bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in Modifiable Health Behaviors During the Pandemic and Effects on Mental Health: Evidence From England
Authors: Gessa Giorgio Di , Zaninotto Paola
Published: December 2021

COVID-19 mitigation efforts (including lockdowns and advice to stay at home as much as possible) are likely to have resulted in changes in health behaviours such as the amount of sleep, physical exercise, alcohol use, and eating. To date, little is known about how and to what extent these changes in health behaviours since the beginning of the pandemic are related to mental health. Using pre-pandemic data from Wave 9 (2018/19) and from two Covid-19 sub-studies (with data collection in June/July and November/December 2020) of the English Longitudinal Study of Ageing, we investigate how changes in health behaviour during the initial months of the pandemic are associated with subsequent mental health among older people. In our regression analyses, we considered depression and anxiety and controlled for pre-pandemic measures of mental health. Between March and June/July 2020, about a third of older people reported less physical activity; one in five less sleep; and one in ten eating less food and drinking more. Compared to respondents who did not change their behaviours, those who reported sleeping and eating both more and less, and who mentioned less physical activity were more likely to report depression and anxiety, even taking into account pre-pandemic mental health. An increase in drinking was also marginally associated with higher depression. Policymakers should encourage older people who have engaged in unhealthier behaviours to modify them to reduce the negative long-term effects on their mental health.
Impact of COVID-19 Mortality on U.S. Life Expectancy by Socioeconomic Rank of County of Residence
Authors: Dukhovnov Denys , Barbieri Magali
Published: December 2021

Mortality disparities due to COVID-19 pandemic in the US accentuated the gap in the targeted public health and education response among disadvantaged communities. We use county data from John Hopkins University of Medicine in conjunction with county socioeconomic decile rankings, and weekly national data from the Centers for Disease Control to uncover the impact of county-level socioeconomic deprivation on the spatio-temporal dynamic of COVID-19 mortality. We estimate that over the course of 2020, the pandemic reduced the life expectancy at birth by 1.33 years (95% CI 1.0-1.56), and by 0.84 years (95% CI 0.59-1.0) by age 85 across all county SES decile groups, relative to the previous year's projection. The highest losses occurred in counties at the ends of the deprivation spectrum, and least affecting those in its middle. Decomposition of the impact of the COVID-19 mortality by seasonal time periods of 2020 reveals that coastal urban and high-SES counties endured a heavy death toll in the initial stages of the pandemic, though managed to cut it by more than a half by the end of 2020. The least affluent, inland, and rural counties have experienced a dramatic and lasting increase in deaths toward the second half of the year. We find that preexisting socioeconomic disparities before COVID-19 remained in force during the pandemic, leaving populations at all ages residing in underserved communities at a greater risk. This both calls into question and further instructs the ongoing public health interventions enabling more effective and equitable infectious disease mitigation strategies.
Joseph T. Freeman and Excellence in Rehabilitation Award Lecture
Authors: Strotmeyer Elsa
Published: December 2021

The Joseph T. Freeman Award lecture will feature an address by the 2021 Freeman Award recipient Pamela Cacchione, PhD, CRNP, BC, FGSA, FAAN, of the University of Pennsylvania. The Joseph T. Freeman Award is a lectureship in geriatrics awarded to a prominent clinician in the field of aging, both in research and practice. The award was established in 1977 through a bequest from a patient's estate as a tribute to Dr. Joseph T. Freeman. The Excellence in Rehabilitation of Aging Persons Award lecture will feature an address by the 2021 Excellence in Rehabilitation Award recipient Gregory Hicks, MPT, PhD of the University of Delaware. The Excellence in Rehabilitation of Aging Persons Award is designed to acknowledge outstanding contributions in the field of the rehabilitation of aging individuals.
Joseph T. Freeman Award: Creating Synergy in Interdisciplinary Aging Research and Practice
Authors: Cacchione Pamela
Published: December 2021

Over 30 years of interdisciplinary practice stimulated many research questions. Early intervention research in sensory impairment, specifically vision and/or hearing impairment was heavily supported by interdisciplinary colleagues from Geriatric Medicine, Nursing, Occupational Therapy, Optometry and Audiology. Challenges and opportunities from this research created a growing interest in developing and designing technologies for older adults. Creating the need for partnerships with engineering. My expertise in aging and access to willing research participants made me an ideal research partner. Effectively expanding my focus beyond sensory impairment interventions to designing and testing robots with older adults. Currently we are testing low cost mobile robots in acute care and the community and are developing and testing a soft robot to assist persons out of a chair as well as turn and lift persons up in bed. The synergy of interdisciplinary practice and research is helping us innovate to improve the lives of older adults.
Challenges Reported by Certified Nursing Assistants During COVID-19: A Qualitative Study
Authors: Reinhardt Joann , Franzosa Emily , Mak Wingyun , Burack Orah
Published: December 2021

