bluuebunny/crossref_metadata_2025 huggingface dataset:
Complementary, Integrative, and Nondrug Therapy Use for Pain Among US Military Veterans on Long-term Opioids
Authors: Goldsmith Elizabeth S. , MacLehose Richard F. , Jensen Agnes C. , Clothier Barbara , Noorbaloochi Siamak , Martinson Brian C. , Donaldson Melvin T. , Krebs Erin E.
Published: August 2020

Background:

Long-term opioid therapy for chronic pain arose amid limited availability and awareness of other pain therapies. Although many complementary and integrative health (CIH) and nondrug therapies are effective for chronic pain, little is known about CIH/nondrug therapy use patterns among people prescribed opioid analgesics.

Objective:

The objective of this study was to estimate patterns and predictors of self-reported CIH/nondrug therapy use for chronic pain within a representative national sample of US military veterans prescribed long-term opioids for chronic pain.

Research Design:

National two-stage stratified random sample survey combined with electronic medical record data. Data were analyzed using logistic regressions and latent class analysis.

Subjects:

US military veterans in Veterans Affairs (VA) primary care who received ≥6 months of opioid analgesics.

Measures:

Self-reported use of each of 10 CIH/nondrug therapies to treat or cope with chronic pain in the past year: meditation/mindfulness, relaxation, psychotherapy, yoga, t’ai chi, aerobic exercise, stretching/strengthening, acupuncture, chiropractic, massage; Brief Pain Inventory-Interference (BPI-I) scale as a measure of pain-related function.

Results:

In total, 8891 (65%) of 13,660 invitees completed the questionnaire. Eighty percent of veterans reported past-year use of at least 1 nondrug therapy for pain. Younger age and female sex were associated with the use of most nondrug therapies. Higher pain interference was associated with lower use of exercise/movement therapies. Nondrug therapy use patterns reflected functional categories (psychological/behavioral, exercise/movement, manual).

Conclusions:

Use of CIH/nondrug therapies for pain was common among patients receiving long-term opioids. Future analyses will examine nondrug therapy use in relation to pain and quality of life outcomes over time.
Predicting Patients at Risk for Prolonged Hospital Stays
Authors: Doctoroff Lauren , Herzig Shoshana J.
Published: August 2020

Background:

Patients with prolonged hospitalizations account for 14% of all hospital days in US hospitals. Predicting which medical patients are at risk for prolonged hospitalizations would allow early proactive management to reduce their length of stay.

Methods:

Using the National Inpatient Sample, we examined risk factors for prolonged hospitalizations among adults hospitalized on the medicine service in 2014. We defined prolonged hospitalizations as those lasting 21 days or longer. We divided the sample into derivation and validation sets, and used logistic regression to identify significant risk factors in the derivation set, which were validated in the validation set. We used the estimates from the model to derive a risk score for prolonged hospitalizations.

Results:

Our sample included 2,997,249 hospitalizations (median age of 66 y, 53.5% female). 1.2% of hospitalizations were 21 days or longer. Patients with prolonged hospitalizations were younger, and had a greater number of chronic diseases. A prolonged hospitalization risk score, derived from the many significant predictors in our model, performed well in discriminating between prolonged and nonprolonged hospitalizations, with c-statistics of 0.80 in both the derivation and validation sets.

Conclusions:

Our predictive model using readily available administrative data was able to discriminate between prolonged and nonprolonged hospitalizations in a national sample of medical patients, and performed well on internal validation. If prospectively validated, such a tool could be of use to hospitals and researchers interested in targeting development, testing, and/or deployment of programs to reduce length of stay.
Cost-effectiveness of Yoga for Chronic Low Back Pain in Veterans
Authors: Groessl Erik J. , Liu Lin , Richard Erin L. , Tally Steven R.
Published: August 2020

Background:

Yoga interventions can improve function and reduce pain in persons with chronic low back pain (cLBP).

Objective:

Using data from a recent trial of yoga for military veterans with cLBP, we analyzed the incremental cost-effectiveness of yoga compared with usual care.

Methods:

Participants (n=150) were randomized to either 2× weekly, 60-minute yoga sessions for 12 weeks, or to delayed treatment (DT). Outcomes were measured at 12 weeks, and 6 months. Quality-adjusted life years (QALYs) were measured using the EQ-5D scale. A 30% improvement on the Roland-Morris Disability Questionnaire (primary outcome) served as an additional effectiveness measure. Intervention costs including personnel, materials, and transportation were tracked during the study. Health care costs were obtained from patient medical records. Health care organization and societal perspectives were examined with a 12-month horizon.

Results:

Incremental QALYs gained by the yoga group over 12 months were 0.043. Intervention costs to deliver yoga were $307/participant. Negligible differences in health care costs were found between groups. From the health care organization perspective, the incremental cost-effectiveness ratio to provide yoga was $4488/QALY. From the societal perspective, yoga was “dominant” providing both health benefit and cost savings. Probabilistic sensitivity analysis indicates an 89% chance of yoga being cost-effective at a willingness-to-pay of $50,000. A scenario comparing the costs of yoga and physical therapy suggest that yoga may produce similar results at a much lower cost.

