bluuebunny/crossref_metadata_2025 huggingface dataset:
Nurse practitioner productivity measurement: An organizational focus and lessons learned
Authors: Lucatorto Michelle A. , Walsh-Irwin Colleen
Published: November 2020

Nurse practitioners (NPs) are valued members of the health care team, and their numbers are growing each year. The volume of literature demonstrating the impact on quality, safety, patient satisfaction, and access measures is substantial and growing. There is a significant lack of measurement methods and outcomes related to NP contributions to organizational productivity. The construction of strategy for measurement of NP productivity is a prerequisite for studies focusing on impact. Models that are being used to measure physician productivity are available to be examined in terms of their applicability to the NP work force. In 2005, the Deputy Under Secretary for Health for Operations and Management directed Veterans Healthcare Administration (VHA) to develop a productivity-based model for physicians using the Medicare Resource-Based Relative Value Scale, which was created in 1992 to provide guidance on determining payment for physician services. In 2015, the VHA set out to set standards for productivity measurements for NPs, physician assistants, and clinical nurse specialists, and in doing so, the physician productivity model was adapted for the NP workforce. The work of adapting the model will be presented in this article. The specific steps in the process of measurement, operational definitions for work activities, and calculations are provided. The article concludes with a discussion of lessons learned and next steps.
The Compounding Effect of Race/Ethnicity and Disability Status on Children’s Health and Health Care by Geography in the United States
Authors: Akobirshoev Ilhom , Mitra Monika , Li Frank S. , Dembo Robert , Dooley Dan , Mehta Amar , Batra Neelesh
Published: November 2020

Objective:

The objective of this study was to examine the potential compounding effect of race/ethnicity, and disability status on children’s health and health care, stratified by selected geographies.

Methods:

We used the 2011/2012 NSCH and the 2012 Boston Survey of Children’s Health for our compounded disparity analysis. We used VanderWheel and Knol method to first predict combined risk ratios of race/ethnicity and disability and then compared them with the observed combined risk ratios.

Results:

We demonstrated that racial/ethnic minority children with disabilities experience additional disparities in health care access outcomes that are greater than the sum of the effects from either characteristic alone. Further, we demonstrate that disparities persist across all selected geographies irrespective of whether children lived in states or metropolitan cities with the best health care systems in the United States.

Conclusions:

Despite reform efforts, our study demonstrates that racial/ethnic minority children with disabilities experience a double burden. Given the deleterious compounded disparities, public health and social service programs at all geographical levels should prioritize identifying participants that face this and tailor programs to meet their needs.
All-cause hospitalization according to demographic group in people living with HIV in the current antiretroviral therapy era
Authors: Rein Sophia M. , Lampe Fiona C. , Johnson Margaret A. , Bhagani Sanjay , Miller Robert F. , Chaloner Clinton , Phillips Andrew N. , Burns Fiona M. , Smith Colette J.
Published: November 2020

Objective:

We investigated differences in all-cause hospitalization between key demographic groups among people with HIV in the UK in the current antiretroviral therapy (ART) era.

Design/Methods:

We used data from the Royal Free HIV Cohort study between 2007 and 2018. Individuals were classified into five groups: MSM, Black African men who have sex with women (MSW), MSW of other ethnicity, Black African women and women of other ethnicity. We studied hospitalizations during the first year after HIV diagnosis (Analysis-A) separately from those more than one year after diagnosis (Analysis-B). In Analysis-A, time to first hospitalization was assessed using Cox regression adjusted for age and diagnosis date. In Analysis-B, subsequent hospitalization rate was assessed using Poisson regression, accounting for repeated hospitalization within individuals, adjusted for age, calendar year, time since diagnosis.

Results:

The hospitalization rate was 30.7/100 person-years in the first year after diagnosis and 2.7/100 person-years subsequently; 52% and 13% hospitalizations, respectively, were AIDS-related. Compared with MSM, MSW and women were at much higher risk of hospitalization during the first year [aHR (95% confidence interval, 95% CI): 2.7 (1.7–4.3), 3.0 (2.0–4.4), 2.0 (1.3–2.9), 3.0 (2.0–4.5) for Black African MSW; other ethnicity MSW; Black African women; other ethnicity women respectively, Analysis-A] and remained at increased risk subsequently [corresponding aIRR (95% CI): 1.7 (1.2–2.4), 2.1 (1.5–2.8), 1.5 (1.1–1.9), 1.7 (1.2–2.3), Analysis-B].

