slowly responded to prolonged vestibule-directed estradiol therapy. The mean age was 66.8 years (± 11.2). The mean pain score was 5 (range = 2–10 on a 0–10 scale). Seven (44%) characterized their pain as debilitating, and 13 (81%) had accompanying urinary symptoms. In 9 patients (56%), ovaries had been removed before natural menopause at ages 27–50 years (mean = 39), followed by minimal or no estrogen therapy. Prolonged estrogen therapy eliminated constant pain in 69% and mitigated it in 31%.

Conclusions

Information about this severe but remediable condition that is associated with lack of estrogen may guide specialists who are treating complex vulvar pain. The patients' clinical histories and therapeutic courses invite a review of estrogen receptor physiology related to urogenital pain conditions.
Endotypes in T1D: B lymphocytes and early onset
Authors: Smith Mia J. , Cambier John C. , Gottlieb Peter A.
Published: June 2020

Purpose of review

Although type 1 diabetes (T1D) is characterized by destruction of the pancreatic beta cells by self-reactive T cells, it has become increasingly evident that B cells also play a major role in disease development, likely functioning as antigen-presenting cells. Here we review the biology of islet antigen-reactive B cells and their participation in autoimmune diabetes.

Recent findings

Relative to late onset, individuals who develop T1D at an early age display increased accumulation of insulin-reactive B cells in islets. This B-cell signature is also associated with rapid progression of disease and responsiveness to B-cell depletion therapy. Also suggestive of B-cell participation in disease is loss of anergy in high-affinity insulin-reactive B cells. Importantly, loss of anergy is seen in patient's healthy first-degree relatives carrying certain T1D risk alleles, suggesting a role early in disease development.

Recent studies indicate that islet-reactive B cells may play a pathogenic role very early in T1D development in young patients, and suggest utility of therapies that target these cells.
Mass cytometry and type 1 diabetes research in the age of single-cell data science
Authors: Rahman Adeeb H. , Homann Dirk
Published: June 2020

Purpose of review

New single-cell tec. hnologies developed over the past decade have considerably reshaped the biomedical research landscape, and more recently have found their way into studies probing the pathogenesis of type 1 diabetes (T1D). In this context, the emergence of mass cytometry in 2009 revolutionized immunological research in two fundamental ways that also affect the T1D world: first, its ready embrace by the community and rapid dissemination across academic and private science centers alike established a new standard of analytical complexity for the high-dimensional proteomic stratification of single-cell populations; and second, the somewhat unexpected arrival of mass cytometry awoke the flow cytometry field from its seeming sleeping beauty stupor and precipitated substantial technological advances that by now approach a degree of analytical dimensionality comparable to mass cytometry.

Recent findings

Here, we summarize in detail how mass cytometry has thus far been harnessed for the pursuit of discovery studies in T1D science; we provide a succinct overview of other single-cell analysis platforms that already have been or soon will be integrated into various T1D investigations; and we briefly consider how effective adoption of these technologies requires an adjusted model for expense allocation, prioritization of experimental questions, division of labor, and recognition of scientific contributions.

The introduction of contemporary single-cell technologies in general, and of mass cytometry, in particular, provides important new opportunities for current and future T1D research; the necessary reconfiguration of research strategies to accommodate implementation of these technologies, however, may both broaden research endeavors by fostering genuine team science, and constrain their actual practice because of the need for considerable investments into infrastructure and technical expertise.
Plant-based diets and bone health: sorting through the evidence
Authors: Hsu Emory
Published: June 2020

Purpose of review

An increase in awareness of vegetarian and vegan (plant-based) diets has brought forth numerous studies on their effects on health. The study of nutrition-based factors affecting bone health is difficult, given the length of time before clinical effects are evident. Furthermore, population-based studies must account for strong confounding influences as effects may be because of association, not causality. Yet, it is highly plausible that dietary factors affect bone remodeling in multiple ways. Plant-based diets may alter macronutrient and micronutrient balance, may cause differences in prebiotic and probiotic effects on gut microbiota, and may subtly change the inflammatory and immune response.

Recent findings

Several recent studies have looked at plant-based nutrition and markers of bone health, using measures such as bone turnover markers, bone mineral density, or fracture rates. Although population based and cross-sectional studies can be prone to confounding effects, a majority did not show differences in bone health between vegetarians/vegans and omnivores as long as calcium and vitamin D intake were adequate. A few prospective cohort or longitudinal studies even demonstrate some benefit to a plant-based diet, but this claim remains unproven.