Discussion/Conclusions:

Yoga is a cost-effective treatment for reducing pain and disability among military veterans with cLBP.
Tailored to Fit
Authors: Purcell Natalie , Becker William C. , Zamora Kara A. , McGrath Sarah L. , Hagedorn Hildi J. , Fabian Eva R. , McCamish Nicole , Seal Karen H.
Published: August 2020

Background:

Veterans Affairs (VA) has rolled out a holistic, multicomponent Whole Health care model nationwide, yet no pragmatic trials have been conducted in real-world clinical settings to compare its effectiveness against other evidence-based approaches for chronic pain management in veterans.

Objectives:

We describe the adaptation of the first large pragmatic randomized controlled trial of the Whole Health model for chronic pain care for diverse VA clinical settings.

Research Design:

Informed by the Promoting Action on Research Implementation in Health Systems implementation framework, we conducted qualitative semistructured interviews to obtain feedback on trial design from VA leadership, frontline clinicians, and veterans with chronic pain at 5 VA enrollment sites. Next, we convened in-person evidence-based quality improvement (EBQI) meetings with study stakeholders (including frontline clinicians and administrators) at each site to discuss study design; review interview themes; and identify site-specific barriers, facilitators, and approaches to implementation. Ethnographic observations from EBQI meetings provided additional insight into implementation strategies.

Subjects:

Seventy-four veteran and VA staff stakeholders were interviewed; 71 stakeholders participated in EBQI meetings.

Results:

At each site, unique clinical contexts and varying resources for Whole Health and pain care delivery affected plans for trial implementation. We present examples of local adaptations that emerged through the formative evaluation process to facilitate implementation and yield a more pragmatic trial design.

Conclusions:

A systematic formative evaluation can facilitate engagement and buy-in of study stakeholders. Locally tailored pragmatic implementation strategies may improve the likelihood of successful trial execution as well as future implementation of evidence-based pain care approaches in real-world clinical settings.
Relation of the Networks Formed by Diabetic Patients Sharing Physicians With Emergency Department Visits and Hospitalizations
Authors: Davis James , Lim Eunjung , Taira Deborah A. , Chen John
Published: August 2020

Objective:

The objective of this study was to evaluate if the networks of diabetic patients sharing physicians are associated with emergency department (ED) visits and hospitalizations.

Study Design:

This is a retrospective cohort study.

Methods:

We used administrative data from a large insurer in Hawaii in 2010. Three types of networks were defined based on patient visits: (1) the total number of links from one patient to other patients sharing a physician; (2) the number of other patients connected by sharing the physician seen the most often; and (3) the number of other patients connected by seeing all the same physicians during the year. The networks were characterized into thirds based on their complexity and analyzed using zero-inflated negative binomial regression models on ED visits and hospitalizations.

Results:

The study included 38,767 diabetes patients with a mean age of 64 years. Patients sharing the most physicians had double the risks of ED visits and hospitalizations. Patients linked by belonging to the largest primary care practices had a 28% reduced odds of ED visits. Patients linked by seeing all of the same physicians during the year had the fewest primary care providers and specialists visits and 25%–50% reductions in ED visits and hospitalizations.

Conclusions:

Networks of diabetic patients sharing all the same physicians were associated with decreased ED visits and hospitalizations. Encouraging diabetic patients to find a provider they like and trust and to stay in the provider’s care may help reduce the risks of adverse events. Physicians building loyalty among their patients may reduce their patients’ risks.
The Utility of 18FDG PET/CT Versus Bone Scan for Identification of Bone Metastases in a Pediatric Sarcoma Population and a Review of the Literature
Authors: Tal Adit L. , Doshi Hiten , Parkar Fauziya , Abraham Tony , Love Charito , Ye Kenny , Yang Rui , Hoang Bang , Loeb David , Chou Alexander , Geller David , Moadel Renee
Published: August 2020

Background:

Outcome of patients with osteosarcoma (OS) and Ewing sarcoma (EWS) is dependent on presence of metastases. Imaging guidelines for OS and EWS include radiographs, computed tomography (CT), and magnetic resonance imaging for primary tumor evaluation and CT chest and bone scintigraphy (BS) for metastatic detection. 18Fluorodeoxyglucose (18FDG) positron emission tomography (PET)/CT has become more common for disease evaluation, yet there is no consensus for its use in this population.

Objective:

We aimed to compare identification of osseous metastases using BS versus 18FDG PET/CT in our patient population. We hypothesized that 18FDG PET/CT is more likely to detect osseous metastases both at diagnosis and relapse.

Materials and Methods:

We performed retrospective chart reviews of pediatric sarcoma patients treated at our institution from 2008 to 2019. Paired BS and 18FDG PET/CT scans were reviewed. Review of the literature was also performed.

Results:

Thirty-three patients had paired BS and 18FDG PET/CT during diagnosis or treatment. Fifteen patients had distant osseous metastases. In the OS cohort, 8/16 patients had osseous metastases; 100% of these patients were detected on 18FDG PET/CT and 75% on BS. Thirty-one bony lesions were seen on imaging in OS patients; 100% of these were identified on 18FDG PET/CT but only 29% on BS. In the EWS cohort, 6/15 patients had osseous metastases; 100% of these patients were detected on 18FDG PET/CT and 50% on BS. Eighteen bony lesions were seen on imaging in EWS patients; 94% of these were identified on 18FDG PET/CT, but only 28% on BS.