Conclusion:

In this setting with universal healthcare, substantial variation exists in hospitalization risk across demographic groups, both in early and subsequent periods after HIV diagnosis, highlighting the need for targeted interventions.
Partial Let-Down and Push-Down Techniques With Complete Cartilage Preservation
Authors: Öztürk Güncel
Published: November 2020

Dorsal hump reduction is one of most commonly performed operations among Caucasian patients because of their nose anatomy. Dorsal preservation techniques in hump reduction are highly favorable, and recent studies have focused on dorsal preservation techniques. In the present research, the authors describe novel approaches for the push-down and let-down techniques in which the cartilage is totally preserved. According to the inclusion and exclusion criteria, the records of 48 patients were assessed (40 females and 8 males). Twenty-seven partial modificated push-down and 21 partial let-down techniques were performed. Participants completed the ROE questionnaire before surgery and at their 1-year follow-up control. The ROE scores before and 1 year after surgery were compared. The median ROE score was 60.0 points before surgery and 93.6 points 1 year after surgery. The ROE score was increased significantly (P < 0.001). A total of 92% of the included patients reported excellent satisfaction with the surgical outcome (ROE score > 85). The present study is the first to show total cartilage preservation with let-down and push-down techniques. These approaches are easy to perform and will lead to better cosmetic results in clinical settings.
Video-based Learning in Surgery
Authors: Yee Andrew , Padovano William M. , Fox Ida K. , Hill Elspeth J. R. , Rowe Amanda G. , Brunt L. Michael , Moore Amy M. , Snyder-Warwick Alison K. , Kahn Lorna C. , Wood Matthew D. , Coert Jan Henk , Mackinnon Susan E.
Published: November 2020

Objective:

To measure surgeon engagement and preferred video duration in a video-based learning program for nerve surgery.

Background:

Educational videos can improve, standardize, and democratize best practices in surgery. To improve care internationally, educators must optimize their videos for learning. However, surgeon engagement and optimal video duration remain undefined.

Methods:

A YouTube channel and a video-based learning website, PASSIO Education (passioeducation.com), were examined from 2011 to 2017. We assessed views, geographic location, audience engagement (average percent of video watched), audience retention (percent of viewers at each timepoint), and usage of short (median 7.4, range 4.1–20.3 min) and long (median 17.2, range 6.1–47.7 min) video formats for the same procedures. A survey of PASSIO Education membership examined preferred video duration.

Results:

Our 117 nerve surgery videos attained over 3 million views with 69% originating outside of the United States. While YouTube achieved more international exposure, PASSIO Education attained a greater mean engagement of 48.4% (14.3% absolute increase, P < 0.0001). Surveyed surgeons (n = 304) preferred longer videos when preparing for infrequent or difficult cases compared with routine cases (P < 0.0001). Engagement declined with video duration, but audience retention between short and long video formats was correlated (τB = 0.52, P < 0.0001).

Conclusions:

For effective spread of best practices, we propose the joint use of YouTube for audience outreach and a surgeon-focused platform to maximize educational value. Optimal video duration is surgeon- and case-dependent and can be addressed through offering multiple video durations and interactive viewing options.
A lateral flow test detecting SARS-CoV-2 neutralizing antibodies
Authors: Zhang Nan , Chen Shuo , Wu Jin V. , Yang Xinhai , Wang Jianfu J.
Published: November 2020

It is of critical importance for COVID-19 survivors, vaccine recipients, and public to know whether they have developed neutralizing antibodies or immunity. Here, we describe a 15 minutes lateral flow test for rapid detection of neutralizing antibodies against SARS-CoV-2. All other currently available neutralization tests require hours or days to complete and have to be performed in a well-equipped laboratory. This lateral flow test is the first of its kind and will serve as a convenient diagnostic tool in management of COVID-19 disease.
A shorter symptom-onset to remdesivir treatment (SORT) interval is associated with a lower mortality in moderate-to-severe COVID-19: A real-world analysis
Authors: Mehta Ravindra M , Bansal Sameer , Bysani Suhitha , Kalpakam Hariprasad
Published: November 2020

Background

Remdesivir is the current recommended anti-viral treatment in moderate-to-severe COVID-19. However, data on several aspects of its use such as impact of timing of therapy, efficacy, and safety in this severity category are limited. The current study aimed to evaluate the impact of timing of remdesivir initiation (symptom-onset to remdesivir treatment [SORT] interval) on in-hospital all-cause mortality in patients with moderate-to-severe COVID-19.

Methods

This retrospective study was conducted between June 25, 2020 and October 3, 2020, at a tertiary care dedicated COVID center in India. Consecutive patients with moderate-to-severe COVID-19 (moderate: SpO2 <94%; severe: SpO2 <90%) were included. Data were collected from the health records of the hospital. Remdesivir was administered along with other standard medications as per protocol. The main outcome was the impact of SORT interval on in-hospital all-cause mortality. Subgroups were formed based on SORT interval. Other measures analyzed included overall in-hospital mortality, length of hospital stay, and safety.

