bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of Chronic Osteomyelitis by an Orthoplastic Team: 7-Year Experience of a University Hospital
Authors: Tierny Chloé , Casoli Vincent , Chadefaux Grégoire , Dauchy Frédéric-Antoine , Fabre Thierry , Belaroussi Yaniss , Delgove Anaïs
Published: June 2021

Background:

Treating chronic osteomyelitis of the lower extremities is challenging. The treatment of acute lower limb trauma by orthoplastic teams has shown good results over the past few decades. This study aimed to characterize surgical outcomes of leg and heel chronic osteomyelitis by an orthoplastic team.

Methods:

The cases of 113 consecutive leg and heel chronic osteomyelitis patients undergoing soft-tissue reconstruction with an orthopedic procedure were reviewed in this retrospective single-center observational study. The main objective was to assess surgical outcomes of skin healing and gait recovery at the 1-year follow-up. The secondary objective was to evaluate the global success rate at the last follow-up.

Results:

The median follow-up was 19.7 months. A free flap was performed for 33 patients (29.2 percent) and a locoregional flap was used in 79 patients (69.9 percent). Seventy-two patients (63.7 percent) had chronic osteomyelitis on continuous bone. The others had a septic pseudarthrosis with a mean bone defect length of 42.9 mm. Forty-four patients (38.9 percent) underwent curettage only, eight (7.1 percent) underwent curettage and cement, 20 (17.7 percent) underwent curettage and bone fixation, and 39 (34.5 percent) underwent the Masquelet technique. At the 1-year follow-up, 72 patients (63.7 percent) had achieved skin healing and had recovered their gait. The success rate at all follow-up time points was 82.3 percent. The median time to achieve skin healing was 6.5 months and that to bone union in cases of septic pseudarthrosis was 7.9 months.

Conclusion:

Orthoplastic management of leg and heel chronic osteomyelitis patients with combined soft-tissue reconstruction using an orthopedic procedure was a viable strategy that offered good results even though the time to complete healing was long.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, III.
Decline in Medicare Utilization and Reimbursement Rates in Ophthalmic Plastic and Reconstructive Surgery
Authors: Gong Jung Ho , Khurana Aditya , Eltorai Adam E. M. , Wagner Lilly H.
Published: June 2021

Background

Analysis of current and past reimbursement patterns for federally funded programs is crucial to develop sustainable future payment models.

Methods

The Centers for Medicare and Medicaid Services Physician Fee Schedule was used to evaluate 26 common ophthalmic plastic and reconstructive surgery (OPRS) procedures. From 2010 to 2019, compound annual growth rate, total percent change, and annual percent change were calculated using inflation-adjusted reimbursement rates. Centers for Medicare and Medicaid Services’ Physician/Supplier Procedure Summary was used to assess the surgical volume of the 26 procedures in ophthalmology and plastic surgery services.

Results

From 2010 to 2019, total billed surgical procedures in OPRS decreased by 57.0%, affecting both ophthalmologists (−54.3%) and plastic surgeons (−80.1%). Over the study period, inflation-adjusted reimbursement rates decreased by 5.6%. Compound annual growth rate was −0.66%, and annual percent change was −0.62%. From 2010 to 2013, reimbursement rates increased by 1.8% each year. In contrast, from 2013 to 2019, reimbursement rates decreased by 1.7% each year (P < 0.0001).

Conclusions

From 2010 to 2019, Medicare utilization has substantially declined for OPRS procedures. Inflation-adjusted Medicare reimbursement rates have decreased for the majority of common procedures since 2013. Surgeons and policymakers need to be aware of these trends to ensure future availability of subspecialty surgical services.
The Economic Impact of Extensor Tendon Lacerations of the Hand in the United States
Authors: Mehrzad Raman , Mookerjee Vikram , Schmidt Scott , Jehle Chris , Rao Vinay , Mehrzad Melorin , Liu Paul Y.
Published: June 2021

Purpose

Extensor tendon lacerations (ETLs) are a common and debilitating injury for thousands of Americans annually. No study has attempted to estimate their economic impact. The objective of this study was to estimate the economic impact of ETLs in America.

Methods

The cost of ETLs to society was estimated using a validated prevalence-based cost of illness model. The primary cohort was defined as all patients with complete ETLs in the United States undergoing surgical repair and, secondarily, the imputed number of patients requiring reoperation within 1 year. For these groups, both direct and indirect costs (lost income, missed workdays, and disability payments) were measured.

Results

The total annual direct medical costs amounted to $14,095.28 per injury and 100,000 population. The total annual indirect labor costs were found to range between $80,842.90 and $150,136.82 per injury and 100,000 population. Hence, the estimated total costs of ETLs are $307 million per year in the United States alone and could be as high as $531 million annually depending on the effects of worker absenteeism on the core production–based industries.