There is no evidence that a plant-based diet, when carefully chosen to maintain adequate calcium and vitamin D levels, has any detrimental effects on bone health. Theoretical findings suggest a long-term plant-based diet may reduce the risk of osteoporosis, through mechanisms that are currently speculative.
Advances in facial nerve management in the head and neck cancer patient
Authors: Crawford Kayva L. , Stramiello Joshua A. , Orosco Ryan K. , Greene Jacqueline J.
Published: June 2020

Purpose of review

The purpose of this review is to summarize best practices in facial nerve management for patients with head and neck cancer. In addition, we provide a review of recent literature on novel innovations and techniques in facial reanimation surgery.

Recent findings

Although recommended when tumor ablation surgery requires facial nerve sacrifice, facial reanimation procedures are not always performed. Concurrent dynamic facial reanimation with masseteric nerve transfers and cable graft repair can preserve native facial muscle function. Static suspension can provide facial support and immediate resting symmetry for patients. Eyelid weight and eye care should not be delayed, particularly in patients with trigeminal sensory deficits. Choice of neural source to innervate a gracilis-free muscle transfer for smile reanimation remains controversial; however, new techniques, such as dual innervation and multivector muscle transfer, may improve aesthetic and functional outcomes.

Management of the facial nerve in the setting of head and neck cancer presents unique challenges. When possible, simultaneous oncologic resection and facial reanimation is ideal given the open surgical field, newly dissected and electrically stimulatable facial nerve branches, as well as minimizing postoperative healing time to prevent postsurgical treatment delays. A coordinated approach to facial nerve management with a multidisciplinary surgical team may help provide optimal, comprehensive care.
Radiation Dose to the Fetus From Computed Tomography of Pregnant Patients—Development and Validation of a Web-Based Tool
Authors: Saltybaeva Natalia , Platon Alexandra , Poletti Pierre-Alexandre , Hinzpeter Ricarda , Merce Marta Sans , Alkadhi Hatem
Published: June 2020

Objective

Estimations of radiation dose absorbed by the fetus from computed tomography (CT) in pregnant patients is mandatory, but currently available methods are not feasible in clinical routine. The aims of this study were to develop and validate a tool for assessment of fetal dose from CT of pregnant patients and to develop a user-friendly web interface for fast fetal dose calculations.

Methods

In the first study part, 750 Monte Carlo (MC) simulations were performed on phantoms representing pregnant patients at various gestational stages. The MC code simulating vendor-independent dose distributions was validated against CT dose index (CTDI) measurements performed on CT scanners of 2 vendors. The volume CTDI–normalized fetal dose values from MC simulations were used for developing the computational algorithm enabling fetal dose assessments from CT of various body regions at different exposure settings. In the institutional review board–approved second part, the algorithm was validated against patient-specific MC simulations performed on CT data of 29 pregnant patients (gestational ages 8–35 weeks) who underwent CT. Furthermore, the tool was compared with a commercially available software. A user-friendly web-based interface for fetal dose calculations was created.

Results

Weighted CTDI values obtained from MC simulations were in excellent agreement with measurements performed on the 2 CT systems (average error, 4%). The median fetal dose from abdominal CT in pregnant patients was 2.7 mGy, showing moderate correlation with maternal perimeter (r = 0.69). The algorithm provided accurate estimates of fetal doses (average error, 11%), being more accurate than the commercially available tool. The web-based interface (www.fetaldose.org) enabling vendor-independent calculations of fetal doses from CT requires the input of gestational age, volume CTDI, tube voltage, and scan region.

Conclusions

A tool for fetal dose assessments from CT of pregnant patients was developed and validated being freely available on a user-friendly web interface.
Surgical Decision-Making in Microvascular Reconstruction of Composite Scalp and Skull Defects
Authors: Vargo James D. , Przylecki Wojciech , Andrews Brian T.
Published: June 2020

Objectives:

Microvascular reconstruction of composite scalp and skull defects requires careful planning of both cranial bone and soft-tissue coverage. The current body of literature has yet to identify a “best practice” approach to achieve these goals.

Methods:

A retrospective chart review was performed. Patients with composite defects who underwent combined microvascular surgery of the scalp and skull were included over a 6-year period. Reconstructions were classified by: microvascular flap, cranioplasty, timing of cranioplasty (primary or delayed), and exposure to radiation.

