bluuebunny/crossref_metadata_2025 huggingface dataset:
Pharmacist perceptions of and views on postgraduate year 3 training
Authors: Dang Yen H , To-Lui Kim P
Published: July 2020

Purpose

To determine the attitudes and perceptions of pharmacy residency program participants regarding proposed expansion of postgraduate year 3 (PGY3) residency training opportunities.

Methods

An online questionnaire was emailed to all directors of ASHP-accredited residency programs with a request to distribute the survey among program participants, including residents, preceptors, coordinators, and other pharmacists working with residents. Survey questions assessed participants’ views and attitudes about PGY3 programs vs other avenues of career advancement, including potential benefits and limitations, program structure, and ramifications for the profession.

Results

Eight hundred forty-five individuals participated in the survey, for a 22.47% response rate. Only 288 pharmacists (34.4%) were familiar with the PGY3 residency training concept. Perceived benefits of PGY3 training, by percentage of respondents citing them, included job specialization (34.41%), an additional year of training (19.93%), and obtaining research skills (5.44%). The main perceived limiting factors included personal finances (21.62%), lack of justification for PGY3 training (13.83%), and time commitments (12.94%). As alternatives to PGY3 training for career advancement, board certifications (49.5%), scholarly activity (19.8%), and leadership in pharmacy organizations (19.2%) were the 3 highest-rated areas. A majority of respondents were opposed to ASHP standardization of PGY3 residency programs (74.3%) and/or had negative preconceptions of the potential impact of expanded PGY3 training initiatives on the job market (80.94%).

Conclusion

Overall, surveyed pharmacy residency program participants were opposed to the concept of expanded PGY3 training initiatives and indicated their view that PGY3 training offers limited benefits in terms of professional development. Participants favored on-the-job training and other avenues of career advancement over PGY3 residency training.
A Rare Pelvic “Mass-Querader”: Acute Urinary Retention Secondary to Hematocolpos in a Preadolescent Patient
Authors: Bezjian Wallace Laurie , Wallace Patrick , Herness Joel
Published: July 2020

We report a case of acute urinary retention in an adolescent female secondary to hematocolpos. A 13-year-old female presented to the emergency department with acute urinary retention and suprapubic abdominal pain for 24 hours. She denied menstruation or sexual history. Bedside bladder ultrasound scan revealed 1.2 L of retained urine and a Foley catheter was placed. A formal renal ultrasound detected a debris-filled structure in the abdomino-pelvic cavity. Follow-up computed tomography of the abdomen and pelvis revealed an 8.5 cm × 9.3 cm × 12.1 cm mass-like structure in the pelvis. No formal pelvic exam was completed and the patient was taken to the operating room for exploratory laparotomy due to concern for large pelvic mass versus tubo-ovarian abscess. However, upon entering the abdominal cavity, no mass was found. At that point, an external genital exam was performed, revealing an imperforate hymen. Hymenotomy resulted in the evacuation of 2.5 L of clotted blood from the vagina and uterus. Hematocolpos resulting in acute urinary retention is exceedingly rare; however, it is an important differential diagnosis that can be ruled in or out by physical exam findings. Although it may be uncomfortable for adolescent patients and physicians, external genital exams should be conducted in young females with acute urinary retention and amenorrhea to evaluate for imperforate hymen. This can ensure appropriate treatment and avoidance of unnecessary invasive procedures.
Children’s objective sleep assessed with wrist-based accelerometers: strong heritability of objective quantity and quality unique from parent-reported sleep
Authors: Breitenstein Reagan S , Doane Leah D , Lemery-Chalfant Kathryn
Published: July 2020

Children’s poor sleep is a risk factor for lower cognitive functioning and internalizing and externalizing problems. It is unclear whether genetic and environmental influences vary based on sleep assessment and no studies to date have examined genetic and environmental contributions to links between multiple objective and subjective sleep indicators. Further, nearly all heritability studies rely on subjective parent- or self-report measures of sleep duration and problems. Given these gaps in the literature, we (1) modeled genetic and environmental influences on multiple objective and subjective sleep indicators and (2) estimated genetic and environmental covariances between objective and subjective sleep indicators in middle childhood. Participants were 608 twin children (MZ = 178, same-sex DZ = 234, opposite-sex DZ = 190) assessed at 8 years of age (SD = 0.63 years). Objective nighttime sleep duration, efficiency, sleep onset latency (SOL), midpoint time, and midpoint variability were collected from actigraph watches worn for 7 nights (Mnights = 6.83, SD = 0.62). Children’s nighttime sleep duration and daytime sleepiness were assessed via parent report. Findings suggested high additive genetic influence on objective sleep quantity and quality, whereas objective SOL, sleep midpoint time, midpoint variability, parent-reported sleep duration, and daytime sleepiness were largely influenced by the shared environment. Common genetic factors explained associations between objective sleep quantity and quality, but genetics did not account for links with parent-reported sleep duration, midpoint time, or midpoint variability. Thus, objective and parent-reported assessments of children’s sleep have unique genetic etiologies and should not be used interchangeably in the sleep literature.
Impact of Sarcopenia on Degenerative Lumbar Spondylosis
Authors: Gibbons Denys , Ahern Daniel P. , Curley Antoinette E. , Kepler Christopher K. , Butler Joseph S.
Published: July 2020