Conclusions

Extensor tendon lacerations incur a significant economic burden to our health care system and are more costly when compared with many other common hand conditions. Specifically, indirect costs are the major contributor toward the total cost these injuries incur on society, accounting for an upward of 91% of the total cost. These results suggest efforts be focused on improving rehabilitation protocols and treatments.

Level of Evidence

Level II—economic and decision analyses.
Navigation-Guided Nasal Endoscopy to Remove the Cavernous Venous Malformation of the Orbital Apex Through the Sphenoid Approach
Authors: Yao-Hua Wang , Jin-Hai Yu , Jun-Hua Hu , Qi-Hua Xu , Qing Huang , Pu-Ying Gan , An-An Wang , Hong-Fei Liao
Published: June 2021

Objective:

To explore the feasibility of navigation-guided sinus endoscopy to remove the cavernous vascular malformation of the orbital apex through the sphenoid approach.

Methods:

A retrospective series of non-control cases were collected. From May 2012 to December 2019, patients with imaging findings of cavernous venous malformation in the orbital apex were collected at the Eye Hospital Affiliated to Nanchang University. All patients underwent navigation guided sinusoscopy through the sphenoid approach to remove the cavernous venous malformation of the orbital apex. Analyze the changes of visual function and postoperative complications before and after operation.

Results:

Twelve patients were collected, including 3 males and 9 females aged between 32 and 59. In 3 patients without visual impairment, the postoperative visual function was still normal. The remaining 9 patients all had visual impairment. Among them, 3 patients had fully recovered normal visual function after operation, 2 patients had improved visual function compared with preoperative, and 4 patients had no change in postoperative visual acuity. There were no complications in 3 of the 12 patients, and 9 patients had transient limited intraocular rotation with mild limitation of diplopia after operation, and all returned to normal within 1 month after surgery.

Conclusion:

Navigation-guided sinus endoscopy through the sphenoid approach to remove the cavernous venous malformation of the orbital apex is an effective and feasible surgical method.
Towards non-invasive heart rate monitoring in free-ranging cetaceans: a unipolar suction cup tag measured the heart rate of trained Risso's dolphins
Authors: Aoki Kagari , Watanabe Yurie , Inamori Daiki , Funasaka Noriko , Sakamoto Kentaro Q.
Published: June 2021

Heart rate monitoring in free-ranging cetaceans to understand their behavioural ecology and diving physiology is challenging. Here, we developed a simple, non-invasive method to monitor the heart rate of cetaceans in the field using an electrocardiogram-measuring device and a single suction cup equipped with an electrode. The unipolar suction cup was placed on the left lateral body surface behind the pectoral fin of Risso's dolphins (Grampus griseus) and a false killer whale (Pseudorca crassidens) in captivity; their heart rate was successfully monitored. We observed large heart rate oscillations corresponding to respiration in the motionless whales during surfacing (a false killer whale, mean 47 bpm, range 20–75 bpm; Risso's dolphins, mean ± s.d. 61 ± 15 bpm, range 28–120 bpm,n= 4 individuals), which was consistent with the sinus arrhythmia pattern (eupneic tachycardia and apneic bradycardia) observed in other cetaceans. Immediately after respiration, the heart rate rapidly increased to approximately twice that observed prior to the breath. Heart rate then gradually decreased at around 20–50 s and remained relatively constant until the next breath. Furthermore, we successfully monitored the heart rate of a free-swimming Risso's dolphin. The all-in-one suction cup device is feasible for field use without restraining animals and is helpful in further understanding the diving physiology of free-ranging cetaceans.

This article is part of the theme issue ‘Measuring physiology in free-living animals (Part II)’.
Future trends in measuring physiology in free-living animals
Authors: Williams H. J. , Shipley J. Ryan , Rutz C. , Wikelski M. , Wilkes M. , Hawkes L. A.
Published: June 2021

Thus far, ecophysiology research has predominantly been conducted within controlled laboratory-based environments, owing to a mismatch between the recording technologies available for physiological monitoring in wild animals and the suite of behaviours and environments they need to withstand, without unduly affecting subjects. While it is possible to record some physiological variables for free-living animals using animal-attached logging devices, including inertial-measurement, heart-rate and temperature loggers, the field is still in its infancy. In this opinion piece, we review the most important future research directions for advancing the field of ‘physiologging’ in wild animals, including the technological development that we anticipate will be required, and the fiscal and ethical challenges that must be overcome. Non-invasive, multi-sensor miniature devices are ubiquitous in the world of human health and fitness monitoring, creating invaluable opportunities for animal and human physiologging to drive synergistic advances. We argue that by capitalizing on the research efforts and advancements made in the development of human wearables, it will be possible to design the non-invasive loggers needed by ecophysiologists to collect accurate physiological data from free-ranging animals ethically and with an absolute minimum of impact. In turn, findings have the capacity to foster transformative advances in human health monitoring. Thus, we invite biomedical engineers and researchers to collaborate with the animal-tagging community to drive forward the advancements necessary to realize the full potential of both fields.