Conclusion:

For patients in our institution with OS or EWS, osseous metastases were more likely detected using 18FDG PET/CT.
Congenital Portosystemic Shunts and Liver Hemangiomas in Children: Is There an Association?
Authors: Kumar Manjusha , Natarajan Kannan , Dunn Rachel , Khan-Serrano Aliyah , Nakar Charles , Rampersad Angeli , Kumar Anil
Published: August 2020

Liver hemangiomas are benign vascular tumors of infancy. They can have vascular shunting mostly arteriovenous and sometimes arterioportal or portosystemic, which improves as hemangiomas involute. In contrast, congenital portosystemic shunts are developmental vascular anomalies that may go undetected for years, with significant sequelae. We describe a child with a history of multiple cutaneous and liver hemangiomas in infancy and later diagnosis of congenital portosystemic shunt. Past experience of a similar patient and a current baby followed for liver hemangiomas with portosystemic shunts, is also shared. Literature is reviewed for known association. We suggest longer-term follow-up for babies with liver hemangiomas.
Temperament and Character Profiles of Ankylosing Spondylitis Patients Compared With Major Depression Patients and Healthy Controls
Authors: Tönük Şükrü Burak , Arısoy Özden , Öztürk Erhan Arif , Boztaş Mehmet Hamid , Çifci Kaygusuz Çiğdem , Erdem Sultanoğlu Tuba
Published: August 2020

Background/Objective

Depressive disorder is common in patients with ankylosing spondylitis (AS), who exhibit specific brain imaging abnormalities resembling those in major depression (MD). We compared temperament and character profiles between patients with AS and MD.

Methods

The study involved 36 patients with AS, 40 with MD, and 36 healthy controls (HCs). The participants were age-, sex-, and education-matched. Depression, anxiety, temperament, and character were evaluated using the Temperament and Character Inventory and physician-rated Hamilton Depression and Anxiety Scales. Disease severity was assessed using the Bath Ankylosing Spondylitis Disease Activity, Radiology, Metrology, and Functionality Indexes; erythrocyte sedimentation rate; and C-reactive protein.

Results

Depression and anxiety scores were highest in MD, lowest in HCs, and intermediate in AS (p < 0.001). Harm avoidance was significantly higher in MD and AS than HCs (p = 0.01). Reward dependency was lower (p = 0.011) and self-transcendence higher in AS only (p = 0.034). Bath Ankylosing Spondylitis Radiology Index was negatively correlated with depression (p = 0.020). Bath Ankylosing Spondylitis Radiology Index and Bath Ankylosing Spondylitis Metrology Index were negatively correlated with harm avoidance (p < 0.05). Disease duration was negatively correlated with self-transcendence (p = 0.027). Harm avoidance was correlated with depression score (p = 0.029). Patients under tumor necrosis factor α inhibitor treatment had lower cooperativeness score (p = 0.022).

Conclusions

Patients with AS had a specific Temperament and Character Inventory pattern. Harm avoidance was common in both AS and MD. In AS, harm avoidance and depression decreased in patients with progression, probably because progressive fusion of the spinal segments causes decrease in pain. Harm avoidance (fear of pain) seemed to be an acting factor for occurrence of depressive symptoms in AS.
Impaired Cardiac Autonomic Control in Women With Fibromyalgia Is Independent of Their Physical Fitness
Authors: Schamne Julio Cezar , Ressetti Juliana Campos , Lima-Silva Adriano Eduardo , Okuno Nilo Massaru
Published: August 2020

Background/Objective

Evidence has suggested abnormal cardiac autonomic responses to exercise in patients with fibromyalgia (FM). However, it is not clear whether the dysautonomia represents a reduced physical fitness rather directly related to FM pathogenesis. Thus, we aimed to verify the cardiac autonomic responses before, during, and after a maximal incremental exercise in women with FM and whether these hypothesized alterations would be dependent with their physical fitness.

Methods

This is a cross-sectional study with 23 FM women and 17 healthy women. The participants performed a maximal incremental cycling test to determine their maximal workload (W
max) and were further matched by their W
max (14 FM patients, W
max: 128.6 ± 16.2 W; and 14 healthy women, W
max: 131.9 ± 15.9 W). Beat-to-beat heart rate (HR) was continuously monitored to calculate HR variability indexes at rest, chronotropic reserve during exercise, and HR recovery.

Results

Heart rate variability indexes related to vagal modulation were significantly lower in FM patients than in healthy women (p < 0.05). The chronotropic reserve and the HR recovery at 30, 120, 180, 300, and 600 seconds after exercise were all lower in FM patients compared with those of healthy women (p < 0.05). Similar findings were found when analysis was performed using the matched physical fitness subgroup.