Results

Of 350 patients treated with remdesivir, 346 were included for the final analysis (males: 270 [78.0%]; median [range] age: 60 [24-94] years). Overall, 243 (70.2%) patients had ≥1 comorbidity; 109 (31.5%) patients had moderate disease, 237 (68.5%) had severe disease, and 50 (14.5%) patients required mechanical ventilation. Of the 346 patients, 76 (22.0%) patients died (moderate: 3 [2.8%], severe: 73 [30.8%]). In the subset of mechanically ventilated patients, 43 (86.0%) died. All-cause mortality was significantly lower in patients with SORT interval ≤9 days (n = 260) compared with those with SORT interval >9 days (n = 86; 18.1% vs 33.7%;P= .004). The odds of death were significantly lower in patients with SORT interval ≤9 days vs >9 days (odds ratio = 0.44; 95% CI, 0.25-0.76;P= .004). Adverse events (transaminitis ≥5 times upper limit of normal or estimated glomerular filtration rate <30ml/min) leading to drug discontinuation were seen in 4 (1.1%) patients.

Conclusion

In this large series of moderate-to-severe COVID-19, initiation of remdesivir ≤9 days from symptom-onset was associated with a significant mortality benefit. These findings indicate a treatment window and reinforce the need for earlier remdesivir initiation in moderate-to-severe COVID-19 infection.
The smartphone: an evolution or revolution in virtual patient healthcare during and beyond the COVID-19 pandemic ? An evaluation and comparison of the smartphone against other currently available wearable technologies in a secondary care setting during the COVID-19 pandemic
Authors: Raza Asif , Mukherjee Subhabrata , Patel Vikash , Kamal Naila , Lichtarowicz-Krynska Ewa
Published: November 2020

Smartphones are now commonly used, for virtual outpatient consultations, to help reduce disease transmission during the COVID-19 pandemic. Nosocomial spread of COVID 19 and hospital acquired infections are usually from staff or students to patients. Reducing non- essential staff numbers on ward rounds may reduce the risk.

We describe the novel use of smartphones, with Microsoft Teams, to live stream inpatient interactions, radiological images, pathology results, charts and patient review between an office-based and ward team (virtual ward round) and for teaching medical students in secondary care. After Research and Ethics, Digital services and Information Governance approval we compared a smartphone and head-worn device (Realwear HMT-1). Data collection was by participant questionnaire. Statistical analysis was performed using the Mann – Whitney test.

There was no statistically significant difference in audio and video feed quality between the smart phone (p value = 0.3) and Realwear device (p value = 0.41). However the smartphone was preferred during ward rounds and was 85% cheaper than the Realwear device. Urology medical staff numbers on the ward were reduced by 50%. Ward round efficiency improved as administrative tasks could be performed by the office team during the virtual ward round.

Virtual ward rounds using smartphones can facilitate remote communication between staff, students and patients. Staff in isolation or shielding can also assist front line colleagues from home. Smarter use of the smart phone may help reduce staff numbers on wards and reduce the number COVID-19 and nosocomial infections, potentially reducing morbidity and mortality locally and globally.
Predicting Response to Radiotherapy of Intracranial Metastases with Hyperpolarized 13C MRI
Authors: Lee Casey Y. , Soliman Hany , Bragagnolo Nadia D. , Sahgal Arjun , Geraghty Benjamin J. , Chen Albert P. , Endre Ruby , Perks William J. , Detsky Jay S. , Leung Eric , Chan Michael , Heyn Chris , Cunningham Charles H.
Published: November 2020

Purpose

Stereotactic radiosurgery (SRS) is used to manage intracranial metastases in a significant fraction of patients. Local progression after SRS can often only be detected with increased volume of enhancement on serial MRI scans which may lag true progression by weeks or months.

Experimental Design

Patients with intracranial metastases (N = 11) were scanned using hyperpolarized 13C MRI prior to treatment with stereotactic radiosurgery (SRS). The status of each lesion was then recorded at six months post-treatment follow-up (or at the time of death).

Results

The positive predictive value of 13C-lactate signal, measured pre-treatment, for prediction of progression of intracranial metastases at six months post-treatment with SRS was 0.8 p < 0.05, and the AUC from an ROC analysis was 0.77 p < 0.05. The distribution of 13C-lactate z-scores was different for intracranial metastases from different primary cancer types (F = 2.46, p = 0.1).