Results:

Forty-five microvascular flaps were performed for 36 patients. Fasciocutaneous flaps were more likely to experience complications than other microvascular flaps (50.0% versus 8.6%, P = 0.008). Forty of the 50 patients (80%) underwent cranioplasty, including 19 autogenous and 21 alloplastic reconstructions. There were 8 total complications: partial flap loss with implant exposure (n = 5), cranioplasty infection (n = 2), and wound dehiscence (n = 1). Alloplastic implants experienced more frequent complications than autologous reconstructions (33.3% versus 5.3%, P = 0.046). Titanium implants demonstrated the higher rates of complications than other groups (P = 0.014). Titanium implants also had more complications relative to poly-ether-ether-ketone implants (60.0% versus 9.1%, P = 0.024). Immediate alloplastic cranioplasty was associated with a significant increase in complications relative to autogenous reconstruction (54.5% versus 5.5%, P = 0.027), and no significant difference in the delayed group (10% versus 0%, P = 0.740).

Conclusion:

According to authors’ knowledge, myofascial flaps yield the lowest complication rate and when possible, autologous cranioplasty is preferred. When defects are too large to accommodate autogenous bone, the authors prefer delayed prefabricated poly-ether-ether-ketone implant reconstruction.
Analysis of Frontal Sinus Fracture Management and Resource Utilization
Authors: Firouzbakht Peter K. , Mohiuddin Ismail S. , Varman Rahul M. , Heinrich Matthew P. , Saa Lisa , Cordero Joehassin
Published: June 2020

Frontal sinus fractures require a large amount of force and often occur in the context of a major trauma. Many patients with these fractures are assessed in an emergent setting where stabilization takes precedence. Delayed diagnosis and treatment of a sinus fracture can result in life-threatening conditions, such as a cerebrospinal fluid (CSF) leak. A number of different treatment algorithms have been proposed, highlighting the complexity of frontal sinus fracture management. The goal of this study is to determine how patients with frontal sinus fractures were treated at Texas Tech University Health Sciences Center and what complications arose as a result of the fracture and subsequent management strategy. Over 9 years, there were 69 reported cases. A total of 63 of these occurred in males (91.3%) versus 6 (8.7%) in females. The majority occurred after a motor vehicle collision (MVC) or a motorcycle collision (MCC). A total of 51 cases were unilateral fractures and 18 were bilateral fractures. Five patients (7.2%) had CSF leakage and 64 (92.8%) did not have CSF leakage. One patient with CSF leakage (20.0%) was managed operatively. Of the 64 patients without CSF leakage, 4 (6.3%) were managed operatively. All operative patients were managed by cranialization. Complications included vision changes, facial pressure, anosmia, facial paresthesia, pneumocephalus, and mucus retention cysts. Vision changes were the most common complication. There did not appear to be any significant difference in complications between the CSF leakage groups, indicating that non-operative management remains a viable option in the management of frontal sinus fractures.
What do editors do? Understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs
Authors: Heraud-Farlow Jacki E. , Walkley Carl R.
Published: June 2020

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. Catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2, A-to-I editing occurs at approximately 50 000–150 000 sites in mice and into the millions of sites in humans. The vast majority of A-to-I editing occurs in repetitive elements, accounting for the discrepancy in total numbers of sites between species. The species-conserved primary role of editing by ADAR1 in mammals is to suppress innate immune activation by unedited cell-derived endogenous RNA. In the absence of editing, inverted paired sequences, such as
Alu
elements, are thought to form stable double-stranded RNA (dsRNA) structures which trigger activation of dsRNA sensors, such as MDA5. A small subset of editing sites are within coding sequences and are evolutionarily conserved across metazoans. Editing by ADAR2 has been demonstrated to be physiologically important for recoding of neurotransmitter receptors in the brain. Furthermore, changes in RNA editing are associated with various pathological states, from the severe autoimmune disease Aicardi-Goutières syndrome, to various neurodevelopmental and psychiatric conditions and cancer. However, does detection of an editing site imply functional importance? Genetic studies in humans and genetically modified mouse models together with evolutionary genomics have begun to clarify the roles of A-to-I editing
in vivo
. Furthermore, recent developments suggest there may be the potential for distinct functions of editing during pathological conditions such as cancer.
The contribution of non-coding regulatory elements to cardiovascular disease
Authors: Villar Diego , Frost Stephanie , Deloukas Panos , Tinker Andrew
Published: June 2020

