Public transport accessibility indicators to urban and regional services in Great Britain.

Public transport accessibility to urban and regional services has been found to relate to various social and economic processes, such as unemployment, transport mode choice, property prices, and public health. A frequent type of measures representing accessibility are location-based. While these offer advantages, like flexibility and ease of interpretation, their estimation usually requires specialized skills and substantial computational resources. To lower these barriers, we have prepared a suite of accessibility indicators for key services across Great Britain at a spatially disaggregated level. The dataset includes ready-to-use public transport accessibility indicators for employment, general practitioners (GP, or family physician), hospitals, grocery stores, supermarkets, primary and secondary schools, and urban centres. It also includes the raw travel time matrix from each origin to every potential destination, a primary input for such indicator estimation. Altogether, this resource offers various levels of application, from direct input into a range of research topics to the foundation for creating comprehensive custom indicators.

Conformation specific antagonistic high affinity antibodies to the RON receptor kinase for imaging and therapy.

The RON receptor tyrosine kinase is an exceptionally interesting target in oncology and immunology. It is not only overexpressed in a wide variety of tumors but also has been shown to be expressed on myeloid cells associated with tumor infiltration, where it serves to dampen tumour immune responses and reduce the efficacy of anti-CTLA4 therapy. Potent and selective inhibitory antibodies to RON might therefore both inhibit tumor cell growth and stimulate immune rejection of tumors. We derived cloned and sequenced a new panel of exceptionally avid anti-RON antibodies with picomolar binding affinities that inhibit MSP-induced RON signaling and show remarkable potency in antibody dependent cellular cytotoxicity. Antibody specificity was validated by cloning the antibody genes and creating recombinant antibodies and by the use of RON knock out cell lines. When radiolabeled with 89-Zirconium, the new antibodies 3F8 and 10G1 allow effective immuno-positron emission tomography (immunoPET) imaging of RON-expressing tumors and recognize universally exposed RON epitopes at the cell surface. The 10G1 was further developed into a novel bispecific T cell engager with a 15 pM EC50 in cytotoxic T cell killing assays.

RNF43 mutations predict response to anti-BRAF/EGFR combinatory therapies in BRAFV600E metastatic colorectal cancer.

Anti-BRAF/EGFR therapy was recently approved for the treatment of metastatic BRAFV600E colorectal cancer (mCRCBRAF-V600E). However, a large fraction of patients do not respond, underscoring the need to identify molecular determinants of treatment response. Using whole-exome sequencing in a discovery cohort of patients with mCRCBRAF-V600E treated with anti-BRAF/EGFR therapy, we found that inactivating mutations in RNF43, a negative regulator of WNT, predict improved response rates and survival outcomes in patients with microsatellite-stable (MSS) tumors. Analysis of an independent validation cohort confirmed the relevance of RNF43 mutations to predicting clinical benefit (72.7% versus 30.8%; P = 0.03), as well as longer progression-free survival (hazard ratio (HR), 0.30; 95% confidence interval (CI), 0.12-0.75; P = 0.01) and overall survival (HR, 0.26; 95% CI, 0.10-0.71; P = 0.008), in patients with MSS-RNF43mutated versus MSS-RNF43wild-type tumors. Microsatellite-instable tumors invariably carried a wild-type-like RNF43 genotype encoding p.G659fs and presented an intermediate response profile. We found no association of RNF43 mutations with patient outcomes in a control cohort of patients with MSS-mCRCBRAF-V600E tumors not exposed to anti-BRAF targeted therapies. Overall, our findings suggest a cross-talk between the MAPK and WNT pathways that may modulate the antitumor activity of anti-BRAF/EGFR therapy and uncover predictive biomarkers to optimize the clinical management of these patients.

Did air pollution continue to affect bike share usage in Seoul during the COVID-19 pandemic?