This article is part of the theme issue ‘Measuring physiology in free-living animals (Part II)’.
Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov.
Authors: Wang Yu-Wen , Ren Wen-Ting , Xu Yuan-You , Zhang Xin-Qi
Published: June 2021

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4–42 °C (optimum, 35 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5). Salt was required for growth (0.5–12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1
 ω7c, 11-methyl C18 : 1
 ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera

Maritimibacter

(95.61–96.05 %) and

Boseongicola

(95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus

Maritimibacter

in the clade of the

Roseobacter

group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60–80 % was calculated to be 68.56–76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T).

Maritimibacter lacisalsi

(Zhong et al. 2015) is considered to diverge from

Maritimibacter alkaliphilus

at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.
A multiscale analysis of early flower development in Arabidopsis provides an
integrated view of molecular regulation and growth control
Authors: Refahi Yassin , Zardilis Argyris , Michelin Gaël , Wightman Raymond , Leggio Bruno , Legrand Jonathan , Faure Emmanuel , Vachez Laetitia , Armezzani Alessia , Risson Anne-Evodie , Zhao Feng , Das Pradeep , Prunet Nathanaël , Meyerowitz Elliot , Godin Christophe , Malandain Grégoire , Jönsson Henrik , Traas Jan
Published: June 2021

The link between gene regulation and morphogenesis of multicellular
organisms is a fundamental problem in biology. We address this question in the
floral meristem of Arabidopsis, which generates new
tissues and organs through complex changes in growth patterns. Starting from
high-resolution time-lapse images, we generated a comprehensive 4-D atlas of
early flower development including cell lineage, cellular growth rates and the
expression patterns of 28 regulatory genes. This information was introduced in
MorphoNet, a web-based open-access platform.

The application of mechanistic computational models indicated that the
molecular network based on the literature only explained a minority of the
expression patterns. This was substantially improved by adding single regulatory
hypotheses for individual genes. We next used the integrated information to
correlate growth with the combinatorial expression of multiple genes. This led
us to propose a set of hypotheses for the action of individual genes in
morphogenesis, not visible by simply correlating gene expression and growth.
This identified the central transcription factor
LEAFY as a potential regulator of heterogeneous
growth, which was supported by quantifying growth patterns in a
leafy mutant. By providing an integrated,
multiscale view of flower development, this atlas should represent a fundamental
step towards mechanistic multiscale-scale models of flower development.
Effectiveness of vaccination against SARS-CoV-2 infection and Covid-19 hospitalization among Finnish elderly and chronically ill – An interim analysis of a nationwide cohort study
Authors: Baum Ulrike , Poukka Eero , Palmu Arto A. , Salo Heini , Lehtonen Toni O. , Leino Tuija
Published: June 2021

Background

In Finland, both mRNA and adenovirus vector (AdV) Covid-19 vaccines have been used after the vaccination campaign started on December 27, 2020. Vaccination of the elderly and chronically ill was prioritized and the interval between doses set to 12 weeks. The objective of this interim analysis was to evaluate first and second dose vaccine effectiveness (VE) in a real-world setting.

Methods

During the first 5 months of the campaign, a register-based cohort study was conducted in the Finnish elderly aged 70+ years and those aged 16–69 years with medical conditions predisposing to severe Covid-19 (chronically ill). Using Cox regression, VE against SARS-CoV-2 infection and Covid-19 hospitalization was estimated comparing the hazard in the vaccinated with that in the unvaccinated.

Results

The cohorts included 901092 elderly (89% vaccinated) and 774526 chronically ill (69% vaccinated) individuals. Three weeks after the first dose, mRNA VE against infection was 45% (95% confidence interval, 36–53%) and 40% (26–51%) in elderly and chronically ill; mRNA VE against hospitalization was 63% (49–74%) and 82% (56–93%). In chronically ill, AdV VE was 42% (32–50) and 62% (42– 75%) against infection and hospitalization, respectively. One week after the second dose, mRNA VE against infection was 75% (65–82%) and 77% (65–85%) in elderly and chronically ill; mRNA VE against hospitalization was 93% (70–98%) and 90% (29–99%).

Conclusions

Covid-19 vaccines protect against SARS-CoV-2 infection and Covid-19 hospitalization. A single dose provides moderate protection in elderly and chronically ill, although 2 doses are clearly superior.

summary

This register-based cohort study demonstrates that Covid-19 vaccines protect against SARS-CoV-2 infection and Covid-19 hospitalization among Finnish elderly and chronically ill. Vaccine effectiveness against hospitalization was moderate after 1 dose and increased to ≥90% after 2 doses.
A novel cell type negatively associated with secondary autoimmunity in alemtuzumab-treated patients is revealed through single-cell longitudinal analysis of clinical trial samples
Authors: Hanamsagar Richa , Chamberlain Mathew , Shankara Srinivas , Marcus Robert , Baker Darren P. , Havari Evis , Klinger Katherine , Nestle Frank O. , de Rinaldis Emanuele , Savova Virginia
Published: June 2021