Sarcopenia is characterized by progressive age-related and systematic loss of skeletal muscle mass, strength, and function. It was classified as an independent disease in 2016; thus, there is a sparsity of research on the association of sarcopenia with lower back pain and spinal diseases. Its prevalence is around 10% worldwide and it has been shown to be detrimental to quality of life in the elderly. Sarcopenia can be clinically identified by assessing muscle mass and physical performance measurements to show reduced strength (eg, grip strength chair rise and knee extensions) or function (eg, walking speed or distance). Radiographic imaging techniques such as computed tomography, ultrasound, or magnetic resonance imaging help diagnose sarcopenia in the lumbar spine by measuring either the cross-sectional area or the fatty infiltrate of the lumbar musculature. The presence of sarcopenia in patients preoperatively may lead to worse postoperative outcomes. Research in the treatment options for sarcopenia presurgery is still in its infancy but exercise (both aerobic and resistance exercise have been found to slow down the rate of decline in muscle mass and strength with aging) and nutrition have been utilized to varying success and show great promise in the future.
Cognitive Function of Recipients of Primary or Secondary Defibrillator Therapy
Authors: Kim JinShil , Park Jin-Kyu , Shin Mi-Seung , Choi Jiin , Kim Sun Hwa , Park Yae Min , On Young Keun , Choi Nayeon , Heo Seongkum
Published: July 2020

Background

The extent to which cognitive function differs between patients who receive implantable cardioverter-defibrillator (ICD) therapy and patients with heart failure (HF) who do not receive ICD therapy remains to be elucidated.

Objectives

The aim of this study was to compare the cognitive function between patients with primary or secondary ICDs and patients with HF without an ICD.

Methods

This descriptive, comparative study included 116 patients who received ICDs and 74 patients with HF who did not receive ICDs. Patients underwent neuropsychological assessment for general cognition, memory, and executive function.

Results

Immediate recall memory loss (18.9%) occurred more often in patients with HF without an ICD than in patients with primary (3.1%) and secondary (7.1%) ICDs (P = .018). After adjusting for age and education, delayed recall memory of patients with HF without ICDs was significantly worse than that of patients with primary ICDs (4.0 vs 6.5; P < .001), whereas delayed recall memory of patients with primary ICDs was better than that of patients with secondary ICDs (6.0 vs 6.5; P = .006). Executive function of patients with HF without ICDs was significantly worse than that of patients with primary (35 vs 58 seconds; P < .001) and secondary (28 vs 58 seconds; P = .0012) ICDs.

Conclusions

Patients with ICDs, regardless of primary or secondary indication, had less impairment of memory and executive function than patients with HF without ICDs, implying that ICD therapy did not interfere with cognitive performance. Cognitive screening as a part of routine care could be helpful for identifying impairment and implementing early cognitive training, especially in patients with HF.
Association of Recognized and Unrecognized Myocardial Infarction With Depressive and Anxiety Disorders in 125,988 Individuals: A Report of the Lifelines Cohort Study
Authors: Iozzia Giulia , de Miranda Azevedo Ricardo , van der Harst Pim , Rosmalen Judith G.M. , de Jonge Peter , Roest Annelieke M.
Published: July 2020

Objective

No previous study has focused on recognition of myocardial infarction (MI) and the presence of both depressive and anxiety disorders in a large population-based sample. The aim of this study was to investigate the association of recognized MI (RMI) and unrecognized MI (UMI) with depressive and anxiety disorders.

Methods

Analyses included 125,988 individuals enrolled in the Lifelines study. Current mental disorders according to the Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) were assessed with the Mini-International Neuropsychiatric Interview. UMI was detected using electrocardiogram in participants who did not report a history of MI. The classification of RMI was based on self-reported MI history together with the use of either antithrombotic medications or electrocardiogram signs of MI. Analyses were adjusted for age, sex, smoking, somatic comorbidities, and physical health–related quality of life as measured by the RAND 36-Item Health Survey in different models.