INTRODUCTION: The role of cycling has become more important in the urban transport system during the Covid-19 pandemic. As public transport passengers have tried to avoid crowded vehicles due to safety concerns, a rapid surge of cycling activities has been noted in many countries. This implies that more cyclists might be exposed to air pollution, potentially leading to health problems in cities like Seoul where the level of air pollution is high. METHODS: We utilised three years of bike sharing programme (Ddareungi) data in Seoul and time series models to examine the changes in the relationship between particulate concentration (PM2.5) and total daily cycling duration before and during the pandemic. RESULTS: We find that cyclists reacted less to the PM2.5 level during the pandemic, potentially due to the lack of covid-secure travel modes. Specifically, our results show significant negative associations between concentrations of PM2.5 and total daily cycling duration before the pandemic (year 2018 and 2019). However, this association became insignificant in 2020. CONCLUSIONS: Building comprehensive cycling infrastructure that can reduce air pollution exposure of cyclists and improving air quality alert systems could help build a more resilient city for the future.

Direct Synthesis of α-Fluoro-α-Triazol-1-yl Ketones from Sulfoxonium Ylides: A One-Pot Approach.

The work reported herein showcases a new route to access α-fluoro-α-triazol-1-yl ketones from sulfoxonium ylides via α-azido-α-fluoro ketone intermediates. In a one-pot, two-step sequence, the ketosulfoxonium reactant initially undergoes insertion of F+ and N3-, followed by a subsequent CuAAC reaction with arylacetylenes to install a 1,4-triazolo moiety. The approach allows for modification to both the sulfoxonium ylide and arylacetylene reactants. Fifteen examples have been reported, with yields ranging between 22% and 75%.

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.

BACKGROUND: Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance. RESULTS: In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels. CONCLUSION: These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.

Changing clinical patterns of Rhegmatogeneous Retinal Detachments during the COVID19 pandemic lockdown in the North West of the UK.

INTRODUCTION: The UK Government imposed a COVID19 lockdown (LD) restricting all but essential activities from 24th March 2020. Subsequently, there has been a significant reduction in casualty attendances nationwide including for ophthalmic emergencies. We aim to study the presentation of rhegmatogenous retinal detachments (RRD) and significant vitreous haemorrhage caused by posterior vitreous detachment (PVD-VH) in three tertiary centres covering most of the North West of England in the 6 weeks before and during the lockdown. METHODS: A retrospective multicenter non-randomised consecutive case series study was designed to collect information on all cases of RRD and PVD-VH requiring surgery presenting to the vitreoretinal departments of Manchester Royal Eye Hospital, East Lancashire NHS Foundation Trust and the Lancashire NHS Foundation Trust from 11th February to 4th May 2020. RESULTS: A total of 137 eyes of 137 patients were identified between the three centres of which 132 eyes were operated for RRD. Of these, 86 (64.7%) were operated pre-LD compared with 46 eyes (34.8%) during LD. Forty-five out of 86 eyes (52.3%) were macula-off pre-LD compared with 31 out of 46 eyes (67.3%) during LD (p = 0.06). There was lower proportion of non-PVD related RRD during LD (11 pre-LD to 1 during LD, p = 0.05). PVR was present in four cases during LD compared to 2 before (p = 0.19). CONCLUSION: There was a clinically significant reduction in the overall incidence of RRD in our centres with an increase in the proportion of macula-off and proliferative vitreoretinopathy during the LD period compared to a similar period before.

The Novel Anti-cMet Antibody seeMet 12 Potentiates Sorafenib Therapy and Radiotherapy in a Colorectal Cancer Model.

RATIONAL: cMet is abnormally regulated in gastrointestinal cancer, and is associated with increased invasiveness of the disease and poor overall survival. There are indications that targeted therapy against cMet, alone or in combination with additional cancer therapies, can help improve treatment outcome. Thus, in the present study we investigated the therapeutic efficacy of a novel cMet-targeting antibody therapy in gastrointestinal cancer models, and assessed potential augmenting effects in combination with tyrosine kinase inhibitor (TKI) targeted therapy or radiotherapy. METHODS: Three different cMet-targeting antibodies were first characterized with respect to antigen binding and effects on cell viability in vitro. The best performing candidate seeMet 12 was then further assessed for effects on colorectal cancer cell growth, proliferation and migration. Combinations with the TKI-inhibitor sorafenib or external beam radiotherapy were then evaluated for potential additive or synergistic effects in vitro using monolayer- and multicellular tumor spheroid assays. Finally, the combination of seeMet 12 and radiotherapy was evaluated in vivo in a proof-of-concept colorectal cancer xenograft study. RESULTS: Dose-dependent therapeutic effects were demonstrated for all three cMet-targeting antibodies. Monotherapy using seeMet 12 resulted in impaired cellular migration/proliferation and reduced tumor spheroid growth. Moreover, seeMet 12 was able to potentiate therapeutic effects in vitro for both sorafenib and radiotherapy treatments. Finally, the in vivo therapy study demonstrated promising results, where a combination of seeMet 12 and fractionated radiotherapy increased median survival by 79% compared to radiotherapy alone, and tripled maximum survival. CONCLUSION: The novel anti-cMet antibody seeMet 12 demonstrated therapeutic effects in cMet positive gastrointestinal cancer cells in vitro. Moreover, the addition of seeMet 12 augmented the effects of sorafenib and radiotherapy. An in vivo proof-of-concept study of seeMet 12 and radiotherapy further validated the results. Thus, cMet-targeted therapy should be further explored as a promising approach to increase therapeutic effects, circumvent treatment resistance, and reduce side effects.

