bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Role for Cytochrome P450 Epoxygenase Metabolites in Septic Shock
Authors: Jones Timothy N. , Janani Leila , Gordon Anthony C. , Al-Beidh Farah , Antcliffe David B.
Published: January 2022

IMPORTANCE:

This is the largest study describing the role of P450 epoxygenase metabolites in septic shock in humans and suggests a novel therapeutic target.

Objectives:

Oxylipins are oxidative breakdown products of cell membrane fatty acids. Animal models have demonstrated that oxylipins generated by the P450 epoxygenase pathway may be implicated in septic shock pathology. However, these mediators are relatively unexplored in humans with septic shock. We aimed to determine if there were patterns of oxylipins that were associated with 28-day septic shock mortality and organ dysfunction.

Design:

Retrospective analysis of samples collected during the Vasopressin versus Norepinephrine as Initial Therapy in Septic Shock trial.

Setting:

ICUs in the United Kingdom.

PARTICIPANTS:

Adults recruited within 6 hours of onset of septic shock.

MAIN OUTCOMES AND MEASURES:

Oxylipin profiling was performed on 404 serum samples from 152 patients using liquid chromatography-mass spectrometry.

Results:

Nonsurvivors were found to have higher levels of 14,15-dihydroxyeicosatrienoic acid (DHET) at baseline than survivors (p = 0.02). Patients with 14,15-DHET levels above the lower limit of quantification of the assay were more likely to die than patients with levels below this limit (hazard ratio, 2.3; 95% CI, 1.2–4.5). Patients with measurable 14,15-DHET had higher levels of organ dysfunction and fewer renal failure-free days than those in whom it was unmeasurable. Considering samples collected over the first week of intensive care stay, measurable levels of DHET species were associated with higher daily Sequential Organ Failure Assessment scores that appeared to be accounted for predominantly by the liver component. Measurable 14,15-DHET showed positive correlation with bilirubin (r
s = 0.38; p < 0.001) and lactate (r
s = 0.27; p = 0.001).

CONCLUSIONS AND RELEVANCE:

The P450 epoxygenase-derived DHET species of oxylipins were associated with organ, particularly liver, dysfunction in septic shock and 14,15-DHET was associated with septic shock mortality. These results support further investigation into the role of the P450 epoxygenase-derived oxylipins in sepsis and suggest that this pathway may offer a novel therapeutic strategy in septic shock.
The anatomy of enjoyment: the flow experience and cardiac surgery
Authors: Jiang Stephanie M. , McQueen Sydney , Mobilio Melanie Hammond , Bisleri Gianluigi , Yanagawa Bobby , Moulton Carol-Anne
Published: January 2022

Purpose of review

In a time of record levels of physician burnout coupled with a global pandemic, protecting physician wellness is critical. The experience of cognitive flow has been found to enhance both wellness and performance. Although flow has been vastly explored in other fields including elite sport, it has not been deeply investigated or applied in cardiac surgery. Here we discuss flow and flow-promoting techniques employed in other fields that may be beneficial within cardiac surgery.

Recent findings

Flow is a prevalent experience among surgeons, amplified during operations. Possible strategies to cultivate flow may be separated into individual skills training, such as mindfulness practice and stress management, institutional changes, such as ensuring adequate resources and protected spaces, and strategies targeting the intersectionality of individuals and systems, such as how workplace culture shapes an individual's experience. These techniques may be applicable within cardiac surgery, especially in training.

Flow has been identified as a key component of a happy and meaningful life, and a potential protector against burnout. Harnessing the benefits of flow may help promote flourishing, particularly in demanding fields, such as cardiac surgery.
Contact Lens Prescribing Trends for Keratoconus at an Academic Medical Center: Increased Utilization of Scleral Lenses for Severe Disease
Authors: Scanzera Angelica C. , Deeley Marc , Joslin Charlotte , McMahon Timothy T. , Shorter Ellen
Published: January 2022

Objectives:

To describe contact lens prescription trends for patients with keratoconus.

Methods:

Demographics, corneal curvature, visual acuity, and type of contact lens prescribed were reviewed for all patients with keratoconus evaluated in the contact lens service in 2010 and 2020.

Results:

There were 292 patients in 2010 and 217 in 2020. In 2010, 69% were using corneal gas-permeable lenses (GP), 16% soft toric, 13% hybrid, and 2% soft sphere with no scleral lens (SL). In 2020, 60% were using corneal GP, 22% SL, 12% soft toric, 5% hybrid, and 1% soft sphere. Mean log of minimum angle of resolution visual acuities with manifest refraction were (represented in mean [SD, range]) 0.42 (0.33, 0–1.3) in 2010 and 0.35 (0.33, 0–1.6) in 2020 improving to 0.19 (0.18, 0–1.3; P≤0.01) and 0.13 (0.14, 0–0.60; P<0.01) with contact lenses. Mean keratometry measurement in patients using SLs was 53.0 diopters (D) (9.9, 42.1–84.5), which was steeper than 46.6 D in patient's using all other lens types in 2010 and 2020 (3.9, 40.9–57.9; P<0.01).