Certified nursing assistants (CNAs) who care for vulnerable nursing home residents faced unprecedented circumstances due to the COVID-19 pandemic. While staff and PPE shortages were ubiquitous and widely known, the focus of this qualitative work was to gain a broader understanding of the numerous challenges they faced. We conducted 10 remote focus groups with CNAs at 5 nursing homes (N=56) in downstate New York. Content analysis was conducted, and emerging themes identified. Results showed a myriad of emotional challenges including helplessness, fear and anxiety. Operational challenges focused on lack of COVID testing capacity, information, and consistent guidance and support, in addition to staff and equipment. Individual challenges included personal experience of COVID illness and that of colleagues, and balancing high concurrent demands of work and family. These results are discussed in the context of developing recommendations to promote future safety, skill refinement and enhanced resilience in the workforce moving forward.
Observing Personality in Everyday Life: How Personality Influences Daily Activities and Mood
Authors: Zhang Shiyang
Published: December 2021

Personality reflects the influence of older adults’ past experiences on their tendencies to engage in certain behaviors and generate emotions. An increasing number of studies have focused on the expression of personality in older adults’ everyday life. Specifically, personality features have been associated with daily activities, affect reactivity, and mood. This symposium draws on Ecological Momentary Assessments and longitudinal analysis to understand how personality is manifested in daily life, and how daily emotional experiences accumulate over time to influence physical health. Lee and colleagues examine how personality is associated with daily activities and find that extraversion is positively associated with activity diversity in two adult samples. Pasquini and colleagues consider the within-person fluctuations in personality traits and demonstrate the possibility of using daily behaviors and affect as markers of extraversion and neuroticism. Zhang and Fingerman assess how positive and negative moods concurrently change in reaction to daily social contacts and confirm that narcissism moderates such associations. Finally, this symposium also focuses on the cumulative effect of daily emotions on physical health. Leger and colleagues address the long-term association between personality (e.g., neuroticism, conscientiousness) and physical health and identify the mediating role of negative reactivity to daily stressors. Collectively, the presentations provide an in-depth analysis of personality’s impact on concrete daily behaviors and emotions, as well as their profound long-term effect on physical health. Our discussion outlines future research directions and highlights how inter-individual differences, simultaneous life events, and social interactions intertwine to influence individuals’ behaviors that occur in natural settings.
Race Differences in Trajectories of Hopelessness Among U.S. Older Adults: Do Social Conditions Matter?
Authors: Mitchell Uchechi , Graetz Elena , Wang Jing
Published: December 2021

Despite being a risk factor for cardiovascular disease, suicidal ideation, and mortality among U.S. older adults, research on hopelessness and how it changes over time are lacking. Although hopelessness generally increases with age, levels of hopelessness may be influenced by race/ethnicity and social or economic factors. This study uses longitudinal data from 8,359 individuals from the Health and Retirement Study to examine race differences in trajectories of hopelessness from 2006 to 2018. We used linear mixed models to estimate trajectories of hopelessness for blacks, whites and Hispanics age 51 and older. The model was fit with a natural spline cubic function to model changes in time trends of hopelessness and the interaction between time and race. Models controlled for demographic characteristics, socioeconomic status, health status, and psychosocial factors that influence hopelessness. We found that older Hispanics have the highest levels of hopelessness, followed by non-Hispanic blacks and non-Hispanic whites. Trajectories of hopelessness were non-linear and differed by race. For older whites, hopelessness increased from 2006-2010 and then decreased until 2018. For older blacks, it decreased the entire time period but did so at a decreasing rate; and, for older Hispanics, hopelessness decreased from 2006-2012 and then increased thereafter. Our study shows that hopelessness generally decreased over time among older adults between 2006 and 2018 in race-specific ways, despite generally increasing with age. These findings suggest that race, age and period effects differentially influence trajectories of hopelessness. Factors contributing to these differences may be related to concurrent social and economic conditions.
Privacy and Smart Speakers in Research With Older Adults
Authors: Quinn Kelly , Chin Jessie , Desai Smit , O'Connell Carrie , Marquez David , Muramatsu Naoko
Published: December 2021

Advances in artificial intelligence and computational linguistics have made smart speakers, such as Amazon Alexa^TM^ and Google Home^TM^, economical and widely available. For older adults particularly, devices with voice interfaces can help to overcome accessibility challenges that often accompany interaction with today’s technologies. However, voice-activation also requires devices to be in a continuous state of ambient listening, which can create a significant privacy risk for the user, one that is often amplified as smart speakers are placed in highly personal home spaces to facilitate their utility. Deployment of these devices in research settings poses additional risk, as traces of data filter through research teams, app developers, and third-party services that support research efforts. This presentation addresses the privacy aspects of deploying Google Home Mini^TM^ speakers in research that examined their feasibility for enhancing physical activity among sedentary older adults. Interviews with participants were conducted in two studies: the first included a demonstration of the device and physical activity program (n=15); and the second included in-home use of devices and a physical activity program (n=15). Content analysis of study documentation, field notes, and interviews revealed specific areas that require additional attention when utilizing smart speakers in research, including the capture of identifying information, protocols for data handling, and requirements for informed consent. These findings are discussed in context with extant literature on individual privacy concerns and behaviors related to smart household devices. Results from this study can inform future research efforts incorporating smart speakers, to mitigate potential risks of privacy violation.
John Henryism and Cognitive Function and Decline
Authors: McSorley V Eloesa , Howard Christopher , James Bryan , Shah Raj , Boyle Patricia , Barnes Lisa
Published: December 2021

