bluuebunny/crossref_metadata_2025 huggingface dataset:
Strength of Improvement Recommendations From Injurious Fall Investigations: A Retrospective Multi-Incident Analysis
Authors: Paulik Olivia , Hallen Jamie , Lapkin Samuel , Green Heidi , Fernandez Ritin
Published: September 2021

Objectives

The aim of this study was to examine the strength of improvement recommendations proposed after investigation of fall incidents in health care facilities that result in major injuries.

Methods

This study was conducted using a retrospective multi-incident analysis design. The study setting was 4 tertiary teaching hospitals, 1 subacute rehabilitation facility, and a residential aged care facility in a metropolitan health district in New South Wales, Australia. Ninety-eight injurious fall incidents during a 2-year period (2015–2016) were investigated. Recommendations were grouped into 3 categories: strong (including environmental modifications, equipment, workflow or process redesign), medium (including changes in communication or documentation processes, staffing numbers and/or skill mix, education to address identified knowledge deficits), and weak (including alerts/warning/labels or expected practice without any associated policy or procedure).

Results

The majority of the incidents (34.7%; n = 34) occurred between 1300 and 1859 hours, 65.3% (n = 64) occurred in the patient’s room, and 79.4% (n = 81) of the injuries were fractures. There were 224 recommendations made for 79 incidents, and 19 incidents did not have any recommendations. The average number of improvement recommendations proposed per incident investigation was 2.3 (SD, 2.1; range, 0–9). Nineteen (8.5%), 80 (35.7%), and 125 (55.8%) recommendations were classified as strong, medium, and weak, respectively. Half of the investigative teams included representatives from more than one professional group. There were a significantly greater number of medium recommendations made by multi-disciplinary teams compared with single-disciplinary teams (odds ratio, 1.83; 95% confidence interval, 1.05–3.21). There was no significant difference in the number of strong and weak recommendations made between the 2 teams.

Conclusions

This study found that only 8.5% of recommendations were classified as strong. This suggests that a major challenge lies in formulating robust recommendations; hence, efforts should focus on enhancing the strength of improvement recommendations.
Working Experience of Managers Who Are Responsible for Promoting and Monitoring Patient Safety in South Korea: Focusing on Small- and Medium-Sized Hospitals
Authors: Yoon Yea Seul , Lee Won , Kang Sunjoo , Kim In Sook , Jang Seung Gyeong
Published: September 2021

Objectives

This study explored the working experience of patient safety managers (PSMs) in small- and medium-sized hospitals (SMHs).

Methods

A qualitative study comprising 3 focus group discussions (6 people each) was conducted. Patient safety managers working in SMHs—hospitals with 100 to 300 beds—were included. Researchers analyzed the transcribed script, and a conventional content analysis was performed to describe PSMs’ working experience.

Results

All the PSMs were nurses and with an average (SD) work experience of 1.51 (1.02) years. Five core themes and 17 subthemes were derived. The PSMs reported that it was difficult to perform patient safety tasks alone and cooperate with other departments. Because of members who did not acknowledge PSMs’ authority as experts, PSMs experienced identity confusion. Lack of an established patient safety culture in SMHs hindered the PSMs from performing patient safety–related duties. The government continues to train PSMs and provide materials; however, they are not suitable for SMHs and thus cannot be used. The PSMs hoped to overcome the system’s initial phase and become professionals.

Conclusions

Patient safety managers faced difficulties because of the lack of guidelines, training, and systems. Nevertheless, they have attempted to overcome these problems themselves, so they can be recognized as professionals. This study’s findings can be used as basic data to provide differentiated support for PSMs, based on hospital size.
Impact of a Review of a Smart Infusion Pump Library in Hematology/Oncology: Tailoring Content to Meet Specialty Needs
Authors: Misko Jeanie , Rawlins Matthew , Ridley Breigh
Published: September 2021

Objectives

Errors involving chemotherapy or intravenous medications may cause serious patient harm. Dose error reduction software (DERS) for “smart” infusion pumps offers additional safety protection for their administration. Our institution uses DERS software hospital-wide; however, the hematology/oncology areas were noted to have reduced compliance with DERS recommendations. In response, we sought to review the DERS content and survey hematology/oncology end users’ satisfaction with the software.

Methods

A multidisciplinary working group was formed to review the current DERS entries for medications, fluids, and blood products. The review included details such as dose, rate, and concentrations. Dose error reduction software compliance was determined using vendor-supplied Continuous Quality Improvement software. An electronic survey assessing clinicians’ satisfaction with the current DERS library and any challenges in its use was conducted before and after the review.

Results

Ninety-one changes were made to 71 medications by the working group. Compliance with the DERS library went from 81.5% before the review to 87.3% after the review (P = 0.257). Fifty-eight survey responses were received (30 prereview and 28 postreview) with improvements in staff satisfaction with the DERS library (83.3%–92.8%, P < 0.05). Near-miss events changed after the review from 2 to 0, and the number of alerts caused by values outside the DERS library reduced from 8788 before the review to 3383 after the review (P ≤ 0.05).