Conclusions:

Scleral lens prescription increased during the past decade; however, corneal GP lenses remain the most frequent lens prescribed for patients with keratoconus in this cohort. Despite being prescribed for patients with the most advanced disease, SLs provide good visual acuity.
Menin Inhibitors in Acute Myeloid Leukemia—What Does the Future Hold?
Authors: Swaminathan Mahesh , Bourgeois Wallace , Armstrong Scott A. , Wang Eunice S.
Published: January 2022

Menin inhibitors constitute a novel class of agents targeting the underlying biology of nucleophosmin (NPM1) mutant and KMT2A (formerly known as MLL1) rearranged (KMT2Ar) acute leukemias. KMT2Ar acute leukemias constitute 5% to 10% of acute leukemias, and NPM1 mutations are identified in 30% of newly diagnosed acute myeloid leukemias (AMLs). In preclinical AML models, small molecule inhibitors of the menin-KMT2A protein-protein interaction induce differentiation, downregulate critical gene expression programs, and confer a survival advantage in patient-derived xenograft models of NPM1 mutant and KMT2Ar AML. Multiple clinical trials evaluating oral menin inhibitors in acute leukemias are ongoing. Preliminary results in relapsed/refractory NPM1 mutant and KMT2Ar AML have shown on-target effects, tolerable toxicity, and promising clinical activity. This review details the current clinical experience of menin inhibitors in AML and discusses how these agents can be successfully integrated into future therapeutic approaches.
Incorporation of FLT3 Inhibitors Into the Treatment Regimens for FLT3 Mutated Acute Myeloid Leukemia
Authors: Perl Alexander E. , Pratz Keith W.
Published: January 2022

Therapeutic outcomes for acute myeloid leukemia patients with Fms-like tyrosine kinase 3 (FLT3) mutations have improved substantially since the discovery of small molecule tyrosine kinase inhibitors. Today, use of FLT3 inhibitors is standard in frontline intensive chemotherapy as well as patients with relapsed or refractory acute myeloid leukemia and FLT3 mutations and increasingly used as for prolonged remission maintenance posttransplant and/or postconsolidation. Yet, FLT3 inhibitors alone are not curative, and best outcomes are seen when the drugs are used as part of combination regimens. Optimizing therapy for patients with FLT3 mutations remains a work in progress. Overall, modern therapeutic approaches generate cure rates for this group at levels that argue against considering these mutations adverse risk. Still, such survivals require intensive therapy and often transplant. Therefore, efforts are underway to determine if lower toxicity regimens can attain comparable outcomes, at least for patients responding optimally. This review will review the various FLT3 inhibitors that are approved or in development, highlight the areas where they have been shown to add value, and identify areas where their use remains controversial.
Improving Efficiency of Multidisciplinary Bedside Rounds in the NICU: A Single Centre QI Project
Authors: Shivananda Sandesh , Osiovich Horacio , de Salaberry Julie , Hait Valoria , Gautham Kanekal S.
Published: January 2022

Introduction:

Inconsistent workflow, communication, and role clarity generate inefficiencies during bedside rounds in a neonatal intensive care unit. These inefficiencies compromise the time needed for essential activities and result in reduced staff and family satisfaction. This study’s primary aim was to reduce the mean duration of bedside rounds by 25% within 3 months by redesigning the rounding processes and applying QI principles. The secondary aims were to improve staff and family experience.

Methods:

We conducted this work in an academic 50-bed neonatal intensive care unit involving 350 staff members. The change interventions included: (i) reinforcing essential value-added activities like standardizing rounding time, the sequencing of patients rounded, sequencing each team member rounding presentations, team preparation, bedside presentation content, and time management; (ii) reducing non-value-added activities; and (iii) moving value-added nonessential activities outside of the rounds.

Results:

The mean duration of rounds decreased from 229 minutes in the pre-implementation to 132 minutes in the postimplementation phase. The proportion of staff showing satisfaction regarding various components of the rounds increased from 5% to 60%, and perceived staff involvement during the rounds increased from 70% to 77%. Ninety-three percent of family experience survey respondents expressed satisfaction at being invited for bedside reporting and being involved in decision-making or care planning. The staff did not report any adverse events related to the new rounds process.

Conclusion:

Redesigning bedside rounds improved staff engagement and workflow, resulting in efficient rounds and better staff experience.
Reducing Avoidable Transfer Delays in the Pediatric Intensive Care Unit for Status Asthmaticus Patients
Authors: Karube Takaharu , Goins Theresa , Karsies Todd J. , Gee Samantha W.
Published: January 2022

Introduction:

Status asthmaticus (acute severe asthma) is one of the most common reasons for Pediatric Intensive Care Unit (PICU) admission. Accordingly, ensuring optimal throughput for patients admitted with status asthmaticus is essential for optimizing PICU capacity. Few studies specifically address effective methods to reduce delays related to PICU discharge. This project aimed to identify and reduce avoidable delays in PICU discharge for status asthmaticus patients.

Methods:

This quality improvement project focused on reducing transfer delays for status asthmaticus patients admitted to the PICU at a freestanding academic children’s hospital. We standardized the transfer criteria, identified barriers to an efficient transfer, and implemented multidisciplinary interventions. The primary aim was to decrease the average duration from fulfilling the transfer criteria to PICU discharge by 15% from the baseline within 8 months of implementation. The balancing measure was readmissions to the PICU for asthma exacerbations within 24 hours from PICU discharge.