Efficiency in Magnocellular Processing: A Common Deficit in Neurodevelopmental Disorders.

Several neurodevelopmental disorders (NDDs) including Developmental Dyslexia (DD), Autism Spectrum Disorder (ASD), but not Attention Deficit Hyperactive Disorder (ADHD), are reported to show deficits in global motion processing. Such behavioral deficits have been linked to a temporal processing deficiency. However, to date, there have been few studies assessing the temporal processing efficiency of the Magnocellular M pathways through temporal modulation. Hence, we measured achromatic flicker fusion thresholds at high and low contrast in nonselective samples of NDDs and neurotypicals (mean age 10, range 7-12 years, n = 71) individually, and group matched, for both chronological age and nonverbal intelligence. Autistic tendencies were also measured using the Autism-Spectrum Quotient questionnaire as high AQ scores have previously been associated with the greater physiological amplitude of M-generated nonlinearities. The NDD participants presented with singular or comorbid combinations of DD, ASD, and ADHD. The results showed that ASD and DD, including those with comorbid ADHD, demonstrated significantly lower flicker fusion thresholds (FFTs) than their matched controls. Participants with a singular diagnosis of ADHD did not differ from controls in the FFTs. Overall, the entire NDD plus control populations showed a significant negative correlation between FFT and AQ scores (r = -0.269, p < 0.02 n = 71). In conclusion, this study presents evidence showing that a temporally inefficient M pathway could be the unifying network at fault across the NDDs and particularly in ASD and DD diagnoses, but not in singular diagnosis of ADHD.

A New Perspective on the Natural Philosophy of Steams and Its Relation to the Steam Engine.

Historians' understanding of the steam engine's evolution suffers from back-projections of nineteenth-century physical science, notably thermodynamics, onto the eighteenth century. The idea of steam as a "working substance" to merely transfer heat is anachronistic in the eighteenth-century context. It has led to serious misconceptions. To correct this misreading, this article uncovers three major areas discussing steam in the eighteenth century: producing a vacuum for fire engines and fire pumps; examining experimentally the bulk properties of steam; and the "chemistry of steams" that included studying effluvia and miasmas and that considered steam responsible for earthquakes, winds, storms, and other natural phenomena. In the eighteenth century, more natural philosophizing about steam (and other matters) was done in and across practical settings in the large than historians have realized. Subsequent understandings and later divisions of knowledge and practice have obscured much.

A Curriculum Domain Adaptation Approach to the Semantic Segmentation of Urban Scenes.

During the last half decade, convolutional neural networks (CNNs) have triumphed over semantic segmentation, which is one of the core tasks in many applications such as autonomous driving and augmented reality. However, to train CNNs requires a considerable amount of data, which is difficult to collect and laborious to annotate. Recent advances in computer graphics make it possible to train CNNs on photo-realistic synthetic imagery with computer-generated annotations. Despite this, the domain mismatch between real images and the synthetic data hinders the models' performance. Hence, we propose a curriculum-style learning approach to minimizing the domain gap in urban scene semantic segmentation. The curriculum domain adaptation solves easy tasks first to infer necessary properties about the target domain; in particular, the first task is to learn global label distributions over images and local distributions over landmark superpixels. These are easy to estimate because images of urban scenes have strong idiosyncrasies (e.g., the size and spatial relations of buildings, streets, cars, etc.). We then train a segmentation network, while regularizing its predictions in the target domain to follow those inferred properties. In experiments, our method outperforms the baselines on two datasets and three backbone networks. We also report extensive ablation studies about our approach.