Conclusions

Review of a hematology/oncology DERS library found improvements that better met the needs of end users. Engagement with relevant stakeholders, in conjunction with ongoing communication and review, is required to improve compliance and satisfaction with DERS.
Ultrasonic Device Complications in Endodontics: An Analysis of Adverse Events From the Food and Drug Administration Manufacturer and User Facility Device Experience
Authors: Rhodes S. Craig
Published: September 2021

Objectives

The author conducted a study to determine the frequency and types of adverse events associated with endodontic ultrasonic devices as reported to the U.S. Food and Drug Administration (FDA) Manufacturer and User Facility Device Experience (MAUDE) database.

Methods

Endodontic ultrasonic device–related adverse events reported to the MAUDE database from January 1, 2016, to October 31, 2020, were accessed and reviewed.

Results

A total of 1258 adverse event reports were submitted to the FDA MAUDE database, as classified under FDA product code ELC (ultrasonic scaler) during the study period. Among these reports, 403 were specific to the dedicated use of the 2 main types of ultrasonic devices used in endodontic treatment: ultrasonic tip devices and irrigation-related devices. Device malfunction-associated events, consisting primarily of device breakage, comprised 393 of the 1258 adverse event reports, whereas the remaining 10 reports were identified as being patient injury–related reports.

Conclusions

The frequency, root causes, and economic costs of ultrasonic tip device breakage remain largely unstudied. Ultrasonic endodontic device–related adverse events and patient injuries occurring within clinical practice may be underreported at the present time. Consequently, the risks and ultimate impacts to patients from ultrasonic endodontic device breakage, malfunction and unknown cause-related adverse events, and patient injuries during their clinical usage remain largely unknown at the present time. Eight of the 10 patient injury–related reports made to the FDA MAUDE database during the period under study, containing descriptions of varying degrees of injury severity, were associated with an irrigation-related device.
Omissions and Deviations From Safe Drug Administration Guidelines in 2 Medical Wards and Risk Factors: Findings From an Observational Study
Authors: Savva Georgios , Merkouris Anastasios , Charalambous Andreas , Papastavrou Evridiki
Published: September 2021

Objectives

This study aimed to record the type and frequency of errors, with an emphasis on omissions, during administration of medicines to inpatients and to investigate associated factors.

Methods

This was a descriptive observational study. The medication process in 2 medical wards was observed by 2 observers using a structured observation form. χ2 Test, Kruskal-Wallis test, and regression analysis were used to explore associations between factors and errors.

Results

From the 665 administrations observed, a total of 2371 errors were detected from which 81.2% were omissions and 18.8% were errors of commission. Omissions in the infection prevention guidelines (46.6%) and in the 5 rights of medication safety principles (35.8%) were a predominant finding. In particular, omitting to hand wash before administering a drug (98.4%), omitting to disinfect the site of injection (37.7%), and omitting to confirm the patient’s name (74.4%) were the 3 most frequently observed omissions. Documentation errors (13.1%) and administration method errors (4.5%) were also detected. Regression analysis has shown that the therapeutic class of the drug administered and the number of medicines taken per patient were the 2 factors with a statistical significance that increased the risk of a higher number of errors being detected.

Conclusions

Errors during drug administration are still common in clinical practice, with omissions being the most common type of error. In particular, omissions in the basic infection and safety regulations seem to be a very common problem. The risk of a higher number of errors being made is increased when a cardiovascular drug is administered and when the number of medicines administered per patient is increased.
Prevalence of COVID-19–Related Social Disruptions and Effects on Psychosocial Health in a Mixed-Serostatus Cohort of Men and Women
Authors: Friedman M. Reuel , Kempf Mirjam-Colette , Benning Lorie , Adimora Adaora A. , Aouizerat Bradley , Cohen Mardge H. , Hatfield Queen , Merenstein Dan , Mimiaga Matthew J. , Plankey Michael W. , Sharma Anjali , Sheth Anandi N. , Ramirez Catalina , Stosor Valentina , Wagner Marc C. E. , Wilson Tracey E. , D'Souza Gypsyamber , Weiss Deborah Jones
Published: September 2021

Objectives:

This study describes prevention behavior and psychosocial health among people living with HIV (PLHIV) and HIV-negative people during the early wave of the coronavirus disease 2019 (COVID-19) pandemic in the United States. We assessed differences by HIV status and associations between social disruption and psychosocial health.

Design:

A cross-sectional telephone/videoconference administered survey of 3411 PLHIV and HIV-negative participants in the Multicenter AIDS Cohort Study/WIHS Combined Cohort Study (MWCCS).

Methods:

An instrument combining new and validated measures was developed to assess COVID-19 prevention efforts, social disruptions (loss of employment, childcare, health insurance, and financial supports), experiences of abuse, and psychosocial health. Interviews were performed between April and June 2020. Associations between social disruptions and psychosocial health were explored using multivariable logistic regression, adjusting for sociodemographics and HIV status.

