bluuebunny/crossref_metadata_2025 huggingface dataset:
A Co-diagnosis of Crohn Disease and Autoimmune Diabetes in an Adolescent Patient
Authors: Chranioti Ioanna , Vartzelis George , Maritsi Despoina , Tsolia Maria
Published: January 2023

Inflammatory bowel disease (IBD) is a lifelong, immune-mediated disorder that often occurs in childhood and is becoming increasingly common worldwide. Diagnosis of IBD in children remains difficult due to the spectrum of symptoms, including gastrointestinal and extraintestinal manifestations. Type 1 diabetes mellitus (T1D) is one of the most common autoimmune diseases in children and adolescents. Classic manifestations of T1D in young people include polyuria, polydipsia, abdominal pain, weight loss, and ketoacidosis. However, children with autoimmunity of pancreatic β-cells may remain euglycemic and asymptomatic for many years. An accurate and prompt diagnosis of IBD and T1D is particularly important in children because they can negatively affect growth, psychosocial function and overall well-being. We present a case in which a previously healthy child was co-diagnosed with Crohn disease and T1D during a routine pediatric evaluation in the outpatient clinic of a peripheral secondary hospital.
Infectious Etiology of Vomiting in Children With Presumed Acute Gastroenteritis in the Absence of Diarrhea: Protocol for a Cohort Study
Authors: Cepińska Aleksandra , Kołodziej Maciej , Podsiadły Edyta , Szajewska Hania
Published: January 2023

Registration number:

NCT05270291, https://clinicaltrials.gov/ct2/show/

Objectives:

In children with acute gastroenteritis (AGE), vomiting often precedes diarrhea. To establish the diagnosis of AGE, enteropathogen detection typically relies on diarrheal stool samples. However, testing requires sufficient stool sample, which may not be easily available. Recent studies suggest that in children presenting to emergency departments with presumed AGE with isolated vomiting, an enteropathogen can be identified using rectal swabs and molecular diagnostic tests. The rate of enteropathogen detection in children with isolated vomiting due to AGE may differ in various populations. Using rectal swabs and molecular diagnostic tests, we plan to assess the proportion of children with isolated vomiting with presumed AGE in whom an enteropathogen can be identified.

Methods:

This will be a cohort study conducted in the emergency department(s) of one or more pediatric hospital(s) in Poland. Children younger than 5 years with the presence of ≥3 episodes of vomiting due to presumed AGE, lasting no longer than 7 days before enrollment, will be recruited. The primary outcome will be the proportion of children with isolated vomiting in whom an enteropathogen is detected. In all eligible participants, rectal swabs will be taken to perform molecular testing for detection of typical viral and bacterial enteropathogens. All children will be followed-up at 14 days after the initial contact to classify them into one of three groups (i.e., vomiting only, vomiting and diarrhea, and diarrhea only).
Salpingitis in an Adolescent Female With Constipation and Abdominal Pain
Authors: Barak Gal , Carroll Matthew R. , Dean Andrea
Published: January 2023

Abdominal pain is one of the most common presenting complaints in the emergency room for pediatric patients. While constipation is one of the most common causes for abdominal pain in pediatrics, serious intra-abdominal pathology must always be excluded. We report a pre-coital post-menarchal adolescent female who presented with severe abdominal pain and constipation and had radiographic findings of salpingitis. It was suspected that uterine and adnexal changes seen on imaging resulted from the fecal mass compressing the genitourinary tract leading to fluid collection manifesting as radiographic evidence of salpingitis. This mechanism is similar to bladder outlet obstruction resulting from compression by intestinal stool burden, leading to urinary stasis, bacteriuria, and ascending urinary tract infection. This case demonstrates how a common pediatric problem, constipation, can lead to a condition rarely found in the pre-coital adolescent population.
Leveraging Electronic Health Record Data for Timely Chronic Disease Surveillance: The Multi-State EHR-Based Network for Disease Surveillance
Authors: Hohman Katherine H. , Martinez Amanda K. , Klompas Michael , Kraus Emily M. , Li Wenjun , Carton Thomas W. , Cocoros Noelle M. , Jackson Sandra L. , Karras Bryant Thomas , Wiltz Jennifer L. , Wall Hilary K.
Published: January 2023

Context:

Electronic health record (EHR) data can potentially make chronic disease surveillance more timely, actionable, and sustainable. Although use of EHR data can address numerous limitations of traditional surveillance methods, timely surveillance data with broad population coverage require scalable systems. This report describes implementation, challenges, and lessons learned from the Multi-State EHR-Based Network for Disease Surveillance (MENDS) to help inform how others work with EHR data to develop distributed networks for surveillance.