Older Black adults in the US have higher prevalence and incidence of dementia and perform lower on cognitive tests than whites. Some of these differences have been attributed to facets of structural racism such as access to and quality of education and fewer socioeconomic resources. Here, we consider whether John Henryism (JH), a measure of self-perceived high-effort coping in the face of chronic environmental and psychosocial stressors, is associated with cognitive function and decline. JH has been associated with adverse cardiovascular health outcomes among African-Americans, especially those with fewer socioeconomic resources. Using data from MARS, we assessed whether JH, measured with an 8-item questionnaire (mean=16.9, sd=4.8, range: 4-27), was associated with level of cognitive function and rate of cognitive decline. We found one standard deviation increase in JH was associated with lower average cognitive function (□=-0.05, 95% CI: -0.09, -0.01). Higher JH was not associated with rate of cognitive decline.
Are Farmers Willing to Substitute Tobacco Cultivation? Evidence From Lichuan City, China
Authors: Wan Xinyu , Jin Jianjun , Ran Shenghong , Guan Tong , Qiu Xin
Published: December 2021

Introduction

Tobacco crop substitution is a critical element in implementing comprehensive tobacco control policies. Understanding tobacco farmers’ willingness or preferences is imperative to implement policies on tobacco crop substitution. This article assesses tobacco farmers’ individual willingness to substitute tobacco cultivation and investigates the factors that influence their willingness in Lichuan City, China.

Methods

We conducted a face-to-face survey with 280 tobacco farmers in Lichuan City of China to assess their willingness to substitute tobacco cultivation. The binary probit model was used to examine the factors influencing farmers’ willingness to substitute tobacco growing.

Results

The results show that fewer than one in five tobacco farmers are willing to substitute tobacco growing with other crops. The main reason for their unwillingness is that they thought the comparative income of growing tobacco was higher and more stable. The regression results show that tobacco farmers with higher education levels and more knowledge of tobacco crop substitution are more willing to take up tobacco crop substitution. Tobacco farmers’ household income decreased the likelihood of their willingness to replace tobacco cultivation. Farmers who perceived the economic benefits and health benefits of tobacco crop substitution are more likely to substitute tobacco cultivation with other crops.

Conclusions

Farmers’ willingness to substitute tobacco cultivation is low. Policy interventions are needed to increase farmers’ willingness to stop growing tobacco and to replace it with other alternative crops.

Implications

Few studies have investigated local farmers’ willingness to substitute tobacco cultivation in China. We found most tobacco farmers in the Lichuan City of China are unwilling to substitute tobacco growing with other crops. Farmers’ low support of tobacco crop substitution is associated with economic factors. Better education and more knowledge of tobacco crop substitution can increase farmers’ willingness to substitute tobacco cultivation.
Minimum Manufacturing Costs, National Prices, and Estimated Global Availability of New Repurposed Therapies for Coronavirus Disease 2019
Authors: Wang Junzheng , Levi Jacob , Ellis Leah , Hill Andrew
Published: December 2021

Background

Currently, only dexamethasone, tocilizumab, and sarilumab have conclusively been shown to reduce mortality of coronavirus disease 2019 (COVID-19). Safe and effective treatments will need to be both affordable and widely available globally to be used alongside vaccination programs. This analysis will estimate and compare potential generic minimum costs of a selection of approved COVID-19 drug candidates with available international list prices.

Methods

We searched for repurposed drugs that have been approved by at least one of the World Health Organization, US Food and Drug Administration, or the United Kingdom National Institute of Health and Care Excellence organizations or at least given emergency use authorization or recommended for off-label prescription. Drug prices were searched for dexamethasone, budesonide, baricitinib, tocilizumab, casirivimab, and imdevimab, and sarilumab, using active pharmaceutical ingredients (APIs) data extracted from global shipping records. This was compared with national pricing data from a range of low-, medium-, and high-income countries. Annual API export volumes from India were used to estimate the current availability of each drug.

Results

Repurposed therapies can be generically manufactured for some treatments at very low per-course costs, ranging from US $2.58 for intravenous (IV) dexamethasone (or US $0.19 orally) and US $4.34 for inhaled budesonide. No export price data were available for baricitinib, tocilizumab, casirivimab, and imdevimab, or sarilumab, but courses of these treatments have higher prices, ranging from US $6.67 for baricitinib to US $875.5 for sarilumab. When comparing international list prices, we found wide variations between countries.

Conclusions

Successful management of COVID-19 will require equitable access to treatment for all populations, not just those able to pay high prices. Dexamethasone and budesonide are widely available and affordable, whereas monoclonal antibodies and IV treatment courses are more expensive.
Epidemiology and Outcomes of Community-Acquired Escherichia coli Pneumonia
Authors: John Teny M , Deshpande Abhishek , Brizendine Kyle , Yu Pei-Chun , Rothberg Michael B
Published: December 2021

Background

E. coli is an under-recognized cause of bacterial community-acquired pneumonia (CAP). The objective of this study was to describe the epidemiology, risk factors, and outcomes of community-acquired Escherichia coli pneumonia in comparison with other gram-negative and pneumococcal pneumonias.