Conclusions

Hyperpolarized 13C imaging has potential as a method for improving outcomes for patients with intracranial metastases, by identifying patients at high risk of treatment failure with SRS and considering other therapeutic options such as surgery.
Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases
Authors: Gado Japheth E. , Harrison Brent E. , Sandgren Mats , Ståhlberg Jerry , Beckham Gregg T. , Payne Christina M.
Published: November 2020

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, comprised of a catalytic domain attached to a carbohydrate binding module (CBM) via a flexible linker, and exhibit a long active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical biological and industrial importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, using the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy. The lengths of the A4, B2, B3, and B4 loops were strongly correlated with functional subtype across the GH7 family. Position-specific classification rules were derived such that specific amino acids at 42 different sequence positions predicted the functional subtype with accuracies greater than 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. We propose these positions play vital roles in the functional variation of GH7 cellulases. Taken together, our results complement numerous experimental findings and present functional relationships that can be applied when prospecting GH7 cellulases from nature, for sequence annotation, and to understand or manipulate function.
Execution of intervention matters more than strategy: A lesson from the spatiotemporal assessment of COVID-19 clusters in Nepal
Authors: Acharya Bipin Kumar , Khanal Laxman , Mahyoub Alnwisi Sameh Mansoor , Ruan Zengliang , Yang Yin , Adhikari Samir Kumar , Pandit Shreejana , Neupane Basanta Kumar , Paudel Binod Kumar , Lin Hualiang
Published: November 2020

The novel coronavirus disease 2019 (COVID-19) has been the biggest public health problem of the present world. As the number of people suffering from the pandemic is rising, it is likely to claim more life and worsen the global health and economy. Nepal, one of the developing countries in the south Asia has been strongly influenced by the pandemic and struggling to contain it with multiple interventions, however, spatiotemporal dynamics of the epidemic and its linkage with various intervention strategies has not been studied yet. Here, we employed the prospective spatial-temporal analysis with SaTScan assessing dynamics of the COVID-19 cases from 23 January to 31 August 2020 at district level in Nepal. The results revealed that COVID-19 dynamics in the early stage of transmission was slower and confined in certain districts. However, from the third week of April, transmission spread rapidly across districts of Province No. 2 and Sudoorpaschim Province, primarily introduced by Nepalese citizens returning from India. Despite nationwide lockdown, nine statistically significant active and emerging clusters were detected between 23 January and 21 July 2020, whereas ten emerging clusters were observed for extended period to 31 August. The population density and population inflow from India crossing the sealed border had significant effects on the elevated risk of the epidemic. The capital city Kathmandu has become the highest-risk active cluster since August when travel restriction has been suspended. Movement restriction appears to be the most effective non-pharmaceutical intervention against the COVID-19 for resource-scarce countries with limited health care facilities. Our findings could be valuable to the health authorities within Nepal and beyond to better allocate resources and improve interventions on the pandemic for containing it efficiently.
COVID-19 case management: The policy model in Morocco context
Authors: Bennis Issam
Published: November 2020

Background

Based on the updated scientific evidence around SARS-CoV-2 diagnostic, health policymakers had to consider that many decisions could enhance or limit the success of the overall COVID-19 control strategy. The purpose of this study is to share alternative COVID-19 case management based on the updated international knowledge.

Methods

This study presents the main information about COVID-19 case management in Morocco from March to October 2020. The NVivo qualitative model content analysis was used to compare and prioritize health decisions with updated scientific evidence.

Results

The lack of molecular diagnostic accuracy using the interpretation of cycles quantification values, was targeted only by allowing all private laboratories to do RT qPCR. However, there is an urgent need for standardisation with accurate molecular SARS-CoV-2 thermocyclers and kits that notify systematic cycles quantification and do more tests per days to control the spread effectively. A predictive tree of the cycle’s range is presented following three steps: 1) the initial clinical definition, 2) the molecular confirmation, 3) and the diagnostic follows up results of the RT qPCR up to 28 days after the onset. At the same time, the seasonal vaccination against influenza and pneumonia could help to reduce COVID-19 deaths.

Conclusions

Until an available SARS-CoV-2 specific vaccine and/or curative effective treatment, updated control strategy in Morocco and similar context countries require to target population living in highly COVID-19 epidemic cities or areas by mass testing with the right interpretation of PCR values changes, associated to seasonal vaccination to foster the immunity.
Synapses from the high-order thalamic nucleus and motor cortex are co-clustered in the distal tuft dendrites of the mouse somatosensory cortex
Authors: Kim Nari , Bahn Sangkyu , Choi Joon Ho , Kim Jinseop S. , Rah Jong-Cheol
Published: November 2020