Program:

Funded by the Centers for Disease Control and Prevention (CDC), MENDS is a data modernization demonstration project that aims to develop a timely national chronic disease sentinel surveillance system using EHR data. It facilitates partnerships between data contributors (health information exchanges, other data aggregators) and data users (state and local health departments). MENDS uses query and visualization software to track local emerging trends. The program also uses statistical and geospatial methods to generate prevalence estimates of chronic disease risk measures at the national and local levels. Resulting data products are designed to inform public health practice and improve the health of the population.

Implementation:

MENDS includes 5 partner sites that leverage EHR data from 91 health system and clinic partners and represents approximately 10 million patients across the United States. Key areas of implementation include governance, partnerships, technical infrastructure and support, chronic disease algorithms and validation, weighting and modeling, and workforce education for public health data users.

Discussion:

MENDS presents a scalable distributed network model for implementing national chronic disease surveillance that leverages EHR data. Priorities as MENDS matures include producing prevalence estimates at various geographic and subpopulation levels, developing enhanced data sharing and interoperability capacity using international data standards, scaling the network to improve coverage nationally and among underrepresented geographic areas and subpopulations, and expanding surveillance of additional chronic disease measures and social determinants of health.
Community Health Improvement Plans and Physical Activity Implementation Strategies: Findings From a Cross-Sectional Survey of US Local Health Departments
Authors: Lightner Joseph S. , Ziegler Nancy , Gardiner Kelsey , Collie-Akers Vicki
Published: January 2023

Objective:

Community Health Improvement Plans (CHIPs) are a foundational public health practice conducted by every accredited health department in the United States. Community Health Improvement Plans may impact community-wide physical activity (PA) by implementing large-scale interventions. However, no studies have evaluated whether, or how, CHIP goals focusing on increasing PA are implemented. This study aims to understand CHIP PA goals, implementation strategies, and implementation outcomes of CHIP nationally.

Design:

This study was a cross-sectional online survey of CHIP implementation.

Setting:

A random sample of accredited local health departments nationally.

Participants:

Local health departments (N = 44) were invited to participate in this study.

Main Outcome Measures:

Constructs from Proctor's Model of Implementation Research and implementation strategies were the main outcomes assessed.

Results:

Most CHIPs included PA goals (72.7%). Goals most commonly focused on changing built environment and infrastructure (25.9%), increasing education and awareness (22.2%), increasing PA programming (18.5%), and partnering with health care (18.5%). Common implementation strategies used were designing and evaluating their CHIPs (72.7%) and developing relationships with stakeholders (72.7%). Respondents reported that CHIPS were able to be adopted, acceptable for the community, and feasible. Community Health Improvement Plans were also reported to be safe, yet respondents reported effectiveness lower than other constructs. Participants reported that individual-level PA was unlikely to change due to their CHIP (mean = 3.39, SD = 1.12).

Conclusions:

Overall, it seems that communities are choosing easily adopted, appropriate, feasible, and safe interventions that may be less effective over those that may produce large-scale improvement in PA behavior. Future research needs to be conducted on the process of CHIP implementation and the potential long-term outcomes. Community Health Improvement Plans may serve as a powerful tool to improve population health if implemented effectively.
Outcomes for Hospitalized Aggressive and Violent Patients When Physical Restraints Are Introduced
Authors: Harris Ché Matthew , Gupta Ishaan , Beydoun Hind , Wright Scott Mitchell
Published: January 2023

Background

Hospital outcomes among patients acting aggressively or violently have not been extensively studied in the United States.

Objectives

The aims of the study are to determine rates of physical restraint use among hospitalized patients who are aggressive/violent and to characterize associations with mortality and utilization metrics.

Design/Setting/Participants

National Inpatient Sample databases from 2016 to 2019 were analyzed with multivariable regression to compare aggressive/violent patients in whom physical restraints were or were not used.

Measures

Prevalence of physical restraint use, in-hospital mortality, length of stay, and total hospital charges were measures.

Results

A total of 40,309 hospitalized patients were coded as having aggressive/violent behavior, of whom 4475 (11.1%) were physically restrained. Physically restrained patients were younger (mean age ± standard error, 42.6 ± 0.64 versus 45.7± 0.41; P < 0.01), more frequently male (71.0% versus 65.4%; P < 0.01), and had less comorbidity (Charlson Index score >3: 7.9% versus 12.5%; P < 0.01) than unrestrained patients. Patients with physical restraints had higher odds of in-hospital mortality (adjusted odds ratio, 2.4, confidence interval [CI], 1.0–5.7; P = 0.04) and lower odds of being discharged to home (adjusted odds ratio, 0.46; CI, 0.38–0.56; P < 0.01) compared with unrestrained patients. Longer hospital stays (adjusted mean difference, 4.1 days CI, 2.1–6.0; P < 0.01) and higher hospitalization charges (adjusted mean difference, $16,996; CI, 6883–27,110; P < 0.01) were observed for those who were physically restrained.