Methods

We conducted a large retrospective cohort study of adult patients admitted with pneumonia to 173 US hospitals included in the Premier Research database from July 2010 to June 2015. Patients were included if they had a principal diagnosis code for pneumonia or a principal diagnosis of respiratory failure or sepsis with a secondary diagnosis of pneumonia and had a positive blood or respiratory culture obtained on hospital day 1. The primary outcome was in-hospital case fatality. Secondary outcomes included intensive care unit admission, invasive mechanical ventilation, and use of vasopressors.

Results

Of 8680 patients with pneumonia and positive blood or respiratory cultures, 1029 (7.7%) had E. coli CAP. Patients with E. coli pneumonia were older and more likely to have a principal diagnosis of sepsis. Patients with E. coli pneumonia had significantly higher case fatality than patients with pneumococcal pneumonia (adjusted odds ratio, 1.55; 95% CI, 1.23–1.97), but it was not significantly different than other gram-negative pneumonias (adjusted odds ratio, 1.06; 95% CI, 0.85–1.32). Approximately 36% of the isolates were resistant to fluoroquinolones; 9.3% were resistant to ceftriaxone.

Conclusions

E. coli is an important cause of severe CAP; with mortality that was higher than pneumococcal pneumonia but similar to other gram-negative pneumonias. The rate of fluoroquinolone resistance was high, and empiric fluoroquinolones should be used with caution in these patients.
Hepatitis C Testing and Linkage to Care Among Adults on Probation in a Large US City
Authors: Kamis Kevin F , Wyles David L , Minturn Matthew S , Scott Tracy , McEwen Dean , Hurley Hermione , Prendergast Scott J , Rowan Sarah E
Published: December 2021

Background

Despite constituting the largest segment of the correctional population, individuals on probation remain largely unstudied with respect to hepatitis C virus (HCV) testing and linkage to care. We implemented an HCV testing and patient navigation program at an adult probation department.

Methods

Adults were tested at a local probation department with a rapid point-of-care HCV antibody (Ab) assay followed by a laboratory-based HCV ribonucleic acid (RNA) assay if anti-HCV positive. All individuals received counseling rooted in harm reduction principles. Individuals testing positive for HCV Ab were immediately linked to a patient navigator in person or via telephone. The patient navigator assisted patients through cure unless the patient was lost to follow-up. Study participation involved an optional survey and optional point-of-care human immunodeficiency virus test.

Results

Of 417 individuals tested, 13% were HCV Ab positive and 65% of those tested for HCV RNA (34 of 52) had detectable HCV RNA. Of the 14 individuals who linked to an HCV treatment provider, 4 completed treatment, as measured by pharmacy fill documentation in the electronic medical record, and 1 obtained sustained virologic response. One hundred ninety-three individuals tested for HIV; none tested positive.

Conclusions

The study cohort had a higher HCV seroprevalence than the general population (13% vs 2%), but linkage to care, completion of HCV treatment, and successful test-of-cure rates were all low. This study indicates that HCV disproportionately impacts adults on probation and prioritizing support for testing and linkage to care could improve health in this population. Colocalization of HCV treatment within probation programs would reduce the barrier of attending a new institution and could be highly impactful.
Clinical Utility of Semistructured Interview and Scales to Assess Withdrawal Syndromes With Dose Reduction or Discontinuation of Selective Serotonin Reuptake Inhibitors or Serotonin Norepinephrine Reuptake Inhibitors
Authors: Cosci Fiammetta , Romanazzo Sara , Mansueto Giovanni , Rontani Petra , Levitan Michelle N. , Halkjœr-Lassen Roseane D. , Quagliato Laiana A. , Nakamura Tomoyuki , Uematsu Ken , Nardi Antonio E. , Oe Misari , Chouinard Virginie-Anne , Chouinard Guy
Published: December 2021

Background

Withdrawal syndromes can occur after dose reduction or discontinuation of selective serotonin reuptake inhibitors (SSRIs) or serotonin-norepinephrine reuptake inhibitors (SNRIs). Few measurement instruments are available to assess them: Diagnostic Clinical Interview for Drug Withdrawal 1–New Symptoms of SSRI and SNRI (DID-W1) and Discontinuation Emergent Signs and Symptoms (DESS) checklist. We assessed their interrater reliability, verified the percent agreement between the two, and tested DESS sensitivity and specificity on the basis of the diagnoses formulated via the DID-W1.

Methods

One-hundred thirty-four subjects who referred for withdrawal at 3 outpatient facilities were enrolled and assessed via the DESS and the DID-W1. Percent agreement and Cohen κ were calculated to measure DID-W1 and DESS interrater reliability, as well as the agreement between DID-W1 and DESS items. Sensitivity and specificity of DESS were derived from the identification of true-positive, false-negative, true-negative, and false-positive on the DID-W1.