Results:

Almost all (97.4%) participants reported COVID-19 prevention behavior; 40.1% participants reported social disruptions, and 34.3% reported health care appointment disruption. Men living with HIV were more likely than HIV-negative men to experience social disruptions (40.6% vs. 32.9%; P < 0.01), whereas HIV-negative women were more likely than women with HIV to experience social disruptions (51.1% vs. 39.8%, P < 0.001). Participants who experienced ≥2 social disruptions had significantly higher odds of depression symptoms [aOR = 1.32; 95% confidence interval (CI): 1.12 to 1.56], anxiety (aOR = 1.63; 95% CI: 1.17 to 2.27), and social support dissatisfaction (aOR = 1.81; 95% CI: 1.26 to 2.60).

Conclusions:

This study builds on emerging literature demonstrating the psychosocial health impact related to the COVID-19 pandemic by providing context specific to PLHIV. The ongoing pandemic requires structural and social interventions to decrease social disruption and address psychosocial health needs among the most vulnerable populations.
A Rare Cause of Peripheral Facial Nerve Palsy: Chondromyxoid Fibroma of the Temporal Bone
Authors: Chrysouli Konstantina , Papanikolaou Vasileios , Chrysovergis Aristeidis , Kyrodimos Efthymios
Published: September 2021

Purpose:

To report a rather rare entity of facial palsy due to chondromyxoid fibroma. The authors present a case along with clinico-pathological features, management, treatment options and follow-up.

Methods:

The authors present a case of a 29-year-old male who suffered from right facial weakness and numbness for a period of 6-months. imaging studies demonstrated a soft, locally invasive tumor, located mainly in the right temporal bone and extended extracranially.

Results:

A surgical procedure of local excision followed by cross-facial nerve grafting was performed.

Conclusions:

Diagnosis should be based on combination of histo-pathologic and radiographic findings, because of its histological similarities to chondrosarcoma.
10 Year Analysis of Pediatric Surgery Fellowship Match and Operative Experience
Authors: Farooqui Zishaan , Cortez Alexander R. , PottsIII John R. , Tiao Gregory M. , von Allmen Daniel , Quillin Ralph C. , Bondoc Alexander J. , Garrison Aaron P.
Published: September 2021

Objective:

This paper aims to evaluate the pediatric surgery training pipeline vis-à-vis the pediatric surgery match and operative experience of pediatric surgery fellows.

Summary of Background Data:

Pediatric surgery remains a competitive surgical subspecialty. However, there is concern that operative experience for pediatric surgery fellows is changing. This paper examines the selectivity of the pediatric surgery match, along with the operative experience of pediatric surgery fellows to characterize the state of pediatric surgery training.

Methods:

The pediatric surgery fellowship match was analyzed from the National Resident Matching Program data from 2010 to 2019. Selectivity among fellowships was compared using analysis of variance with Dunnett test. Operative log data for pediatric fellows was analyzed using the Accreditation Council for Graduate Medical Education case logs from 2009 to 2019. Linear regression analysis was used to evaluate trends in operative volume over time.

Results:

Pediatric surgery had the highest proportion of unmatched applicants (47.2% ± 5.3%) and lowest proportion of unfilled positions (1.4% ± 1.6%) when compared to other National Resident Matching Program surgical fellowships. Accreditation Council for Graduate Medical Education case log analysis revealed a statistically significant decrease in cases for graduating fellows (–5.3 cases/year, P < 0.05). Total index cases decreased (–4.7 cases/year, P < 0.01, R2 = 0.83) such that graduates in 2019 completed 59 fewer index operations than graduates in 2009.

Conclusion:

Although pediatric surgery fellowship remains highly selective there has been a decline in the operative experience for graduating fellows. This highlights the need for evaluation of training paradigms and operative exposure in pediatric surgery to ensure the training of competent pediatric surgeons.
FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
Authors: Fell Christopher W , Hagelkruys Astrid , Cicvaric Ana , Horrer Marion , Liu Lucy , Li Joshua Shing Shun , Stadlmann Johannes , Polyansky Anton A , Mereiter Stefan , Tejada Miguel Angel , Kokotović Tomislav , Scaramuzza Angelica , Twyman Kimberly A , Morrow Michelle M , Juusola Jane , Yan Huifang , Wang Jingmin , Burmeister Margit , Andersen Thomas Levin , Wirnsberger Gerald , Holmskov Uffe , Perrimon Norbert , Zagrović Bojan , Monje Francisco J , Moeller Jesper Bonnet , Penninger Josef M , Nagy Vanja
Published: September 2021