Results:

The analysis included 623 patients. Following interventions, the time from fulfilling transfer criteria to PICU discharge decreased from 9.8 hours to 6.8 hours, a 30.6% reduction from baseline. Improvements were sustained for 6 months. In the preintervention group, three patients were readmitted to the PICU within 24 hours of transferring out of the PICU, but no patient was readmitted during the postintervention period.

Conclusions:

Standardizing transfer criteria and implementing multidisciplinary strategies can reduce avoidable PICU discharge delays for patients with status asthmaticus. The application of a similar approach could potentially reduce avoidable delays for other conditions in the PICU.
Improving Quality and Efficiency in Pediatric Emergency Department Behavioral Health Care
Authors: Emerson Beth L. , Setzer Erika , Blake Eileen , Siew Lawrence
Published: January 2022

Introduction:

Many children with behavioral health concerns increasingly utilize the emergency department for assessment and care. These visits are increasing in frequency, length, and cost, further stressing already limited resources. To improve the quality of care in this population, we developed a multidisciplinary improvement initiative to decrease the length of stay by 10% (from 5.2 hours), increase suicide screening to 90%, and improve patient and family experience by 10% (from 89.7).

Methods:

We leveraged a multidisciplinary team to map care processes, standardize suicide risk screening, optimize staffing, and develop a brochure to demystify patients’ and families’ visits. We developed dashboards and a call-back system following discharge to understand engagement in post-acute care plans. We utilized run charts to identify signals of nonrandom variation.

Results:

We reduced overall length of stay from 5.2 to 4 hours, improved patient experience scores from 89.7 to 93.2, and increased the suicidality screening rate from 0% to 94%. There was no change in the 72-hour return rate in this population.

Conclusions:

Engagement of a multidisciplinary team, with strategic implementation of improvements, measurably improved many aspects of care for pediatric patients with behavioral health crises in the emergency department setting. Recidivism, however, remains unchanged in this population and continues as a goal for future work.
In Vitro and In Vivo Pathogenicity of A. alternata to Sugar beet and Assessment of Sensitivity to Fungicides
Authors: Haque Md Ehsanul , Parvin Most Shanaj
Published: January 2022

A. alternata is a weak and opportunistic pathogen, but recently this pathogen has been reported in major sugar beet growing regions in the US. Therefore, we were interested to investigate the in-vitro and in-vivo pathogenesis of A. alternata to sugar beet seed, seedlings, tissue slices, stecklings, and roots. The in-vitro study demonstrated that A. alternata reduces seed germination, causes damping-off of seedlings, and decomposes beet tissue. The in-vivo study showed the same inoculum responsible for Alternaria leaf spots, and black circular spots on beetroot. Furthermore, we did a preliminary study to determine in vitro sensitivities of some fungicides to determine the effective concentration that inhibited 50% of radial mycelial growth (EC50 values) of A. alternata. The results indicated that EC50 values ranged from 0.0023 to 0.0058 for PROLINE, from 0.0004 to 0.0021 for OMEGA, and from 0.0027 to 0.0053 for Super TIN. Among the potential fungicides, the efficiency of quinone outside inhibitors (QoI- PRIAXOR) was relatively higher to inhibit the radial growth of A. alternata, irrespective of concentrations.
A Phase 2 open-label study to determine the safety and efficacy of weekly dosing of ATL1102 in patients with non-ambulatory Duchenne muscular dystrophy
Authors: Woodcock IR , Tachas G , Desem N , Houweling PJ , Yiu EM , Kean M , Emmanuel J , Kennedy R , Carroll K , de Valle K , Adams J , Lamandé SR , Coles C , Tiong C , Villano D , Button P , Hogrel J-Y , Catling-Seyffer S , Delatycki MB , Ryan MM ,   ATL1102 in DMD clinical trial group
Published: January 2022

Background

ATL1102 is a 2’MOE gapmer antisense oligonucleotide to the CD49d alpha subunit of VLA-4. ATL1102 inhibits expression of CD49d on lymphocytes, thereby reducing their survival, activation and migration to sites of inflammation. Children with Duchenne muscular dystrophy (DMD) have dystrophin deficient muscles. These are susceptible to contraction induced injury which triggers the immune system, exacerbating muscle damage. CD49d is a biomarker of disease severity in DMD, with increased numbers of high CD49d expressing T cells correlating with more severe and progressive weakess, despite corticosteroid treatment.

Methods

This Phase 2 open label study assessed the safety, efficacy and pharmacokinetic profile of ATL1102 administered as 25 mg weekly by subcutaneous injection for 24 weeks in 9 non-ambulatory boys with DMD aged 10–18 years. Participants receiving corticosteroid therapy were allowed into the study if on a stable dose for at least 3 months. The main objective was to assess safety and tolerability of ATL1102. Secondary objectives included the effect of ATL1102 on lymphocyte numbers in the blood, functional changes in upper limb function as assessed by Performance of Upper Limb test (PUL 2.0) and upper limb strength using MyoGrip and MyoPinch compared to baseline.