Conclusions

The documented cardiac autonomic abnormalities at rest, during, and after exercise in FM patients persist even when physical fitness status is taken in account. Thus, strategies to attenuate the dysautonomia in FM patients must be considered.
Brevibacterium rongguiense sp. nov., isolated from freshwater sediment
Authors: Deng Tongchu , Lu Huibin , Qian Youfen , Chen Xingjuan , Yang Xunan , Guo Jun , Sun Guoping , Xu Meiying
Published: August 2020

A Gram stain-positive, non-spore-forming, non-motile and rod-shaped actinomycete, strain 5221T, was isolated from the sediment of a river collected at Ronggui in the Pearl River Delta, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a distinct lineage within the genus

Brevibacterium

and had the highest sequence similarity to

Brevibacterium pityocampae

Tp12T (96.7 %), followed by

Brevibacterium daeguense

2C6-41T (96.5 %),

Brevibacterium samyangense

SST-8T (96.0 %) and

Brevibacterium ravenspurgense

20T (95.9 %). The results of chemotaxonomic analyses, including detecting anteiso-C15 : 0, anteiso-C17 : 0, and C16 : 0 as the major cellular fatty acids, diphosphatidylglycerol, phosphatidylglycerol and three phosphoglycolipids as the polar lipids, MK-8(H2) as the major menaquinone, and a DNA G+C content of 72.4 mol%, supported that strain 5221T is a member of the genus

Brevibacterium

. Furthermore, low sequence similarities of 16S rRNA gene sequences, differences in fatty acid compositions and differential physiological characteristics such as enzyme activity and carbon sources utilization ability distinguished the isolate from its close relatives. Therefore, strain 5221T represents a novel species of the genus

Brevibacterium

, for which the name Brevibacterium rongguiense sp. nov. is proposed, with the type strain 5221T (=GDMCC 1.1766T=KACC 21700T).
Metabacillus sediminilitoris sp. nov., a marine bacterium isolated from a tidal sediment
Authors: Mao Haiyan , Wei Yuli , Gao Yuxin , Pei Jiahao , Zhang Yan , Fang Jiasong
Published: August 2020

A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain DSL-17T, was isolated from a tidal sediment of the East China Sea and characterized phylogenetically and phenotypically. The strain could grow at 16–47 °C (optimum 37 °C), at pH 6.0–10.0 (optimum 6.0) and with 1–7% (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSL-17T was related to members of the genus

Metabacillus

and shared the highest similarity with

Metabacillus litoralis

SW-211T (98.6 %), followed by

Metabacillus halosaccharovorans

E33T (97.9 %),

Metabacillus crassostreae

JSM 100118T (97.7 %),

Metabacillus niabensis

4T19T (97.7 %) and

Metabacillus malikii

NCCP-662T (97.5 %). 16S rRNA gene sequence similarities between strain DSL-17T and other members of the genus

Metabacillus

were below 96.6 %. The sole respiratory quinone was MK-7. Strain DSL-17T had a cell-wall peptidoglycan based on meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), three unidentified glycolipids and six unidentified lipids. The strain had iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and iso-C16 : 0 as major fatty acids. The G+C content of the genomic DNA was 35.7 mol%. The combined genotypic and phenotypic data indicated that strain DSL-17T represents a novel species of the genus

Metabacillus

, for which the name Metabacillus sediminilitoris sp. nov. is proposed The type strain is DSL-17T (=MCCC 1K03777T=DSM 109843T).
Nocardia macrotermitis sp. nov. and Nocardia aurantia sp. nov., isolated from the gut of the fungus-growing termite Macrotermes natalensis
Authors: Benndorf René , Schwitalla Jan W. , Martin Karin , de Beer Z. Wilhelm , Vollmers John , Kaster Anne-Kristin , Poulsen Michael , Beemelmanns Christine
Published: August 2020

The taxonomic positions of two novel aerobic, Gram-stain-positive Actinobacteria, designated RB20T and RB56T, were determined using a polyphasic approach. Both were isolated from the fungus-farming termite Macrotermes natalensis. Results of 16S rRNA gene sequence analysis revealed that both strains are members of the genus

Nocardia

with the closest phylogenetic neighbours

Nocardia miyunensis

JCM12860T (98.9 %) and

Nocardia nova

DSM44481T (98.5 %) for RB20T and

Nocardia takedensis

DSM 44801T (98.3 %),

Nocardia pseudobrasiliensis

DSM 44290T (98.3 %) and

Nocardia rayongensis

JCM 19832T (98.2 %) for RB56T. Digital DNA–DNA hybridization (DDH) between RB20T and

N. miyunensis

JCM12860T and

N. nova

DSM 44481T resulted in similarity values of 33.9 and 22.0 %, respectively. DDH between RB56T and

N. takedensis

DSM44801T and

N. pseudobrasiliensis

DSM44290T showed similarity values of 20.7 and 22.3 %, respectively. In addition, wet-lab DDH between RB56T and

N. rayongensis

JCM19832T resulted in 10.2 % (14.5 %) similarity. Both strains showed morphological and chemotaxonomic features typical for the genus