Alemtuzumab, a humanized anti-CD52 monoclonal antibody, is an approved treatment for relapsing forms of multiple sclerosis (RMS). While its efficacy has been demonstrated in clinical studies, its use is associated with unpredictable non-MS autoimmunity manifesting months or years after treatment. Approximately 40% of treated patients present with autoimmune thyroid events, 2% with platelet deficiency (immune thrombocytopenia; ITP)1, and 0.34% with autoimmune nephropathies2. The lack of predictive biomarkers necessitates careful monitoring in clinical practice with a Risk Management Plan or Risk Evaluation and Mitigation Strategy (RMP/REMS) in place for early detection of these autoimmune events. We carried out a longitudinal single-cell analysis of PBMCs in a small subset of alemtuzumab-treated patients from the phase 3 CARE-MS I (CAMMS323) study3 and identified a novel platelet lineage cell negatively associated with thyroid autoimmunity. This discovery raises the possibility that a shared underlying mechanism may contribute to the incidence of thyroid autoimmunity and ITP in alemtuzumab-treated patients.

Highlights

A novel platelet-lineage cell type present in peripheral blood is uncovered and characterized

Depletion and/or transcriptomic changes in this cell type are associated with increased incidence of secondary autoimmunity in MS patients on Alemtuzumab.

Retrospective single-cell analysis studies can uncover novel insights and lead to future biomarker development
Effects of pharmacogenomic (PGx) testing on clinical pain management prescriptions, a retrospective study
Authors: Tagwerker Christian , Carias-Marines Mary Jane , Smith David J.
Published: June 2021

Current deficits in effectively utilizing PGx testing in clinical practice include limited awareness and training of healthcare professionals, routine ordering of assays investigating up to 5 genes and lack of concise reporting of dosing guidelines and drug-drug-interactions. A novel deep sequencing (>1000X) PGx panel is described encompassing 23 genes and 141 SNPs or indels combined with PGx dosing guidance, drug-gene-interaction (DGI) and drug-drug-interaction (DDI) reporting to prevent adverse drug reaction events. During a 2-year period, patients (n = 171) were monitored in a pain management clinic. Urine toxicology, PGx reports, and progress notes were studied retrospectively for changes in prescription regimens before and after the PGx report was made available to the provider.

Among patient PGx reports with medication lists provided (n = 146) 57.5% showed one or more moderate and 5.5% at least one serious pharmacogenetic interaction. 66% of patients showed at least one moderate and 15% one or more serious drug-gene or drug-drug-interaction. A significant number of active changes in prescriptions based on the PGx reports provided was observed for 85 patients (83%) for which a specific drug was either discontinued, switched within the defined drug classes of the report or a new drug added.

Preventative action was observed for all serious interactions and only moderate interactions were tolerated for lack of other alternatives. This study demonstrates a successful implementation of PGx testing utilizing an extended PGx panel combined with a customized, informational report to help improve clinical outcomes.
Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope
Authors: Dolton Garry , Rius Cristina , Hasan Md Samiul , Wall Aaron , Szomolay Barbara , Behiry Enas , Whalley Thomas , Southgate Joel , Fuller Anna ,   The COVID-19 Genomics UK (COG-UK) consortium, Morin Théo , Topley Katie , Tan Li Rong , Goulder Philip J. R. , Spiller Owen B. , Rizkallah Pierre J. , Jones Lucy C. , Connor Thomas R. , Sewell Andrew K.
Published: June 2021

The adaptive immune system protects against infection via selection of specific antigen receptors on B-cells and T-cells. We studied the prevalent CD8 ‘killer’ T-cell response mounted against SARS-CoV-2 Spike269-277 epitope YLQPRTFLL via the most frequent Human Leukocyte Antigen (HLA) class I worldwide, HLA A*02. The widespread Spike P272L mutation has arisen in at least 14 different SARS-CoV-2 lineages to date, including in lineages identified as variants of concern. P272L was common in the B.1.177 lineage associated with establishing the ‘second wave’ in Europe. The large CD8 T-cell response seen across a cohort of HLA A*02+ convalescent patients, comprising of over 120 different TCRs, failed to respond to the P272L. Sizable populations (0.01%-0.2%) of total CD8 T-cells from individuals vaccinated against SARS-CoV-2 stained with HLA A*02-YLQPRTFLL multimers but failed to bind to the P272L reagent. Viral escape at prevalent T-cell epitopes restricted by high frequency HLA may be particularly problematic when vaccine immunity is focussed on a single protein such as SARS-CoV-2 Spike and provides a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlights the urgent need for monitoring T-cell escape in new SARS-CoV-2 variants.