Results

ATL1102 was generally safe and well tolerated. No serious adverse events were reported. There were no participant withdrawals from the study. The most commonly reported adverse events were injection site erythema and skin discoloration. There was no statistically significant change in lymphocyte count from baseline to week eight (mean change -0.56×109/L 95%CI -1.52, 0.40), week twelve (mean change -0.53×109/L 95%CI -1.65, 0.58) or week twenty-four (mean change -0.28×109/L 95%CI -1.10, 0.55) of dosing however, the CD3+CD49d+ T lymphocytes were statistically significantly higher at week 28 compared to week 24, four weeks past the last dose (mean change 0.40×109/L 95%CI 0.05, 0.74; p=0.030). Functional muscle strength, as measured by the PUL2.0, EK2 and Myoset grip and pinch measures, and MRI fat fraction of the forearm muscles were stable throughout the trial period.

Conclusion

ATL1102, a novel antisense drug being developed for the treatment of inflammation that exacerbates muscle fibre damage in DMD, appears to be safe and well tolerated in non-ambulant boys with DMD. The apparent stabilisation observed on multiple muscle disease progression parameters assessed over the study duration support the continued development of ATL1102 for the treatment of DMD.
Association between oral health and hyperuricemia in Korean adults: Korea National Health and Nutrition Examination Survey 2016-2019
Authors: Park Junyong , son Minkook , Lee Sung Won , Chung Won Tae , Lee Sang Yeob
Published: January 2022

Hyperuricemia plays an essential role in the development of gout. Despite the clinical importance of hyperuricemia, a direct relationship between oral health and hyperuricemia has not been established. Therefore, we aim to investigate the association between oral health and hyperuricemia in Korean adults.

We selected 17,584 subjects from the Korea National Health and Nutrition Examination Survey 2016–2019 database. Oral health-related variables included the number of dental caries, regular tooth brushing, use of secondary oral products, and regular dental examination. The odds ratio (OR) and 95% confidence intervals (CIs) for hyperuricemia were calculated using a multivariable-adjusted logistic regression model.

In all subjects, oral health status with dental caries and oral health behaviors, including tooth brushing; secondary oral products; and regular dental examination, were significantly associated with hyperuricemia. The adjusted OR and 95% CIs for hyperuricemia comparing more than three dental caries with no dental caries were 1.28 (1.08–1.51). The adjusted OR and 95% CIs for hyperuricemia in regular tooth brushing, use of secondary oral products, and regular dental examination were 0.78 (0.67–0.91), 0.91 (0.82–1.00), and 0.86 (0.78–0.95), respectively. Notably, the association between oral health and hyperuricemia was more prominent in male subjects. In addition, when subjects were grouped by the scoring system regarding oral health, the prevalence of hyperuricemia was lower in groups with a better oral health score.

In conclusion, we demonstrated that oral health status and behaviors were associated with hyperuricemia, especially in males. Further complementary studies are needed to confirm the definite association between oral health and hyperuricemia.
Discrepancy review: A feasibility study of a novel peer review intervention to reduce undisclosed discrepancies between registrations and publications
Authors:   TARG Meta-Research Group & Collaborators, Thibault Robert T. , Hardwicke Tom E. , Clark Robbie W. A. , Pennington Charlotte R. , Nilsonne Gustav , O'Mahony Aoife , Drax Katie , Thompson Jacqueline , Munafò Marcus R.
Published: January 2022

Background

Undisclosed discrepancies often exist between study registrations and their associated publications. Discrepancies can increase risk of bias, and when undisclosed, they disguise this increased risk of bias from readers. To remedy this issue, we developed an intervention called discrepancy review. We provided journals with peer reviewers specifically assigned to check for undisclosed discrepancies between registrations and manuscripts submitted to journals.

Objectives

We aimed to (1) evaluate the feasibility of incorporating discrepancy review as a regular practice at scientific journals and the feasibility of conducting a trial on discrepancy review; (2) explore the benefits and time required to incorporate discrepancy review as a regular practice at scientific journals; and (3) refine the discrepancy review process.

Method

We performed discrepancy review on 18 manuscripts submitted to Nicotine and Tobacco Research and 3 manuscripts submitted to the European Journal of Personality. We iteratively refined the discrepancy review process based on feedback from discrepancy reviewers, editors, and authors. We then assessed whether revised manuscripts addressed recommendations from discrepancy reviewers and identified potential outcome measures for use in a future trial of discrepancy review.

Results

Registrations were generally too imprecise to be effectively evaluated by our original discrepancy review process so we developed a simplified, semi-structured process. Authors addressed the majority of discrepancy reviewer comments and there was no opposition to running a trial from authors, editors, or discrepancy reviewers. Clinical trial registrations were more precise but less comprehensive than registrations on the Open Science Framework, suggesting they should be evaluated in separate trials. Outcome measures for a trial of discrepancy review on clinical trial registration could include the presence of primary or secondary outcome discrepancies and whether publications that are not the primary report from a clinical trial registration are clearly described as such. Outcome measures for a trial on Open Science Framework registrations could include assessments of whether registrations are permanent, as well as an overarching subjective assessment of the impact of discrepancies.

