bluuebunny/crossref_metadata_2025 huggingface dataset:
159 Geographic Accessibility and Capacity of Day Care Services for People with Dementia
Authors: Pierse Tom , Cullinan John , Keogh Fiona , O'Shea Eamon
Published: September 2019

Background

Day care is an important service for some people with dementia and their carers. In Ireland, day care services for people with dementia are delivered by a mix of dementia specific day-care centres and generic centres that cater for people with dementia to various degrees. In this paper we map the geographic variation in the supply of day care services for people with dementia relative to potential need.

Methods

Using a national HSE survey of day care centres, we estimate the current supply of day care services for people with dementia in both generic and dementia specific centres by combining a number of qualitative and quantitative measures. To identify the variation in supply, we map day care provision at local and regional levels to the number of people with dementia in the area. To consider geographic accessibility, we map and analyse the population living outside the catchment area of the day care centres.

Results

There is significant variation across the country in the existing capacity of day care centres to cater for people with dementia. The number of places per 100 persons with dementia varies from 9 to 16 across the Community Health Organisation areas. We show that 20 per cent of people with dementia are not living within a 15km radius of a day care centre that caters for people with dementia.

Conclusion

Day care has a place in the menu of service for people with dementia living in the community. As the number of people with dementia grows, investment in day care centres needs to be targeted to areas of greatest need. In many parts of the country, the current day care centres have limited capacity to provide a service for people with dementia that live in their catchment area. There is considerable geographical inequity in day care provision for people with dementia across the country.
Caring for and assessing pediatric patients: Aspects to consider as a pharmacy practitioner
Authors: Eiland Lea S , Meyers Rachel S
Published: September 2019

Purpose

Pharmacists care for patients of all ages. Pediatric patients are not smaller versions of adults; thus, they provide a unique challenge to pharmacists. Basic components of patient assessment and considerations for medication dosing and administration for pediatric patients are reviewed here.

Each pediatric patient is different, and physiological changes occur as a patient ages. Growth, vital signs, and laboratory tests are common assessments for all patients. However, there are unique factors to consider within the pediatric population, and a pharmacist must understand how to assess and interpret these data for pediatric patients of all ages. Additionally, individualized medication dosing is based on patient factors such as age, weight, or body surface area in this population. Key information about the administration of medications and understanding of dosage formulations for this patient population is an area where pharmacists can make recommendations to prescribers and counsel patients and caregivers in order to improve patient outcomes and increase adherence.

Conclusion

Patient assessment by the pharmacist is a key step in developing a patient treatment plan. Assessment factors in the pediatric population can differ from those in the adult population. A working knowledge of differences within the pediatric population and understanding how to assess them is essential for providing optimal patient care to this population.
Pediatric-to-adult healthcare transitions: Current challenges and recommended practices
Authors: Hobart Catherine B , Phan Hanna
Published: September 2019

Purpose

An overview of the pediatric-to-adult healthcare transition (HCT) process, including stakeholders, challenges, and fundamental components that present opportunities for pharmacists and pharmacy technicians, is provided.

Pediatric-to-adult HCT programs should be longitudinal in nature, be patient focused, and be coproduced by patients, caregivers, and care team members. Educational components of HCT programs should include knowledge and skills in disease state management and self-care; safe and effective use of medications, as well as other treatment modalities; and healthcare system navigation, including insurance issues. Interprofessional involvement in HCT is encouraged; however, roles for each discipline involved are not clearly delineated in current guidelines or literature. Possible influencing elements in achieving successful pediatric-to-adult HCT outcomes include those that are related to patient and/or caregiver factors, clinician awareness, availability of resources, and ability to achieve financial sustainability.

Conclusion

The use of structured pediatric-to-adult HCT programs is currently recommended to optimize patient and health-system outcomes. Given the importance of medication-related knowledge and healthcare system navigation skills to successful care transitions, there are opportunities for pharmacists and pharmacy technicians to contribute to HCT programs.
Does Implant Surface Texture Affect the Risk of Capsular Contracture in Subglandular Breast Augmentation and Breast Augmentation-Mastopexy?
Authors: Lista Frank , Austin Ryan E , Saheb-Al-Zamani Maryam , Ahmad Jamil
Published: September 2019

Background

Previous studies have reported decreased rates of capsular contracture associated with the use of textured surface breast implants placed in the subglandular plane during breast augmentation. However, since the publication of these studies, our understanding of the pathophysiology of capsular contracture, as well as the surgical techniques utilized to minimize bacterial contamination of the implant, have advanced considerably.

Objectives

The purpose of this study was to re-evaluate the relation between implant surface texturization and capsular contracture rates for breast implants placed in the subglandular plane during primary breast augmentation.