Conclusions

Physically restrained aggressive/violent patients had worse in-hospital outcomes compared with their unrestrained counterparts. Avoiding physical restraints whenever possible should be considered when managing this confrontational yet vulnerable patient population. When restraints are needed, providers must thoughtfully bear in mind heightened risks for worse outcomes.
A Persistent Left-Sided Superior Vena Cava Detected on a O-15-H2O PET/CT of the Heart
Authors: Overgaard David Lyse , Tolbod Lars Poulsen , Gormsen Lars Christian , Madsen Michael Alle
Published: January 2023

A persistent left-sided superior vena cava (PLSVC) is an uncommon finding with a prevalence of up to 0.5% in the general population. The PLSVC appears when the left anterior cardinal vein fails to regress as the ligament of Marshall during embryologic development. It is usually asymptomatic and discovered incidentally; however, its recognition is important because it might complicate invasive cardiovascular procedures. In this case, we report an incidental finding of a PLSVC detected on the O-15-H2O PET/CT of a patient who was referred for myocardial perfusion imaging.
68Ga-FAPI PET/MRI and 18F-FDG PET/CT in a Case With Extensive Portal Vein Tumor Thrombus
Authors: Yao Xilan , Liu Weiting , Ou Xiaohong
Published: January 2023

18F-FDG PET/CT has been reported to be useful in differentiating tumor thrombus and bland thrombus. There are few reports on 68Ga-FAPI PET imaging features of tumor thrombus. Herein, we report a 46-year-old man with extensive tumor thrombus in the portal vein due to hepatic malignancy on 18F-FDG PET/CT and 68Ga-FAPI PET/MRI.
Does Facial Fracture Management Require Opioids? A Pilot Trial of a Narcotic-Minimizing Analgesia Protocol for Operative Facial Trauma
Authors: Knudsen Margarete Grace , Kotha Vikas S. , Wee Corinne , Lesko Robert P. , Swanson Marco , Kumar Anand , Davidson Edward H.
Published: January 2023

Opioid minimization in the acute postoperative phase is timely in the era of the opioid epidemic. The authors hypothesize that patients with facial trauma receiving multimodal, narcotic-minimizing pain management in the perioperative period will consume fewer morphine milligram equivalents (MMEs) while maintaining adequate pain control compared with a traditional analgesia protocol. An IRB-approved pilot study evaluating isolated facial trauma patients compared 10 consecutive prospective patients of a narcotic-minimizing pain protocol beginning in August 2020 with a retrospective, chart-reviewed cohort of 10 consecutive patients before protocol implementation. The protocol was comprised of multimodal nonopioid pharmacotherapy given preoperatively (acetaminophen, celecoxib, and pregabalin). Postoperatively, patients received intravenous (IV) ketorolac, scheduled acetaminophen, ibuprofen, and gabapentin. Oxycodone was reserved for severe uncontrolled pain. The control group had no standardized protocol, though opioids were ad libitum. Consumed MMEs and verbal Numeric Rating Scale (vNRS) pain scores (0–10) were prospectively tracked and compared with retrospective data. Descriptive and inferential statistics were run. At all recorded postoperative intervals, narcotic-minimizing subjects consumed significantly fewer MMEs than controls [0–8 h, 21.5 versus 63.5 (P = 0.002); 8–16 h, 4.9 versus 20.6 (P = 0.02); 16–24 h, 3.3 versus 13.9 (P = 0.03); total 29.5 versus 98.0 (P = 0.003)]. At all recorded postoperative intervals, narcotic-minimizing subjects reported less pain (vNRS) than controls (0–8 h, 7.7 versus 8.1; 8–16 h, 4.4 versus 8.0; 16–24 h 4.3 versus 6.9); significance was achieved at the 8 to 16-hour time point (P = 0.006). A multimodal, opioid-sparing analgesia protocol significantly reduces opioid use in perioperative facial trauma management without sacrificing satisfactory pain control for patients.
Applying and Testing a Crowdsourcing Platform to Support Home-Based Simulation
Authors: Clarke Krystina M. , Barari Ahmad , Hogue Andrew , Dubrowski Adam
Published: January 2023

The purpose of this report is to: (1) highlight challenges of transitioning the delivery of simulation from centralized, in-person laboratory to decentralized, home-based, online format; (2) suggest a solution that involves the use of crowdsourcing community-based 3-dimensional printers to produce affordable simulators; and (3) present exploratory research and a test case aiming to identify crowdsourcing frameworks to accomplish this. We present a test case that shows the potential of the proposed solution to scale up the decentralized simulation practices during and beyond the COVID-19 pandemic. As a largely uncharted territory, the test case highlighted successes and areas for improvement that need to be addressed through both theoretical and empirical research and testing before full implementation and scale-up.
The Clinical Development of Levodopa Inhalation Powder
Authors: Hauser Robert A. , LeWitt Peter A. , Waters Cheryl H. , Grosset Donald G. , Blank Burkhard
Published: January 2023