Conclusion

We found that discrepancy review could feasibly be introduced as a regular practice at journals interested in this process. A full trial of discrepancy review would be needed to evaluate its impact on reducing undisclosed discrepancies.
Phenotypic Pliancy and the Breakdown of Epigenetic Polycomb Mechanisms
Authors: Lambros Maryl , Sella Yehonatan , Bergman Aviv
Published: January 2022

Epigenetic regulatory mechanisms allow multicellular organisms to develop distinct specialized cell identities despite having the same total genome. Cell-fate choices are based on gene expression programs and environmental cues that cells experience during embryonic development, and are usually maintained throughout the life of the organism despite new environmental cues. The evolutionarily conserved Polycomb group (PcG) proteins form Polycomb Repressive Complexes that help orchestrate these developmental choices. Post-development, these complexes actively maintain the resulting cell fate, even in the face of environmental perturbations. Given the crucial role of these polycomb mechanisms in providing phenotypic fidelity (i.e. maintenance of cell fate), we hypothesize that their dysregulation after development will lead to decreased phenotypic fidelity allowing dysregulated cells to sustainably switch their phenotype in response to environmental changes. We call this abnormal phenotypic switchingphenotypic pliancy. We introduce a general computational evolutionary model that allows us to test our systems-level phenotypic pliancy hypothesisin-silicoand in a context-independent manner. We find that 1) phenotypic fidelity is an emergent systems-level property of PcG-like mechanism evolution, and 2) phenotypic pliancy is an emergent systems-level property resulting from this mechanism’s dysregulation. Since there is evidence that metastatic cells behave in a phenotypically pliant manner, we hypothesize that progression to metastasis is driven by the emergence of phenotypic pliancy in cancer cells as a result of PcG mechanism dysregulation. We corroborate our hypothesis using single-cell RNA-sequencing data from metastatic cancers. We find that metastatic cancer cells are phenotypically pliant in the same manner as predicted by our model.

Significance Statement

We introduce the concept of cellular phenotypic pliancy– sustained abnormal phenotypic switching in response to environmental changes– and demonstrate that such behavior can be caused by dysregulation of Polycomb mechanisms. To overcome the incomplete knowledge about these mechanisms in higher organisms, we develop an abstract computational model to study the emergence of phenotypic pliancy from a general systems-level view by confirming our hypothesis over a wide range of simulated gene-regulatory networks and Polycomb mechanism patterns. We corroborate our hypothesis and model predictions using single-cell RNA-seq metastatic cancer datasets. Our hypothesis has the potential to shed light on a general phenomenon for complex diseases where abnormal phenotypic switching is relevant.
Interplay between murine sex-biased gene expression and hepatic zonation revealed by single nucleus RNA sequencing
Authors: Goldfarb Christine N. , Karri Kritika , Pyatkov Maxim , Waxman David J.
Published: January 2022

The zonation of liver metabolic processes is well-characterized; however, little is known about the cell type-specificity and zonation of sexually dimorphic gene expression or its growth hormone (GH)-dependent transcriptional regulators. We address these issues using single nucleus RNA sequencing of 32,000 nuclei representing nine major liver cell types. Nuclei were extracted from livers from young adult male and female mice, from male mice infused with GH continuously to mimic the female plasma GH pattern, and from mice treated with TCPOBOP, a xenobiotic agonist ligand of the liver nuclear receptor CAR (Nr1i3). Analysis of these rich transcriptomic datasets revealed: 1) expression of sex-biased genes and their key GH-dependent transcriptional regulators is primarily restricted to hepatocytes and is not a feature of liver non-parenchymal cells; 2) many sex-biased transcripts show sex-dependent zonation within the liver lobule; 3) gene expression is substantially feminized in both periportal and pericentral hepatocytes when male mice are infused with GH continuously; 4) sequencing nuclei increases the sensitivity for detecting thousands of nuclear-enriched lncRNAs and enables determination of their liver cell type-specificity, sex bias and hepatocyte zonation profiles; 5) the periportal to pericentral hepatocyte cell ratio is significantly higher in male than female liver; and 6) TCPOBOP exposure disrupts sex-specific gene expression and hepatocyte zonation within the liver lobule. These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects on both protein-coding genes and lncRNAs.

Synopsis

Single nucleus RNA-seq analysis elucidated the cell type-specificity and zonation of the sex-biased murine liver transcriptome, including thousands of long non-coding RNAs. Xenobiotic exposure induced widespread dysregulation, including both gain and loss of sex-biased gene expression and changes in zonation.
Redefining the architecture of ferlin proteins: insights into multi-domain protein structure and function
Authors: Dominguez Matthew J. , McCord Jon J. , Sutton R. Bryan
Published: January 2022

Ferlins are complex, multidomain proteins whose functions involve membrane fusion, membrane repair, and exocytosis. Progress in studying the domain composition of ferlins has been problematic due to the large size of the ferlin proteins and the difficulty in computing accurate residue ranges for each respective ferlin protein domain. However, recent advances in in silico protein folding methods have significantly enhanced the understanding of the domain structure of these complex proteins. To compute unbiased domain boundaries, we used RoseTTAFold to assemble full-length models for each of the six human ferlin proteins (dysferlin, myoferlin, otoferlin, Fer1L4, Fer1L5, and Fer1L6). Despite the differences in amino acid sequence between the ferlin proteins, the domain ranges and the distinct subdomains in some of the ferlin domains were remarkably consistent. Further, the RoseTTAFold/AlphaFold2 in silico boundary prediction methods allowed us to describe and characterize a previously unknown C2 domain, ubiquitous in all human ferlins, which we refer to as C2-FerA. At present, the ferlin domain-domain interactions implied by the full-length in silico models are predicted to have a low accuracy; however, the use of RoseTTAFold and AlphaFold2 as a domain finder has proven to be a powerful research tool in understanding ferlin structure.
Effects of transcranial magnetic stimulation on the human brain recorded with intracranial electrocorticography: First-in-human study
Authors: Wang Jeffrey B. , Bruss Joel E. , Oya Hiroyuki , Uitermarkt Brandt D. , Trapp Nicholas T. , Gander Phillip E. , Howard Matthew A. , Keller Corey J. , Boes Aaron D.
Published: January 2022