Nocardia

, such as the presence of meso-diaminopimelic acid (A2pm) within the cell wall, arabinose and galactose as major sugar components within whole cell-wall hydrolysates, the presence of mycolic acids and major phospholipids (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol), and the predominant menaquinone MK-8 (H4, ω-cyclo). The main fatty acids for both strains were hexadecanoic acid (C16 : 0), 10-methyloctadecanoic acid (10-methyl C18 : 0) and cis-9-octadecenoic acid (C18 : 1 ω9c). We propose two novel species within the genus

Nocardia

: Nocardia macrotermitis sp. nov. with the type strain RB20T (=VKM Ac-2841T=NRRL B65541T) and Nocardia aurantia sp. nov. with the type strain RB56T (=VKM Ac-2842T=NRRL B65542T).
The Species Awareness Index (SAI): a Wikipedia-derived conservation culturomics metric for public biodiversity awareness
Authors: Millard Joseph W , Gregory Richard D , Jones Kate , Freeman Robin
Published: August 2020

Threats to global biodiversity are well-known, but slowing currents rates of biodiversity loss remains an ongoing challenge. The Aichi Targets set out 20 goals on which the international community should act to alleviate biodiversity decline, one of which (Target 1) aimed to raise public awareness of the importance of biodiversity. Whilst conventional indicators for Target 1 are of low spatial and temporal coverage, conservation culturomics has demonstrated how biodiversity awareness can be quantified at the global scale. Following the Living Planet Index methodology, here we introduced the Species Awareness Index (SAI), an index of changing species awareness on Wikipedia. We calculated this index at the page level for 41,197 IUCN species across 10 Wikipedia languages, incorporating over 2 billion views. Bootstrapped indices for the page level SAI show that overall awareness of biodiversity is marginally increasing, although there are differences among taxonomic classes and languages. Among taxonomic classes, overall awareness of reptiles is increasing fastest, and amphibians slowest. Among languages, overall species awareness for the Japanese Wikipedias is increasing fastest, and the Chinese and German Wikipedias slowest. Although awareness of species on Wikipedia as a whole is increasing, and is significantly higher in traded species, over the period 2016-2020 change in interest appears not to be strongly related to the trade of species or animal pollinators. As a data source for public biodiversity awareness Wikipedia could be integrated into the Biodiversity Engagement Indicator, thereby incorporating a more direct link to biodiversity itself.
Coherent Optical Scattering and Interferometry (COSI) for label-free multiparameter quantitative imaging of intra-thrombus stabilityin vitro
Authors: Zheng Y. , Montague S. J. , Lim Y. J. , Xu T. , Xu T. , Gardiner E. E. , Lee W. M.
Published: August 2020

Although existing microfluidicsin vitroassays recapitulate blood vessel microenvironment using surface-immobilized agonists under biofluidic flows, these assays do not quantify intra-thrombus mass and activities of adhesive platelets at agonist margin and uses fluorescence labeling, therefore limiting clinical translation potential. Here, we describe a real time label-freein vitroquantitative imaging flow assay calledCoherentOpticalScattering and phaseInterferometry (COSI) that evaluates both intra-thrombus and adhesive-only platelet dynamics using only changes in refractive index. By combining coherent optical scattering and optical interferometry, we evaluated and quantified both intra-thrombus mass with picogram accuracy and adhesive platelet-only events/dynamics with high spatial-temporal resolution (400 nm/s) under fluid shear stress using only changes in refractive index. Using oblique illumination, COSI provide a ∼ 4 µm thin axial slice that quantifies the magnitude of physical of surface adhesive platelets (spreading, adhesion and consolidation) in a developing thrombus without labelling under fluid shear stress. We achieve real time visualization of recruitment of single platelet into thrombus and further correlate it to the developing mass of a thrombus. The adhesive platelet activity exhibit stabilized surface activity of around 2 µm/s and intra-thrombus mass exchange were balanced at around 1 picogram after treatment of a broad range metalloproteinase inhibitor (250 µM GM6001).

Significance

The combination of phase imaging with transmitted light and backscattering imaging via oblique illumination in COSI unpicked intra-thrombus mass and adhesive platelet-only activity events at picogram and sub-micrometer precision with millisecond time resolution under fluid shear stress. COSI maps the longitudinal time dynamics of adhesive platelets along changing thrombus mass under metalloproteinase inhibition, and demonstrates potential for real-time correlative microfluidic label-free imaging for flow-dependent biological adhesive events.
NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge
Authors: Guebre-Xabier Mimi , Patel Nita , Tian Jing-Hui , Zhou Bin , Maciejewski Sonia , Lam Kristal , Portnoff Alyse D. , Massare Michael J. , Frieman Matthew B. , Piedra Pedro A. , Ellingsworth Larry , Glenn Gregory , Smith Gale
Published: August 2020

There is an urgent need for a safe and protective vaccine to control the global spread of SARS-CoV-2 and prevent COVID-19. Here, we report the immunogenicity and protective efficacy of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length SARS-CoV-2 spike (S) glycoprotein stabilized in the prefusion conformation. Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. Following intranasal and intratracheal challenge with SARS-CoV-2, immunized macaques were protected against upper and lower infection and pulmonary disease. These results support ongoing phase 1/2 clinical studies of the safety and immunogenicity of NVX-CoV2327 vaccine (NCT04368988).