Cardiovascular disease collectively accounts for a quarter of deaths worldwide. Genome-wide association studies across a range of cardiovascular traits and pathologies have highlighted the prevalence of common non-coding genetic variants within candidate loci. Here, we review genetic, epigenomic and molecular approaches to investigate the contribution of non-coding regulatory elements in cardiovascular biology. We then discuss recent insights on the emerging role of non-coding variation in predisposition to cardiovascular disease, with a focus on novel mechanistic examples from functional genomics studies. Lastly, we consider the clinical significance of these findings at present, and some of the current challenges facing the field.
Nicotinamide Riboside supplementation does not alter whole-body or skeletal muscle metabolic responses to a single bout of endurance exercise
Authors: Stocks Ben , Ashcroft Stephen P. , Joanisse Sophie , Elhassan Yasir S. , Lavery Gareth G. , Dansereau Linda C. , Philp Ashleigh M. , Wallis Gareth A. , Philp Andrew
Published: June 2020

Oral supplementation of the NAD+precursor Nicotinamide Riboside (NR) has been reported to increase Sirtuin (SIRT) signalling, mitochondrial biogenesis and endurance capacity in rodent skeletal muscle. However, whether NR supplementation can elicit a similar response in human skeletal muscle is unclear. This study aimed to assess the effect of 7-day NR supplementation on exercise-induced transduction and transcriptional responses in skeletal muscle of young, healthy, recreationally active human volunteers. In a double-blinded, randomised, counter-balanced, crossover design, eight male participants (age: 23 ± 4 years, VO2peak: 46.5 ± 4.4 mL·kg-1·min-1) received one week of NR or cellulose placebo (PLA) supplementation (1000 mg·d-1) before performing one hour of cycling at 60% Wmax. Muscle biopsies were collected prior to supplementation and pre-, immediately and three-hours post-exercise from the medial vastus lateralis, whilst venous blood samples were collected throughout the trial. Global acetylation, auto-PARylation of PARP1, acetylation of p53Lys382and MnSODLys122were unaffected by NR supplementation or exercise. Exercise led to an increase in AMPKThr172(1.6-fold), and ACCSer79(4-fold) phosphorylation, in addition to an increase in PGC-1α (∼5-fold) and PDK4 (∼10-fold) mRNA expression, however NR had no additional effect on this response. There was also no effect of NR supplementation on substrate utilisation at rest or during exercise or on skeletal muscle mitochondrial respiration. Finally, NR supplementation blunted the exercise induced activation of skeletal muscle NNMT mRNA expression, but had no effect on mRNA expression of NMRK1, NAMPT or NMNAT1, which were not significantly affected by NR supplementation or exercise. In summary, one week of NR supplementation does not augment skeletal muscle signal transduction pathways implicated in mitochondrial adaptation to endurance exercise.
Efficient Cas9 multiplex editing using unspaced gRNA arrays engineering in aPotato virus Xvector
Authors: Uranga Mireia , Aragonés Verónica , Selma Sara , Vázquez-Vilar Marta , Orzáez Diego , Daròs José-Antonio
Published: June 2020

Systems based on the clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated proteins (Cas) have revolutionized genome editing in many organisms, including plants. Most CRISPR-Cas strategies in plants rely on genetic transformation usingAgrobacterium tumefaciensto supply the gene editing reagents, such as the Cas nucleases or the guide RNA (gRNA). While the Cas nucleases are constant elements in editing approaches, gRNAs are target-specific and a screening process is usually required to identify those most effective. Plant virus-derived vectors are an alternative for the fast and efficient delivery of gRNAs into adult plants, due to the virus capacity for genome amplification and systemic movement, a strategy known as virus-induced genome editing (VIGE). In this work, we engineeredPotato virus X(PVX) to build a vector able to easily express one or more gRNAs in adult solanaceous plants. Using the PVX-based vector,Nicotiana benthamianagenes were efficiently targeted, producing nearly 80% indels in a transformed line that constitutively expressedStreptococcus pyogenesCas9. Interestingly, results showed that the PVX vector allows expression of arrays of unspaced gRNAs achieving highly efficient multiplex editing in a few days in adult plant tissues. We also demonstrate that genome modifications are inherited in plants regenerated from infected tissues. In sum, the new PVX VIGE vector allows easy, fast and efficient expression of gRNAs arrays for multiplex CRISPR-Cas genome editing and will be a useful tool for functional gene analysis and precision breeding across diverse plant species, particularly in important crops of the familySolanaceae.
Phasic activation of dorsal raphe serotonergic neurons increases pupil-linked arousal
Authors: Cazettes Fanny , Reato Davide , Morais João P. , Renart Alfonso , Mainen Zachary F.
Published: June 2020