Oral levodopa is the most effective treatment for Parkinson disease, but OFF periods emerge over time. Gastrointestinal dysfunction and food effects impact levodopa absorption, contributing to unpredictable control of OFF periods. Inhaled levodopa powder (Inbrija) is approved for on-demand treatment of OFF periods in patients receiving oral levodopa–dopa decarboxylase inhibitors. The 84-mg dose is administered via a breath-actuated inhaler. It provides pulmonary delivery of levodopa to the systemic circulation and is taken when a patient has an OFF period in between doses of regular oral levodopa medication. The pivotal SPAN-PD trial in patients experiencing OFF periods on oral dopaminergic therapy showed that levodopa inhalation powder 84 mg produced significant improvement in Unified Parkinson Disease Rating Scale Part III score, as measured 30 minutes postdose at week 12, and improvement was seen as early as 10 minutes. More patients in the levodopa inhalation powder group turned ON within 60 minutes of treatment and remained ON at 60 minutes than in the placebo group. Levodopa inhalation powder can also be used to treat early-morning OFF periods and, when used for up to 12 months, produced no clinically significant differences in pulmonary function compared with an untreated cohort. Levodopa inhalation powder 84 mg increased plasma levodopa concentration rapidly and with less variability than oral levodopa/carbidopa (25/100 mg). Most common adverse event associated with levodopa inhalation powder is cough, found in ~15% of patients in the SPAN-PD trial; otherwise, reported adverse events were consistent with those known to be associated with oral levodopa.
Evaluation of microbial safety and cross-contamination sources in
button mushroom (Agaricus bisporus)
production
Authors: Kim Jin-Hee , Choi Song Yi , Hwang In Jun , Hyun Jeong Eun , Kim Sun Ae , Ban Ga-Hee , Kim Se-Ri
Published: January 2023

This study aimed to investigate the contamination sources of button mushrooms by
assessing the microbial load on the mushrooms and in the agricultural inputs
that come into contact with the mushroom. A total of 234 samples including
mushrooms, compost, casing soil, and tools from A, B, C, and D farms were tested
for sanitary indicators (aerobic bacteria, coliforms, and Escherichia
coli) and foodborne pathogens (E. coli O157:H7,
Salmonella spp., Staphylococcus aureus,
and Listeria monocytogenes). To identify the contamination
source, E. coli was isolated and analyzed using MLST
(Multi-Locus Sequence Typing). The number of aerobic bacteria remained
consistent during composting (⟩7 log CFU/g); however, the occurrence of
coliforms and E. coli was reduced to the detection limit
(⟨1.0 log). Salmonella spp. and L.
monocytogenes were detected in the raw material; however, they were
inactivated during composing. More than 6.0 log of aerobic bacteria and 3.0 log
of coliforms were observed in the casing soil from A, B, and C farms and in the
gloves from the C farm. MLST indicated that the STs of E. coli
isolated from casing soil layer and from the harvested mushrooms were identical
at ST 189. Therefore, cross contamination occurred through the casing soil
layer, and this could contribute to E. coli contamination in
mushrooms. It is necessary to practice hygiene guidelines, such as sterilization
of casing soil, worker hygiene, and facility sanitation, to minimize the
potential of microbial contamination in mushrooms.
Anti-inflammatory activities of polysaccharides isolated from
Aloe saponaria Haw grown in Namhae
Authors: Kang Jae Ran , Kim Gyoung Min , Shin Jung Hye
Published: January 2023

To identify the physiological activity of Saponaria aloe cultivated in the
Namhae-gun, polysaccharides, as the main physiologically active substances, were
isolated and their antioxidant and anti-inflammatory activities were confirmed.
Hot-air dried saponaria were extracted with hot water (80°C, 24 h) and
then the extracts were freeze dried (HWE). HWE was dialyzed using 3.5 kDa
dialysis membrane and only intra-dialysis solution was taken and freeze dried
(IDS) for experiment. Total polysaccharide content was higher in IDS (195.32
mg/g) than HWE however, anthraquinone content was lower in IDS. Total phenolic
compounds (TPC) contents of HWE and IDS were 594.04 and 1,047.23 mg/100 g,
respectively. The IC50 values of
2,2-Azinobis-(3-ethylbenzo-thiazoline-6-sulphonate (ABTS) and
1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities were higher
1.7 and 1.8 folds in HWE than IDS, respectively. The MTT assay showed that the
sample concentrations below than 100 μg/mL were
sufficient to exert anti-inflammatory activity in lipopolysaccharide (LPS)
induced RAW 264.7 cells. The production levels of nitric oxide (NO) and reactive
oxygen species (ROS) were significantly decreased in 100
μg/mL of HWE (p⟨0.01) and IDS
(p⟨0.001) treated group than those in LPS only treated group. The
expression levels of tumor necrosis faction (TNF)-α and
interleukin (IL)-6 were significantly lower in all treated samples than in the
LPS only treated group. However, there was no significant difference between the
HWE and IDS-treated group. The expression activity of
IL-1β was no significant difference among all
samples.
The impact of vaccination frequency on COVID-19 public health outcomes: A model-based analysis
Authors: Stoddard Madison , Yuan Lin , Sarkar Sharanya , van Egeren Debra , Mangalaganesh Shruthi , Nolan Ryan P. , Rogers Michael S. , Hather Greg , White Laura F. , Chakravarty Arijit
Published: January 2023