Methods

Retrospective chart review was performed of all primary subglandular breast augmentation procedures involving the use of either smooth or textured round silicone gel implants, with or without simultaneous mastopexy. The primary outcome measures included clinically significant capsular contracture (Baker grade III/IV) and revision surgery for capsular contracture.

Results

Between 2010 and 2017, 526 patients underwent primary subglandular breast augmentation with either smooth (n = 212) or textured (n = 314) round silicone gel implants; 248 patients underwent breast augmentation, whereas 278 underwent breast augmentation-mastopexy. Average follow-up was 756 days in the textured group and 461 days in the smooth group. Five cases of capsular contracture were observed in the textured group, and 7 cases of capsular contracture were observed in the smooth group (P = 0.20).

Conclusions

Smooth surface implants placed in the subglandular plane were not at a significantly increased risk of capsular contracture compared with textured surface implants. We suggest that adherence to a surgical technique focused on minimizing bacterial contamination of the implant is of greater clinical significance than implant surface characteristics when discussing capsular contracture.

Level of Evidence: 4
Left Interhemispheric Craniotomy for Resection of Cavernous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: September 2019

Thalamic cavernous malformations pose variable surgical challenges given that the location and size of the lesion often determine the approach surgical trajectory. The patient in this case has a large thalamic cavernous malformation that results in a mass effect on the third ventricle and directly abuts the lateral ventricle. A small interhemispheric craniotomy is performed to allow for an anterior interhemispheric transcallosal approach to the lesion. The lateral ventricle is accessed, and the septum is removed to enhance visualization of the surgical field. A small rim of normal parenchyma on the lateral margin of the thalamus is transgressed, and the cavernous malformation is entered. The lesion is removed in a piecemeal manner. Use of counter traction assists with the piecemeal removal. The lighted suction is critical during inspection and manipulation of the lesion within the resection cavity given the limited lighting deep within the cavity. The lesion was removed completely, and postoperative imaging confirms gross total resection. The patient gave informed consent for surgery and video recording. The institutional review board approval was deemed unnecessary. Used with permission from the Barrow Neurological Institute.
Randomized crossover study investigating resident retention of menopause-related knowledge after completion of learning modules
Authors: Shinnick Julia K. , Raker Christina , Hampton B. Star , Eger Renee
Published: September 2019

Objective:

The aim of this study was to evaluate residents’ retention of menopause-based knowledge immediately after, and 3 months after completion of, self-administered modules that varied by menopause-related topic and delivery format.

Methods:

Prospective crossover study of Obstetrics and Gynecology and Family Medicine residents at one institution over the 2017 to 2018 academic year. Residents were randomized to a series of three PowerPoints (Microsoft, Redwood, WA), each <30 slides, administered during regularly scheduled didactics. Each series contained three subjects (Menopause Basics [MB], Hormone Therapy [HT], and Genitourinary Syndrome of Menopause [GSM]) delivered through three different presentation styles (typical presentation [typical], pictures and a narration [pictures], and interactive to reveal information [interactive]). Knowledge and comfort were assessed through baseline, immediate postexposure, and 3-month follow-up surveys containing 24 knowledge questions (multiple choice) and 10 comfort and satisfaction questions (5-point Likert scale and multiple choice). Statistical tests were applied with P<0.05 considered significant.

Results:

Thirty-three residents completed the 3-month follow-up. Immediately postexposure, knowledge and comfort increased from baseline for all topics (P < 0.05). When formats were grouped together to investigate retention by topic, the HT topic demonstrated a sustained increase in knowledge on 3-month follow-up (P = 0.047). The typical format of the GSM topic had significantly better retention than the picture format (P = 0.027). All formats were associated with a significant increase in comfort (all P < 0.01).

Conclusions:

Participation in this specialized menopause curriculum led to short-term increases in objectively assessed menopause-related knowledge. Tailoring self-administered learning modules to learning styles did not, however, effectively enhance overall knowledge retention on 3-month follow-up, though comfort in managing menopause remained increased.

Video Summary:

http://links.lww.com/MENO/A474.
Retrospective analysis of phytoSERM for management of menopause-associated vasomotor symptoms and cognitive decline: a pilot study on pharmacogenomic effects of mitochondrial haplogroup and APOE genotype on therapeutic efficacy
Authors: Wang Yiwei , Hernandez Gerson , Mack Wendy J. , Schneider Lon S. , Yin Fei , Brinton Roberta D.
Published: September 2019

Objective:

PhytoSERM is a selective estrogen receptor beta (ERβ) modulator comprised of three phytoestrogens: genistein, daidzein, and S-equol. The PhytoSERM formulation promotes estrogenic action in the brain while largely inactive or inhibitory in reproductive tissue. A phase Ib/IIa clinical trial (ClinicalTrial.gov ID: NCT01723917) of PhytoSERM demonstrated safety and pharmacokinetics profile of PhytoSERM. While this study was not powered for efficacy analysis, we conducted a pilot, retrospective analysis to identify potential responders to PhytoSERM treatment, and to determine the optimal populations to pursue in a phase II clinical trial of efficacy of the PhytoSERM formulation.