Variations in pupil size under constant luminance are closely coupled to changes in arousal state [1–5]. It is assumed that such fluctuations are primarily controlled by the noradrenergic system [6–9]. Phasic activity of noradrenergic axons precedes pupil dilations associated with rapid changes in arousal [7,9], and is believed to be driven by unexpected uncertainty [1,10–16]. However, the role of other modulatory pathways in the control of pupil-linked arousal has not been as thoroughly investigated, but evidence suggests that noradrenaline may not be alone [7,17,18]. Administration of serotonergic drugs seems to affect pupil size [19–23], but these effects have not been investigated in detail. Here, we show that transient serotonin (5-HT) activation, like noradrenaline, causes pupil-size changes. We used phasic optogenetic activation of 5-HT neurons in the dorsal raphe nucleus (DRN) in head-fixed mice locomoting in a foraging task. 5-HT-driven modulations of pupil size were maintained throughout the photostimulation period and sustained for several seconds after the end of the stimulation. The activation of 5-HT neurons increased pupil size additively with locomotor speed, suggesting that 5-HT transients affect pupil-linked arousal independently from locomotor states. We found that the effect of 5-HT on pupil size depended on the level of environmental uncertainty, consistent with the idea that 5-HT may report a salience or surprise signal [24]. Together, these results challenge the classic view of the neuromodulatory control of pupil-linked arousal, revealing a tight relationship between the activation of 5-HT neurons and changes in pupil size.
Healthy aging interventions reduce non-coding repetitive element transcripts
Authors: Wahl Devin , Cavalier Alyssa N. , Smith Meghan , Seals Douglas R. , LaRocca Thomas J.
Published: June 2020

Transcripts from non-coding repetitive elements (RE) in the genome may be involved in aging. However, they are often ignored in transcriptome studies on healthspan and lifespan, and their role in healthy aging interventions has not been characterized. Here, we analyze RE in RNA-seq datasets from mice subjected to robust healthspan- and lifespan-increasing interventions including calorie restriction, rapamycin, acarbose, 17-α-estradiol, and Protandim. We also examine RE transcripts in long-lived transgenic mice, and in mice subjected to high-fat diet, and we use RNA-seq to investigate the influence of aerobic exercise on RE transcripts with aging in humans. We find that: 1) healthy aging interventions/behaviors globally reduce RE transcripts, whereas aging and age-accelerating treatments increase RE expression; and 2) reduced RE expression with healthy aging interventions is associated with biological/physiological processes mechanistically linked with aging. Thus, RE transcript dysregulation and suppression are likely novel mechanisms underlying aging and healthy aging interventions, respectively.
Effects of H2A.B incorporation on nucleosome structures and dynamics
Authors: Kohestani Havva , Wereszczynski Jeff
Published: June 2020

The H2A.B histone variant is an epigenetic regulator involved in transcriptional upregulation, DNA synthesis, and splicing that functions by replacing the canonical H2A histone in the nucleosome core particle. Introduction of H2A.B results in less compact nucleosome states with increased DNA unwinding and accessibility at the nucleosomal entry and exit sites. Despite being well characterized experimentally, the molecular mechanisms by which H2A.B incorporation alters nucleosome stability and dynamics remain poorly understood. To study the molecular mechanisms of H2A.B, we have performed a series of conventional and enhanced sampling molecular dynamics simulation of H2A.B and canonical H2A containing nucleosomes. Results of conventional simulations show that H2A.B weakens protein/protein and protein/DNA interactions at specific locations throughout the nucleosome. These weakened interactions result in significantly more DNA opening from both the entry and exit sites in enhanced sampling simulations. Furthermore, free energy profiles show that H2A.B containing nucleosomes have significantly broader free wells, and that H2A.B allows for sampling of states with increased DNA breathing, which are shown to be stable on the hundreds of nanoseconds timescale with further conventional simulations. Together, our results show the molecular mechanisms by which H2A.B creates less compacted nucleosome states as a means of increasing genetic accessibility and gene transcription.