Highlights

Full-length SARS-CoV-2 prefusion spike with Matrix-M1™ (NVX-CoV2373) vaccine.

Induced hACE2 receptor blocking and neutralizing antibodies in macaques.

Vaccine protected against SARS-CoV-2 replication in the nose and lungs.

Absence of pulmonary pathology in NVX-CoV2373 vaccinated macaques.
Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling
Authors: Liu Po-Yu , Wu Wei-Kai , Chen Chieh-Chang , Panyod Suraphan , Sheen Lee-Yan , Wu Ming-Shiang
Published: August 2020

Sequencing of the 16S rRNA gene by Illumina next-generation sequencing is broadly used in microbiome studies. Different hypervariable regions of the 16S rRNA gene, V3V4 (amplified with primers 341F–805R) or V4 (V4O; primers 515F–806R), are selected, depending on the targeted resolution. However, in population-based clinical studies, combining V3V4 and V4 data from different studies for a meta-analysis is challenging. Reads generated by short-read (150-bp) high-throughput sequencing platforms do not fully recover the V4 region read-length. Here, we evaluated the compatibility of 16S rRNA V3V4 and V4 amplicons for microbiome profiling. We compared taxonomic compositions obtained by the analysis of V3V4 and V4 amplicons, and V4 fragments trimmed from V3V4 amplicons. We also evaluated an alternative V4 region (V4N; primers 519F–798R) designed for efficient stitching with 150-bp paired-end sequencing. First, we simulated a global investigation of environmental prokaryotesin silico. This revealed that V4O primers recovered the highest proportion of fragments (81.7%) and most phyla, including archaea. Empirical sequencing of standard (mock) and human fecal samples revealed biased patterns of each primer that were similar to the ones determined byin silicosimulation. Further, for human fecal microbiome profiling, the between-sample variance was greater than the systematic bias of each primer. The use of trimmed V4 fragments and single-end amplicons resulted in the same systematic bias. In conclusion, paired-end V4O sequencing yielded the most accurate data for both, simulation and mock community sequencing; the V4O amplicons were compatible with trimmed V4 sequences for microbiome profiling.

IMPORTANCE

Next-generation sequencing of the 16S rRNA gene is a commonly used approach for clinical microbiome studies. Different amplicons of the 16S rRNA hypervariable regions are used in different studies, which creates incompatible sequence features when comparing and integrating data among studies by using 16S denoising pipelines. Here we compared the type of data and coverage obtained when different 16S rRNA amplicons were analyzed.In silicoand empirical analyses of the human fecal microbiome revealed that the V3V4 amplicons are compatible with V4 amplicons after trimming up to the same region. These observations demonstrate that reconciling the compatibility of clinical microbiome data from different studies improve not only the sample size but also the confidence of the hypothesis tested.
SuperStructure: a Parameter-Free Super-Structure Identifier for SMLM Data
Authors: Marenda M. , Lazarova E. , van de Linde S. , Gilbert N. , Michieletto D.
Published: August 2020

Single-Molecule Localisation Microscopy (SMLM) allows the quantitative mapping of molecules at high resolution. However, understanding the non-random interaction of proteins requires the identification of more complex patterns than those typified by standard clustering tools. Here we introduce SuperStructure, a parameter-free algorithm to quantify structures made of inter-connected clusters, such as protein gels. SuperStructure works without a priori assumptions and is thus an ideal methodology for standardised analysis of SMLM data.
Safety and data quality of EEG recorded simultaneously with multi-band fMRI
Authors: Egan Maximillian K. , Larsen Ryan , Wirsich Jonathan , Sutton Brad P. , Sadaghiani Sepideh
Published: August 2020

Purpose

Simultaneously recorded electroencephalography and functional magnetic resonance imaging (EEG-fMRI) is highly informative yet technically challenging. Until recently, there has been little information about EEG data quality and safety when used with newer multi-band (MB) fMRI sequences. Here, we measure the relative heating of a MB protocol compared with a standard single-band (SB) protocol considered to be safe. We also evaluated EEG quality recorded concurrently with the MB protocol on humans.

Materials and Methods

We compared radiofrequency (RF)-related heating at multiple electrodes and magnetic field magnitude,B1+RMS, of a MB fMRI sequence with whole-brain coverage (TR = 440 ms, MB factor = 4) against a previously recommended, safe SB sequence using a phantom outfitted with a 64-channel EEG cap. Next, 9 human subjects underwent eyes-closed resting state EEG-fMRI using the MB sequence. Additionally, in three of the subjects resting state EEG was recorded also during the SB sequence and in an fMRI-free condition to directly compare EEG data quality across scanning conditions. EEG data quality was assessed by the ability to remove gradient and cardioballistic artifacts along with a clean spectrogram.

Results

The heating induced by the MB sequence was lower than that of the SB sequence by a factor of 0.73 ± 0.38. This is consistent with an expected heating ratio of 0.64, calculated from the square of the ratio ofB1+RMSvalues of the sequences. In the resting state EEG data, gradient and cardioballistic artifacts were successfully removed using traditional template subtraction. All subjects showed an individual alpha peak in the spectrogram with a posterior topography characteristic of eyes-closed EEG. The success of artifact rejection for the MB sequence was comparable to that in traditional SB sequences.