New in Version 2

Updated as P272L now seen in 14 different SARS-CoV-2 lineages including the B.1.1.7/Alpha (UK variant) lineage

Atomic structures of HLA A*02-YLQPRTFLL and HLA A*02-YLQLRTFLL added

Pierre Rizkallah added as an author and author list changed to reflect the contributions of Aaron Wall and Anna Fuller to the newly added datasets
Is Second dose of vaccination useful in previously SARS-CoV-2 infected Health Care Workers?
Authors: De Ponfilly Gauthier Pean , Pilmis Benoît , El Kaibi Iheb , Castreau Nathalie , Laplanche Sophie , Le Monnier Alban
Published: June 2021

Vaccines are the most important public health measure to protect people from COVID-19 worldwide. In addition, healthcare workers account for a large number of infected people. Then, protecting this population from COVID-19 seems crucial in the preservation of healthcare systems. In a context of few doses available, serological assays could be useful to decide whether one or two doses are needed. Our results show that a first dose of BNT162b2 mRNA vaccine seems to act as a boost after SARS-CoV-2 infection in healthcare workers with a previous SARS-CoV-2 infection and a second dose might not be required.
Sex-specific survival bias and interaction modeling in coronary artery disease risk prediction
Authors: Surakka Ida , Wolford Brooke N , Ritchie Scott C , Hornsby Whitney E , Sutton Nadia R. , Gabrielsen Maiken Elvenstad , Skogholt Anne Heidi , Thomas Laurent , Inouye Michael , Hveem Kristian , Willer Cristen J
Published: June 2021

Background

The 10-year Atherosclerotic Cardiovascular Disease (ASCVD) risk score is the standard approach to predict risk of incident cardiovascular events and recently, addition of CAD polygenic scores (PGSCAD) have been evaluated. Although age and sex strongly predict the risk of CAD, their interaction with genetic risk prediction has not been systematically examined.

Objectives

This study performed an in-depth evaluation of age and sex effects in genetic CAD risk prediction.

Methods

The population-based Norwegian HUNT2 cohort of 51,036 individuals was used as the primary dataset. Findings were replicated in the UK Biobank (372,410 individuals). Models for 10-year CAD risk were fitted using Cox proportional hazards and Harrell’s concordance index, sensitivity, and specificity were compared.

Results

Inclusion of age and sex interactions of PGSCAD to the prediction models increased C-index and sensitivity likely countering the observed survival bias in the baseline. The sensitivity for females was lower than males in all models including genetic information. The two-step approach identified a total of 82.6% of incident CAD cases (74.1% by ASCVD risk score and an additional 8.5% by the PGSCAD interaction model).

Conclusion

These findings highlight the importance and complexity of genetic risk in predicting CAD. There is a need for modeling age and sex-interactions terms with polygenic scores to optimize detection of individuals at high-risk, those who warrant preventive interventions. Sex-specific studies are needed to understand and estimate CAD risk with genetic information.

CONDENSED ABSTRACT

This study used two large population-based longitudinal datasets to evaluate genetic prediction of CAD including age and sex interactions. The model fit and sensitivity of the prediction models increased when including age and sex interaction of PGSCAD to the prediction models likely countering the observed survival bias in the baseline. The sensitivity for females was lower than for males in all models including genetic information. Our results highlight the importance and complexity of genetic risk and suggest including age and sex interactions with polygenic scores to identify more high-risk individuals for preventive interventions.
Host-parasite coevolution promotes innovation through deformations in fitness landscapes
Authors: Gupta Animesh , Zaman Luis , Strobel Hannah M. , Gallie Jenna , Burmeister Alita R. , Kerr Benjamin , Tamar Einat S. , Kishony Roy , Meyer Justin R.
Published: June 2021

During the struggle for survival, populations occasionally evolve new functions that give them access to untapped ecological opportunities. Theory suggests that coevolution between species can promote the evolution of such innovations by deforming fitness landscapes in ways that open new adaptive pathways. We directly tested this idea by using high throughput gene editing-phenotyping technology (MAGE-Seq) to measure the fitness landscape of a virus, bacteriophage λ, as it coevolved with its host, the bacterium Escherichia coli. Through computer simulations of λ’s evolution on the empirical fitness landscape, we showed that λ was more likely to evolve to use a new receptor if it experienced a shift in its fitness landscape caused by coevolution. This result was further validated by additional laboratory experiments. This study provides direct evidence for the role of coevolution in driving evolutionary novelty and provides a quantitative framework for predicting evolution in coevolving ecological communities.
OSCAR: a framework to identify and quantify cells in densely packed three-dimensional biological samples
Authors: Ledesma-Terrón Mario , Pérez-Dones Diego , Míguez David G.
Published: June 2021