The posterior medial nucleus of the thalamus (POm) and vibrissal primary motor cortex (vM1) convey essential information to the barrel cortex (S1BF) regarding whisker position and movement. Therefore, understanding the relative spatial relationships of these two inputs is critical prerequisites to acquire insight into how S1 synthesizes information to interpret the location of an object. Using array tomography, we identified the locations of synapses from vM1 and POm on distal tuft dendrites of L5 pyramidal neurons. We found that synapses from vM1 and POm are spatially clustered on the same set of dendrites with unusually high density. Furthermore, the clusters of vM1 and POm synapses colocalize each other. These findings suggest that synaptic clusters, but not dendritic branches, act as functional units and cooperatively contribute to nonlinear dendritic responses.
Human coronaviruses disassemble processing bodies
Authors: Kleer Mariel , Mulloy Rory P. , Robinson Carolyn-Ann , Evseev Danyel , Bui-Marinos Maxwell P. , Castle Elizabeth L. , Banerjee Arinjay , Mubareka Samira , Mossman Karen , Corcoran Jennifer A.
Published: November 2020

A dysregulated proinflammatory cytokine response is characteristic of severe coronavirus infections caused by SARS-CoV-2, yet our understanding of the underlying mechanism responsible for this imbalanced immune response remains incomplete. Processing bodies (PBs) are cytoplasmic membraneless ribonucleoprotein granules that control innate immune responses by mediating the constitutive decay or suppression of mRNA transcripts, including many that encode proinflammatory cytokines. PB formation promotes turnover or suppression of cytokine RNAs, whereas PB disassembly corresponds with the increased stability and/or translation of these cytokine RNAs. Many viruses cause PB disassembly, an event that can be viewed as a switch that rapidly relieves cytokine RNA repression and permits the infected cell to respond to viral infection. Prior to this report, no information was known about how human coronaviruses (hu CoVs) impacted PBs. Here, we show SARS-CoV-2 and the common cold hu CoVs, OC43 and 229E, induced PB loss. We screened a SARS-CoV-2 gene library and identified that expression of the viral nucleocapsid (N) protein from SARS-CoV-2 was sufficient to mediate PB disassembly. RNA fluorescentin situhybridization revealed that N protein-mediated PB loss correlated with elevated RNA for PB-localized transcripts encoding TNF and IL-6. Ectopic expression of the N proteins from five other human coronaviruses (OC43, MERS, 229E, NL63 and SARS-CoV-1) did not cause significant PB disassembly, suggesting that this feature is unique to SARS-CoV-2 N protein. These data suggest that SARS-CoV-2-mediated PB disassembly contributes to enhanced proinflammatory cytokine production observed during severe SARS-CoV-2 infection.
Multi-session delivery of synchronous rTMS and sensory stimulation induces long-term plasticity
Authors: Zhong Ming , Cywiak Carolina , Metto Abigael C. , Liu Xiang , Qian Chunqi , Pelled Galit
Published: November 2020

Background

Combining training or sensory stimulation with non-invasive brain stimulation has shown to improve performance in healthy subjects and improve brain function in patients after brain injury. However, the plasticity mechanisms and the optimal parameters to induce long-term and sustainable enhanced performance remain unknown.

Objective

This work was designed to identify the protocols of which combining sensory stimulation with repetitive transcranial magnetic stimulation (rTMS) will facilitate the greatest changes in fMRI activation maps in the rat’s primary somatosensory cortex (S1).

Methods

Several protocols of combining forepaw electrical stimulation with rTMS were tested, including a single stimulation session compared to multiple, daily stimulation sessions, as well as synchronous and asynchronous delivery of both modalities. High-resolution fMRI was used to determine how pairing sensory stimulation with rTMS induced short and long-term plasticity in the rat S1.

Results

All groups that received a single session of rTMS showed short-term increases in S1 activity, but these increases did not last three days after the session. The group that received a stimulation protocol of 10 Hz forepaw stimulation that was delivered simultaneously with 10 Hz rTMS for five consecutive days demonstrated the greatest increases in the extent of the evoked fMRI responses compared to groups that received other stimulation protocols.

Conclusions

Our results provide direct indication that pairing peripheral stimulation with rTMS induces long-term plasticity, and this phenomenon appears to follow a time-dependent plasticity mechanism. These results will be important to lead the design of new training and rehabilitation paradigms and training towards achieving maximal performance in healthy subjects.