The brain extracellular matrix (ECM) is enriched in chondroitin sulphate proteoglycans (CSPGs) with variable sulphate modifications that intimately participate in brain maturation and function. Very little is known about how the changing biophysical properties of the CSPGs are signalled to neurons. Here, we report Fibrinogen C Domain Containing 1 (FIBCD1), a known chitin-binding receptor of the innate immune system, to be highly expressed in the hippocampus and to specifically bind CSPGs containing 4-O sulphate modification (CS-4S). Cultured Fibcd1 knockout (KO) neurons lack phenotypic and transcriptomic responses to CSPG stimulation. Further, Fibcd1 KO mice exhibit accumulation of CS-4S, likely resulting in deficits of hippocampal-dependent learning tasks and abrogated synaptic remodelling, a phenotype rescued by enzymatic digestion of CSPGs. Likewise, neuronal specific knockdown of a Fibcd1 orthologue in flies results in neuronal morphological changes at the neuromuscular junctions and behavioural defects. Finally, we report two undiagnosed patients with a complex neurodevelopmental disorder with deleterious variants in FIBCD1, strongly implicating FIBCD1 in the development of the disease. Taken together, our results demonstrate that FIBCD1 is a novel, evolutionarily conserved component of ECM sulphation recognition that is crucial for neuronal development and function.
INTEGUMENT-SPECIFIC TRANSCRIPTIONAL REGULATION IN THE MID-STAGE OF FLAX SEED DEVELOPMENT INFLUENCES THE RELEASE OF MUCILAGE AND THE SEED OIL CONTENT
Authors: Miart Fabien , Fontaine Jean-Xavier , Mongelard Gaëlle , Wattier Christopher , Lequart-Pillon Michelle , Bouton Sophie , Molinié Roland , Dubrulle Nelly , Fournet Françoise , Demailly Hervé , Roulard Romain , Dupont Loïc , Boudaoud Arezki , Thomasset Brigitte , Gutierrez Laurent , Van Wuytswinkel Olivier , Mesnard François , Pageau Karine
Published: September 2021

Flax (Linum usitatissimum L.) seed oil, which accumulates in the embryo, and mucilage, which is synthesized in the seed coat, are of great economic importance for food, pharmaceutical as well as chemical industries. Theories on the link between oil and mucilage production in seeds consist in the spatio-temporal competition of both compounds for photosynthates during the very early stages of seed development. In this study, we demonstrate a positive relationship between seed oil production and seed coat mucilage extrusion in the agronomic model, flax. Three recombinant inbred lines were selected for low, medium and high mucilage and seed oil contents. Metabolite and transcript profiling (1H NMR and DNA oligo-microarrays) was performed on the seeds during seed development. These analyses showed main changes in the seed coat transcriptome during the mid-phase of seed development (25 Days Post-Anthesis), once the mucilage biosynthesis and modification processes are thought to be finished. These transcriptome changes comprised genes that are putatively involved in mucilage chemical modification and oil synthesis, as well as gibberellic acid (GA) metabolism. The results of these integrative biology approach, suggest that transcriptional regulations of seed oil and fatty acid (FA) metabolism could occur in the seed coat during the mid-stage of seed development, once the seed coat carbon supplies have been used for mucilage biosynthesis and mechanochemical properties of the mucilage secretory cells.
Kif11 overexpression rescues cognition, long-term potentiation, and spine defects in mouse and cell models of Alzheimer’s disease
Authors: Lucero Esteban M. , Freund Ronald K. , Johnson Noah R. , Dooling Breanna , Sullivan Emily , Prikhodko Olga , Ahmed Md. Mahiuddin , Dell’Acqua Mark L. , Chial Heidi J. , Potter Huntington
Published: September 2021

Competitive inhibition of kinesin motor proteins by amyloid-beta (Aβ) may contribute to alterations in the neuronal microtubule cytoskeleton that can disrupt plasticity mechanisms required for learning and memory, such as long-term potentiation (LTP), thus contributing to synaptic dysfunction and cognitive impairments associated with Alzheimer’s disease (AD). Here, we tested the hypothesis that overexpression of the microtubule motor protein KIF11 (Kinesin-5/Eg5) will rescue Aβ-mediated synaptic dysfunction and cognitive impairments. We found that overexpression ofKif11prevented spatial learning and LTP deficits in the 5xFAD mouse model of AD and rescued Aβ-mediated decreases in postsynaptic dendritic spine density in neuronal cultures. Together, these data suggest that KIF11 function is important for preserving synaptic structures and functions that are critical for learning and memory and for protection against Aβ-mediated loss of cognition in AD.

Highlights

Deficits in cognition and long-term potentiation in the 5xFAD mouse model of Alzheimer’s disease are prevented byKif11overexpression.

Aβ-mediated dendritic spine loss is blocked byKif11overexpression.
Tetragonisca angustularesin gathering behaviour ofSchizolobium parahyba
Authors: Regnier Leonardo
Published: September 2021

Tetragonisca angustulais a very important stingless bees species. This study aimed to report the resin gathering behaviour of this species of a possible new resin source:Schizolobium parahyba. Evaluations of temperature, number of bees in gathering activity, time and season were used to characterize bee’s behaviour. Resin gathering activities were concentered between 10 and 14 hours, with a moderate linear positive correlation index with the temperature. No bee activity was observed when temperatures were below 16.69°C. Gathering suffered extreme reduction during winter and greater activity in summer. Bees exploration were concentered on the younger leafs and apical portion ofS. parahyba. Older leafs were mainly ignored, and gradually the exploring activity was constantly migrating to most young parts, while apical exploration was consistent all the studied period.
Large-scale miRNA-Target Data Analysis to Discover miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans
Authors: Chang Haowu , Zhang Tianyue , Zhang Hao , Su Lingtao , Qin Qing-Ming , Li Guihua , Li Xueqing , Wang Li , Zhao Tianheng , Zhao Enshuang , Zhao Hengyi , Liu Yuanning , Stacey Gary , Xu Dong
Published: September 2021