We have developed an Object Segmentation, Counter and Analysis Resource (OSCAR) that is designed specifically to quantify densely packed biological samples with reduced signal-to-background ratio. OSCAR uses as input three dimensional images reconstructed from confocal 2D sections stained with dies such as nuclear marker and immunofluorescence labeling against specific antibodies to distinguish the cell types of interest. Taking advantage of a combination of arithmetic, geometric and statistical algorithms, OSCAR is able to reconstruct the objects in the 3D space bypassing segmentation errors due to the typical reduced signal to noise ration of biological tissues imaged in toto. When applied to the zebrafish developing retina, OSCAR is able to locate and identify the fate of each nuclei as a cycling progenitor or a terminally differentiated cell, providing a quantitative characterization of the dynamics of the developing vertebrate retina in space and time with unprecedented accuracy.
Automated movement assessment in stroke rehabilitation
Authors: Ahmed Tamim , Thopalli Kowshik , Rikakis Thanassis , Turaga Pavan , Kelliher Aisling , Huang Jia-Bin , Wolf Steve
Published: June 2021

We are developing a system for long term Semi-Automated Rehabilitation At the Home (SARAH) that relies on low-cost and unobtrusive video-based sensing. We present a cyber-human methodology used by the SARAH system for automated assessment of upper extremity stroke rehabilitation at the home. We propose a hierarchical model for automatically segmenting stroke survivor’s movements and generating training task performance assessment scores during rehabilitation. The hierarchical model fuses expert therapist knowledge-based approaches with data-driven techniques. The expert knowledge is more observable in the higher layers of the hierarchy (task and segment) and therefore more accessible to algorithms incorporating high level constraints relating to activity structure (i.e. type and order of segments per task). We utilize an HMM and a Decision Tree model to connect these high level priors to data driven analysis. The lower layers (RGB images and raw kinematics) need to be addressed primarily through data driven techniques. We use a transformer based architecture operating on low-level action features (tracking of individual body joints and objects) and a Multi-Stage Temporal Convolutional Network(MS-TCN) operating on raw RGB images. We develop a sequence combining these complimentary algorithms effectively, thus encoding the information from different layers of the movement hierarchy. Through this combination, we produce a robust segmentation and task assessment results on noisy, variable and limited data, which is characteristic of low cost video capture of rehabilitation at the home. Our proposed approach achieves 85% accuracy in per-frame labeling, 99% accuracy in segment classification and 93% accuracy in task completion assessment. Although the methodology proposed in this paper applies to upper extremity rehabilitation using the SARAH system, it can potentially be used, with minor alterations, to assist automation in many other movement rehabilitation contexts (i.e. lower extremity training for neurological accidents).
Dopamine-independent state inference mediates expert reward guided decision making
Authors: Blanco-Pozo Marta , Akam Thomas , Walton Mark E.
Published: June 2021

Rewards are thought to influence future choices through dopaminergic reward prediction errors (RPEs) updating stored value estimates. However, accumulating evidence suggests that inference about hidden states of the environment may underlie much adaptive behaviour, and it is unclear how these two accounts of reward-guided decision-making should be integrated. Using a two-step task for mice, we show that dopamine reports RPEs using value information inferred from task structure knowledge, alongside information about recent reward rate and movement. Nonetheless, although rewards strongly influenced choices and dopamine, neither activating nor inhibiting dopamine neurons at trial outcome affected future choice. These data were recapitulated by a neural network model in which frontal cortex learned to track hidden task states by predicting observations, while basal ganglia learned corresponding values and actions via dopaminergic RPEs. Together, this two-process account reconciles how dopamine-independent state inference and dopamine-mediated reinforcement learning interact on different timescales to determine reward-guided choices.
Genetic basis and dual adaptive role of floral pigmentation in sunflowers
Authors: Todesco Marco , Bercovich Natalia , Kim Amy , Imerovski Ivana , Owens Gregory L. , Ruiz Óscar Dorado , Holalu Srinidhi V. , Madilao Lufiani L. , Jahani Mojtaba , Légaré Jean-Sébastien , Blackman Benjamin K. , Rieseberg Loren H.
Published: June 2021

Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here we analyze the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation at a single MYB transcription factor, HaMYB111, through accumulation of UV-absorbing flavonol glycosides. As expected, different patterns of ultraviolet pigments in flowers have a strong effect on pollinator preferences. However, variation for floral ultraviolet patterns is also associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Larger ultraviolet patterns, which are found in drier environments, limit transpiration, therefore reducing water loss. The dual role of floral UV patterns in pollination attraction and abiotic responses reveals the complex adaptive balance underlying the evolution of floral traits.
Evolutionary graph theory beyond pairwise interactions: higher-order network motifs shape times to fixation in structured populations
Authors: Kuo Yang Ping , Carja Oana
Published: June 2021