Methods:

In this retrospective analysis involving 46 participants (n = 16, placebo; n = 18, 50 mg/d PhytoSERM; and n = 12, 100 mg/d PhytoSERM), the therapeutic effect of PhytoSERM was stratified by 2 genetic risk modulators for Alzheimer's disease: mitochondrial haplogroup and APOE genotype.

Results:

Our retrospective responder analysis indicated that participants on 50 mg of daily PhytoSERM (PS50) for 12 weeks significantly reduced hot flash frequency compared with their baseline (mean [95% CI])−1.61, [−2.79, −0.42], P = 0.007). Participants on 50 mg of PhytoSERM also had significantly greater reduction in hot flash frequency at 12 weeks compared with the placebo group (−1.38, −0.17 [median PS50, median placebo], P = 0.04). Fifty milligrams of daily PhytoSERM also preserved cognitive function in certain aspects of verbal learning and executive function. Our analysis further suggests that mitochondrial haplogroup and APOE genotype can modify PhytoSERM response.

Conclusion:

Our data support a precision medicine approach for further development of PhytoSERM as a safe and effective alternative to hormone therapy for menopause-associated hot flash and cognitive decline. While definitive determination of PhytoSERM efficacy is limited by the small sample size, these data provide a reasonable rationale to extend analyses to a larger study set powered to address statistical significance.
Predicting Development of Bilateral Menière's Disease Based on cVEMP Threshold and Tuning
Authors: Noij Kimberley S. , Herrmann Barbara S. , Guinan John J. , Rauch Steven D.
Published: September 2019

Objective:

To investigate if the cervical vestibular evoked myogenic potential (cVEMP) is predictive for developing bilateralMenière'sdisease (MD).

Study Design:

Retrospective cohort study.

Setting:

Tertiary care center.

Patients:

Records of 71 patients previously diagnosed with unilateral MDat our institution who underwent cVEMP testing between 2002 and 2011 were screened.

Intervention:

Patients were contacted to answer a questionnaire to identify which patients had developed bilateral disease. Based on questionnaires and medical charts, 49 patients with a follow-up time of at least 5 years were included. The 49 originally asymptomatic ears are referred to as “study ears.” Previously reported cVEMP criteria (original criteria) applied to study-ear cVEMPs separated them intoMenière-like and normal-like groups.

Main Outcome Measure:

The main purpose was to determine if previously obtained cVEMP thresholds and tuning ratios of unilateral MD patients could predict who develops bilateral disease.

Results:

From the 49 included patients, 12 developed bilateral disease (24.5%). The study ears characterized by original cVEMP criteria asMenière-like were significantly more likely to develop bilateral disease compared with the normal-like study ears. The original criteria predicted development of bilateral disease with a positive predictive value (PPV) and negative predictive value (NPV) of 58.3% and 86.5% respectively. ROC curves were used to revise cVEMP criteria for predicting the progression to bilateral disease. A revised criterion combining three cVEMP metrics, reached a PPV and NPV of 85.7% and 93.7%.

Conclusion:

cVEMP threshold and tuning in unilateral MD patients are predictive of which patients will develop bilateral disease.
Improving the safety of chemotherapy process by a risks management tool
Authors: Ouasrhir Abdelali , Bourhaleb Zouhour , Rahhali Rabie , Boukhatem Noureddine
Published: September 2019

Objectives:

Chemotherapy compounding is a main step of chemotherapy cancer process. This step is formed by many parts. A multidisciplinary team is assembled to define critical points and failures linked to this process and proposed different actions to secure them and improve chemotherapy cancer process.

Methodology:

By a prospective analysis risks tool: the failure modes, effects, and criticality analysis (FMECA), anticancer drug process compounding was sequenced in many parts. During the brainstorming, different ideas expressed and were classified into an Ishikawa cause–effect diagram. The criticality indexes (CI) are calculated from occurrence, severity, and the detection probability.