Although growing evidence shows that microRNA (miRNA) regulates plant growth and development, miRNA regulatory networks in plants are not well understood. Current experimental studies cannot characterize miRNA regulatory networks on a large scale. This information gap provides a good opportunity to employ computational methods for global analysis and to generate useful models and hypotheses. To address this opportunity, we collected miRNA-target interactions (MTIs) and used MTIs from Arabidopsis thaliana and Medicago truncatula to predict homologous MTIs in soybeans, resulting in 80,235 soybean MTIs in total. A multi-level iterative bi-clustering method was developed to identify 483 soybean miRNA-target regulatory modules (MTRMs). Furthermore, we collected soybean miRNA expression data and corresponding gene expression data in response to abiotic stresses. By clustering these data, 37 MTRMs related to abiotic stresses were identified including stress-specific MTRMs and shared MTRMs. These MTRMs have gene ontology (GO) enrichment in resistance response, iron transport, positive growth regulation, etc. Our study predicts soybean miRNA-target regulatory modules with high confidence under different stresses, constructs miRNA-GO regulatory networks for MTRMs under different stresses and provides miRNA targeting hypotheses for experimental study. The method can be applied to other biological processes and other plants to elucidate miRNA co-regulation mechanisms.
OrBITS: Label-free and time-lapse monitoring of patient derived organoids for advanced drug screening
Authors: Deben Christophe , De La Hoz Edgar Cardenas , Le Compte Maxim , Van Schil Paul , Hendriks Jeroen M. , Lauwers Patrick , Yogeswaran Suresh Krishan , Lardon Filip , Pauwels Patrick , Van Laere Steven , Bogaerts Annemie , Smits Evelien , Vanlanduit Steve , Lin Abraham
Published: September 2021

Background

Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications.

Methods

Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, namedOrganoidBrightfieldIdentification-basedTherapyScreening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification.

Results

OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D®-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, intra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification.

Conclusions

Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.
The transitivity of the Hardy-Weinberg law
Authors: Graffelman Jan , Weir Bruce S.
Published: September 2021

The reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit, is addressed. The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in practical genetic data analysis with multi-allelic markers is explored. In general, results of statistical tests for Hardy-Weinberg equilibrium obtained with polymorphisms that are reduced by deletion or joining of alleles are seen to be consistent with the formulated transitivity principle. We also show how the transitivity principle allows one to identify equilibrium-offending alleles, and how it can provide clues to genotyping problems and evolutionary changes. For microsatellites, which are widely used in forensics, the transitivity principle implies one expects similar results for statistical tests that use length-based and sequence-based alleles. High-quality autosomal microsatellite databases of the US National Institute of Standards and Technology are used to illustrate the use of the transitivity principle in testing both length-based and sequence-based microsatellites for Hardy-Weinberg proportions. Test results for Hardy-Weinberg proportions for the two types of microsatellites are seen to be largely consistent and can detect allele imbalance.
Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA
Authors: Bewg W. Patrick , Harding Scott A. , Engle Nancy L. , Vaidya Brajesh N. , Zhou Ran , Reeves Jacob , Horn Thomas W. , Joshee Nirmal , Jenkins Jerry W. , Shu Shengqiang , Barry Kerrie W. , Yoshinaga Yuko , Grimwood Jane , Schmitz Robert J. , Schmutz Jeremy , Tschaplinski Timothy J. , Tsai Chung-Jui
Published: September 2021

As the focus for CRISPR edited plants moves from proof-of-concept to real world applications, precise gene manipulation will increasingly require concurrent multiplex editing for polygenic traits. A common approach for editing across multiple sites is to design one gRNA per target; however, this complicates construct assembly and increases the possibility of off-target mutations. In this study, we utilized one gRNA to targetMYB186, a known positive trichome regulator, as well as its paralogsMYB138andMYB38at a consensus site for mutagenesis inPopulus tremula×P. albaINRA 717-1B4. Unexpected duplications ofMYB186andMYB138resulted in a total of eight alleles for the three targeted genes in the hybrid poplar. Deep sequencing and PCR analyses confirmed editing across all eight targets in nearly all of the resultant glabrous mutants, ranging from small indels to large genomic dropouts, with no off-target activity detected at four potential sites. This highlights the effectiveness of a single gRNA targeting conserved exonic regions for multiplex editing. Additionally, cuticular wax and whole leaf analyses showed a complete absence of triterpenes in the trichomeless mutants, hinting at a previously undescribed role for the non-glandular trichomes of poplar.