SIGNIFICANCE

Nature has evolved a plethora of mechanisms for altering the physical and chemical properties of chromatin fibers as a means of controlling gene expression. These epigenetic processes may serve to increase or decrease DNA accessibility, manage the recruitment of remodeling factors, or tune the stability of the nucleosomes that make up chromatin. Here, we have used both conventional and enhanced sampling molecular dynamics simulations to understand how one of these epigenetic mechanisms, the substitution of canonical H2A proteins with the H2A.B variant, exerts its influence on the structures and dynamics of the nucleosome. Results show at the molecular level how this variant alters inter-molecular interactions to increase DNA accessibility as a means of increasing genetic accessibility and gene transcription.
Evaluation of Seed or Grain Storage Technologies from Indian Farming Societies Using A Hybrid and Multi-Attribute Approach
Authors: Maity Aniruddha , Mukherjee Anirban , Ray Mrinmoy , Pramanik Pragati , Parmar Sanjay S , Manjunatha N , Kumar Sanjay , Wasnik Vinod Kumar , Shubha Kumari
Published: June 2020

Soon after the introduction of green revolution, a parallel increment in percent food grain production and losses has been reported in India, which impedes the mission of achieving food security in India. In parts, among the major causes of these losses are the reluctance among farmers, especially of small holding, towards adoption of scientific storage methods/technologies and inability of the national agencies to meet the challenges imposed by the supply of surplus grains to them by the farmers. Although sets of traditional and improved grain storage technologies exist among Indian farming communities, a controversial account about their effectiveness and performance is available in the literature which negatively impacts the endeavour of bringing rapid developmental in the farming society. In a developing nation like India, a large section of farmers is often either unaware of the modern technologies or cannot logistically access them. They often rely on the traditional or semi-modern technologies without having a comprehensive account of the benefit and economic feasibility of the modern technologies. This impedes the vision of rapid development of the farmers and the process of infusing emerging technologies in the society. In order to develop an informative argument about the performance of the existing technologies, a nearly comprehensive study has been undertaken to compare the different traditional and improved grain storage structures used by Indian farmers. Both qualitative and quantitative parameters were compared individually and simultaneously to achieve their effect on performance individually and in unison. Another objective of the study was to test the applicability of hybrid and multi-attribute approach, based on Analytic Hierarchy Process (AHP) and the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) for the performance evaluation and ranking of the attributes and structures. Finally, based on analysis and ideas borrowed out of literature a set of theoretical and conceptual guidelines to assist improvement in these structures was brought in. The study will help understand the status of grain storage technologies in the developing, resource-poor society and also increase the adoption and access of farmers to better post-harvest seed storage technologies.
Neighborhood income and physical distancing during the COVID-19 pandemic in the U.S.
Authors: Jay Jonathan , Bor Jacob , Nsoesie Elaine , Lipson Sarah Ketchen , Jones David K. , Galea Sandro , Raifman Julia
Published: June 2020

Introduction

Although physical distancing has been the primary strategy to reduce the spread of COVID-19 in the U.S., people’s ability to distance may vary by socioeconomic characteristics, leading to higher transmission risk in low-income neighborhoods.

Methods

We used mobility data from a large, anonymized sample of smartphone users to assess the relationship between neighborhood median household income and physical distancing during the COVID-19 epidemic. We assessed changes in several behaviors including: spending the day entirely at home; working outside the home; and visits to supermarkets, parks, hospitals, and other locations. We also assessed differences in effects of state policies on physical distancing across neighborhood income levels.

Results

We found a strong gradient between neighborhood income and physical distancing. Compared to January and February 2020, the proportion of individuals spending the day entirely at home in April 2020 increased by 10.9 percentage points in low-income neighborhoods and by 27.1 percentage points in high-income neighborhoods. During April 2020, people in low-income neighborhoods were more likely to work outside the home, compared to people in higher-income neighborhoods, but not more likely to visit non-work locations. State physical distancing orders were associated with a 1.5 percentage-point increase (95% CI [0.9, 2.1], p < 0.001) in staying home in low-income neighborhoods and a 2.4 percentage point increase (95% CI [1.4, 3.4], p < 0.001) in high-income neighborhoods.