Results:

The sum of CIs of 18 identified failure modes was CI = 3607 for the decentralized system and CI = 726 after the new organization of compounding process. The chemotherapy production step represents 37.17% (CI = 1341) of all failures in the old process. The greatest risk reductions between the old and the new process concerned the risk of ‘Double check missing before delivery to the ward’ by a factor reduction of 28.0). Among the CIs remaining superior to 100, there was one failure: ‘Typing error during prescription’ (CI = 144).

Conclusion:

Modification of the chemotherapy-compounding process by centralization, training program, and implementation of procedures resulted in an important risk reduction as shown by risk analysis. Our study illustrates the usefulness of risk analysis methods in the healthcare system. A systematic use of risk analysis is needed to improve the safety of high-risk activities in healthcare processes.
Basic determinants of child growth in sub-Saharan Africa: cross-sectional survey analysis of positive deviants in poor households
Authors: Amugsi Dickson A. , Dimbuene Zacharie T.
Published: September 2019

Background

Childhood malnutrition is a significant public health problem confronting countries across the globe. Nonetheless, recent evidence suggests a downward trend in undernutrition among children globally. Despite the progress made at the global level, sub-Saharan Africa did not experience significant improvement in the past decades. The objective of this study was to investigate the basic determinants associated with linear growth among children under 5 years living in poor households.

Methods

The study used nationally representative cross-sectional survey data from Ghana, Kenya, Democratic Republic of Congo (DRC), Nigeria and Mozambique. The participants are children aged 0–59 months (N=24,264) living in poor households. The DHS obtained information on children through face-to-face interviews with mothers. The height of the children was also measured and used to compute the height-for-age Z-scores (HAZ). In this study, HAZ is categorised into HAZ>-2 standard deviations (SD) (not stunted/better growth) and HAZ<-2 SD (stunted/poor growth).

Results

A unit change in maternal years of education was associated with increased odds of better growth among children living in poor households in DRC [adjusted odds ratio (aOR)= 1.03, 95% CI=1.01,1.07)], Ghana (aOR=1.06, 95% CI=1.01,1.11), Kenya (aOR=1.03, 95% CI= 1.01, 1.05) and Nigeria (aOR=1.08, 95%=1.06,1.10). Maternal antenatal attendance of at least four visits was associated positively with better child growth in DRC (aOR=1.32, 95% CI=1.05, 1.67) and Ghana (aOR=1.67, 95% CI=1.19, 2.33). In Ghana, Mozambique and DRC, breastfeeding was associated significantly with the likelihood of better linear growth when only socio-demographic correlates were included in the models but disappeared after the inclusion of child-level covariates. In Nigeria, normal maternal weight was associated with increased odds (aOR=1.24, 95% CI=1.08, 1.43) of positive growth among children living in poor households, so was overweight (aOR=1.51, 95% CI= 1.24, 1.83). In all the countries except Ghana, child biological factors such as sex and age were associated with reduced odds of better growth.

Conclusions

The socio-demographic factors included in this analysis have the potential to promote linear growth of children under 5 years living in poor households. Interventions aimed at fostering linear growth among children living in poverty should target at enhancing these factors.
Secrets of the hospital underbelly: patterns of abundance of antimicrobial resistance genes in hospital wastewater vary by specific antimicrobial and bacterial family
Authors: Perry Meghan R. , Lepper Hannah C. , McNally Luke , Wee Bryan A. , Munk Patrick , Warr Amanda , Moore Barbara , Kalima Pota , Philip Carol , de Roda Husman Ana Maria , Aarestrup Frank M. , Woolhouse Mark , van Bunnik Bram A.D.
Published: September 2019

Background

Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater.

Methods

Sewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates.

Results

Microbiota and ARG composition varied between collection points and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, P=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06 - 1.16, P<0.001). Furthermore, analysing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage (carbapenem rate ratio (RR) 1.91, 95% confidence intervals (CI) 1.01 – 3.72, P=0.07, and vancomycin RR 10.25, CI 2.32 – 49.10, P<0.01). Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance (odds ratio (OR) 1.62, CI 1.33 – 2.00, P<0.001, and OR 1.65, CI 1.21 – 2.30, P=0.006 respectively).