While the rapid deployment of SARS-CoV-2 vaccines had a significant impact on the ongoing COVID-19 pandemic, rapid viral immune evasion and waning neutralizing antibody titers have degraded vaccine efficacy. Nevertheless, vaccine manufacturers and public health authorities have a number of levers at their disposal to maximize the benefits of vaccination. Here, we use an agent-based modeling framework coupled with the outputs of a population pharmacokinetic model to examine the impact of boosting frequency and durability of vaccinal response on vaccine efficacy. Our work suggests that repeated dosing at frequent intervals (multiple times a year) may offset the degradation of vaccine efficacy, preserving their utility in managing the ongoing pandemic. Our work relies on assumptions about antibody accumulation and the tolerability of repeated vaccine doses. Given the practical significance of potential improvements in vaccinal utility, clinical research to better understand the effects of repeated vaccination would be highly impactful. These findings are particularly relevant as public health authorities worldwide seek to reduce the frequency of boosters to once a year or less. Our work suggests practical recommendations for vaccine manufacturers and public health authorities and draws attention to the possibility that better outcomes for SARS-CoV-2 public health remain within reach.
Effect of high-intensity interval training on body composition and glucose control in type 2 diabetes: a systematic review and meta-analysis
Authors: Cai Yidan , Long Zhuan , Guo Zhicheng
Published: January 2023

Background

Diabetes mellitus(DM) has become the third chronic noncommunicable disease worldwide, and is one of the most common chronic diseases in almost all countries. Type 2 diabetes(T2DM) is the most common group of DM, accounting for more than 90% of the DM population.

Objectives

This systematic review is conducted to compare the impact of HIIT and MICT on body composition and glucose control in T2DM, and to determine the suitable intervention for HIIT and the more effective forms of HIIT on T2DM.

Methods

Seven databases were searched from their inception to 21 November 2022 for randomized controlled trial(RCT) with HIIT and MICT intervention. The effect size was completed by using standardized mean difference (SMD) and standard deviation. Body mass(BM), body mass index (BMI), percent fat mass (PFM), fat mass (FM), fat-free mass (FFM), VO2peak, HbA1c, fasting plasma glucose(FPG), and fasting plasma insulin(FPI) were included in the meta-analysis as outcomes.

Results

15 RCTs with 371 T2DM were conducted in accordance with our inclusion criteria. The results of the meta-analysis revealed that compared to MICT, HIIT had significant effects on VO2peak(SMD=0.4, 95%CI: 0.08 to 0.73, p=0.02) and HbA1c(SMD=-0.24, 95%CI: -0.48 to -0.01, p=0.04), while there were no significant differences in body composition, FPG, and FPI.

Conclusion

HIIT provides similar or more benefits on body composition, cardiorespiratory fitness(CRF), and glucose control relative to MICT, which might be influenced by duration, frequency, and HIIT interval. For people with T2DM, HIIT can achieve more improvement in CRF and glucose control than MICT and appear to be more time-saving.
Immunogenicity and safety of Quadrivalent Influenza HA vaccine compared with Trivalent Influenza HA vaccine and evaluation of Quadrivalent Influenza HA vaccine batch-to-batch consistency in Indonesian children and adults
Authors: Fadlyana Eddy , Dhamayanti Meita , Tarigan Rodman , Prodjosoewojo Susantina , Rahmadi Andri Reza , Sari Rini Mulia , Rusmil Kusnandi , Kartasasmita Cissy B
Published: January 2023

Background

One of the newest strategies developed by the Global Influenza Strategy has been to broaden the composition of the current influenza vaccine formulations from trivalent products to quadrivalent products. This study aimed to assess the immunogenicity and safety of Quadrivalent Influenza HA vaccine (QIV) compared with Trivalent Influenza HA vaccine (TIV) and to evaluate three consecutive batches of QIV equivalence in Indonesian children and adults.

Methods and findings

This was an open-labeled, bridging clinical study involving unprimed healthy children and adults aged 9–40 years. A total of 540 subjects were enrolled in this study and randomized into four arm groups. Each subject received one dose of TIV or QIV with three different batch codes. Serology tests were performed at baseline and 28 days after vaccination. Hemagglutination inhibition (HI) antibody titers were analyzed for Geometric Mean Titer (GMT), seroprotection, and seroconversion rates. Solicited, unsolicited, and serious adverse events were observed up to 28 days after vaccination. A total of 537 subjects completed the study per protocol and were analyzed for immunogenicity criteria. All randomized subjects were analyzed for safety criteria. The percentage of the subjects with anti-HI titer ≥1:40 28 days after QIV vaccination was 99.5% for A/H1N1; 99.5% for A/H3N2; 93.1% for B/Texas, and 99.0% for B/Phuket. The seroprotection, GMT, and seroconversion rates of QIV were not significantly different from those of TIV for the common vaccine strains (p> 0.01) and were significantly different from those of TIV for the added B/Phuket strains (p< 0.01). Most solicited injection-site and systemic reactions with either vaccine were mild to moderate and resolved within a few days.