Results

Both tools showed excellent interrater reliability (DID-W1 Cohen κ = 0.958; DESS Cohen κ = 0.81–1). The degree of agreement between DID-W1 and DESS items was poor or fair (Cohen κ < 0.40) for some items and moderate (Cohen κ = 0.41–0.60) for others. Sensitivity and specificity of DESS were 0.937 (true-positive = 60, false-negative = 4) and 0.285 (true-negative = 20, false-positive = 50), respectively.

Conclusions

DID-W1 was a reliable method to identify and diagnose withdrawal syndromes. The DESS checklist showed to be a useful tool for detecting withdrawal SSRI/SNRI symptoms when the aim is to achieve high sensitivity to identify true positives.
EDS-related Feeding Difficulties: Preventing the Placement of a Surgical Feeding Tube
Authors: Kilgore Alexandra L. , Hawa Juliette T. , Liu Edwin , Belkind-Gerson Jaime , Santucci Kourtney Kuss
Published: December 2021

Feeding difficulties due to functional gastrointestinal (GI) symptoms (i.e., nausea, pain, and bloating) are well described in patients with hypermobile-type Ehlers-Danlos Syndrome. These symptoms are particularly difficult to treat when there is comorbid dysautonomia, usually manifesting as postural orthostatic tachycardia syndrome. Here, we describe a successful trial of multidisciplinary rehabilitative interventions to avoid placement of a surgical feeding tube in such a patient. Main components of intervention were intensive pelvic floor physiotherapy and biofeedback, occupational therapy focused on coping with feeding-related symptoms, psychology support, and medications targeting histamine blockade and enhancing intestinal motility.
Surgical Outcomes of Pancreatectomy with Resection of the Portal Vein and/or Superior Mesenteric Vein and Jejunal Vein for Pancreatic Head Cancer
Authors: Nagakawa Yuichi , Jang Jin-Young , Kawai Manabu , Kim Song Cheol , Inoue Yosuke , Matsuyama Ryusei , Heo Jin Seok , Honda Masayuki , Sugiura Teiichi , Ohtsuka Masayuki , Mizuno Shugo , Kwon Wooil , Uemura Kenichiro , Han Ho-Seong , Sugimoto Motokazu , Okano Keiichi , Nakamura Masafumi , Wada Keita , Kumamoto Yusuke , Osakae Hiroaki , Tsuchida Akihiko , Yoon Yoo-Seok , Park Joon Seong , Yamaue Hiroki , Endo Itaru
Published: December 2021

Objective:

The aim of this study was to investigate the safety and survival benefits of portal vein and/or superior mesenteric vein (PV/SMV) resection with jejunal vein resection (JVR) for pancreatic ductal adenocarcinoma (PDAC).

Summary Background Data:

Few studies have shown the surgical outcome and survival of pancreatic resection with JVR, and treatment strategies for patients with PDAC suspected of jejunal vein (JV) infiltration remain unclear.

Methods:

In total, 1260 patients who underwent pancreatectomy with PV/ SMV resection between 2013 and 2016 at 50 facilities were included; treatment outcomes were compared between the PV/SMV group (PV/ SMV resection without JVR; n = 824), PV/SMV-J1 V group (PV/SMV resection with first jejunal vein resection; n = 394), and PV/SMV-J2,3 V group (PV/SMV resection with second jejunal vein or later branch resection; n = 42).

Results:

Postoperative complications and mortality did not differ between the three groups. The postoperative complication rate associated with PV/ SMV reconstruction was 11.9% in PV/SMV group, 8.6% in PV/SMV-J1 V group, and 7.1% in PV/SMV-J2,3V group; there were no significant differences among the three groups. Overall survival did not differ between PV/SMV and PV/SMV-J1 V groups (median survival; 29.2 vs 30.9 months, P = 0.60). Although PV/SMV-J2,3 V group had significantly shorter survival than PV/SMV group who underwent upfront surgery (P = 0.05), no significant differences in overall survival of patients who received preoperative therapy. Multivariate survival analysis revealed that adjuvant therapy and R0 resection were independent prognostic factors in all groups.

Conclusion:

PV/SMV resection with JVR can be safely performed and may provide satisfactory overall survival with the pre-and postoperative adjuvant therapy.
Role of SAGA complex subunits in gene regulation of Candida albicans
Authors: Rashid Saima , Correia Mesquita Tuana Oliveira , Whiteway Malcolm
Published: December 2021

The SAGA (Spt-Ada-Gcn5-acetyltransferase) is an evolutionary conserved multidomain co-activator complex involved in gene regulation through its histone acetyltransferase (HAT) and deubiquitinase (DUB) functions. It is well studied in Saccharomyces cerevisiae, and recent reports from humans and Drosophila expand its importance from gene transcription regulation to transcription elongation, protein stability and telomere maintenance. In Candida albicans, little is known about the components of the SAGA complex and their influence in morphogenesis and stress response. In this work, we analysed individual components of the SAGA complex, their role in morphogenesis and responses to different signalling cues. We initially analysed conditionally repressed strains of SAGA complex subunits involved in the HAT function of the complex: Tra1, Ngg1, Spt7, Spt8, Taf5, Taf6, Taf9, and Taf10. It appears that the Tra1 might be essential for the viability of C. albicans, as we failed to obtain homozygous deletions although it showed detectible growth in the conditionally repressed strain. Also, we observed that TBP- associated factors are essential in C. albicans, possibly due to their role in the transcription initiation factor TFIID instead of SAGA. We also detected that the Spt8 repressed mutant was extensively invasive in YPD at 300C while a repressed Ngg1 was considerably less invasive compared to its wild type. Also, we have seen that the mutations affecting TBP-binding ability confer susceptibility to drugs, temperature, osmotic, oxidative and DNA damage stress. Further, it seems that the modules of SAGA complex might have antagonistic roles in expression regulation but this needs more in-depth study.
Investigation of the MFS drug transporter family in Candida parapsilosis using CRISPR-Cas9
Authors: Zhao Fang , Butler Geraldine
Published: December 2021