Conclusions

We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.
Noise-Assisted MEMD-Based Phase-Connectivity Analysis to Personalize Closed-Loop DBS Therapy in Epilepsy Patients
Authors: Farahmand Sina , Sobayo Tiwalade , Mogul David J.
Published: September 2019

Deep brain stimulation (DBS) is a treatment that has been explored for controlling seizures in patients with intractable epilepsy. Many clinical and pre-clinical studies using DBS therapy determine stimulation parameters through trial and error. The same stimulation parameters are often applied to the whole cohort, which consequently produces mixed results of responders and non-responders. In this paper, an adaptive non-linear analytical methodology is proposed to extract stimulation frequency and location(s) from endogenous brain dynamics of epilepsy patients, using phase-synchrony and phase-connectivity analysis, as seizures evolve. The proposed analytical method was applied to seizures recorded using depth electrodes implanted in hippocampus and amygdala in three patients. A reduction in phase-synchrony was observed in all patients around seizure onset. However, phase-synchrony started to gradually increase from mid-ictal and achieved its maximum level at seizure termination. This result suggests that hyper-synchronization of the epileptic network may be a crucial mechanism by which the brain naturally terminates seizure. Stimulation frequency and locations that matched the network phase-synchrony at seizure termination were extracted using phase-connectivity analysis. One patient with temporal lobe epilepsy (TLE) had a stimulation frequency ∼15 Hz with the stimulation locations confined to the hippocampus. The other two patients with extra-temporal lobe epilepsy (ETE) had stimulation frequency ∼90 Hz with at least one stimulation location outside of hippocampus. These results suggest that DBS parameters should vary based on the patient’s underlying pathology. The proposed methodology provides an algorithm for tuning DBS parameters for individual patients in an effort to increase the clinical efficacy of the therapy.
kinfitr: Reproducible PET Pharmacokinetic Modelling in R
Authors: Matheson Granville J.
Published: September 2019

Quantification of Positron Emission Tomography (PET) data is performed using pharmacokinetic models. There exist many models for describing this data, each of which may describe the data better or worse depending on the specific application, and there are both theoretical, practical and empirical reasons to select any one model over another. As such, effective PET modelling requires a high degree of flexibility, while effective communication of all steps taken through scientific publications is not always feasible. Reproducible research practices address these concerns, in that researchers share analysis code, and data if possible, such that all steps are recorded, allowing an independent researcher to reproduce the results and assess their veracity. In this article, I presentkinfitr: a software package for performing kinetic modelling using the open-source R language, in a reproducible manner. The R community has a strong culture of reproducible research, and the language consists of numerous tools which allow both effective and easy sharing and communication of analysis code. The package is written in such a way as to allow the analyst the freedom to use and rapidly exchange between approaches, and to assess goodness of fit, with 14 different kinetic models currently implemented using a consistent syntax, as well as tools for working with the data. By providing open-source tools for kinetic modelling, including documentation and examples, it is hoped that this will extend access to methodology for research groups lacking software engineering expertise, as well as simplify and thereby encourage transparent and reproducible reporting.
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
Authors: Chen Yuhao , Brook Thomas C. , Soe Cho Zin , O’Neill Ian , Alcon-Giner Cristina , Leelastwattanagul Onnicha , Phillips Sarah , Caim Shabhonam , Clarke Paul , Hall Lindsay J. , Hoyles Lesley
Published: September 2019

Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis, nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella as previous studies have focussed on recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for isolates. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. ‘healthy’) encoded multiple β-lactamases, which may prove problematic when defining treatment regimens for NEC or sepsis, and suggest ‘healthy’ preterm infants contribute to the resistome. No difference was observed between isolates recovered from ‘healthy’ and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Using a curated dataset of Klebsiella oxytoca, K. grimontii and K. michiganensis whole-genome sequences, metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut, and highlight the importance of refined analyses with curated sequence databases when studying closely related species present in metagenomic data.
Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage
Authors: Janissen Richard , Eslami-Mossallam Behrouz , Artsimovitch Irina , Depken Martin , Dekker Nynke H.
Published: September 2019

Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examined the E. coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identified, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We further identified two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlie elongation-rate switching, and RNA cleavage deficiency that underpins different long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.
Trypsin treatment unlocks barrier for zoonotic coronaviruses infection
Authors: Menachery Vineet D. , Dinnon Kenneth H. , Yount Boyd L. , McAnarney Eileen T. , Gralinski Lisa E. , Hale Andrew , Graham Rachel L. , Scobey Trevor , Anthony Simon J. , Wang Lingshu , Graham Barney , Randell Scott H. , Lipkin W. Ian , Baric Ralph S.
Published: September 2019