To design population topologies that can accelerate rates of solution discovery in directed evolution problems or in evolutionary optimization applications, we must first systematically understand how population structure shapes evolutionary outcome. Using the mathematical formalism of evolutionary graph theory, recent studies have shown how to topologically build networks of population interaction that increase probabilities of fixation of beneficial mutations, at the expense, however, of longer fixation times, which can slow down rates of evolution under elevated mutation rate. Here we find that moving beyond dyadic interactions is fundamental to explain the trade-offs between probability and time to fixation. We show that higher-order motifs, and in particular three-node structures, allow tuning of times to fixation, without changes in probabilities of fixation. This gives a near-continuous control over achieving solutions that allow for a wide range of times to fixation. We apply our algorithms and analytic results to two evolutionary optimization problems and show that the rate at which evolving agents learn to navigate their environment can be tuned near continuously by adjusting the higher-order topology of the agent population. We show that the effects of population structure on the rate of evolution critically depend on the optimization landscape and find that decelerators, with longer times to fixation of new mutants, are able to reach the optimal solutions faster than accelerators in complex solution spaces. Our results highlight that no one population topology fits all optimization applications, and we provide analytic and computational tools that allow for the design of networks suitable for each specific task.
Risk modelling of single cell populations revealed the heterogeneity of immune infiltration in hepatocellular carcinoma
Authors: Wang Lu , Chen Yifan , Mao Fengbiao , Sun Zhongsheng , Liu Xiangdong
Published: June 2021

Hepatocellular carcinoma (HCC) is one of the most common primary hepatic malignancies. E2F transcription factors play an important role in the tumorigenesis and progression of HCC, mainly through the RB/E2F pathway. Prognostic models for HCC based on gene signatures have been developed rapidly in recent years; however, their discriminating ability at the single cell level remains elusive, which could reflect the underlying mechanisms driving the sample bifurcation. In this study, we constructed and validated a predictive model based on E2F expression, successfully stratifying HCC patients into two groups with different survival risks. Then we used a single-cell dataset to test the discriminating ability of the predictive model on infiltrating T cells, demonstrating remarkable cellular heterogeneity as well as altered cell fates. We identified distinct cell subpopulations with diverse molecular characteristics. We also found that the distribution of cell subpopulations varied considerably across onset stages among patients, providing fundamental basis for patient-oriented precision evaluation. Moreover, single-sample gene set enrichment analysis revealed that subsets of CD8+ T cells with significantly different cell adhesion level could be associated with different patterns of tumor cell dissemination. Therefore, our findings linked the conventional prognostic gene signature to the immune microenvironment and cellular heterogeneity at the single-cell level, thereby providing deeper insights into the understanding of HCC tumorigenesis.
Negative curvature-promoting lipids instruct nuclear ingression of low autophagic potential vacuoles
Authors: Garcia Manon , Kumanski Sylvain , Elías-Villalobos Alberto , Soulet Caroline , Moriel-Carretero María
Published: June 2021

Membrane contact sites are functional nodes at which organelles exchange information through moving ions, proteins and lipids, thus driving the reorganization of metabolic pathways and the adaptation to changing cues. The nuclear-vacuole junction of Saccharomyces cerevisiae is among the most extensive and better-known organelle contact sites, described to expand in response to various metabolic stresses. While using genotoxins with unrelated purposes, we serendipitously discovered a phenomenon that we describe as the most extreme and intimate contact ever reported between nuclei and vacuoles: the vacuole becomes completely internalized in the nucleus. We define lipids supporting negative curvature, such as phosphatidic acid and sterols, as bona-fide drivers of this event. Functionally, we purport that internalized vacuoles are low efficiency ones whose removal from the cytoplasm optimizes cargo interaction with functional vacuoles. Thus, our findings also point to nucleus-vacuole interactions as important for metabolic adaptation. Yet, rather than by inter-organelle exchanges, the underlying mechanism literally concurs with vacuolar sequestration.
Markovian Weighted Ensemble Milestoning (M-WEM): Long-time Kinetics from Short Trajectories
Authors: Ray Dhiman , Stone Sharon Emily , Andricioaei Ioan
Published: June 2021

We introduce a rare-event sampling scheme, named Markovian Weighted Ensemble Milestoning (M-WEM), which inlays a weighted ensemble framework within a Markovian milestoning theory to efficiently calculate thermodynamic and kinetic properties of long-timescale biomolecular processes from short atomistic molecular dynamics simulations. M-WEM is tested on the Müller-Brown potential model, the conformational switching in alanine dipeptide, and the millisecond timescale protein-ligand unbinding in a trypsin-benzamidine complex. Not only can M-WEM predict the kinetics of these processes with quantitative accuracy, but it also allows for a scheme to reconstruct a multidimensional free energy landscape along additional degrees of freedom which are not part of the milestoning progress coordinate. For the ligand-receptor system, the experimental residence time, association and dissociation kinetics, and binding free energy could be reproduced using M-WEM within a simulation time of a few hundreds of nanoseconds, which is a fraction of the computational cost of other currently available methods, and close to four orders of magnitude less than the experimental residence time. Due to the high accuracy and low computational cost, the M-WEM approach can find potential application in kinetics and free-energy based computational drug design.
Characterization of an operon required for growth on cellobiose in Clostridioides difficile
Authors: Hasan Md Kamrul , Dhungel Babita Adhikari , Govind Revathi
Published: June 2021