The function of specific transporters is a key feature underlying drug resistance in Candida species. Drug transporters fall into two main classes – ATP-binding cassette (ABC) transporters, and the major facilitator superfamily (MFS) transporters. Some members of the drug/H (+) antiporter (DHA1) of the MFS superfamily have been shown to function as multidrug transporters. We targeted 16 genes belonging to five families that compose one branch of the DHA1 transporter group. These include MDR1/FLR1, associated with multidrug resistance in C. albicans (3 members); TPO4, associated with polyamine transport (1 member); NAG3/4, associated with transport of N-acetyl glucosamine (2 members); TPO2/3, associated with polyamine transport (1 member); and TPO1/FLU1, possibly associated with fluconazole resistance (9 members). We used CRISPR-Ca9 based gene editing to explore the function of of the five families in C. parapsilosis.

All 16 members were individually disrupted by introducing stop codons in the first third of the open reading frames (editing), or by deleting the whole gene. In addition, members of each family were disrupted together, including all 9 members of the TPO1/FLU1 family. CPAR2_603010, CPAR2_207540, and CPAR2_301760 all belonged to the MDR1 family. Editing CPAR2_603010 conferred sensitivity to fluconazole and voriconazole, though disrupting the other two genes had no effect. The azole sensitivity of the CPAR2_603010 edited strain was reverted by introducing the wild type sequence. Disrupting CPAR2_603010 or CPAR2_301760 individually did not affect sensitivity to 4-nitroquinoline 1-oxide. However, the double disruptant was sensitive. Disrupting CPAR2_300760, a member of the TPO1/FLU1 family, resulted in sensitivity to mycophenolic acid. Whole genome sequencing analysis of a strain in which all nine TPO1 genes were disrupted revealed that few off-target effects introduced by the CRISPR-Cas9 system, as few unexpected changes were found after eight rounds of transformation.
Complex sphingolipids: Vital determinants of drug susceptibility, membrane integrity and pathogenesis of Candida glabrata
Authors: Shahi Garima , Kumar Mohit , Khandelwal Nitesh Kumar , Sarkar Parijat , Kumari Sonam , Chauhan Neeraj , Chattopadhyay Amitabha , Gaur Naseem A. , Prasad Rajendra
Published: December 2021

Complex Sphingolipids (SLs) are unique to fungi, which apart from being novel drug targets, also appear to act as molecular signals, in diverse biological processes. In this study, we have specifically blocked the key synthesis step of SLs metabolism by disruption of the uncharacterized CgIPT1 gene, which based on homology with other Candida spp., predicted to mediate the conversion of MIPC to M(IP)2C. We followed fusion based PCR homologous recombination method for IPT1 deletion by using dominant markerNAT1. The knockout was selected on a nourseothricin drug plate and confirmed by gene specific PCR and by checking M(IP)2C levels. We observed that the specific accumulation of MIPC or lack of M(IP)2C in C. glabrata displayed increased susceptibility to both imidazole’s (ketoconazole, miconazole and clotrimazole) and triazoles (fluconazole, itraconazole and posaconazole). RNA Sequencing of Cgipt1Δcells revealed no major impact on of expression levels of common MDR determinants albeit a distinct imbalances in expression of lipid homeostasis genes was evident. The Fluorescence Recovery after Photobleaching (FRAP) experiments confirmed that plasma membrane in Cgipt1Δ cells display a reduction in micro-viscosity leading to increase in drug diffusion and susceptibility of Cgipt1Δcells. Interestingly, the Cgipt1Δ also exhibit attenuated virulence in a murine model. Together, our data confirms the relevance of M(IP)2C in governing drug susceptibility and virulence in C. glabrata.
Exploration of anti EFG1 locked nucleic acid gapmers to control Candida albicans filamentation
Authors: Araújo Daniela , Mil-Homens Dalila , Jørgensen Per Trolle , Fialho Arsénio M. , Wengel Jesper , Henriques Mariana , Silva Sónia
Published: December 2021

Introduction:

Antisense oligonucleotides (ASOs) have been successfully utilized to silence gene expression for the treatment of many genetic human diseases, and particularly the locked nucleic acid (LNA) chemical modification is extensively used with this propose. However, LNA-modified ASOs have never been exploited for controlling virulence genes of Candida.