Traditionally, the emergence of coronaviruses (CoVs) has been attributed to a gain in receptor binding in a new host. Our previous work with SARS-like viruses argued that bats already harbor CoVs with the ability to infect humans without adaptation. These results suggested that additional barriers limit the emergence of zoonotic CoV. In this work, we describe overcoming host restriction of two MERS-like bat CoVs using exogenous protease treatment. We found that the spike protein of PDF2180-CoV, a MERS-like virus found in a Ugandan bat, could mediate infection of Vero and human cells in the presence of exogenous trypsin. We subsequently show that the bat virus spike can mediate infection of human gut cells, but is unable to infect human lung cells. Using receptor-blocking antibodies, we show that infection with the PDF2180 spike does not require MERS-CoV receptor DPP4 and antibodies developed against the MERS spike receptor-binding domain and S2 portion are ineffective in neutralizing the PDF2180 chimera. Finally, we found that addition of exogenous trypsin also rescues replication of HKU5-CoV, a second MERS-like group 2c CoV. Together, these results indicate that proteolytic cleavage of the spike, not receptor binding, is the primary infection barrier for these two group 2c CoVs. Coupled with receptor binding, proteolytic activation offers a new parameter to evaluate emergence potential of CoVs and offer a means to recover previously unrecoverable zoonotic CoV strains.

Importance

Overall, our studies demonstrate that proteolytic cleavage is the primary barrier to infection for a subset of zoonotic coronaviruses. Moving forward, the results argue that both receptor binding and proteolytic cleavage of the spike are critical factors that must be considered for evaluating the emergence potential and risk posed by zoonotic coronaviruses. In addition, the findings also offer a novel means to recover previously uncultivable zoonotic coronavirus strains and argue that other tissues, including the digestive tract, could be a site for future coronavirus emergence events in humans.
Phylogenetic, sequence and structural analysis of Insulin superfamily proteins reveals an indelible link between evolution and structure-function relationship
Authors: S. Shrilakshmi , Kundapura Shankar V. , Dey Debayan , Kulal Ananda , Ramagopal Udupi A.
Published: September 2019

The insulin superfamily proteins (ISPs), in particular, insulin, IGFs and relaxins are key modulators of animal physiology. They are known to have evolved from the same ancestral gene and have diverged into proteins with varied sequences and distinct functions, but maintain a similar structural architecture stabilized by highly conserved disulphide bridges. A recent surge of sequence data and the structures of these proteins prompted a need for a comprehensive analysis which connects the evolution of these sequences in the light of available functional and structural information and their interaction with cognate receptors. This study reveals a) unusually high sequence conservation of IGFs (>90%), which has never been reported before. In fact, it was interesting to observe that the functional domains (excluding signal peptide) of human, horse, pig and Ord’s kangaroo rat are 100% identical. (b) an updated definition of the signature motif of the relaxin family (c) a non-canonical C-peptide cleavage site in a few killifish insulin sequences and so on. We also provide a structure-based rationale for such conservation by introducing a concept called binding partners imposed evolutionary constraints. Furthermore, the high conservation of IGFs appears to represent a classic case of resistance to sequence diversity exerted by physiologically important interactions with multiple partners. Furthermore, we propose a probable mechanism for C-peptide cleavage in killifish insulin sequences.
Insertions ofP{lacW}andP{EP}artificial transposons on the chromosomal divisions ofDrosophila melanogasterare not randomly distributed
Authors: Marian Bologa Alexandru , Cristian Ghita Iulian , Cristian Ratiu Attila , Al. Alexandru Ecovoiu
Published: September 2019

Herein we describe the distribution of P{lacW} and P{EP} artificial transposons in the genome of Drosophila melanogaster. A total number of 5,560 P{lacW} and 3,786 P{EP} insertions available on FlyBase were extracted from this database and ordered according to the chromosomal regions they hit. Comparative bioinformatics analysis revealed that the insertion’s patterns are similar for P{lacW} and P{EP}. The two patterns are significantly correlated for chromosomes X, 2L, 2R and 3L, but not for 3R.

Fourier analysis revealed a periodic behaviour in the distribution of insertions, which approximates insertional hotspots. Our results raise questions concerning if and how the local chromosomal landscape affects the insertion patterns of different but related transposons.
Miocene and Pliocene speciation ofRussulasubsectionRoseinaein temperate forests of eastern North America
Authors: Looney Brian P. , Adamčík Slavomír , Matheny P. Brandon
Published: September 2019

Numerous lineages of mushroom-forming fungi have been subject to bursts of diversification throughout their evolutionary history, events that can impact our ability to infer well-resolved phylogenies. However, groups that have undergone quick genetic change may have the highest adaptive potential. As the second largest genus of mushroom-forming fungi,Russulaprovides an excellent model for studying hyper-diversification and processes in evolution that drives it. This study focuses on the morphologically defined group –RussulasubsectionRoseinae. Species hypotheses based on morphological differentiation and multi-locus phylogenetic analyses are tested in theRoseinaeusing different applications of the multi-species coalescent model. Based on this combined approach, we recognize fourteen species inRoseinaeincluding the Albida and wholly novel Magnarosea clades. Reconstruction of biogeographic and host association history suggest that parapatric speciation in refugia during glacial cycles of the Pleistocene drove diversification within theRoseinae, which is found to have a Laurasian distribution with an evolutionary origin in the Appalachian Mountains of eastern North America. Finally, we detect jump dispersal at a continental scale that has driven diversification since the most recent glacial cycles.
Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene
Authors: Qiao Wenjing , Puentes Jácome Luz A. , Tang Xianjin , Lomheim Line , Yang Minqing Ivy , Gaspard Sarra , Avanzi Ingrid Regina , Wu Jichun , Ye Shujun , Edwards Elizabeth A.
Published: September 2019

Intensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient γ-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3µM/day to ∼12µM/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from β (0.77±0.15), α (0.55±0.09), γ (0.13±0.02) to δ (0.06±0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance ofPelobacterandDehalobacter, especially in the α-HCH and δ-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.
Mate-finding dispersal reduces local mate limitation and sex bias in dispersal
Authors: Mishra Abhishek , Tung Sudipta , Sruti V.R. Shree , Srivathsa Sahana V. , Dey Sutirth
Published: September 2019

Sex-biased dispersal (SBD) often skews the local sex ratio in a population. This can result in a shortage of mates for individuals of the less-dispersive sex. Such mate limitation can lead to Allee effects in populations that are small or undergoing range expansion, consequently affecting their survival, growth, stability and invasion speed.

Theory predicts that mate shortage can lead to either an increase or a decrease in the dispersal of the less-dispersive sex. However, neither of these predictions have been empirically validated.

To investigate how SBD-induced mate limitation affects dispersal of the less-dispersive sex, we used Drosophila melanogaster populations with varying dispersal propensities. To rule out any mate-independent density effects, we examined the behavioral plasticity of dispersal in presence of mates as well as same-sex individuals with differential dispersal capabilities.

In the presence of high-dispersive mates, the dispersal of both male and female individuals was significantly increased. However, the magnitude of this increase was much larger in males than in females, indicating that the former show greater mate-finding dispersal. Moreover, the dispersal of either sex did not change when dispersing alongside high- or low-dispersive individuals of the same sex. This suggested that the observed plasticity in dispersal was indeed due to mate-finding dispersal, and not mate-independent density effects.

Strong mate-finding dispersal can diminish the magnitude of sex bias in dispersal. This can modulate the evolutionary processes that shape range expansions and invasions, depending on the population size. In small populations, mate-finding dispersal can ameliorate Allee effects. However, in large populations, it can dilute the effects of spatial sorting.
Hsa_circ_0001947 suppresses acute myeloid leukemia progression by sponging hsa-miR-329-5p and regulating CREBRF expression
Authors: Han Fengjiao , Zhong Chaoqin , Li Wei , Wang Ruiqing , Zhang Chen , Yang Xinyu , Ji Chunyan , Ma Daoxin
Published: September 2019

Acute myeloid leukemia (AML) is a heterogeneous group of diseases resulting from clonal transformation of hematopoietic precursors through the acquisition of chromosomal rearrangements and multiple gene mutations. Accumulating evidence has indicated that aberrantly expressed circular RNAs (circRNAs) are involved in cancer development and progression. However, their clinical values and biological roles in AML remain unclear. In this study, we identified the aberrantly down-regulated profile of hsa_circ_0001947 in AML through microarray analysis and validated it with quantitative reverse transcription polymerase chain reaction (qRT-PCR). Then, we explored the clinical significance, biological functions and regulatory mechanisms of hsa_circ_0001947 in AML patients. The results showed that lower hsa_circ_0001947 expression was positively correlated with higher leukemia cells in bone marrow or peripheral blood, indicating poor prognosis. Further, bioinformatics analysis demonstrated hsa_circ_0001947-hsa-miR-329-5p-CREBRF network. Down-regulation of hsa_circ_0001947 by siRNA promoted cell proliferation, inhibited apoptosis, reduced drug resistance of AML cells, and also decreased the expression of its targeted gene, CREBRF. The mimics of hsa-miR-329-5p reduced drug resistance and decreased the expression of CREBRF, while its inhibitor manifested anti-leukemia effects and increased CREBRF expression. In vivo studies revealed that silencing hsa_circ_0001947 promoted the tumor growth in BALB/c nude mice. Collectively, our findings suggest that hsa_circ_0001947 functions as a tumor inhibitor to suppress AML cell proliferation through hsa-miR-329-5p/CREBRF axis, which would be a novel target for AML therapy.
DETECTing Merkel cell Polyomavirus in Merkel Tumours
Authors: Arora Reety , Gupta Komal , Vijaykumar Anjali , Krishna Sudhir
Published: September 2019

Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer caused either by Merkel cell polyomavirus (MCV) T antigen expression, post integration (∼80% cases), or by UV mediated DNA damage. Interestingly, overall survival of patients suffering from MCV positive Merkel cell carcinoma is better, making this differential information of significant diagnostic and prognostic value. Also, MCV as a causative agent also provides a direct target for therapy in virus positive MCC patients. Currently, the methods used for diagnosis of MCV in tumours are often tedious, discordant and unreliable. In this study we used a guided molecular scissors based - DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR) technique to develop anin vitromolecular diagnostic tool for MCV positive MCC. DETECTR couples recombinase polymerase based amplification of target MCV DNA with Cas12a mediated detection. CRISPR diagnostics couple specific detection followed by cutting of the pathogenic DNA by the Cas enzyme – gRNA complex, with non-specific cutting of ssDNA that provides a measurable visual cue. To detect MCV DNA in MCC tumours, we designed Cas12a gRNAs targeting the MCV DNA and tested their targeting efficiency, and sensitivity using a fluorophore quencher labeled reporter assay. We show that this sophisticated MCV DETECTR system can detect MCV integrated in Merkel tumour rapidly, specifically and with femto-molar sensitivity. This new MCV DNA detecting system is promising and we hope it can be coupled with histopathological and immunohistochemical studies to diagnose the viral status of MCC in clinics in the near future.
Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments
Authors: Lynch Eric M. , Kollman Justin M.
Published: September 2019

Many enzymes assemble into defined oligomers, providing a mechanism for cooperatively regulating enzyme activity. Recent studies in tissues, cells, andin vitrohave described a mode of regulation in which enzyme activity is modulated by polymerization into large-scale filaments1–5. Enzyme polymerization is often driven by binding to substrates, products, or allosteric regulators, and tunes enzyme activity by locking the enzyme in high or low activity states1–5. Here, we describe a unique, ultrasensitive form of polymerization-based regulation employed by human CTP synthase 2 (CTPS2). High-resolution cryoEM structures of active and inhibited CTPS2 filaments reveal the molecular basis of this regulation. Rather than selectively stabilizing a single conformational state, CTPS2 filaments dynamically switch between active and inactive filament forms in response to changes in substrate and product levels. Linking the conformational state of many CTPS2 subunits in a filament results in highly cooperative regulation, greatly exceeding the limits of cooperativity for the CTPS2 tetramer alone. The structures also reveal a link between conformational state and control of ammonia channeling between the enzyme’s two active sites. This filament-based mechanism of enhanced cooperativity demonstrates how the widespread phenomenon of enzyme polymerization can be adapted to achieve different regulatory outcomes.
Cell cycle regulation of mitochondrial protein import revealed by genome-scale pooled bimolecular fluorescence complementation screening
Authors: Blakely Kim , Mero Patricia , Arnold Roland , Saleem Ayesha , Misquitta Christine , Kasimer Dahlia , Kumar Sachin , Uetrecht Andrea , Brown Kevin A. , Datti Alessandro , Hood David , Kim Philip , Moffat Jason
Published: September 2019

A central focus of systems biology is the functional mapping of protein-protein interactions under physiological conditions. Here we describe MaGiCaL-BiFC, a lentivirus-based bimolecular fluorescence protein-fragment complementation approach for the high-throughput, genome-scale identification of protein-protein interactions in mammalian cells. After developing and validating this methodology using known protein-protein interaction pairs, we constructed genome-scale pooled BiFC libraries using the human ORFeome cDNA collection. These pooled libraries, containing ∼ 12,000 unique human cDNAs, were used to screen for candidate interaction partners of the mitochondrial transmembrane protein TOMM22. Following infection of cells with the TOMM22 bait and the pooled cDNA libraries, cells harboring candidate TOMM22 interacting proteins were isolated from the cell pool via fluorescence activated cell sorting, and identified via microarray analysis. This approach identified several known interaction partners of TOMM22, as well as novel physical and functional partners that link the mitochondrial network to proteins involved in diverse cellular processes. Notably, protein kinase CK2 was identified as a novel physical interaction partner of human TOMM22. We found that this association occurs preferentially during mitosis and involves direct phosphorylation of TOMM22, an event that may lead to attenuation of mitochondrial protein import. Together, this data contributes to the growing body of evidence suggesting eloquent coordination between cell cycle progression and mitochondrial physiology. Importantly, through high-throughput screening and focused validation, our study demonstrates the power of the MaGiCaL-BiFC approach to uncover novel functional protein-protein interactions, including those involving proteins with membrane-spanning domains, or of a transient nature, all within their native cellular environment.