Discussion

People in lower-income neighborhoods have faced barriers to physical distancing, particularly the need to work outside the home. State physical distancing policies have not mitigated these disparities.
A new subclass of exoribonuclease resistant RNA found in multipleFlaviviridaegenera
Authors: Szucs Matthew J. , Nichols Parker J. , Jones Rachel A. , Vicens Quentin , Kieft Jeffrey S.
Published: June 2020

Viruses have developed innovative strategies to exploit the cellular machinery and overcome the host antiviral defenses, often using specifically structured RNA elements. Examples are found in flaviviruses; during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5’ to 3’ exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease resistant RNA structure (xrRNA) located in the viral genome’s 3’untranslated region (UTR). Although known to exist in severalFlaviviridaegenera the full distribution and diversity of xRNAs in this virus family was unknown. Using the recent high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNA in thePegivirus, Pestivirus, and Hepacivirusgenera. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Our findings thus require adjustments of previous xrRNA classification schemes and expand on the previously known distribution of the xrRNA inFlaviviridae, indicating their widespread distribution and illustrating their importance.

IMPORTANCE

TheFlaviviridaecomprise one of the largest families of positive sense single stranded (+ssRNA) and it is divided into theFlavivirus,Pestivirus,Pegivirus, andHepacivirusgenera. The genusFlaviviruscontains many medically relevant viruses such as Zika Virus, Dengue Virus, and Powassan Virus. In these, a part of the virus’s RNA twists up into a very special three-dimensional shape called an xrRNA that blocks the ability of the cell to “chew up” the viral RNA. Hence, part of the virus’ RNA remains intact, and this protected part is important for viral infection. This was known to occur in Flaviviruses but whether it existed in the other members of the family was not known. In this study, we not only identified a new subclass of xrRNA found in Flavivirus but also in the remaining three genera. The fact that this process of viral RNA maturation exists throughout the entireFlaviviridaefamily makes it clear that this is an important but underappreciated part of the infection strategy of these diverse human pathogens.
DeepFRET: Rapid and automated single molecule FRET data classification using deep learning
Authors: Thomsen Johannes , Sletfjerding Magnus B. , Stella Stefano , Paul Bijoya , Jensen Simon Bo , Malle Mette G. , Montoya Guillermo , Petersen Troels C. , Hatzakis Nikos S.
Published: June 2020

Single molecule Förster Resonance energy transfer (smFRET) is a mature and adaptable method for studying the structure of biomolecules and integrating their dynamics into structural biology. The development of high throughput methodologies and the growth of commercial instrumentation have outpaced the development of rapid, standardized, and fully automated methodologies to objectively analyze the wealth of produced data. Here we present DeepFRET, an automated standalone solution based on deep learning, where the only crucial human intervention in transiting from raw microscope images to histogram of biomolecule behavior, is a user-adjustable quality threshold. Integrating all standard features of smFRET analysis, DeepFRET will consequently output common kinetic information metrics for biomolecules. We validated the utility of DeepFRET by performing quantitative analysis on simulated, ground truth, data and real smFRET data. The accuracy of classification by DeepFRET outperformed human operators and current commonly used hard threshold and reached >95% precision accuracy only requiring a fraction of the time (<1% as compared to human operators) on ground truth data. Its flawless and rapid operation on real data demonstrates its wide applicability. This level of classification was achieved without any preprocessing or parameter setting by human operators, demonstrating DeepFRET’s capacity to objectively quantify biomolecular dynamics. The provided a standalone executable based on open source code capitalises on the widespread adaptation of machine learning and may contribute to the effort of benchmarking smFRET for structural biology insights.
Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation
Authors: Henderson Rory , Edwards Robert J , Mansouri Katayoun , Janowska Katarzyna , Stalls Victoria , Kopp Megan , Haynes Barton F. , Acharya Priyamvada
Published: June 2020

The glycan shield of the beta-coronavirus (β-CoV) Spike (S) glycoprotein provides protection from host immune responses, acting as a steric block to potentially neutralizing antibody responses. The conformationally dynamic S-protein is the primary immunogenic target of vaccine design owing to its role in host-cell fusion, displaying multiple receptor binding domain (RBD) ‘up’ and ‘down’ state configurations. Here, we investigated the potential for RBD adjacent, N-terminal domain (NTD) glycans to influence the conformational equilibrium of these RBD states. Using a combination of antigenic screens and high-resolution cryo-EM structure determination, we show that an N-glycan deletion at position 234 results in a dramatically reduced population of the ‘up’ state RBD position. Conversely, glycan deletion at position N165 results in a discernable increase in ‘up’ state RBDs. This indicates the glycan shield acts not only as a passive hinderance to antibody meditated immunity but also as a conformational control element. Together, our results demonstrate this highly dynamic conformational machine is responsive to glycan modification with implications in viral escape and vaccine design.
The nucleus is a quality control center for non-imported mitochondrial proteins
Authors: Shakya Viplendra P.S. , Barbeau William A. , Xiao Tianyao , Knutson Christina S. , Hughes Adam L.
Published: June 2020