Results

Participants with RMI had significantly higher odds of having any depressive and any anxiety disorder as compared with participants without MI (depressive disorder: odds ratio [OR] = 1.86, 95% confidence interval [CI] = 1.38–2.52; anxiety disorder: OR = 1.60, 95% CI = 1.32–1.94) after adjustment for age and sex. Participants with UMI did not differ from participants without MI (depressive disorder: OR = 1.60, 95% CI = 0.96–2.64; anxiety disorder: OR = 0.73, 95% CI = 0.48–1.11). After additional adjustment for somatic comorbidities and low physical health–related quality of life, the association between RMI with any depressive disorder was no longer statistically significant (OR = 1.18; 95% CI =0.84–1.65), but the association with any anxiety disorder remained (OR = 1.27, 95% CI = 1.03–1.57).

Conclusions

Recognition of MI seems to play a major role in the occurrence of anxiety, but not depressive, disorders.
A New Experimental Lymphedema Model
Authors: Aksoyler Dicle , Bitik Ozan , Menku Ozdemir Fethiye Damla , Gokoz Ozay , Uzun Hakan , Yeniceri Berna , Nasir Serdar Nazif
Published: July 2020

Background

Our aim was to create a new rodent hind limb lymphedema model lacking the fibrosis effect induced by radiotherapy and subjected to the inhibition of lymphangiogenesis via sirolimus (rapamycin) to maintain a chronic lymphedema model and investigate its reliability for human treatment modalities.

Methods

Forty-two Sprague-Dawley rats were randomly assigned to 7 groups: (1) surgery control, (2) vehicle-surgery control, (3) vehicle control, (4) rapamycin control, (5) surgery with 1 mg/kg per day rapamycin, (6) surgery with 1.5 mg/kg per day rapamycin, and (7) surgery with 2 mg/kg per day rapamycin. All surgeries were performed on the right hind limbs, with the left hind limbs also considered as a control. The drug and its solvent were administered daily into the relevant groups intraperiteonally. The presence of lymphedema was investigated by weekly limb circumference measurements, microcomputed tomography, fluorescence lymphography using indocyanine green dye, and microscopic evaluation at the end of the sixth week to determine any histological changes in the hind limbs.

Results

In group 1, lymphedema was observed for 2 weeks (P = 0.032), whereas in groups 5, 6, and 7, lymphedema lasted for 3 weeks (P < 0.05.) Fluorescence using indocyanine green revealed that the edema was totally resolved after 6 weeks of surgery by a well-developed superficial lymphatic organization instead of the normal distinct vessel structure. Histologically, groups 1, 5, 5, and 7 demonstrated a significant increase in both the number of macrophages (P < 0.001) and newly formed lymphatic vessels in the right side surgically treated hind limb (P < 0.05).

Conclusions

Despite the extreme surgical destruction and lymphangiogenesis inhibition in the rat model, the sustained lymphedema did not last >3 weeks. Because of the rapid neolymphangiogenesis in murines and a different wound healing mechanism, they should not be considered as an appropriate model for research on human lymphedema in first place.
Anthropometric Changes in the Upper Lip Between the Standing Position in the Clinic and Supine Position on the Operative Table in Secondary Cleft Lip Nasal Deformities
Authors: Han Kihwan , Kim Taeki , Kim Junhyung , Choi Jaehoon , Shin Youngmin , Jeong Woonhyeok
Published: July 2020

Background

We evaluated changes in lip height and length by position in cleft lip nasal deformity patients who underwent treatment with Millard technique.

Methods

A retrospective review of the medical records and an anthropometric analysis of photographs were performed in 209 cases of cleft lip nasal deformity. In the photogrammetric analysis, the lip height and length were calculated with respect to the intercanthal width. To evaluate the change in the difference between the cleft- and noncleft-side measurements between the standing and supine positions, the difference between the cleft- and noncleft-side measurements (Δnc-c) was calculated. We identified which patients and surgical factors affected the difference between the cleft- and noncleft-side measurements between the standing and supine positions (Δst-sp).

Results

From a total of 120 cases, cases with missing medical charts and clinical photographs were excluded, and 89 cases were included in this study. The discrepancy between the cleft-side lip height and noncleft-side lip height was significantly different between the standing and supine positions (P = 0.007). According to the univariate regression analysis, Δst-sp (sbal-cphi) had a significant positive correlation with body mass index (P = 0.044). In the final multiple linear regression analysis, body mass index had a significant positive correlation with Δst-sp (sbal-cphi, P = 0.044).