Highlights

A single rTMS session induced short-term changes but they were not sustainable

Multi-session delivery of rTMS paired with sensory stimulation induced long-term plasticity

rTMS paired with sensory stimulation induced plasticity via time-dependent mechanism

Delivery of sensory stimulation only did not induce long-term plasticity
Resource uptake and the evolution of moderately efficient enzymes
Authors: Labourel Florian , Rajon Etienne
Published: November 2020

Enzymes speed up reactions that would otherwise be too slow to sustain the metabolism of self-replicators. Yet, most enzymes seem only moderately efficient, exhibiting kinetic parameters orders of magnitude lower than their expected physically achievable maxima and spanning over surprisingly large ranges of values. Here, we question how these parameters evolve using a mechanistic model where enzyme efficiency is a key component of individual competition for resources. We show that kinetic parameters are under strong directional selection only up to a point, above which enzymes appear to evolve under near-neutrality, thereby confirming the qualitative observation of other modeling approaches. While the existence of a large fitness plateau could potentially explain the extensive variation in enzyme features reported, we show using a population genetics model that such a widespread distribution is an unlikely outcome of evolution on a common landscape, as mutation-selection-drift balance occupy a narrow area even when very moderate biases towards lower efficiency are considered. Instead, differences in the evolutionary context encountered by each enzyme should be involved, such that each evolves on an individual, unique landscape. Our results point to drift and effective population size playing an important role, along with the kinetics of nutrient transporters, the tolerance to high concentrations of intermediate metabolites, and the reversibility of reactions. Enzyme concentration also shapes selection on kinetic parameters, but we show that the joint evolution of concentration and efficiency does not yield extensive variance in evolutionary outcomes when documented costs to protein expression are applied.
A motion aftereffect from viewing other people’s gaze
Authors: Randall William , Guterstam Arvid
Published: November 2020

Recent work suggests that our brains may generate subtle, false motion signals streaming from other people to the objects of their attention, aiding social cognition. For instance, brief exposure to static images depicting other people gazing at objects made subjects slower at detecting subsequent motion in the direction of gaze, suggesting that looking at someone else’s gaze caused a directional motion adaptation. Here we confirm, using a more stringent method, that viewing static images of another person gazing in a particular direction, at an object, produced motion aftereffects in the opposite direction. The aftereffect was manifested as a change in perceptual decision threshold for detecting left versus right motion. The effect disappeared when the person was looking away from the object. These findings suggest that the attentive gaze of others is encoded as an implied agent-to-object motion that is sufficiently robust to cause genuine motion aftereffects, though subtle enough to remain subthreshold.
Mechanistic analysis of enhancer sequences in the Estrogen Receptor transcriptional program
Authors: Tabe-Bordbar Shayan , Song You Jin , Lunt Bryan J. , Prasanth Kannanganattu V. , Sinha Saurabh
Published: November 2020

Background

Estrogen Receptor α (ERα) is a major lineage determining transcription factor (TF) in mammary gland development, orchestrating the expression of thousands of genes. Dysregulation of ERα-mediated transcriptional program results in abnormal cell proliferation and cancer. Transcriptomic and epigenomic profiling of breast cancer cell lines has revealed large numbers of enhancers involved in this regulatory program, but how these enhancers encode function in their sequence remains poorly understood.

Results

A subset of ERα-bound enhancers are transcribed into short bidirectional RNA (enhancer RNA or eRNA), and this property is believed to be a reliable marker of active enhancers. We therefore analyze thousands of ERα-bound enhancers and build quantitative, mechanism-aware models to discriminate eRNAs from non-transcribing enhancers based on their sequence. Our thermodynamics-based models provide insights into the roles of specific TFs in ERα-mediated transcriptional program, many of which are supported by the literature. We use in silico perturbations to predict TF-enhancer regulatory relationships and integrate these findings with experimentally determined enhancer-promoter interactions to construct a gene regulatory network. We also demonstrate that the model can prioritize breast cancer-related sequence variants while providing mechanistic explanations for their function. Finally, we experimentally validate the model-proposed mechanisms underlying three such variants.

Conclusions

We modeled the sequence-to-expression relationship in ERα-driven enhancers and gained mechanistic insights into the workings of a major transcriptional program. Our model is consistent with the current body of knowledge and its predictions are confirmed by experimental observations. We believe this to be a promising approach to analysis of regulatory sequences and variants.
Development of Targetable Multi-Drug Nanoparticles for Glioblastoma Treatment and In Vitro Evaluation in Glioblastoma Stem Cells
Authors: Smiley Shelby B. , Yun Yeonhee , Ayyagari Pranav , Shannon Harlan E. , Pollok Karen E. , Vannier Michael W. , Das Sudip K. , Veronesi Michael C.
Published: November 2020

Glioblastoma (GBM) is a malignant brain tumor with a poor long-term prognosis. The current median survival is approximately fifteen to twenty months with the standard of care therapy which includes surgery, radiation, and chemotherapy. An important factor contributing to recurrence of GBM is high resistance of GBM cancer stem cells (CSCs) to several anticancer drugs, for which a systemically delivered single drug approach will be unlikely to produce a viable cure. Therefore, multidrug therapies have the potential to improve the survival time. Currently, only temozolomide (TMZ), which is a DNA alkylator, affects overall survival in GBM patients. CSCs regenerate rapidly and over-express a methyl transferase which overrides the DNA-alkylating mechanism of TMZ, leading to drug resistance. Idasanutlin (RG7388, R05503781) is a potent, selective MDM2 antagonist that additively kills GBM CSCs when combined with TMZ. Nanotechnology is an emerging field that shows great promise in drug delivery and diagnostics. The ability to combine both therapy and imaging allows real time assessment of drug delivery in vivo for the field of theranostics.