Conclusions

QIV was immunogenic and well-tolerated and had immunogenicity and safety profiles compared with TIV for all common strains. The immunogenicity of the three batches of QIV was equivalent for the four strains.

Clinical Trial registration

NCT03336593
Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection
Authors: Talmi Frank Dalit , Byas Alex D. , Murrieta Reyes , Weger-Lucarelli James , Rückert Claudia , Gallichotte Emily , Yoshimoto Janna A. , Allen Chris , Bosco-Lauth Angela M. , Graham Barbara , Felix Todd A. , Brault Aaron , Ebel Gregory D.
Published: January 2023

Error-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure.

Author Summary

WNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.
Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions
Authors: Alyami R. Y. , Cleary D. W. , Forster J. , Feelisch M. , Ardern-Jones M. R.
Published: January 2023

Background

The skin microbiome is increasingly recognised as a critical component of the innate skin immune response and is central to the pathogenesis of many inflammatory skin disorders including atopic dermatitis. Previous studies have not looked in detail at the impact of changing both sampling methodology and hypervariable region sequencing for skin microbiome analysis.

Objectives

We set out to undertake a detailed analysis comparing microbe population diversity and resolution at the single species level by swab, tape, scrape and scrape then swab sampling assayed by hypervariable region sequencing.

Methods

In triplicate samples from the antecubital fossa were taken from healthy volunteers for 16s RNA analysis by primer amplification for hypervariable regions 1-3, and 3-4.

Results

Alpha (phylogenetic) diversity was the greatest with tape sampling and V1-3 analysis, whereas for V4, tape and swab were equivalent. Scrape sampling showed lower alpha diversity at both V1-3 and V4. All measures of beta diversity showed the scrape methodology yielded a lesser diversity than the others. Phyla composition was similar across all sampling methodologies. Minor differences in composition were noted between V1-3 and V4 sequencing, but V1-3 was optimal for identification of firmicutes (including staphylococci).

Conclusions

In the methodological planning of skin microbiome analysis skin scientists need to consider the microbes of interest to choose the optimal hypervariable region to sequence, and harmonisation of methodological approaches would be beneficial to the field. For detection of staphylococci on flexural skin, we would recommend tape sampling with analysis of V1-3.

What’s already known about this topic?

Previous microbiome studies have utilised many different methodologies, but a detailed comparison of their utility in skin research has not been undertaken

Methodological choices in skin microbiome analysis affect both sensitivity to detect diversity and sensitivity to identify at a species level

Optimisation to detect diversity and species identification can require different approaches

What does this study add?

Our study compared a matrix the four most widely utilised skin sampling methodologies and the two principle means for hypervariable gene analysis.

We show that alpha diversity is optimal with tape sampling

Additionally, in contrast to gut microbiome analyses, in the skin hypervariable region V1-3 analysis is superior to V4 when the species of interest are staphylococci.
A First Ultrastructural and Immuno-Labelling Investigation of Western Red Cedar Leaves
Authors: Gowen Brent E. , Noshad David
Published: January 2023

A first morphological analysis of the leaves ofThuja plicata(Western Red Cedar, WRC), a commercially valuable tree species, is presented. The ultrastructural and immuno-labelling analyses were only possible after applying modifications to standard transmission electron microscopy (TEM) preparatory methodology to fully embed cedar leaves. We demonstrate an application of the technique after leaf exposure to the fungiDidymascella thujina(cedar leaf blight, CLB). The leaves resulting defence response was visualized to two plant defence proteins, β-1,3 Glucanase and Chitinase. The TEM methodology modifications presented may generally apply to other plant species resistant to morphological analyses due to their thick leaf cuticles. The technique requires no more equipment than found in any basic Transmission Electron Microscopy Facility.
Identification of levoglucosan degradation pathways in bacteria and sequence similarity network analysis
Authors: Kaur Arashdeep , Scott Nichollas E. , Herisse Marion , Goddard-Borger Ethan D. , Pidot Sacha , Williams Spencer J.
Published: January 2023

Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degradingPaenarthrobacterspp. (Paenarthrobacter nitrojuajacolisLG01 andPaenarthrobacter histidinolovoransLG02) that were isolated from soil by metabolic enrichment using levoglucosan as the sole carbon source. Genome sequencing and proteomics analysis revealed the expression of a series of genes encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan β-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and an associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident, while the expressed genes contained a range of putative sugar phosphate isomerases/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbours of LgdA revealed that homologues of LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One group of sugar phosphate isomerase/xylose isomerase homologues (named LgdB3) was identified with limited distribution that is mutually exclusive with LgdB2, and we propose that they may fulfill a similar function. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds, suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight diversity within the LGDH pathway, through which bacteria utilize levoglucosan as a nutrient source.
Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus
Authors: Tschurikow Xenia , Gadzekpo Aaron , Tran Mai P. , Chatterjee Rakesh , Sobucki Marcel , Zaburdaev Vasily , Göpfrich Kerstin , Hilbert Lennart
Published: January 2023

Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Low amphiphile concentrations induce rounding of droplets, followed by splitting and, ultimately, full dispersal at higher concentrations. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of the complex organization of transcription in biological cells using relatively simple, DNA sequence-programmable nanostructures, opening novel ways to control mesoscopic organization of synthetic nanomaterials.

GRAPHICAL ABSTRACT
Kar4 is Required for the Normal Pattern of Meiotic Gene Expression
Authors: Park Zachory M. , Remillard Matthew , Rose Mark D.
Published: January 2023

Kar4p, the yeast homolog of the mammalian methyltransferase subunit METTL14, is required for the initiation of meiosis and has at least two distinct functions in regulating the meiotic program. Cells lacking Kar4p can be driven to sporulate by co-overexpressing the master meiotic transcription factor,IME1, and the translational regulator,RIM4, suggesting that Kar4p functions at both the transcriptional and translational level to regulate meiosis. Using microarray analysis and RNA sequencing, we found thatkar4Δ/Δ mutants have a largely wild type transcriptional profile with the exception of two groups of genes that show delayed and reduced expression: (1) a set of Ime1p-dependent early genes as well asIME1, and (2) a set of late genes dependent on the mid-meiotic transcription factor, Ndt80p. The early gene expression defect is rescued by overexpressingIME1, but the late defect is only suppressed by overexpression of bothIME1andRIM4. Mass spectrometry analysis identified several genes involved in meiotic recombination with strongly reduced protein levels, but with little to no reduction in transcript levels inkar4Δ/Δ afterIME1overexpression. The low levels of these proteins were rescued by overexpression ofRIM4andIME1, but not by the overexpression ofIME1alone. These data expand our understanding of the role of Kar4p in regulating meiosis and provide key insights into a potential mechanism of Kar4p’s later meiotic function that is independent of mRNA methylation.

Author Summary

Kar4p is required at two stages during meiosis. Cells lacking Kar4p have a severe loss of mRNA methylation and arrest early in the meiotic program, failing to undergo either pre-meiotic DNA synthesis or meiotic recombination. The early block is rescued by overexpression of the meiotic transcription factor,IME1. Thekar4Δ/Δ cells show delayed and reduced expression of a set of Ime1p-dependent genes expressed early in meiosis as well as a set of later genes that are largely Ndt80p-dependent. Overexpression ofIME1rescues the expression defect of these early genes and expedites the meiotic program in the wild type S288C strain background. However,IME1overexpression is not sufficient to facilitate sporulation inkar4Δ/Δ. Completion of meiosis and sporulation requires the additional overexpression of a translational regulator,RIM4.

Analysis ofkar4Δ/Δ’s proteome during meiosis withIME1overexpression revealed that proteins important for meiotic recombination have reduced levels that cannot be explained by equivalent reductions in transcript abundance.IME1overexpression by itself rescues the defect associated with a catalytic mutant of Ime4p, implying that the early defect reflects mRNA methylation. The residual defects in protein levels likely reflect the loss of a non-catalytic function of Kar4p, and the methylation complex, which requires overexpression ofRIM4to suppress.
Transcriptomic impacts and potential routes of detoxification in a lampricide-tolerant teleost exposed to TFM and niclosamide
Authors: Lawrence M.J. , Grayson P. , Jeffrey J.D. , Docker M.F. , Garroway C.J. , Wilson J.M. , Manzon R.G. , Wilkie M.P. , Jeffries K.M.
Published: January 2023

Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America often relies on the application of 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide mixtures to kill larval sea lamprey. Selectivity of TFM against lampreys appears to be due to differential detoxification ability in these jawless fishes compared to bony fishes, particularly teleosts. However, the proximate mechanisms of tolerance to the TFM and niclosamide mixture and the mechanisms of niclosamide toxicity on its own are poorly understood, especially among non-target fishes. Here, we used RNA sequencing to identify specific mRNA transcripts and functional processes that responded to niclosamide or a TFM:niclosamide mixture in bluegill (Lepomis macrochirus). Bluegill were exposed to niclosamide or TFM:niclosamide mixture, along with a time-matched control group, and gill and liver tissues were sampled at 6, 12, and 24 h. We summarized the whole-transcriptome patterns through gene ontology (GO) term enrichment and through differential expression of detoxification genes. The niclosamide treatment resulted in an upregulation of several transcripts associated with detoxification (cyp, ugt, sult, gst), which may help explain the relatively high detoxification capacity in bluegill. Conversely, the TFM:niclosamide mixture resulted in an enrichment of processes related to arrested cell cycle and growth, and cell death alongside a diverse detoxification gene response. Detoxification of both lampricides likely involves the use of phase I and II biotransformation genes. Our findings strongly suggest that the unusually high tolerance of bluegill to lampricides is due to these animals having an inherently high capacity and flexible detoxification response to such compounds.
Evaluation of quantitative synchrotron radiation micro-X-ray fluorescence in rice grain
Authors: Limmer Matt A. , Webb Samuel M. , Seyfferth Angelia L.
Published: January 2023