Conclusions

Our study shows thatB1+RMSis a useful indication of the relative heating of fMRI protocols. This observation indicates that simultaneous EEG-fMRI recordings using this MB sequence can be safe in terms of RF-related heating, and that EEG data recorded using this sequence is of acceptable quality after traditional artifact removal techniques.
Accurate identification and quantification of commensal microbiota bound by host immunoglobulins
Authors: Jackson Matthew A. , Pearson Claire , Ilott Nicholas E. , Huus Kelsey E. , Hegazy Ahmed N. , Webber Jonathan , Finlay B. Brett , Macpherson Andrew J. , Powrie Fiona , Lam Lilian H.
Published: August 2020

Background

Identifying which taxa are targeted by immunoglobulins can uncover important host-microbe interactions. Immunoglobulin binding of commensal taxa can be assayed by sorting bound bacteria from samples and using amplicon sequencing to determine their taxonomy, a technique most widely applied to study Immunoglobulin A (IgA-Seq). Previous experiments have scored taxon binding in IgA-Seq datasets by comparing abundances in the IgA bound and unbound sorted fractions. However, as these are relative abundances, such scores are influenced by the levels of the other taxa present and represent an abstract combination of these effects. Diversity in the practical approaches of prior studies also warrants benchmarking of the individual stages involved. Here, we provide a detailed description of the design strategy for an optimised IgA-Seq protocol. Combined with a novel scoring method for IgA-Seq datasets that accounts for the aforementioned effects, this platform enables accurate identification and quantification of commensal gut microbiota targeted by host immunoglobulins.

Results

Using germ-free andRag1−/−mice as negative controls, and a strain-specific IgA antibody as a positive control, we determine optimal reagents and fluorescence activated cell sorting (FACS) parameters for IgA-Seq. Using simulated IgA-Seq data, we show that existing IgA-Seq scoring methods are influenced by pre-sort relative abundances. This has consequences for the interpretation of case-control studies where there are inherent differences in microbiota composition between groups. We show that these effects can be addressed using a novel scoring approach based on posterior probabilities. Finally, we demonstrate the utility of both the IgA-Seq protocol and probability-based scores by examining both novel and published data fromin vivodisease models.

Conclusions

We provide a detailed IgA-Seq protocol to accurately isolate IgA-bound taxa from intestinal samples. Using simulated and experimental data, we demonstrate novel probability-based scores that adjust for the compositional nature of relative abundance data to accurately quantify taxon-level IgA binding. All scoring approaches are made available in the IgAScores R package. These methods should improve the generation and interpretation of IgA-Seq datasets and could be applied to study other immunoglobulins and sample types.
Suppression of p16 alleviates the senescence-associated secretory phenotype
Authors: Buj Raquel , Leon Kelly E. , Aird Katherine M.
Published: August 2020

Oncogene induced senescence (OIS) is characterized by increased expression of the cell cycle inhibitor p16, leading to a hallmark cell cycle arrest. Suppression of p16 in this context drives proliferation, senescence bypass, and contributes to tumorigenesis. OIS cells are also characterized by the expression and secretion of a widely variable group of factors collectively termed the senescence-associated secretory phenotype (SASP). The SASP can be both beneficial and detrimental and affects the microenvironment in a highly context-dependent manner. The relationship between p16 suppression and the SASP remains unclear. Here, we show that knockdown of p16 decreases expression of the SASP factors and pro-inflammatory cytokinesIL6andCXCL8in both RASG12V-and BRAFV600E-induced senescence. Notably, this is likely not due to suppression of senescence asLMNB1and cyclin A expression remain low and p21 remains high. Moreover, low p16 expression in both cancer cell lines and patient samples correspond to decreased SASP gene expression, suggesting this is a universal effect of loss of p16 expression. Together, our data suggest that p16 transcriptionally regulates SASP gene expression, which has implications for understanding how p16 modulates both the senescent and tumor microenvironment.
In vivo CRISPR screening for phenotypic targets of themir-35-42family inC. elegans
Authors: Yang Bing , Schwartz Matthew , McJunkin Katherine
Published: August 2020

Identifying miRNA target genes is difficult, and delineating which targets are the most biologically important is even more difficult. We devised a novel strategy to test the phenotypic impact of individual microRNA–target interactions by disrupting each predicted miRNA-binding site by CRISPR–Cas9 genome editing inC. elegans. We developed a multiplexed negative selection screening approach in which edited loci are deep sequenced, and candidate sites are prioritized based on apparent selection pressure against mutations that disrupt miRNA binding. Importantly, our screen was conducted in vivo on mutant animals, allowing us to interrogate organism-level phenotypes. We used this approach to screen for phenotypic targets of the essentialmir-35-42family. By generating 1130 novel 3′UTR alleles across all predicted targets, we identifiedegl-1as a phenotypic target whose derepression partially phenocopies themir-35-42mutant phenotype by inducing embryonic lethality and low fecundity. These phenotypes can be rescued by compensatory CRISPR mutations that retargetmir-35to the mutantegl-13′UTR. This study demonstrates that the application of in vivo whole organismal CRISPR screening has great potential to accelerate the discovery of phenotypic negative regulatory elements in the noncoding genome.
MYCN drives chemoresistance in small cell lung cancer while USP7 inhibition can restore chemosensitivity
Authors: Grunblatt Eli , Wu Nan , Zhang Huajia , Liu Xiaoli , Norton Justin P. , Ohol Yamini , Leger Paul , Hiatt Joseph B. , Eastwood Emily C. , Thomas Rhiana , Ibrahim Ali H. , Jia Deshui , Basom Ryan , Eaton Keith D. , Martins Renato , Houghton A. McGarry , MacPherson David
Published: August 2020