ONE SENTENCE SUMMARY

Targeting conserved sequences with a single gRNA allowed efficient mutagenesis of a multigene family and the recovery of trichomeless and triterpene-free poplar mutants.
Pro-apoptotic caspase deficiency reveals a cell-extrinsic mechanism of NK cell regulation
Authors: Olsen Tayla M. , Tan Wei Hong , Knudsen Arne C. , Rongvaux Anthony
Published: September 2021

Abstract

Regulated cell death is essential for the maintenance of cellular and tissue homeostasis. In the hematopoietic system, genetic defects in apoptotic cell death generally produce the accumulation of immune cells, inflammation and autoimmunity. In contrast, we found that genetic deletion of caspases of the mitochondrial apoptosis pathway reduces natural killer (NK) cell numbers and makes NK cells functionally defectivein vivoandin vitro. Caspase deficiency results in constitutive activation of a type I interferon (IFN) response, due to leakage of mitochondrial DNA and activation of the cGAS/STING pathway. The NK cell defect in caspase-deficient mice is independent of the type I IFN response, but the phenotype is partially rescued by cGAS or STING deficiency. Finally, caspase deficiency alters NK cells in a cell-extrinsic manner. Type I IFNs and NK cells are two essential effectors of antiviral immunity, and our results demonstrate that they are both regulated in a caspase-dependent manner. Beyond caspase-deficient animals, our observations may have implications in infections that trigger mitochondrial stress and caspase-dependent cell death.
Rapid, multianalyte detection of opioid metabolites in wastewater
Authors: Kumar Narendra , Rana Muhit , Geiwitz Michael , Khan Niazul Islam , Catalano Matthew , Ortiz-Marquez Juan C. , Kitadai Hikari , Weber Andrew , Dweik Badawi , Ling Xi , van Opijnen Tim , Argun Avni , Burch Kenneth S.
Published: September 2021

By monitoring opioid metabolites, wastewater-based epidemiology (WBE) could be an excellent tool for real-time information on consumption of illicit drugs. A key limitation of WBE is the reliance on costly laboratory-based techniques that require substantial infrastructure and trained personnel, resulting in long turnaround times. Here, we present an aptamer-based graphene field effect transistor (AptG-FET) platform for simultaneous detection of three different opioid metabolites. This platform provides a reliable, rapid, and inexpensive method for quantitative analysis of opioid metabolites in wastewater (WW). The platform delivers a limit of detection (LOD) 2-3 orders of magnitude lower than previous reports, but in line with the concentrations range (pg/ml to ng/ml) of these opioid metabolites present in real samples. To enable multianalyte detection we developed a facile, reproducible, and high yield fabrication process producing twenty G-FETs with integrated side gate platinum (Pt) electrodes on a single chip. Our devices achieved the simultaneous and selective multianalyte detection of three different metabolites: Noroxycodone (NX), 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), and Norfentanyl (NF) in wastewater.
Characterization of aquaporin1b (AQP1b) mRNA in mud loach (Misgurnus mizolepis) in response to heavy metal and immunostimulant stimuli
Authors: Lee Sang Yoon , Nam Yoon Kwon , Kim Yi Kyung
Published: September 2021

Aquaporins (AQPs) facilitate the transport of water or other small solutes into cells in the presence of osmotic gradients. However, the current understanding of piscine AQP gene with cellular stress responses has been still limitedly exemplified. In present study, we characterized the mud loach AQP1b gene at the nucleotide and amino acid levels. We identified three AQP 1b transcript variants (mmAQP1b_tv1, mmAQP1b_tv2, and mmAQP1b_tv3). Then, we examined the AQP1b promoter region and observed several transcription factor binding sites (TFBS) for nuclear factor of activated T-cells (NFAT), SRY-box, c-AMP responsive element binding protein (CREB), GATA binding factor, and hepatic nuclear factor-1. Interestingly, mmAQP1b transcription was differentially modulated by heavy metal or immunostimulant challenge. Further studies to deepen the knowledge of fish AQP-mediated adaptation response potentially relevant to molecular pathogenesis are warranted.

Summary statement

We identified mud loach AQP1b transcript variants and consensus sequences involved in stress or innate immunity in promotor region. AQP1b transcription was differentially modulated by heavy metal or immunostimulant challenge.
Tumor Suppressor p53 Restrains Cancer Cell Dissemination by Modulating Mitochondrial Dynamics
Authors: Phan Thi Tuyet Trinh , Lin Yu-Chun , Chou Yu-Ting , Wu Chien-Wei , Lin Lih-Yuan
Published: September 2021

Tumor suppressor p53 plays a central role in preventing tumorigenesis. Here, we unravel how p53 modulates mitochondrial dynamics to restrain the metastatic properties of cancer cells. p53 inhibits the mammalian target of rapamycin complex 1 (mTORC1) signaling to attenuate the protein level of mitochondrial fission process 1 (MTFP1), which fosters the pro-fission dynamin-related protein 1 (Drp1) phosphorylation. This regulatory mechanism allows p53 to restrict cell migration and invasion governed by Drp1-mediated mitochondrial fission. Downregulating p53 expression or elevating the molecular signature of mitochondrial fission correlates with aggressive tumor phenotypes and poor prognosis in cancer patients. Upon p53 loss, exaggerated mitochondrial fragmentation stimulates the activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling resulting in epithelial-to-mesenchymal transition (EMT)-like changes in cell morphology, accompanied by accelerated matrix metalloproteinase-9 (MMP9) expression and invasive cell migration. Notably, blocking the activation of mTORC1/MTFP1/Drp1/ERK1/2 axis completely abolishes the p53 deficiency-driven cellular morphological switch, MMP9 expression, and cancer cell dissemination. Our findings unveil a hitherto unrecognized mitochondria-dependent molecular mechanism underlying the metastatic phenotypes of p53-compromised cancers.
Effect of dietary zinc supplementation on the gastrointestinal microbiota and host gene expression in theShank3B−/−mouse model of autism spectrum disorder
Authors: Wong Giselle C. , Jung Yewon , Lee Kevin , Fourie Chantelle , Handley Kim M. , Montgomery Johanna M. , Taylor Michael W.
Published: September 2021