Conclusion

In our results, the difference in vertical lip height is easy to underestimate in the supine position during surgery. Therefore, surgeons should verify lip height with the patient in the sitting or standing position during the operation to avoid undercorrecting lips with short heights.
Fortiea necridiiformans sp. nov., a soil-dwelling cyanobacterium from Pachmarhi Biosphere Reserve, India
Authors: Saraf Aniket , Dawda Himanshu G. , Suradkar Archana , Agre Vaibhav , Singh Prashant
Published: July 2020

Cyanobacterial strain PS4G was isolated from seepage soil sampled at Pachmarhi, Madhya Pradesh, India, and was characterized using a polyphasic approach. The results of morphological analysis showed that strain PS4G had unique morphological characteristics which were not observed in the other described species of the genus Fortiea. In the 16S rRNA gene phylogenetic analysis inferred using Bayesian inference, maximum-likelihood and neighbour-joining methods, strain PS4G clustered within the clade consisting of the members of the genus Fortiea. Furthermore, in the secondary structure analysis using the D1–D1′ helix and BoxB regions of 16S–23S ITS, strain PS4G showed marked differences in comparison with other members of the genus Fortiea. Overall, the morphological, phylogenetic and folded 16S–23S ITS secondary structure examination indicated that strain PS4G represents a novel species of the genus Fortiea. In accordance with the International Code of Nomenclature of Algae, Fungi and Plants we describe a novel species of Fortiea with the name Fortiea necridiiformans sp. nov.
Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence
Authors: Khonyongwa Kirstin , Taori Surabhi K. , Soares Ana , Desai Nergish , Sudhanva Malur , Bernal Will , Schelenz Silke , Curran Lisa A.
Published: July 2020

Background

The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions among vulnerable inpatients.

Aims

This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a London Teaching Hospital Trust.

Methods

Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset >14d of admission. Test performance of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections (OHAI) was compared to previous years.

Results

58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years.

Conclusion

Early diagnosis and isolation of COVID-19 would help reduce transmission. A single CTNS has limited value in segregating patients into positive and negative pathways.
Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling
Authors: Sugino Ken , Miyares Rosa L. , Espinosa-Medina Isabel , Chen Hui-Min , Potter Christopher J , Lee Tzumin
Published: July 2020

Acquiring both lineage and cell-type information during brain development could elucidate transcriptional programs underling neuronal diversification. This is now feasible with single-cell RNA-seq combined with CRISPR-based lineage tracing, which generates genetic barcodes with cumulative CRISPR edits. This technique has not yet been optimized to deliver high-resolution lineage reconstruction of protracted lineages.Drosophilaneuronal lineages are an ideal model to consider, as multiple lineages have been morphologically mapped at single-cell resolution. Here we find the parameter ranges required to encode a representative neuronal lineage emanating from 100 stem cell divisions. We derive the optimum editing rate to be inversely proportional to lineage depth, enabling encoding to persist across lineage progression. Further, we experimentally determine the editing rates of a Cas9-deaminase in cycling neural stem cells, finding near ideal rates to map elongatedDrosophilaneuronal lineages. Moreover, we propose and evaluate strategies to separate recurring cell-types for lineage reconstruction. Finally, we present a simple method to combine multiple experiments, which permits dense reconstruction of protracted cell lineages despite suboptimum lineage encoding and sparse cell sampling.
Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment
Authors: Paul Arghadwip , Samantray Suman , Anteghini Marco , Strodel Birgit
Published: July 2020

The amlyoid-β peptide (Aβ) is closely linked to the development of Alzheimer’s disease. Molecular dynamics (MD) simulations have become an indispensable tool for studying the behavior of this peptide at the (sub)molecular level, thereby providing insight into the molecular basis of Alzheimer’s disease. General key aspects of MD simulations are the force field used for modeling the peptide or protein and its environment, which is important for accurate modeling of the system of interest, and the length of the simulations, which determines whether or not equilibrium is reached. In this study we address these points by analyzing 30-µs MD simulations acquired for Aβ40 using seven different force fields. We assess the convergence of these simulations based on the convergence of various structural properties and of NMR and fluorescence spectroscopic observables. Moreover, we calculate Markov state models for each of the seven MD simulations, which provide an unprecedented view of the thermodynamics and kinetics of the amyloid-β peptide. This further allows us to provide answers for pertinent questions, like:Which force fields are suitable for modeling Aβ?(a99SB-UCB and a99SB-ILDN/TIP4P-D);What does Aβ peptide really look like?(mostly extended and disordered) and;How long does it take MD simulations of Aβ to attain equilibrium?(20–30 µs). We believe the analyses presented in this study will provide a useful reference guide for important questions relating to the structure and dynamics of Aβin particular, and by extension other similar disordered peptides.
Tet1isoforms differentially regulate gene expression, synaptic transmission and memory in the mammalian brain
Authors: Greer C.B. , Wright J. , Weiss J.D. , Lazerenko R.M. , Moran S.P. , Zhu J. , Chronister K.S. , Jin A.Y. , Kennedy A.J. , Sweatt J.D. , Kaas G.A.
Published: July 2020