Transcranial magnetic stimulation (TMS) is increasingly used as a noninvasive technique for neuromodulation in research and clinical applications, yet its mechanisms are not well understood. Here, we present the first in-human study evaluating the effects of TMS using intracranial electrocorticography (iEEG) in neurosurgical patients. We first evaluated safety in a gel-based phantom. We then performed TMS-iEEG in 20 neurosurgical participants with no adverse events. Next, we evaluated brain-wide intracranial responses to single pulses of TMS to the dorsolateral prefrontal cortex (dlPFC) (N=10, 1414 electrodes). We demonstrate that TMS preferentially induces neuronal responses locally within the dlPFC at sites with higher electric field strength. Evoked responses were also noted downstream in the anterior cingulate and anterior insular cortex, regions functionally connected to the dlPFC. These findings support the safety and promise of TMS-iEEG in humans to examine local and network-level effects of TMS with higher spatiotemporal resolution than currently available methods.
Close kin dyads indicate intergenerational dispersal and barriers
Authors: Schmidt Thomas L , Elfekih Samia , Cao Li-Jun , Wei Shu-Jun , Al-Fageeh Mohamed B , Nassar Majed , Al-Malik Abdulaziz , Hoffmann Ary A
Published: January 2022

The movement of individuals through continuous space is typically constrained by dispersal ability and dispersal barriers. A range of approaches have been developed to investigate these. Kindisperseis a new approach that infers intergenerational dispersal (σ) from close kin dyads, and appears particularly useful for investigating taxa that are difficult to observe individually. This study, focusing on the mosquitoAedes aegypti, shows how the same close kin data can also be used for barrier detection. We empirically demonstrate this new extension of the method using genome-wide sequence data from 266Ae. aegypti. First, we use the spatial distribution of full-sib dyads collected within one generation to infer past movements of ovipositing female mosquitoes. These dyads indicated the relative barrier strengths of two roads, and performed favourably against alternative genetic methods for detecting barriers. The difference in variance between the sib and first cousin spatial distributions was used to infer movement over the past two generations, providing estimates of intergenerational dispersal (σ = 81.5-197.1 m.gen-1/2) and density (ρ = 833-4864 km-2). Dispersal estimates showed general agreement with those from mark-release-recapture studies. Barriers, σ, ρ, and neighbourhood size (331-526) can inform forthcoming releases of dengue-suppressingWolbachiabacteria into this mosquito population.
A local translation program regulates centriole amplification in the airway epithelium
Authors: Liu Helu , Li Huijun , Jiang Zhihua , Jin Shibo , Song Rui , Yang Ying , Li Jun , Huang Jingshu , Zhang Xiaoqing , Dong Xuesong , Mori Munemasa , Fritzler Marvin J , He Lin , Cardoso Wellington , Lu Jining
Published: January 2022

Biogenesis of organelles requires targeting of a subset of proteins to specific subcellular domains by signal peptides or mechanisms controlling mRNA localization and local translation. How local distribution and translation of specific mRNAs for organelle biogenesis is achieved remains elusive and likely to be dependent on the cellular context. Here we identify Trinucleotide repeat containing-6a (Tnrc6a), a component of the miRNA pathway, distinctively localized to apical granules of differentiating airway multiciliated cells (MCCs) adjacent to centrioles. In spite of being enriched in TNRC6A and the miRNA-binding protein AGO2, they lack enzymes for mRNA degradation. Instead, we found these apical granules enriched in components of the mRNA translation machinery and newly synthesized proteins suggesting that they are specific hubs for target mRNA localization and local translation in MCCs. Consistent with this,Tnrc6aloss of function prevented formation of these granules and led to a broad reduction, rather than stabilization of miRNA targets. These included downregulation of key genes involved in ciliogenesis and was associated with defective multicilia formation both in vivo and in primary airway epithelial cultures. Similar analysis of Tnrc6a disruption in yolk sac showed stabilization of miRNA targets, highlighting the potential diversity of these mechanisms across organs.

Highlights

Tnrc6ais expressed in the lung selectively in differentiating multiciliated cells (MCC) adjacent to centrioles.

TNRC6A localizes to apical granules containing AGO2, miRNAs and their targets, but lacking mRNA degradation enzymes.

TNRC6A granules are enriched in components of the mRNA translation machinery and show evidence of concentrated newly-synthesized proteins

Loss ofTnrc6ain the lung leads to reduction, not stabilization of miRNA targets.