Shank genes are implicated in ~1% of people with autism and mice with Shank3 knock out mutations exhibit autism-like behaviours. Zinc deficiency and gastrointestinal problems can be common among people with autism, and zinc is a key element required for SHANK protein function and gut development. InShank3B−/−mice, a supplementary zinc diet reverses autism behaviours. We hypothesise that dietary zinc may alter the gut microbiome, potentially affecting the gut-microbiome-brain axis, which may contribute to changes in autism-like behaviours. To test this, four types of gastrointestinal samples (ileum, caecum, colon, faecal) were collected from wild-type and knock-outShank3B−/−mice on either control or supplemented-zinc diets. Cage, genotype and zinc diet each contributed significantly to bacterial community variation (accounting for 12.8%, 3.9% and 2.3% of the variation, respectively). Fungal diversity differed significantly between wild-type and knock-outShank3B−/−mice on the control zinc diet, and the fungal biota differed among gut locations. RNA-seq analysis of host (mouse) transcripts revealed differential expression of genes involved in host metabolism that may be regulated by the gut microbiota and genes involved in anti-microbial interactions. By utilising theShank3B−/−knock-out mouse model we were able to examine the influence of – and interactions between – dietary zinc and ASD-linked host genotype. These data broaden understanding of the gut microbiome in autism and pave the way towards potential microbial therapeutics for gastrointestinal problems in people with autism.

Importance

Previously, supplemental dietary zinc in the Shank3B−/−mouse model of autism spectrum disorder resulted in observations of ASD behaviours reversal; in this study we also used theShank3B−/−mouse model to examine the influence of – and interaction between – dietary zinc and ASD-linked host genotype. Sample location along the gastrointestinal tract, genotype and zinc diet explained some of the variation in the microbiota data, with notable bacterial differences between treatment groups. Differential expression of host genes between treatment groups, including antimicrobial interaction genes and gut microbiota-regulated host metabolism genes, suggests that the interplay between gut microbes, the gastrointestinal tract and the brain may play a major role towards the observed amelioration of ASD behaviours seen previously with supplemented dietary zinc. These results widen the scope towards manipulating both dietary zinc and the microbiota itself to ameliorate ASD-related behaviours and associated gastrointestinal issues.
Advanced understanding of prokaryotic biofilm formation using a cost-effective and versatile multi-panel adhesion (mPAD) mount
Authors: Schulze Stefan , Schiller Heather , Solomonic Jordan , Telhan Orkan , Costa Kyle , Pohlschroder Mechthild
Published: September 2021

Most microorganisms exist in biofilms, which comprise aggregates of cells surrounded by an extracellular matrix that provides protection from external stresses. Based on the conditions under which they form, biofilm structures vary in significant ways. For instance, biofilms that develop when microbes are incubated under static conditions differ from those formed when microbes encounter the shear forces of a flowing liquid. Moreover, biofilms develop dynamically over time. Here, we describe a cost-effective, 3D-printed coverslip holder that facilitates surface adhesion assays under a broad range of standing and shaking culture conditions. This multi-panel adhesion (mPAD) mount further allows cultures to be sampled at multiple time points, ensuring consistency and comparability between samples and enabling analyses of the dynamics of biofilm formation. As a proof of principle, using the mPAD mount for shaking, oxic cultures, we confirm previous flow chamber experiments showing that Pseudomonas aeruginosa wild type and a phenazine deletion mutant (Δphz) form similar biofilms. Extending this analysis to anoxic conditions, we reveal that microcolony and biofilm formation can only be observed under shaking conditions and are decreased in the Δphz mutant compared to wild-type cultures, indicating that phenazines are crucial for the formation of biofilms if oxygen as an electron acceptor is not available. Furthermore, while the model archaeon Haloferax volcanii does not require archaella for attachment to surfaces under static conditions, we demonstrate that H. volcanii mutants that lack archaella are negatively affected in their early stages of biofilm formation under shaking conditions.