The quantification of antibody elements and receptors subunit expression using qPCR: The design of VH, VL, CH, CL, FcR subunits primers for a more holistic view of the immune system.

The expression levels of immunoglobulin elements and their receptors are important markers for health and disease. Within the immunoglobulin locus, the constant regions and the variable region families are associated with certain pathologies, yet a holistic view of the interaction between the expressions of the multiple genes remain to be fully characterized. There is thus an important need to quantify antibody elements, their receptors and the receptor subunits in blood (PBMC cDNA) for both screening and detailed studies of such associations. Leveraging on qPCR, we designed primers for all Vκ1-6, VH1-7, Vλ1-11, nine CH isotypes, Cκ, Cκ, Cλ1 &3, FcεRI α,ß, and γ subunits, all three FcγR and their subunits, and FcαR. Validating this on a volunteer PBMC cDNA, we report a qPCR primer set repertoire that can quantify the relative expression of all the above genes to the GAPDH housekeeping gene, with implications and uses in both clinical monitoring and research.

The Stapled Peptide PM2 Stabilizes p53 Levels and Radiosensitizes Wild-Type p53 Cancer Cells.

The tumor suppressor p53 is a key mediator of cellular stress and DNA damage response cascades and is activated after exposure to ionizing radiation. Amplifying wild-type p53 expression by targeting negative regulators such as MDM2 in combination with external beam radiotherapy (EBRT) may result in increased therapeutic effects. The novel stapled peptide PM2 prevents MDM2 from suppressing wild-type p53, and is thus a promising agent for therapeutic combination with EBRT. Effects of PM2 and potential PM2-induced radiosensitivity were assessed in a panel of cancer cell lines using 2D cell viability assays. Western Blot and flow cytometric analyses were used to investigate the mechanisms behind the observed effects in samples treated with PM2 and EBRT. Finally, PM2-treatment combined with EBRT was evaluated in an in vitro 3D spheroid model. PM2-therapy decreased cell viability in wild-type p53, HPV-negative cell lines. Western Blotting and flow cytometry confirmed upregulation of p53, as well as initiation of p53-mediated apoptosis measured by increased cleaved caspase-3 and Noxa activity. Furthermore, 3D in vitro tumor spheroid experiments confirmed the superior effects of the combination, as the only treatment regime resulting in growth inhibition and complete spheroid disintegration. We conclude that PM2 induces antitumorigenic effects in wt p53 HPV-negative cancer cells and potentiates the effects of EBRT, ultimately resulting in tumor eradication in a 3D spheroid model. This strategy shows great potential as a new wt p53 specific tumor-targeting compound, and the combination of PM2 and EBRT could be a promising strategy to increase therapeutic effects and decrease adverse effects from radiotherapy.

Restricted fluid bolus volume in early septic shock: results of the Fluids in Shock pilot trial.

OBJECTIVE: To determine the feasibility of Fluids in Shock, a randomised controlled trial (RCT) of restricted fluid bolus volume (10 mL/kg) versus recommended practice (20 mL/kg). DESIGN: Nine-month pilot RCT with embedded mixed-method perspectives study. SETTING: 13 hospitals in England. PATIENTS: Children presenting to emergency departments with suspected infection and shock after 20 mL/kg fluid. INTERVENTIONS: Patients were randomly allocated (1:1) to further 10 or 20 mL/kg fluid boluses every 15 min for up to 4 hours if still in shock. MAIN OUTCOME MEASURES: These were based on progression criteria, including recruitment and retention, protocol adherence, separation, potential trial outcome measures, and parent and staff perspectives. RESULTS: Seventy-five participants were randomised; two were withdrawn. 23 (59%) of 39 in the 10 mL/kg arm and 25 (74%) of 34 in the 20 mL/kg arm required a single trial bolus before the shock resolved. 79% of boluses were delivered per protocol in the 10 mL/kg arm and 55% in the 20 mL/kg arm. The volume of study bolus fluid after 4 hours was 44% lower in the 10 mL/kg group (mean 14.5 vs 27.5 mL/kg). The Paediatric Index of Mortality-2 score was 2.1 (IQR 1.6-2.7) in the 10 mL/kg group and 2.0 (IQR 1.6-2.5) in the 20 mL/kg group. There were no deaths. Length of hospital stay, paediatric intensive care unit (PICU) admissions and PICU-free days at 30 days did not differ significantly between the groups. In the perspectives study, the trial was generally supported, although some problems with protocol adherence were described. CONCLUSIONS: Participants were not as unwell as expected. A larger trial is not feasible in its current design in the UK. TRIAL REGISTRATION NUMBER: ISRCTN15244462.