Tnrc6ais required for efficient centriole amplification and multicilia formation.
Microbial GWAS studies revealing combinations of Omicron RBD mutations existed and may contribute to antibody evasion and ACE2 binding
Authors: Ou Xumin , Yang Zhishuang , Zhu Dekang , Mao Sai , Wang Mingshu , Jia Renyong , Chen Shun , Liu Mafeng , Yang Qiao , Wu Ying , Zhao Xinxin , Zhang Shaqiu , Huang Juan , Gao Qun , Liu Yunya , Zhang Ling , Peopplenbosch Maikel , Pan Qiuwei , Cheng Anchun
Published: January 2022

Since Omicron variant of SARS-CoV-2 was first detected in South Africa (SA), it has now dominated in United Kingdom (UK) of Europe and United State (USA) of North America. A prominent feature of this variant is the gathering of spike protein mutations, in particularly at the receptor binding domain (RBD). These RBD mutations essentially contribute to antibody resistance of current immune approaches. During global spillover, combinations of RBD mutations may exist and synergistically contribute to antibody resistance in fact. Using three geographic-stratified genome wide association studies (GWAS), we observed that RBD combinations exhibited a geographic pattern and genetical associated, such as five common mutations in both UK and USA Omicron, six or two specific mutations in UK or USA Omicron. Although the UK specific RBD mutations can be further classified into two separated sub-groups of combination based on linkage disequilibrium analysis. Functional analysis indicated that the common RBD combinations (fold change, -11.59) alongside UK or USA specific mutations significantly reduced neutralization (fold change, -38.72, -18.11). As RBD overlaps with angiotensin converting enzyme 2(ACE2) binding motif, protein-protein contact analysis indicated that the common RBD mutations enhanced ACE2 binding accessibility and were further strengthened by UK or USA-specific RBD mutations. Spatiotemporal evolution analysis indicated that UK-specific RBD mutations largely contribute to global spillover. Collectively, we have provided genetic evidence of RBD combinations and estimated their effects on antibody evasion and ACE2 binding accessibility.
Cannabis Use and Sleep Quality in Daily Life: a Daily Diary Study of Adults Starting Cannabis for Health Concerns
Authors: Tervo-Clemmens Brenden , Schmitt William , Wheeler Grace , Cooke Megan , Schuster Randi M. , Hickey Sarah , Pachas Gladys , Evins A. Eden , Gilman Jodi
Published: January 2022

Background

Legalization of cannabis for medical uses has proceeded without well-controlled studies. Real world patterns of medical cannabis use are highly variable and rarely overseen by a physician. Smartphone assessments that capture ecologically valid patterns of medical cannabis use and health symptoms may help clarify risks and benefits.

Methods

As part of a larger, randomized trial (NCT03224468), adults (N=181) seeking cannabis for insomnia, pain, or anxiety or depressive symptoms were randomized to obtain a medical cannabis card immediately (MCC) or to a waitlist control (WLC) and completed 12-weeks of daily web-based surveys on cannabis use and three health outcomes: sleep, pain, and depressive symptoms.

Results

Completion rates in this long-term, daily survey design were high (median completed assessments: 72 out of 90 days). Daily reports of cannabis use were consistent with monthly interview assessments and urinalysis. The MCC group increased cannabis use frequency following randomization, while WLC did not. Within the MCC group, self-reported sleep quality was significantly higher on cannabis use days, compared to nonuse days. The MCC group displayed long-term sleep improvements, paralleled by increased cannabis frequency. Daily associations between cannabis use and self-reported pain or depressive symptoms were not significant.

Conclusion

Cannabis use is associated with same day improvements in self-reported sleep quality, but not pain or depressive symptoms, although sleep improvements occurred within the context of potentially risky increases in use. Long-term, web-based assessments of cannabis appear valid and feasible, providing a robust method for future real-world effectiveness studies with expanded and objective measures.

Funding/Support

This work was funded by R01DA042043; PI: JMG.
Auto-Detection and Segmentation of Involved Lymph Nodes in HPV-Associated Oropharyngeal Cancer Using a Convolutional Deep Learning Neural Network
Authors: Taku Nicolette , Wahid Kareem A. , van Dijk Lisanne V. , Sahlsten Jaakko , Jaskari Joel , Kaski Kimmo , Fuller C. David , Naser Mohamed A.
Published: January 2022

Purpose

Segmentation of involved lymph nodes on head and neck computed tomography (HN-CT) scans is necessary for the radiotherapy treatment planning of human papilloma virus (HPV) associated oropharynx cancers (OPC). We aimed to train a deep learning convolutional neural network (DL-CNN) to identify and segment involved lymph nodes on contrast-enhanced HN-CT scans.

Methods

90 patients who underwent levels II-IV neck dissection for newly diagnosed, clinically node-positive, HPV-OPC were identified. Ground-truth segmentation of all radiographically and pathologically involved nodes was manually performed on pre-surgical HN-CT scans, which were randomly divided into training/validation dataset (n=70) and testing dataset (n=20). A 5-fold cross validation was used to train 5 separate DL-CNN sub-models based on a residual U-net architecture. Validation and testing segmentation masks were compared to ground-truth segmentation masks using overlap-based, volume-based, and distance-based metrics. A lymph auto-detection model was developed by thresholding segmentation model outputs, and 20 node-negative HN-CT scans were added to the test set to further evaluate auto-detection capabilities. Model discrimination of lymph node “positive” and “negative” HN-CT scans was evaluated using the area under the receiver operating characteristic curve (AUC).