Importance

Due to the versatility of the mPAD mount, we anticipate that it will aid the analysis of biofilm formation in a broad range of bacteria and archaea. Thereby, it contributes to answering critical biological questions about the regulatory and structural components of biofilm formation and understanding this process in a wide array of environmental, biotechnological, and medical contexts.
An open label, adaptive, phase 1 trial of high-dose oral nitazoxanide in healthy volunteers: an antiviral candidate for SARS-CoV-2
Authors: Walker Lauren E , FitzGerald Richard , Saunders Geoffrey , Lyon Rebecca , Fisher Michael , Martin Karen , Eberhart Izabela , Woods Christie , Ewings Sean , Hale Colin , Rajoli Rajith KR , Else Laura , Dilly-Penchala Sujan , Amara Alieu , Lalloo David G , Jacobs Michael , Pertinez Henry , Hatchard Parys , Waugh Robert , Lawrence Megan , Johnson Lucy , Fines Keira , Reynolds Helen , Rowland Timothy , Crook Rebecca , Byrne Kelly , Mozgunov Pavel , Jaki Thomas , Khoo Saye , Owen Andrew , Griffiths Gareth , Fletcher Thomas E
Published: September 2021

Repurposing approved drugs may rapidly establish effective interventions during a public health crisis. This has yielded immunomodulatory treatments for severe COVID-19, but repurposed antivirals have not been successful to date because of redundancy of the target in vivo or suboptimal exposures at studied doses. Nitazoxanide is an FDA approved antiparasitic medicine, that physiologically-based pharmacokinetic (PBPK) modelling has indicated may provide antiviral concentrations across the dosing interval, when repurposed at higher than approved doses. Within the AGILE trial platform (NCT04746183) an open label, adaptive, phase 1 trial in healthy adult participants was undertaken with high dose nitazoxanide. Participants received 1500mg nitazoxanide orally twice-daily with food for 7 days. Primary outcomes were safety, tolerability, optimum dose and schedule. Intensive pharmacokinetic sampling was undertaken day 1 and 5 with Cmin sampling on day 3 and 7. Fourteen healthy participants were enrolled between 18th February and 11th May 2021. All 14 doses were completed by 10/14 participants. Nitazoxanide was safe and well tolerated with no significant adverse events. Moderate gastrointestinal disturbance (loose stools) occurred in 8 participants (57.1%), with urine and sclera discolouration in 12 (85.7%) and 9 (64.3%) participants, respectively, without clinically significant bilirubin elevation. This was self-limiting and resolved upon drug discontinuation. PBPK predictions were confirmed on day 1 but with underprediction at day 5. Median Cmin was above the in vitro target concentration on first dose and maintained throughout. Nitazoxanide administered at 1500mg BID with food was safe and well tolerated and a phase 1b/2a study is now being initiated in COVID-19 patients.
Universal inverse square relationship between heart rate variability and heart rate
Authors: Maltsev Anna V. , Monfredi Oliver , Maltsev Victor A.
Published: September 2021

In our previous study, we analyzed heart rate variability and heart rate from a large variety of cardiac preparations (including humans, living animals, Langendorff-perfused isolated hearts, and single sinoatrial nodal cells) in diverse species, combining our data with those of previously published articles. The analysis revealed that regardless of conditions, heart rate variability (for the purposes of the study assessed as standard deviation of beat-to-beat intervals) vs. heart rate follows a universal exponential decay-like relationship. Numerical simulations of diastolic interval variability by adding a randomly fluctuating term (Iper) to net current revealed a similar relationship. In the present study, using a Taylor series, we found that this relationship is, in fact, inverse square, and we derive an explicit formula for the standard deviation (sd) of the cycle length (CL) as a function of heart rate (HR) with biophysically meaningful parameters: sd(CL)=sd(Iper)*(60,000/mean(HR) -APD)^2/(ΔV*C), where CL is in ms, HR in beats per minute, Iper in pA, APD in ms is an average AP duration of pacemaker cells, C in pF is cell membrane capacitance, and ΔV is the magnitude of diastolic depolarization in mV. This relationship gives direct insight into heart rate variability mechanisms at the basic level of individual pacemaker cells, i.e. their intrinsic CL variability linked to stochastic operation of ion channels (both Ca release and cell membrane channels) generating Iper. Our explicit formula may be also used for a more precise biomedical interpretation of heart rate variability after respective corrections for heart rate.
Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock
Authors: Meek Stephen , Watson Tom , Eory Lel , McFarlane Gus , Wynne Felicity J. , McCleary Stephen , Dunn Laura E.M. , Charlton Emily M. , Criag Chloe , Shih Barbara , Regan Tim , Taylor Ryan , Sutherland Linda , Gossner Anton , Chintoan-Uta Cosmin , Fletcher Sarah , Beard Philippa M. , Hassan Musa A. , Grey Finn , Hope Jayne C. , Stevens Mark P. , Nowak-Imialek Monika , Niemann Heiner , Ross Pablo J. , Tait-Burkard Christine , Brown Sarah M. , Lefevre Lucas , Thomson Gerard , McColl Barry W. , Lawrence Alistair B. , Archibald Alan L. , Steinbach Falko , Crooke Helen R. , Gao Xuefei , Liu Pentao , Burdon Tom
Published: September 2021

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how pluripotent stem cells (PSCs) can provide a limitlessin vitrosupply of genetically and experimentally tractable macrophages from livestock. Porcine and bovine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics ofex vivoprimary macrophages. Pig PSCdMs were productively infected by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and African Swine Fever Virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, Pig PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied in parental stem cells, or directly by lentiviral vector transduction. PSCs and differentiated derivatives therefore provide a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in livestock.