The dynamic regulation of DNA methylation in post-mitotic neurons is necessary for memory formation and other adaptive behaviors. Ten-eleven translocation 1 (TET1) plays a part in these processes by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), thereby initiating active DNA demethylation. However, attempts to pinpoint its exact role in the nervous system have been hindered by contradictory findings, perhaps due in part, to a recent discovery that two isoforms of theTet1gene are differentially expressed from early development into adulthood. Here, we demonstrate that both the shorter transcript (Tet1S) encoding an N-terminally truncated TET1 protein and a full-lengthTet1(Tet1FL) transcript encoding canonical TET1 are co-expressed in the adult brain. We show thatTet1Sis the predominantly expressed isoform, and is highly enriched in neurons, whereasTet1FLis generally expressed at lower levels and more abundant in glia, suggesting their roles are at least partially cell-type specific. Using viral-mediated, isoform- and neuron-specific molecular tools, we find thatTet1Srepression enhances, whileTet1FLimpairs, hippocampal-dependent memory. In addition, the individual disruption of the two isoforms leads to contrasting changes in basal synaptic transmission and the dysregulation of unique gene ensembles in hippocampal neurons. Together, our findings demonstrate that eachTet1isoform serves a distinct role in the mammalian brain.
Microplastic shape, concentration and polymer type affect soil properties and plant biomass
Authors: Lozano Yudi M. , Lehnert Timon , Linck Lydia T. , Lehmann Anika , Rillig Matthias C.
Published: July 2020

Microplastics are an increasing concern in terrestrial systems. These particles can be incorporated into the soil in a wide range of shapes and polymers, reflecting the fact that manufacturers produce plastics in a variety of physical and chemical properties matching their intended use.Despite of this, little is known about the effects that the addition into the soil of microplastics of different shapes, polymer type and concentration levels may have on soil properties and plant performance.

To fill this gap, we selected four microplastic shapes: fibers, films, foams and fragments; and for each shape we selected three microplastics made of one of the following polymers: polyester, polyamide, polypropylene, polyethylene, polyethylenterephthalat, polyurethane, polystyrene and polycarbonate. In a glasshouse experiment, each microplastic was added to a soil from a dry grassland at a concentration of 0.1%, 0.2%, 0.3% and 0,4%. A carrot (Daucus carota) plant grew in each pot during four weeks. At harvest, shoot and root mass, soil aggregation and microbial activity were measured.

Our results showed that all microplastic shapes increased shoot and root masses. As concentration increased, microfibers increased plant biomass probably as fibers may hold water in the soil for longer. In contrast, microfilms decreased biomass with concentration, likely because they can create channels in the soil that promote water evaporation affecting plant performance. All microplastic shapes decreased soil aggregation, probably since microplastics may introduce fracture points in the aggregates affecting their stability and also due to potential negative effects on soil biota. The latter may also explain the decrease in microbial activity with, for example, polyethylene films. Similar to plant biomass, microfilms decreased soil aggregation with increasing concentration.

Our study tested the microplastic shape mediation and dissimilarity hypotheses, highlighting the importance of microplastic shape, polymer type and concentration when studying the effects of microplastics on terrestrial systems.
Exploring the quality of protein structural models from a Bayesian perspective
Authors: Arroyuelo Agustina , Vila Jorge A. , Martin Osvaldo A.
Published: July 2020

We explore how ideas and practices common in Bayesian modeling can be applied to help assess the quality of 3D protein structural models. As the wordmodelis used in both Bayesian Statistics and Protein Science, throughout this article we deliberately use the wordmodelto discuss statistical models andstructureto discuss protein 3D models, thus avoiding potential confusions. The basic premise of our approach, is that the evaluation of a Bayesian statistical model’s fit may reveal aspects of the quality of a structure, when the fitted data are related to protein structural properties. Therefore, we fit a Bayesian hierarchical linear model to experimental and theoretical13CαChemical Shifts. Then, we propose two complementary approaches for the evaluation of such fitting: 1) in terms of theexpected differencesbetween experimental and posterior predicted values; 2) in terms of theleave-one-out cross validation point-wise predictive accuracy. Finally, we present visualizations that can help interpret these evaluations. The analyses presented in this article are aimed to aid in detecting problematic residues in protein structures. The code developed for this work is available on:https://github.com/BIOS-IMASL/Hierarchical-Bayes-NMR-Validation.
UNCG RNA tetraloop as a formidable force-field challenge for MD simulations
Authors: Mráziková Klaudia , Mlýnský Vojtěch , Kührová Petra , Pokorná Pavlína , Kruse Holger , Krepl Miroslav , Otyepka Michal , Banáš Pavel , šponer Jiří
Published: July 2020

Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ffs) remains far from satisfactory even after decades of development, as apparent from a problematic structural description of some important RNA motifs. Actually, some of the smallest RNA molecules belong to the most challenging systems for MD simulations and, among them, the UNCG tetraloop is saliently difficult. We report a detailed analysis of UNCG MD simulations, depicting the sequence of events leading to the loss of the UNCG native state during MD simulations. We identify molecular interactions, backbone conformations and substates that are involved in the process. The total amount of MD simulation data analyzed in this work is close to 1.3 millisecond. Then, we unravel specificffdeficiencies using diverse quantum mechanical/molecular mechanical (QM/MM) and QM calculations. Comparison between the MM and QM methods shows discrepancies in the description of the 5’-flanking phosphate moiety and both signature sugar-base interactions. Our work indicates that poor behavior of the UNCG tetraloop in simulations is a complex issue that cannot be attributed to one dominant and straightforwardly correctable factor. Instead, there is a concerted effect of multipleffinaccuracies that are coupled and amplifying each other. We attempted to improve the simulation behavior by some carefully-tailored interventions but the results are still far from satisfactory, underlying the difficulties in development of accurate nucleic acidsffs.
Breathing Behaviors in Common Marmoset (Callithrix jacchus)
Authors: Bishop Mitchell , Turk Ariana , Adeck Afuh , SheikhBahaei Shahriar
Published: July 2020

The respiratory system maintains homeostatic levels of oxygen (O2) and carbon dioxide (CO2) in the body through rapid and efficient regulation of frequency and depth (tidal volume) of breathing. Many studies on homeostatic control of breathing have been done on rodent animal models, in which they have relatively reduced chemosensitivities when compared with primates. The use of common marmoset (Callithrix jacchus), a New World non-human primate model, in neuroscience is increasing, however, the data on their breathing is limited and their respiratory behaviors have yet to be characterized. Using Whole-body Plethysmography in room air as well as in hypoxic (low O2) and hypercapnic (high CO2) conditions, we defined breathing behaviors in awake, freely behaving marmosets. Additionally, we optimized an analysis toolkit for unsupervised analysis of respiratory activities in common marmoset. Our data indicate that marmosets’ exposure to hypoxia decreased metabolic rate and increased sigh rate. However, the hypoxic condition did not augment the ventilatory response. Hypercapnia, on the other hand, increased both the frequency and tidal volume. In this study, we described breathing behaviors of common marmosets in a variety of O2and CO2conditions.
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data
Authors: Kong Sungsik , Kubatko Laura S.
Published: July 2020

Abstract

Interspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methodsHyDeand theD-statistic (i.e., the ABBA-BABA test), and the population clustering approachesstructureand ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for theD-statistic andHyDe, and the accuracy of the estimates ofγas measured by the mean squared error forHyDe, structure, and ADMIXTURE. BothHyDeand theD-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although theD-statistic often has an unacceptably high FDR. The estimates ofγinHyDeare impressively robust and accurate whereasstructureand ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., whenγis close to 0). Moreover, the posterior distribution estimated usingstructureexhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.
Residence Time Analysis of RNA Polymerase Transcription Dynamics: A Bayesian Sticky HMM Approach
Authors: Kilic Zeliha , Sgouralis Ioannis , Pressé Steve
Published: July 2020

The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed “residence time”, reports on the initiation, elongation and termination stages of transcription. At the single molecule level, this information can be obtained from dual ultra-stable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP’s transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov models that treats all residence times, for an E. Coli RNAP, on an equal footing without a priori discriminating between long and short residence times. In addition, our method has two additional advantages, we provide: full distributions around key point statistics; and directly treat the sequence-dependence of RNAP’s elongation rate.

By applying our approach to experimental data, we find: no emergent separation between long and short residence times warranted by the data; force dependent average residence time transcription elongation dynamics; limited effects of GreB on average backtracking durations and counts; and a slight drop in the average residence time as a function of applied force in RNaseA’s presence.

STATEMENT OF SIGNIFICANCE

Much of what we know about RNA Polymerase, and its associated transcription factors, relies on successfully discriminating between what are believed to be short and long residence times in the data. This is achieved by applying pause-detection algorithms to trace analysis. Here we propose a new method relying on Bayesian sticky hidden Markov models to interpret time traces provided by dual optical trapping experiments associated with transcription elongation of RNAP. Our method does not discriminate between short and long residence times from the offset in the analysis. It allows for DNA site-dependent transition probabilities of RNAP to neighboring sites (thereby accounting for chemical variability in site to site transitions) and does not demand any time trace pre-processing (such as denoising).
Brazilian dental students and COVID-19: a survey on knowledge and perceptions
Authors: Aragao Maria Gerusa Brito , Gomes Francisco Isaac Fernandes , de Melo Letícia Pinho Maia Paixão , Corona Silmara Aparecida Milori
Published: July 2020