EFG1is an important determinant of virulence that is involved in the switch from yeast to filamentous forms in C. albicans. Thus, our main goal was to explore LNA antisense gapmers for controlling EFG1gene expression and to block C. albicans filamentation.

Methods:

A set of five LNA-modified gapmers were designed with different chemical modifications (phosphorothioate backbone (PS) and/or palmitoyl-2’-amino-LNA) and ASO length. The in vitro performance of the different ASOs was evaluatedon their ability to control EFG1 gene expression, by qRT-PCR, and to reduce C. albicans’ filamentation, through filaments’ enumeration by microscopy. The in vivo therapeutic potential of ASOs was assessed using a G. mellonella model of infection, through a survival assay.

Results:

In vitro results showed that all ASOs were able to reduce the levels of EFG1gene expression, consequently reducing the levels of C. albicans filamentation around 50%. Interestingly, in vivo tests showed that the LNA-modified gapmer with PS backbone and palmitoyl-2’-amino-LNA was more effective at preventing G. mellonella infections.

Conclusions:

Undeniably, this work promotes the development of a novel approach for the treatment of Candida infections based on the delivery of ASOs coupled with LNA chemical modification.
Identification of genome-wide alternative splicing events in sequential, isogenic clinical isolates of Candida albicans reveals a mechanism important for drug resistance and tolerance to cellular stress
Authors: Muzafar Suraya , Chauhan Neeraj , Sharma Ravi Datta , Prasad Rajendra
Published: December 2021

Alternative gene splicing (AS) is a process by which a single gene can give rise to different protein isoforms, generating proteome diversity. Despite recent advances in our understanding of AS in basic cellular processes, the role of AS in drug resistance and fungal pathogenesis is poorly understood. In Candida albicans, approximately 6% of the genes contain introns. Considering this low and random distribution of introns, we focused our study on alternative splicing (AS) and its impact on the development of drug resistance, an area largely unexplored in this yeast. We performed comparative RNA sequencing of sequential isogenic azole sensitive and resistant isolates of C. albicans. The analysis revealed differential expression of splice junctions/isoforms in 14 genes, between the drug sensitive and resistant isolates. Furthermore, C. albicans WT cells exposed to antifungal drugs, heat stress or metal deficiency also showed differential expression of isoforms for the genes undergoing AS. In this study we present data on the effect of AS on the function of SOD3. The C. albicans SOD3 has a single intron and is important for the removal of superoxide radicals. The overexpression of the two isoforms of SOD3 in its null background highlighted importance of spliced isoform in complementing the susceptibility to menadione. However, the two isoforms did not differ in rescuing the susceptibility of sod3Δ/Δto Amphotericin B. Collectively, these data suggest that AS may be a novel mechanism in C. albicans for stress adaptation and overcoming drug resistance.
FunHoMic: A Marie Skłodowska-Curie Innovative Training Network for the study of the Fungus-Host-Microbiota interplay
Authors: Cole Nathaniel , Marsaux Benoît , Rosati Diletta , Delavy Margot , Kosmala Daria , Xie Zixuan , Kaune Ann-Kristin , Valentine Marisa , Chakraborty Sayoni , Kaur Manjyot , Alaban Leovigildo Rey , Morelli Moran , Fróis-Martins Ricardo , Walker Alan , Van den Abbeele Pieter , Netea Mihai , Bougnoux Marie-Elisabeth , Manichanh Chaysavanh , Munro Carol , Hube Bernhard , Jacobsen Ilse , Roget Karine , Thomas Vincent , Queiroz Karla , Leibundgut-Landmann Salomé , Brown Alistair , d'Enfert Christophe
Published: December 2021

Introduction

The FunHoMic project is a Marie Skłodowska-Curie Innovative Training Network comprising 13 PhD students, 8 academic partners and 3 industry partnersaimingto understand the interplay between fungi, hostsand microbiota to improve prevention and treatment of fungal infections.

Importance

About 2 billion people suffer fungal infections, which have a mortality rate close to that of malaria or breast cancer. Candida albicans has a high clinical and economic burden, making it of particular interest to the FunHoMic project. 70% of women experience at least one episode of vulvovaginal candidiasis (“thrush”) during their lifetime; 8% suffer recurring infections. C. albicans may live as a commensal but can cause symptoms when the fungus-host-microbiota equilibrium is disrupted. Infections by C. albicans have a significant clinical impact, with fatalities in severe cases. Many factors are associated with C. albicans infections; intensive care, neutropenic and diabetic patients are most at risk of systemic infection. Rising antifungal drug resistance has led to certain C. albicans infections having no treatment option.

Aim

The FunHoMic consortium combines projectson fungal pathogenesis, immunology, microbial ecology and’omics technologies to understand and exploit interactions between fungus, host and microbiota. Identification of novel bio markers on the fungal side such as genetic polymorphisms or on the host side such asmicrobiota profiles, metabolites and/or immune markers can lead to patient classification based on relative risk of infection. This could be the beginning of personalised management for fungal infections using preventive or therapeutic interventions like new antifungals, immune modulators or Live Biotherapeutic Products (LBPs).