Results

In the DL-CNN validation phase, all sub-models yielded segmentation masks with median DSC ≥ 0.90 and median volume similarity score of ≥ 0.95. In the testing phase, the DL-CNN produced consensus segmentation masks with median Dice of 0.92 (IQR, 0.89-0.95), median volume similarity of 0.97 (IQR, 0.94-0.99), and median Hausdorff distance of 4.52 mm (IQR, 1.22-8.38). The detection model achieved an AUC of 0.98.

Conclusion

The results from this single-institution study demonstrate the successful automation of lymph node segmentation for patients with HPV-OPC using a DL-CNN. Future studies, including external validation using a larger dataset, are necessary to clarify the role of the DL-CNN in the routine radiation oncology treatment planning workflow.
STAT3 regulates cytokine production downstream of TNFR1 in part by inducing expression of TNFAIP3/A20
Authors: Antonia Ricardo , Karelehto Eveliina , Toriguchi Kan , Matli Mary , Warren Robert , Pfeffer Lawrence M. , Donner David B.
Published: January 2022

Background

Previous work demonstrated that the Signal Transducer and Activator of Transcription 3 (STAT3) is activated downstream of the Type 1 TNF Receptor. However, whether and how STAT3 regulates gene expression downstream of TNFR1 has not been elucidated.

Methods

Global transcriptome analysis by RNA sequencing was performed in wild type and STAT3 knockout mouse embryonic fibroblasts (MEFs) stimulated with TNF. The fold changes in gene expression were assessed bioinformatically. Results of the RNA sequencing were validated at the protein level by using multiplex cytokine assays and immunoblotting.

Results

Stimulation of MEFs with TNF or an agonist antibody to TNFR1 activated STAT3, and this was inhibited by pharmacological inhibition of Jak2 and cSrc. At 4 hours after TNF stimulation, STAT3 knockout MEFs had a greater level than WT MEFs of induction of the chemokines Ccl2, Cxcl1 and Cxcl10 at the RNA and protein levels. Mechanistically, this was due STAT3 promoting the expression of Tnfaip3/A20, a ubiquitin modifying enzyme that inhibits inflammation, in wild-type MEFs at early timepoints after TNFR1 stimulation. In STAT3 knockout MEFs TNF failed to induce the expression of Tnfaip3/A20 or GM-CSF when acting through TNFR1. Expression of A20 into STAT3 knockout MEFs suppressed cytokine expression.

Conclusion

STAT3 limits the induction of Ccl2, Cxcl1 and Cxcl10 in response to TNFR1 activation by promoting the expression of Tnfaip3/A20. On the other hand, STAT3 promotes the expression of GM-CSF in response to TNFR1 stimulation. These results show that STAT3 modulates inflammatory signaling by TNF in normal cells.
SAIBR: A simple, platform-independent method for spectral autofluorescence correction
Authors: Rodrigues Nelio T.L. , Bland Tom , Borrego-Pinto Joana , Ng KangBo , Hirani Nisha , Gu Ying , Foo Sherman , Goehring Nathan W.
Published: January 2022

Biological systems are increasingly viewed through the lens of mathematics, physics, and systems approaches that demand accurate quantification of gene expression and local protein concentrations. Such approaches have benefited greatly from the revolution in genetic engineering sparked by CRISPR/Cas9. By facilitating the tagging of genes at their genomic loci, CRISPR/Cas9 allows us to use fluorescence to monitor proteins that are expressed at or near endogenous levels under native regulatory control. However, due to their typically lower expression levels, quantitative experiments using endogenously-tagged genes can run into limits imposed by autofluorescence (AF). AF is often a particular challenge in the illumination bands occupied by the most efficient fluorescent proteins (GFP, mNeonGreen). Stimulated by our work in C. elegans, we describe and validate Spectral Autofluorescence Image correction By Regression (SAIBR), a simple, platform-independent protocol, and associated GUI-based FIJI plugin to correct for autofluorescence using standard filter sets and illumination conditions. Fully validated for use in C. elegans embryos and tested in diverse systems, including starfish oocytes and fission yeast, SAIBR achieves accurate quantitation of fluorophore signal and enables reliable detection and quantification of even weakly expressed proteins. Thus, SAIBR provides a highly accessible, low barrier way to incorporate AF correction as standard for researchers working on a broad variety of cell and developmental systems.

Summary Statement

Implemented as an easy-to-use Fiji Plugin, SAIBR provides effective autofluorescence correction for cells and tissues using standard imaging conditions.
Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
Authors: Guellil Meriam , van Dorp Lucy , Inskip Sarah A. , Dittmar Jenna M. , Saag Lehti , Tambets Kristiina , Hui Ruoyun , Rose Alice , D’Atanasio Eugenia , Kriiska Aivar , Varul Liivi , Koekkelkoren A.M.H.C. , Goldina Rimma D. , Cessford Craig , Solnik Anu , Metspalu Mait , Krause Johannes , Herbig Alexander , Robb John E. , Houldcroft Charlotte J. , Scheib Christiana L.
Published: January 2022

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7 - 1.13 × 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with late Neolithisation and implicating Bronze Age migrations6 in the distribution of HSV-1 through Eurasia.