This study evaluated the knowledge and perception of Brazilian dental students about COVID-19 and the undergraduate clinical practice during the outbreak by a self-administered web-based questionnaire. A social network campaign on Instagram was raised to approach the reach population. The survey covered demographic and academic profile, general knowledge, preventive measures, and perception about the COVID-19. Descriptive statistics were used to identify frequencies and distributions of variables, which were compared by type of institution and current year of enrollment using Chi-square or Fisher’s exact tests (α=0.05). A total of 833 valid responses were received over 10 days. Students were able to identify the incubation period, main symptoms, and contagious routes of the disease but struggled in recognizing the name of the virus responsible for the pandemics. Hand washing before and after a dental appointment with a patient (97.7%) followed by use of barriers to protect mucosa (97.2%) were the more frequently recognized measures to prevent COVID-19 spread in the dental office. As for the perception of COVID-19, 73.2% of the dental students perceive the disease as severe, while only 11.1% of them think that COVID-19 is severe only for people presenting risk factors. Dental student’s knowledge and perception were associated with the type of institution and year of enrollment. In summary, the dental students demonstrated an acceptable general knowledge about COVID-19, but dental schools will need to address gaps in knowledge and control measures and perceptions to ensure a safer return to presential activities.
Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19
Authors: Ando Shiho , Matsuzawa Yuki , Tsurui Hiromichi , Mizutani Testuya , Hall Damien , Kuroda Yutaka
Published: July 2020

After several weeks of “lockdown” as the sole answer to the COVID-19 pandemic, many countries are restarting their economic and social activities. However, balancing the re-opening of society against the implementation of non-pharmaceutical measures needed for minimizing interpersonal contacts requires a careful assessment of the risks of infection as a function of the confinement relaxation strategies. Here, we present a stochastic coarse grained model that examines this problem. In our model, people are allowed to move between discrete positions on a one-dimensional grid with viral infection possible when two people are collocated at the same site. Our model features three sets of adjustable parameters, which characterize (i) viral transmission, (ii) viral detection, and (iii) degree of personal mobility, and as such, it is able to provide a qualitative assessment of the potential for second-wave infection outbreaks based on the timing, extent, and pattern of the lockdown relaxation strategy. In line with general expectations, our model predicts that a full lockdown yields the best results, namely, the lowest number of total infections. A less anticipated result was that when personal mobility is increased beyond a critical level, the risk of infection rapidly reaches a constant value, which depends solely on the population density. Furthermore, according to our model, confinement alone is not effective if it is not accompanied by a detection capacity (coupled with quarantine) that surpasses 40% of the patients during their symptomatic phase. The results of our simulation also showed that keeping the virus transmission probability to less than 0.4, which can be achieved in real life by respecting social distancing or wearing masks, is as effective as imposing a mild lockdown. Finally, we note that detection and quarantine of pre-symptomatic patients, even with a probability as low as 0.2, would reduce the final numbers of infections by a factor of ten or more.

Availability

http://domserv.lab.tuat.ac.jp/COVID19.html (under preparation)
Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy
Authors: Newman Christina M. , Ramuta Mitchell D. , McLaughlin Matthew T. , Wiseman Roger W. , Karl Julie A. , Dudley Dawn M. , Stauss Miranda R. , Maddox Robert J. , Weiler Andrea M. , Bliss Mason I. , Fauser Katrina N. , Haddock Luis A. , Shortreed Cecilia G. , Haj Amelia K. , Accola Molly A. , Heffron Anna S. , Bussan Hailey E. , Reynolds Matthew R. , Harwood Olivia E. , Moriarty Ryan V. , Stewart Laurel M. , Crooks Chelsea M. , Prall Trent M. , Neumann Emma K. , Somsen Elizabeth D. , Burmeister Corrie B. , Hall Kristi L. , Rehrauer William M. , Friedrich Thomas C. , O’Connor Shelby L. , O’Connor David H.
Published: July 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16 to November 19, 2020, 4,704 surveillance samples were collected from volunteers and tested for SARS-CoV-2 at 5 sites. A total of 21 samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, while 8 were negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the RT-LAMP assay’s false-negative rate from July 16 to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or less and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP negative pools (2,493 samples) testing positive in the more sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
High-resolution positron emission microscopy of patient-derived tumor organoids
Authors: Khan Syamantak , Shin June Ho , Ferri Valentina , Cheng Ning , Noel Julia E. , Kuo Calvin , Sunwoo John B. , Pratx Guillem
Published: July 2020