Small cell lung cancer (SCLC) is an aggressive neuroendocrine cancer characterized by initial chemosensitivity followed by emergence of chemoresistant disease. To study roles for MYCN amplification in SCLC progression and chemoresistance, we developed a genetically engineered mouse model of MYCN-overexpressing SCLC. In treatment-naïve mice, MYCN overexpression promoted cell cycle progression, suppressed infiltration of cytotoxic T cells, and accelerated SCLC. MYCN overexpression also suppressed response to cisplatin–etoposide chemotherapy, with similar findings made upon MYCL overexpression. We extended these data to genetically perturb chemosensitive patient-derived xenograft (PDX) models of SCLC. In chemosensitive PDX models, overexpression of either MYCN or MYCL also conferred a switch to chemoresistance. To identify therapeutic strategies for MYCN-overexpressing SCLC, we performed a genome-scale CRISPR–Cas9 sgRNA screen. We identified the deubiquitinase USP7 as a MYCN-associated synthetic vulnerability. Pharmacological inhibition of USP7 resensitized chemoresistant MYCN-overexpressing PDX models to chemotherapy in vivo. Our findings show that MYCN overexpression drives SCLC chemoresistance and provide a therapeutic strategy to restore chemosensitivity.
Distinct kinesin motors drive two types of maize neocentromeres
Authors: Swentowsky Kyle W. , Gent Jonathan I. , Lowry Elizabeth G. , Schubert Veit , Ran Xia , Tseng Kuo-Fu , Harkess Alex E. , Qiu Weihong , Dawe R. Kelly
Published: August 2020

A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.
LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy
Authors: Nichterwitz Susanne , Nijssen Jik , Storvall Helena , Schweingruber Christoph , Comley Laura Helen , Allodi Ilary , Lee Mirjam van der , Deng Qiaolin , Sandberg Rickard , Hedlund Eva
Published: August 2020

Somatic motor neurons are selectively vulnerable in spinal muscular atrophy (SMA), which is caused by a deficiency of the ubiquitously expressed survival of motor neuron protein. However, some motor neuron groups, including oculomotor and trochlear (ocular), which innervate eye muscles, are for unknown reasons spared. To reveal mechanisms of vulnerability and resistance in SMA, we investigate the transcriptional dynamics in discrete neuronal populations using laser capture microdissection coupled with RNA sequencing (LCM-seq). Using gene correlation network analysis, we reveal a TRP53-mediated stress response that is intrinsic to all somatic motor neurons independent of their vulnerability, but absent in relatively resistant red nucleus and visceral motor neurons. However, the temporal and spatial expression analysis across neuron types shows that the majority of SMA-induced modulations are cell type–specific. Using Gene Ontology and protein network analyses, we show that ocular motor neurons present unique disease-adaptation mechanisms that could explain their resilience. Specifically, ocular motor neurons up-regulate (1) Syt1, Syt5, and Cplx2, which modulate neurotransmitter release; (2) the neuronal survival factors Gdf15, Chl1, and Lif; (3) Aldh4, that protects cells from oxidative stress; and (4) the caspase inhibitor Pak4. Finally, we show that GDF15 can rescue vulnerable human spinal motor neurons from degeneration. This confirms that adaptation mechanisms identified in resilient neurons can be used to reduce susceptibility of vulnerable neurons. In conclusion, this in-depth longitudinal transcriptomics analysis in SMA reveals novel cell type–specific changes that, alone and combined, present compelling targets, including Gdf15, for future gene therapy studies aimed toward preserving vulnerable motor neurons.
InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction
Authors: Roslova Maria , Smeets Stef , Wang Bin , Thersleff Thomas , Xu Hongyi , Zou Xiaodong
Published: August 2020

A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
Anaerobic fixed-target serial crystallography
Authors: Rabe Patrick , Beale John H. , Butryn Agata , Aller Pierre , Dirr Anna , Lang Pauline A. , Axford Danny N. , Carr Stephen B. , Leissing Thomas M. , McDonough Michael A. , Davy Bradley , Ebrahim Ali , Orlans Julien , Storm Selina L. S. , Orville Allen M. , Schofield Christopher J. , Owen Robin L.
Published: August 2020

Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitrogen cryo-stream at 100 K) enable, is data collection of dioxygen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for dioxygen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the `sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent L-arginine hydroxylase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.