Author Correction: The effects of Antibody Engineering CH and CL in Trastuzumab and Pertuzumab recombinant models: Impact on antibody production and antigen-binding.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

The effects of red surrounds on visual magnocellular and parvocellular cortical processing and perception.

More than 50 years ago, Hubel and Wiesel identified a subpopulation of geniculate magnocellular (M) neurons that are suppressed by diffuse red light. Since then, many human psychophysical studies have used red and green backgrounds to study the effects of M suppression on visual task performance, as a means to better understand neurodevelopmental disorders such as dyslexia and schizophrenia. Few of these studies have explicitly assessed the relative effects of red backgrounds on the M and P (parvocellular) pathways. Here we compared the effects of red and green diffuse background illumination on well-accepted cortical M and P signatures, both physiologically through nonlinear analysis of visual evoked potentials (VEPs; N = 15), and psychophysically through pulsed and steady pedestal perceptual thresholds (N = 9 with gray pedestals and N = 8 with colored pedestals). Red surrounds reduced P-generated temporal nonlinearity in the VEPs, but they did not influence M-generated VEP signatures. The steady and pulsed pedestal results suggest that red surrounds can have different effects on M and P contrast sensitivities, depending on whether the target is colored gray or red, presented centrally or peripherally, or whether it is brighter or dimmer than the surround. Our results highlight difficulties in interpreting the effects of red backgrounds on human VEPs or perception in terms of M specific suppression.

Effect of VH-VL Families in Pertuzumab and Trastuzumab Recombinant Production, Her2 and FcγIIA Binding.

Many therapeutic antibodies are humanized from animal sources. In the humanization process, complementarity determining region grafting is tedious and highly prone to failure. With seven known VH families, and up to six known κ VL families, there are choices aplenty. However, the functions of these families remain largely enigmatic. To study the role of these V-region families, we made 84 recombinant combinations of the various VH and VL family whole IgG1 variants of both Trastuzumab and Pertuzumab. We managed to purify 66 of these to investigate the biophysical characteristics: recombinant protein production, and both Her2 and FcγIIA binding. Our findings revealed combinations that showed improved recombinant antibody production and both antigen and receptor binding kinetics. These findings show the need to rethink antibodies as a whole protein, relooking of the functions of the antibody domains, and the need to include immunoglobulin receptor investigations for effective antibody therapeutics development.

The effects of Antibody Engineering CH and CL in Trastuzumab and Pertuzumab recombinant models: Impact on antibody production and antigen-binding.

Current therapeutic antibodies such as Trastuzumab, are typically of the blood circulatory IgG1 class (Cκ/ CHγ1). Due to the binding to Her2 also present on normal cell surfaces, side effects such as cardiac failure can sometimes be associated with such targeted therapy. Using antibody isotype swapping, it may be possible to reduce systemic circulation through increased tissue localization, thereby minimising unwanted side effects. However, the effects of such modifications have yet to be fully characterized, particularly with regards to their biophysical properties in antigen binding. To do this, we produced all light and heavy chain human isotypes/subtypes recombinant versions of Trastuzumab and Pertuzumab, and studied them with respect to recombinant production and Her2 binding. Our findings show that while the light chain constant region changes have no major effects on production or Her2 binding, some heavy chain isotypes, in particularly, IgM and IgD isotypes, can modulate antigen binding. This study thus provides the groundwork for such isotype modifications to be performed in the future to yield therapeutics of higher efficacy and efficiency.