Organoid tumor models have found application in a growing array of cancer studies due to their ability to closely recapitulate the structural and functional characteristics of solid tumors. However, organoids are too small to be compatible with common radiological tools used in oncology clinics. Here, we present a microscopy method to image18F-fluorodeoxyglucose in patient-derived tumor organoids with spatial resolution up to 100-fold better than that of clinical positron emission tomography (PET). When combined with brightfield imaging, this metabolic imaging approach functionally mirrors clinical PET/CT scans and provides a quantitative readout of cell glycolysis. In particular, the specific avidity of a tumor for FDG, or lack thereof, was maintained when the tumor cells were grownex vivoas tumor organoids. In addition, cisplatin treatment caused a dose-dependent decrease in the metabolic activity of these organoids, with the exception of one patient whose tumor was also resistant to cisplatin treatment. Thus, FDG-imaging of organoids could be used to predict the response of individual patients to different treatments and provide a more personalized approach to cancer care.
Natural food intake patterns do not synchronize peripheral clocks
Authors: Xie Xiaobin , Kukino Ayaka , Calcagno Haley E. , Berman Alec , Garner Joseph P. , Butler Matthew P.
Published: July 2020

Food is thought to synchronize circadian clocks in the body, but this is based on time-restricted feeding (TRF) protocols. To test whether naturalistic feeding patterns are sufficient to phase-shift and entrain peripheral tissues, we measured circadian rhythms of the liver, kidney, and submandibular gland inmPer2Lucmice under different feeding schedules. In ad lib feeding as well as in a schedule designed to mimic the ad lib pattern, PER2::LUC bioluminescence peaked during the night as expected. Surprisingly, shifting the scheduled feeding by 12h caused only small advances (<3h). To isolate the effects of feeding from the light-dark cycle, clock phase was then measured in mice acclimated to scheduled feeding and housed in constant darkness. In these conditions, peripheral clock phases were better predicted by the rest-activity cycle than the food schedule. Under natural feeding patterns, the master pacemaker in the brain sets the phase of peripheral organs independent of feeding behavior.
Digital spatial profiling of coronary plaques from persons living with HIV reveals high levels of STING and CD163 in macrophage enriched regions
Authors: Wanjalla Celestine N. , Guo Liang , Fuller Daniela T. , Mashayekhi Mona , Bailin Samuel , Gabriel Curtis L. , Temu Tecla , Gong Jingjing , Liang Yan , Virmani Renu , Finn Aloke V. , Kalams Spyros A. , Mallal Simon A. , Miner Jonathan J. , Beckman Joshua A. , Koethe John R.
Published: July 2020

Background

Chronic innate and adaptive immune activation may contribute to high prevalence of cardiovascular disease in persons living with HIV (PLWH).

Methods

We assessed coronary plaques from deceased PLWH (n=6) and HIV-negative (n=6) persons matched by age and gender. Formalin-fixed, paraffin-embedded 5μm thick sections were processed using Movat, hematoxylin and eosin, immunohistochemical and immunofluorescence stains. Immune cell populations were measured using surface antibodies, and immune-related protein expression from macrophage rich, T-cell rich and perivascular adipose tissue regions using GeoMx®digital spatial profiling.

Results

Coronary plaques from PLWH and HIV-negative persons had similar plaque area and percent stenosis. Percent CD163+cells as measured by immunohistochemical staining was significantly higher in PLWH, median 0.29% (IQR 0.11-0.90) vs. 0.01% (IQR 0.0013-0.11) in HIV-negative plaque, p = 0.02 (Figure 1A). Other surface markers of innate cells (CD68+, p=0.18), adaptive immune cells (CD3+, p=0.39; CD4+, p=0.09; CD8+, p=0.18) and immune trafficking markers (CX3CR1+, p=0.09) within the coronary plaque trended higher in HIV-positive plaques but did not reach statistical significance. GeoMx®digital spatial profiling showed higher differential protein expression of CD163 (scavenger receptor for hemoglobin-haptoglobin complex), stimulator of interferon gamma (STING, a cytosolic DNA sensor), CD25 and granzyme-B in the HIV-positive compared to HIV-negative, p<0.05(Figure 1B).

Conclusions

Increased inflammation within the coronary plaques of PLWH is characterized by more innate and adaptive immune cells. Higher STING expression in PLWH suggests that immune response to viral antigens within the plaque might be a driver above other stimulants. STING inhibitors are available and could be investigated as a future therapeutic target in PWH if these results are replicated with a larger number of plaques.

Graphical Abstract

Highlights

Immunohistochemical and fluorescent stains combined with GeoMx®digital spatial profiling allowed for deep characterization of immune cells within intact coronary plaques and perivascular adipose tissue

Coronary plaques from HIV-positive persons had higher proportion of CD163+immune cells compared to HIV-negative persons

Differential protein expression of immune-rich regions of interest within intact 5μm sections of coronary plaques revealed higher levels of stimulator of interferon gamma (STING) in HIV-positive persons