Cellobiose metabolism is linked to the virulence properties in numerous bacterial pathogens. Here, we characterized a putative cellobiose PTS operon of Clostridiodes difficile to investigate the role of cellobiose metabolism in C. difficile pathogenesis. Our gene knockout experiments demonstrated that the putative cellobiose operon enables uptake of cellobiose into C. difficile and allows growth when cellobiose is provided as the sole carbon source in minimal medium. Additionally, using reporter gene fusion assays and DNA pull-down experiments, we show that its transcription is regulated by CelR, a novel transcriptional repressor protein, which directly binds to the upstream region of the cellobiose operon to control its expression. We have also identified cellobiose metabolism to play a significant role in C. difficile physiology as observed by the reduction of sporulation efficiency when cellobiose uptake was compromised in the mutant strain. In corroboration to in vitro study findings, our in vivo hamster challenge experiment showed a significant reduction of pathogenicity by the cellobiose mutant strain in both the primary and the recurrent infection model- substantiating the role of cellobiose metabolism in C. difficile pathogenesis.
Structure of the mini-RNA-guided endonuclease CRISPR-CasΦ3
Authors: Carabias Arturo , Fuglsang Anders , Temperini Piero , Pape Tillmann , Sofos Nicholas , Stella Stefano , Erlendsson Simon , Montoya Guillermo
Published: June 2021

CRISPR-CasΦ is a novel family of miniaturized RNA-guided endonucleases from phages 1,2. These novel ribonucleoproteins (RNPs) provide a compact scaffold gathering all key activities of a genome editing tool2. Here, we provide the first structural insight into CasΦ singular DNA targeting and cleavage mechanism by determining the cryoEM structure of CasΦ3 with the triple strand R-loop generated after DNA cleavage. The structure reveals the unique machinery for target unwinding to form the crRNA-DNA hybrid and cleaving the target DNA. The protospacer adjacent motif (PAM) is recognised by the target strand (T-strand) and non-target strand (NT-strand) PAM interacting domains (TPID and NPID). Unwinding occurs after insertion of the conserved α1 helix disrupting the dsDNA, thus facilitating the crRNA-DNA hybrid formation. The NT-strand is funnelled towards the RuvC catalytic site, while a long helix of TPID separates the displaced NT-strand and the crRNA-DNA hybrid avoiding DNA re-annealing. The crRNA-DNA hybrid is directed to the stop (STP) domain that splits the hybrid guiding the T-strand towards the RuvC active site. The conserved RuvC insertion of the CasΦ family is extended along the hybrid, interacting with the phosphate backbone of the crRNA. A cluster of hydrophobic residues anchors the RuvC insertion in a cavity of the STP domain. The assembly of the hybrid promotes the shortening of the RuvC insertion, thus pulling the STP towards the RuvC active site to activate catalysis. These findings illustrate why CasΦ unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. Site-directed mutagenesis in key residues support CasΦ3 target DNA and non-specific ssDNA cutting mechanism. Our analysis provides new avenues to redesign the compact CRISPR-CasΦ nucleases for genome editing.
Injectable Nanoparticle-Based Hydrogels Enable the Safe and Effective Deployment of Immunostimulatory CD40 Agonist Antibodies
Authors: Correa Santiago , Gale Emily C. , Mayer Aaron T. , Xiao Zunyu , Liong Celine , Klich John H. , Brown Ryanne A. , Meany Emily L. , Saouaf Olivia M. , Maikawa Caitlin L. , Grosskopf Abigail K. , Mann Joseph L. , Idoyaga Juliana , Appel Eric A.
Published: June 2021

When properly deployed, the immune system can eliminate deadly pathogens, eradicate metastatic cancers, and provide long-lasting protection from diverse diseases. Unfortunately, realizing these remarkable capabilities is inherently risky as disruption to immune homeostasis can elicit dangerous complications or autoimmune disorders. While current research is continuously expanding the arsenal of potent immunotherapeutics, there is a technological gap when it comes to controlling when, where, and how long these drugs act on the body. Here, we explore the ability of a slow-releasing injectable hydrogel depot to reduce the problematic dose-limiting toxicities of immunostimulatory CD40 agonist (CD40a) while maintaining their potent anti-cancer efficacy. We leverage a previously described polymer-nanoparticle (PNP) hydrogel system that exhibits shear-thinning and yield-stress properties that we hypothesized would improve locoregional delivery of the CD40a immunotherapy. Using PET imaging, we demonstrate that prolonged hydrogel-based delivery redistributes CD40a exposure to the tumor and the tumor draining lymph node (TdLN), thereby reducing weight loss, hepatotoxicity, and cytokine storm associated with standard treatment. Moreover, CD40a-loaded hydrogels mediate improved local cytokine induction in the TdLN and improve treatment efficacy in the B16F10 melanoma model. PNP hydrogels, therefore, represent a facile, drug-agnostic method to ameliorate immune-related adverse effects and explore locoregional delivery of immunostimulatory drugs.