Concentrations of nutrients and contaminants in rice grain affect human health, specifically through the localization and chemical form of elements. Methods to spatially quantify the concentration and speciation of elements are needed to protect human health and characterize elemental homeostasis in plants. Here, an evaluation was carried out using quantitative synchrotron radiation microprobe X-ray fluorescence (SR-µXRF) imaging by comparing average rice grain concentrations of As, Cu, K, Mn, P, S and Zn measured with rice grain concentrations from acid digestion and ICP-MS analysis for 50 grain samples. Better agreement was found between the two methods for high-Z elements. Regression fits between the two methods allowed quantitative concentration maps of the measured elements. These maps revealed that most elements were concentrated in the bran, although S and Zn permeated into the endosperm. Arsenic was highest in the ovular vascular trace (OVT), with concentrations approaching 100 mg kg−1 in the OVT of a grain from a rice plant grown in As-contaminated soil. Quantitative SR-µXRF is a useful approach for comparison across multiple studies but requires careful consideration of sample preparation and beamline characteristics.
Low-density tissue scaffold imaging by synchrotron radiation propagation-based imaging computed tomography with helical acquisition mode
Authors: Duan Xiaoman , Li Naitao , Cooper David M. L. , Ding Xiao Fan , Chen Xiongbiao , Zhu Ning
Published: January 2023

Visualization of low-density tissue scaffolds made from hydrogels is important yet challenging in tissue engineering and regenerative medicine (TERM). For this, synchrotron radiation propagation-based imaging computed tomography (SR-PBI-CT) has great potential, but is limited due to the ring artifacts commonly observed in SR-PBI-CT images. To address this issue, this study focuses on the integration of SR-PBI-CT and helical acquisition mode (i.e. SR-PBI-HCT) to visualize hydrogel scaffolds. The influence of key imaging parameters on the image quality of hydrogel scaffolds was investigated, including the helical pitch (p), photon energy (E) and the number of acquisition projections per rotation/revolution (N
p), and, on this basis, those parameters were optimized to improve image quality and to reduce noise level and artifacts. The results illustrate that SR-PBI-HCT imaging shows impressive advantages in avoiding ring artifacts with p = 1.5, E = 30 keV and N
p = 500 for the visualization of hydrogel scaffolds in vitro. Furthermore, the results also demonstrate that hydrogel scaffolds can be visualized using SR-PBI-HCT with good contrast while at a low radiation dose, i.e. 342 mGy (voxel size of 26 µm, suitable for in vivo imaging). This paper presents a systematic study on hydrogel scaffold imaging using SR-PBI-HCT and the results reveal that SR-PBI-HCT is a powerful tool for visualizing and characterizing low-density scaffolds with a high image quality in vitro. This work represents a significant advance toward the non-invasive in vivo visualization and characterization of hydrogel scaffolds at a suitable radiation dose.
Monitoring surface dynamics of electrodes during electrocatalysis using in situ synchrotron FTIR spectroscopy
Authors: Cheng Weiren , Xu Yanzhi , Yang Chenyu , Su Hui , Liu Qinghua
Published: January 2023

Monitoring the surface dynamics of catalysts under working conditions is important for a deep understanding of the underlying electrochemical mechanisms towards efficient energy conversion and storage. Fourier transform infrared (FTIR) spectroscopy with high surface sensitivity has been considered as a powerful tool for detecting surface adsorbates, but it faces a great challenge when being adopted in surface dynamics investigations during electrocatalysis due to the complication and influence of aqueous environments. This work reports a well designed FTIR cell with tunable micrometre-scale water film over the surface of working electrodes and dual electrolyte/gas channels for in situ synchrotron FTIR tests. By coupling with a facile single-reflection infrared mode, a general in situ synchrotron radiation FTIR (SR-FTIR) spectroscopic method is developed for tracking the surface dynamics of catalysts during the electrocatalytic process. As an example, in situ formed key *OOH is clearly observed on the surface of commercial benchmark IrO2 catalysts during the electrochemical oxygen evolution process based on the developed in situ SR-FTIR spectroscopic method, which demonstrates its universality and feasibility in surface dynamics studies of electrocatalysts under working conditions.