To develop a multi-drug therapy using multi-functional nanoparticles (NPs) that preferentially target the GBM CSC subpopulation and provide in vivo preclinical imaging capability. Polymer-micellar NPs composed of poly(styrene-b-ethylene oxide) (PS-b-PEO) and poly(lactic-co-glycolic) acid (PLGA) were developed investigating both single and double emulsion fabrication techniques as well as combinations of TMZ and RG7388. The NPs were covalently bound to a 15-base-pair CD133 aptamer in order to target the CD133 antigen expressed on the surface of GBM CSC subpopulation. For theranostic functionality, the NPs were also labelled with a radiotracer, Zirconium-89 (89Zr). The NPs maintained a small size of less than 100 nm, a low negative charge and exhibited the ability to effectively target and kill the CSC subpopulation. In addition, the conjugation of the CD133 aptamer was able to promote killing in CSCs leading to the justification of a targeted nanosystem to potentially improve localized therapy in future in vivo models. This work has provided a potentially therapeutic option for GBM specific for CSC targeting and theranostic imaging.
Symptoms suggestive of COVID-19 in households with and without children: a descriptive survey
Authors: Grove Grace , Ziauddeen Nida , Alwan Nisreen A
Published: November 2020

Background

Exploring transmission and symptoms of COVID-19 in children is vital, given that schools have recently fully reopened.

Objectives

This study aimed to characterise the nature and duration of symptoms suggestive of COVID-19 in UK households, and examine whether the symptoms varied between households with and without children and between adults and children from March to May 2020 in the UK.

Methods

An online questionnaire posted on social media (Mumsnet, Twitter, Facebook) was used to gather demographic and symptom information within UK households.

Results

Results from 508 households (1057 adults and 398 children) were available for analysis. 64.1% of respondent households with children and 59.1% of households without children had adults with symptoms suggestive of COVID-19. The proportion of adults that reported being symptomatic was 46.1% in households with children (and 36.7% in households without children. In 37.8% of households with at least one adult and one child with symptoms, the child’s onset of symptoms started before the adult. Of all children, 35.7% experienced symptoms, with almost a quarter experiencing fluctuating symptoms for more than 2 weeks compared to almost half of symptomatic adults. In general, children had a shorter (median 5 days) and milder illness course than adults (median 10 days). Fatigue was the most common symptom in adults (79.7%) and cough was the most common symptom in children (53.5%). Chest tightness, shortness of breath, fatigue, muscle ache and diarrhoea were more common in adults than children, while cough and fever were equally common.

Conclusion

Children had shorter and milder illness than adults, but in almost a quarter of children symptoms lasted more than 2 weeks. In over a third of both adult-child symptomatic households, the child was the first to become ill. Child to adult transmission and clinical presentation in children need to be further characterised.

Synopsis

Study question.

What is the nature and duration of symptoms suggestive of COVID-19 in UK households with and without children during March and May 2020? Do the symptoms vary between adults and children?

What’s already known.

There has been uncertainty about the extent to which children get and transmit SARS-CoV-2 within households. Symptoms associated with SARS-CoV-2 infection are well described in adults but symptoms and their duration are less well-characterised in children.

What this study adds

On average, children had shorter and milder illness than adults, but still symptoms lasted more than 2 weeks in a significant proportion of children. In over a third of both adult and child symptomatic households, the child was the first to become ill.
Replacing theSpCas9HNH domain by deaminases generates compact base editors with an alternative targeting scope
Authors: Villiger Lukas , Schmidheini Lukas , Mathis Nicolas , Rothgangl Tanja , Marquart Kim , Schwank Gerald
Published: November 2020

Base editors are RNA-guided deaminases that enable site-specific nucleotide transitions. The targeting scope of these Cas-deaminase fusion proteins critically depends on the availability of a protospacer adjacent motif (PAM) at the target locus and is limited to a window within the CRISPR-Cas R-loop, where single stranded (ss)DNA is accessible to the deaminase. Here, we reason that the Cas9-HNH nuclease domain sterically constrains ssDNA accessibility, and demonstrate that omission of this domain expands the editing window. By exchanging the HNH nuclease domain with an adenosine deaminase we furthermore engineer adenine base editor variants (HNHx-ABE) with PAM-proximally shifted editing windows. This work expands the targeting scope of base editors, and provides base editor variants that are substantially smaller. It moreover informs of potential future directions in Cas9 protein engineering, where the HNH domain could be replaced by other enzymes that act on ssDNA.
Spatiotemporal model of cellular mechanotransduction via Rho and YAP
Authors: Novev Javor K. , Heltberg Mathias L. , Jensen Mogens H. , Doostmohammadi Amin
Published: November 2020

How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization.