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the MarieSklodowska-Curie grant agreement No 812969.
Candida auris gene expression: modulation upon caspofungin treatment
Authors: Alves Lysangela , Amatuzzi Rafaela , Zamith-Miranda Daniel , Martins Sharon , Nosanchuk Joshua
Published: December 2021

Candida auris has emerged as a serious worldwide threat by causing invasive infections in humans that are frequently resistant to one or more conventional antifungal medications, resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective treatment approaches to combat this fungus. To date, there is little information about C. auris gene expression regulation in response to antifungal treatment. Our integrated analyses focused on the comparative transcriptomics of C. auris in the presence and absence of caspofungin as well as a detailed analysis of the yeast's extracellular vesicle (EV)-RNA composition. The results showed that genes coding oxidative stress response, ribosomal proteins, cell wall, and cell cycle were significantly up-regulated in the presence of caspofungin, whereas transcriptional regulators and proteins related to nucleus were down-regulated. The mRNAs in the EVswere associated with the stress responses induced by caspofungin and the ncRNA content of the EVs shifted during caspofungin treatment. Altogether, the results provide further insights into the fungal response to caspofungin and demonstrate that analyses of C. auris growth under antifungal stress can elucidate resistance and survival mechanisms of this fungus in response to medical therapy.
Genome-wide analysis of experimentally evolved Candida auris reveals multiple novel mechanisms of multidrug-resistance
Authors: Carolus Hans , Pierson Siebe , Mun?oz José F. , Subotić Ana , Cruz Rita B. , Cuomo Christina A. , Van Dijck Patrick
Published: December 2021

Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug-resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes and echinocandins. We show the stepwise accumulation of multiple novel mutations in genes known and unknown in antifungal drug resistance, albeit almost all new for C. auris. Echinocandin resistance was accompanied by a codon deletion in FKS1hot spot 1 and a substitution in FKS1 ‘novel’ hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1; a segmental duplication of chromosome 1 containing ERG11; and a whole chromosome 5 duplication, which contains TAC1b. The latter was associated with increased expression of ERG11, TAC1band CDR2, but not CDR1. The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential and diversity for MDR development in C. auris, even in a clade until now not associated with MDR (clade II),hereby stressing its clinical importance and the urge for future research.
A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities
Authors: da Costa Naíla Barbosa , Hébert Marie-Pier , Fugère Vincent , Terrat Yves , Fussmann Gregor F. , Gonzalez Andrew , Shapiro B. Jesse
Published: December 2021

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria.

IMPORTANCE

Glyphosate-based herbicides (GBHs) such as Roundup may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remains unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here we used freshwater mesocosm experiments to show that GBHs strongly select for ARGs, particularly multidrug efflux pumps. These selective effects are evident after just a few days, and at glyphosate concentrations that are high but still within short-term (1-4 day) regulatory limits. The ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes, and to a lesser extent by mutations in EPSPS. GBHs are therefore likely to select for higher ARG frequencies in natural streams, lakes, and ponds.
Development of a sensitive trial-ready poly(GP) CSF biomarker assay for C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis
Authors: Wilson Katherine M , Katona Eszter , Glaria Idoia , Swift Imogen J. , Sogorb-Esteve Aitana , Heller Carolin , Bouzigues Arabella , Heslegrave Amanda J , Patil Saurabh , Mohapatra Susovan , Liu Yuanjing , Goyal Jaya , Sanchez-Valle Raquel , Laforce Robert , Synofzik Matthis , Rowe James B. , Finger Elizabeth , Vandenberghe Rik , Butler Chris R. , Gerhard Alexander , van Swieten John , Seelaar Harro , Borroni Barbara , Galimberti Daniela , Mendonça Alexandre de , Masellis Mario , Tartaglia Carmela , Otto Markus , Graff Caroline , Ducharme Simon , Malaspina Andrea , Zetterberg Henrik , Boyanapalli Ramakrishna , Rohrer Jonathan D , Isaacs Adrian M
Published: December 2021

A GGGGCC repeat expansion in the C9orf72 gene is the most common cause of genetic frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). As potential therapies targeting the repeat expansion are now entering clinical trials, sensitive biomarker assays of target engagement are urgently required. We utilised the single molecule array (Simoa) platform to develop an immunoassay for measuring poly(GP) dipeptide repeat proteins (DPRs) generated by the repeat expansion in CSF of people with C9orf72-associated FTD/ALS. We show the assay to be highly sensitive and robust, passing extensive qualification criteria including low intra- and inter-plate variability, a high precision and accuracy in measuring both calibrators and samples, dilutional parallelism, tolerance to sample and standard freeze-thaw and no haemoglobin interference. We used this assay to measure poly(GP) DPRs in the CSF of samples collected through the Genetic FTD Initiative. We found it had 100% specificity and 100% sensitivity and a large window for detecting target engagement, as the C9orf72 CSF sample with the lowest poly(GP) signal had 8-fold higher signal than controls and on average values from C9orf72 samples were 38-fold higher than controls, which all fell below the lower limit of quantification of the assay. These data indicate that a Simoa-based poly(GP) DPR assay is suitable for use in clinical trials to determine target engagement of therapeutics aimed at reducing C9orf72 repeat-containing transcripts.