Mitochondrial import deficiency causes cellular stress due to the accumulation of non-imported mitochondrial precursor proteins. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we catalog the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment inS. cerevisiae. We find that a number of non-imported mitochondrial proteins localize to the nucleus, where they are eliminated by proteasome-based nuclear protein quality control. Recognition of mitochondrial precursors by the nuclear quality control machinery requires the presence of an N-terminal mitochondrial targeting sequence (MTS), and impaired breakdown of precursors leads to their buildup in nuclear-associated foci. These results identify the nucleus as a key destination for the disposal of non-imported mitochondrial precursors.
Role of Anti-SARS-CoV-2 antibodies in different cohorts: Can they provide clues for appropriate patient triaging?
Authors: Mutnal Manohar B. , Mohammad Amin A. , Arroliga Alejandro C. , Hua Yinan , Wang Liping , Koss William , Rao Arundhati
Published: June 2020

The emergence of coronavirus disease 2019 (COVID-19) has become a major global health crisis. Currently, diagnosis is based on molecular techniques, which detect the viral nucleic acids when present at detectable levels. The serum IgG response againstSARS-CoV-2was examined by using an ELISA-based assay. Serum samples, along with nasopharyngeal specimens were collected from various cohorts and analyzed by ELISA and rRT-PCR, respectively. A total of 167 serum samples were tested for serum IgG antibodies againstSARS-CoV-2in outpatient cohorts, 15 (8.9%) were positive by rRT-PCR and the remaining 152 (91%) were negative. We used these data to generate two different assay cutoffs for serum IgG assay and investigated percent concordance with rRT-PCR test results. The emergency department data revealed, out of 151 nasopharyngeal swabs, 4 (2.6%) were positive by rRT-PCR and 18 (11.9%) were positive for serum IgG assay. Among the 18 patients that were positive for serum IgG, 13 (72.2%) exhibited 1-3 symptoms of COVID-19 and 5 (27.7%) patients did not present with any COVID-19 related symptoms, per CDC criteria. All 4 (100%) patients that were positive by rRT-PCR had symptoms of COVID-19 disease. A longitudinal study from the inpatient population suggested there was a sharp increase in the serum IgG titers in 5 patients, a moderate increase in 1 patient and a plateau in 3 patients. Sero-prevalence of COVID-19 disease in pre-procedure patients was 5.5%. Our findings suggest serological tests can be used for appropriate patient triaging when performed as an adjunct to existing molecular testing.
Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance
Authors: Padhi Aditya K. , Shukla Rohit , Tripathi Timir
Published: June 2020

SARS-CoV-2 is rapidly evolving with the continuous emergence of new mutations. There is no specific antiviral therapy for COVID-19, and the use of Remdesivir for treating COVID-19 will likely continue before clinical trials are completed. Due to the lengthening pandemic and evolving nature of the virus, predicting potential residues prone to mutations is crucial for the management of Remdesivir resistance. We used a rational ligand-based interface design complemented with mutational mapping to generate a total of 100,000 mutations and provide insight into the functional outcome of mutations in the Remdesivir-binding site in nsp12. After designing 56 residues in the Remdesivir binding site of nsp12, the designs retained 96-98% sequence identity, which suggests that SARS-CoV-2 attains resistance and develops further infectivity with very few mutations in the nsp12. We also identified affinity-attenuating Remdesivir binding designs of nsp12. Several mutants acquired decreased binding affinity with Remdesivir, which suggested drug resistance. These hotspot residues had a higher probability of undergoing selective mutations in the future to develop Remdesivir and related drug-based resistance. A comparison of 21 nsp12 Remdesivir-bound designs to the 13 EIDD-2801-bound nsp12 designs suggested that EIDD-2801 would be more effective in preventing the emergence of resistant mutations and against Remdesivir-resistance strains due to the restricted mutational landscape. Combined with the availability of more genomic data, our information on mutation repertoires is critical to guide scientists to rational structure-based drug discovery. Knowledge of the potential residues prone to mutation improves our understanding and management of drug resistance and disease pathogenesis.