For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio’s time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.
Genetic Modification to Design a Stable Yeast-expressed Recombinant SARS-CoV-2 Receptor Binding Domain as a COVID-19 Vaccine Candidate
Authors: Chen Wen-Hsiang , Wei Junfei , Kundu Rakhi Tyagi , Adhikari Rakesh , Liu Zhuyun , Lee Jungsoon , Versteeg Leroy , Poveda Cristina , Keegan Brian , Villar Maria Jose , de Araujo Leao Ana C. , Rivera Joanne Altieri , Gillespie Portia M. , Pollet Jeroen , Strych Ulrich , Zhan Bin , Hotez Peter J. , Bottazzi Maria Elena
Published: November 2020

Background

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has now spread worldwide to infect over 110 million people, with approximately 2.5 million reported deaths. A safe and effective vaccine remains urgently needed.

Method

We constructed three variants of the recombinant receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein (residues 331-549) in yeast as follows: (1) a “wild type” RBD (RBD219-WT), (2) a deglycosylated form (RBD219-N1) by deleting the first N-glycosylation site, and (3) a combined deglycosylated and cysteine-mutagenized form (C538A-mutated variant (RBD219-N1C1)). We compared the expression yields, biophysical characteristics, and functionality of the proteins produced from these constructs.

Results and conclusions

These three recombinant RBDs showed similar secondary and tertiary structure thermal stability and had the same affinity to their receptor, angiotensin-converting enzyme 2 (ACE-2), suggesting that the selected deletion or mutations did not cause any significant structural changes or alteration of function. However, RBD219-N1C1 had a higher fermentation yield, was easier to purify, was not hyperglycosylated, and had a lower tendency to form oligomers, and thus was selected for further vaccine development and evaluation.

General significance

By genetic modification, we were able to design a better-controlled and more stable vaccine candidate, which is an essential and important criterion for any process and manufacturing of biologics or drugs for human use.
KusakiDB v1.0: a novel approach for validation and completeness of protein orthologous groups
Authors: Ghelfi Andrea , Nakamura Yasukazu , Isobe Sachiko
Published: November 2020

Plants have quite a low coverage in the major protein databases despite their roughly 350,000 species. Moreover, the agricultural sector is one of the main categories in bioeconomy. In order to manipulate and/or engineer plant-based products, it is important to understand the essential fabric of an organism, its proteins. Therefore, we created KusakiDB, which is a database of orthologous proteins, in plants, that correlates three major databases, OrthoDB, UniProt and RefSeq. KusakiDB has an orthologs assessment and management tools in order to compare orthologous groups, which can provide insights not only under an evolutionary point of view but also evaluate structural gene prediction quality and completeness among plant species. KusakiDB could be a new approach to reduce error propagation of functional annotation in plant species. Additionally, this method could, potentially, bring to light some orthologs unique to a few species or families that could have evolved at a high evolutionary rate or could have been a result of a horizontal gene transfer.

Availability and Implementation

The software is implemented in R. It is available athttp://pgdbjsnp.kazusa.or.jp/app/kusakidband athttps://hub.docker.com/r/ghelfi/kusakidbunder the MIT license.

Contact:

andreaghelfi@kazusa.or.jp

Supplementary information

Supplementary data are available atBioinformaticsonline.
DR2S: An Integrated Algorithm Providing Reference-Grade Haplotype Sequences from Heterozygous Samples
Authors: Klasberg Steffen , Schmidt Alexander H. , Lange Vinzenz , Schöfl Gerhard
Published: November 2020

Background

High resolutionHLAgenotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation.

Results

Here, we report onDR2S, an R package that leverages the strengths of two sequencing technologies – the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio’s SMRT sequencing or ONT’s nanopore sequencing – to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised forHLAand KIR genes,DR2Sis applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition,DR2Sintegrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases.

Conclusions

DR2Sis a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such asHLAorKIR. It has been used by biologists to successfully characterise and submit more than 500HLAalleles and more than 500KIRalleles to theIPD-IMGT/HLAandIPD-KIRdatabases.
Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy
Authors: Navikas Vytautas , Leitao Samuel M. , Grussmayer Kristin S. , Descloux Adrien , Drake Barney , Yserentant Klaus , Werther Philipp , Herten Dirk-Peter , Wombacher Richard , Radenovic Aleksandra , Fantner Georg E.
Published: November 2020

High-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffractional resolution.