Synthetic white balancing for intra-operative hyperspectral imaging

Hyperspectral imaging shows promise for surgical applications to non-invasively provide spatially-resolved, spectral information. For calibration purposes, a white reference image of a highly-reflective Lambertian surface should be obtained under the same imaging conditions. Standard white references are not sterilizable, and so are unsuitable for surgical environments. We demonstrate the necessity for in situ white references and address this by proposing a novel, sterile, synthetic reference construction algorithm. The use of references obtained at different distances and lighting conditions to the subject were examined. Spectral and color reconstructions were compared with standard measurements qualitatively and quantitatively, using $\Delta E$ and normalised RMSE respectively. The algorithm forms a composite image from a video of a standard sterile ruler, whose imperfect reflectivity is compensated for. The reference is modelled as the product of independent spatial and spectral components, and a scalar factor accounting for gain, exposure, and light intensity. Evaluation of synthetic references against ideal but non-sterile references is performed using the same metrics alongside pixel-by-pixel errors. Finally, intraoperative integration is assessed though cadaveric experiments. Improper white balancing leads to increases in all quantitative and qualitative errors. Synthetic references achieve median pixel-by-pixel errors lower than 6.5% and produce similar reconstructions and errors to an ideal reference. The algorithm integrated well into surgical workflow, achieving median pixel-by-pixel errors of 4.77%, while maintaining good spectral and color reconstruction.Comment: 22 pages, 10 figure

Diversity analysis of released varieties of Indian cardamom using ISSR markers reveal narrowing genetic base

311-322Elettaria cardamomum Maton the small cardamom of commerce is a monotypic genus in India under the family Zingiberaceae. Genetic diversity studies using inter simple sequence repeat (ISSR) markers were conducted on a total of 13 released varieties of cardamom including selections and hybrids from different research stations in South India along with a popular variety Njallani and a wild relative Aframomum sps as checks. ISSR markers however, revealed relatively high level of genetic redundancy among the tested varieties with the exception of a few. Nonetheless, unweighted pair group method of arithmetic average (UPGMA) based cluster analysis of the similarity matrix differentiated all the varieties tested with the exception of two and segregated the wild relative Aframomum. Considerable reduction of polymorphism percentage was observed on exclusion of Aframomum while studying ISSR polymorphism which could be an indicator of the narrowing genetic base in the released varieties. Morphological data were compiled based on International Plant Genetic Resources Institute (IPGRI) cardamom descriptor and revealed moderate variability among the varieties. The results highlighted the requirement of molecular characterization of unutilized germplasm accessions, related wild species, and exotic relatives using specific molecular markers to help refine breeding efforts and introgression of new alleles for further improvement and enhancement of genetic base of cultivated cardamom

A new view of electrochemistry at highly oriented pyrolytic graphite

Major new insights on electrochemical processes at graphite electrodes are reported, following extensive investigations of two of the most studied redox couples, Fe(CN)64–/3– and Ru(NH3)63+/2+. Experiments have been carried out on five different grades of highly oriented pyrolytic graphite (HOPG) that vary in step-edge height and surface coverage. Significantly, the same electrochemical characteristic is observed on all surfaces, independent of surface quality: initial cyclic voltammetry (CV) is close to reversible on freshly cleaved surfaces (>400 measurements for Fe(CN)64–/3– and >100 for Ru(NH3)63+/2+), in marked contrast to previous studies that have found very slow electron transfer (ET) kinetics, with an interpretation that ET only occurs at step edges. Significantly, high spatial resolution electrochemical imaging with scanning electrochemical cell microscopy, on the highest quality mechanically cleaved HOPG, demonstrates definitively that the pristine basal surface supports fast ET, and that ET is not confined to step edges. However, the history of the HOPG surface strongly influences the electrochemical behavior. Thus, Fe(CN)64–/3– shows markedly diminished ET kinetics with either extended exposure of the HOPG surface to the ambient environment or repeated CV measurements. In situ atomic force microscopy (AFM) reveals that the deterioration in apparent ET kinetics is coupled with the deposition of material on the HOPG electrode, while conducting-AFM highlights that, after cleaving, the local surface conductivity of HOPG deteriorates significantly with time. These observations and new insights are not only important for graphite, but have significant implications for electrochemistry at related carbon materials such as graphene and carbon nanotubes

CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin

The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.</p

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain–behavior relationships after stroke

The goal of the Enhancing Neuroimaging Genetics through Meta‐Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well‐powered meta‐ and mega‐analytic approaches. ENIGMA Stroke Recovery has data from over 2,100 stroke patients collected across 39 research studies and 10 countries around the world, comprising the largest multisite retrospective stroke data collaboration to date. This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral and demographics data. Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large‐scale stroke lesion analysis are described, and challenges unique to this type of big data collaboration in stroke research are discussed. Finally, future directions and limitations, as well as recommendations for improved data harmonization through prospective data collection and data management, are provided

"If we use the strength of diversity among researchers we can only improve the quality and impact of our research": Issues of equality, diversity, inclusion, and transparency in the process of applying for research funding

This paper sets out the recommendations that have emerged from a six-month-long exploration and discussion of the processes that take place before research is submitted for funding: the ‘pre-award’ environment. Our work concentrated on how this environment is experienced by researchers at all career stages and from a variety of backgrounds, demographics, and disciplines, as well as by research managers and research support professionals. In the later stages of our exploration, representatives from research funders were also involved in the discussions. The primary component of this project was an analysis of pre-award activities and processes at UK universities, using information collated from workshops with researchers and research management and support staff. The findings of this analysis were presented as a workflow diagram, which was then used to surface issues relating to equality, diversity, inclusion, and transparency in context. The workflow diagram and the issues highlighted by it were used to structure discussions at a symposium for a range of research stakeholders, held in Bristol, UK, in January 2023. The recommendations set out in this paper are drawn from discussions that took place at that event. This paper is not an exhaustive landscape analysis, nor a review of existing research and practice in the area of pre-award processes or of recent thinking on the topics of equality, diversity, and inclusion (EDI). Instead, it aims to summarise and encapsulate the suggestions put forward by the stakeholders during the symposium. These recommendations, from experienced professionals working in the field, are based on their encounters with the issues raised in the project. They do not solely relate to those working on pre-award processes, but may also apply to funders, policymakers, university leaders, and professional associations, since many of the challenges flagged in our research are systemic and cultural, and reach far beyond the research office

Spinal Cord Atrophy Predicts Progressive Disease in Relapsing Multiple Sclerosis

Objective A major challenge in multiple sclerosis (MS) research is the understanding of silent progression and Progressive MS. Using a novel method to accurately capture upper cervical cord area from legacy brain MRI scans we aimed to study the role of spinal cord and brain atrophy for silent progression and conversion to secondary progressive disease (SPMS). Methods From a single-center observational study, all RRMS (n = 360) and SPMS (n = 47) patients and 80 matched controls were evaluated. RRMS patient subsets who converted to SPMS (n = 54) or silently progressed (n = 159), respectively, during the 12-year observation period were compared to clinically matched RRMS patients remaining RRMS (n = 54) or stable (n = 147), respectively. From brain MRI, we assessed the value of brain and spinal cord measures to predict silent progression and SPMS conversion. Results Patients who developed SPMS showed faster cord atrophy rates (-2.19%/yr) at least 4 years before conversion compared to their RRMS matches (-0.88%/yr, p &lt; 0.001). Spinal cord atrophy rates decelerated after conversion (-1.63%/yr, p = 0.010) towards those of SPMS patients from study entry (-1.04%). Each 1% faster spinal cord atrophy rate was associated with 69% (p &lt; 0.0001) and 53% (p &lt; 0.0001) shorter time to silent progression and SPMS conversion, respectively. Interpretation Silent progression and conversion to secondary progressive disease are predominantly related to cervical cord atrophy. This atrophy is often present from the earliest disease stages and predicts the speed of silent progression and conversion to Progressive MS. Diagnosis of SPMS is rather a late recognition of this neurodegenerative process than a distinct disease phase. ANN NEUROL 202

Impact of Rapid Urbanization on the Rates of Infection by Vibrio cholerae O1 and Enterotoxigenic Escherichia coli in Dhaka, Bangladesh

Bangladesh is a country where acute dehydrating diarrhea or cholera is common and is seen at least two times every year and additionally in natural disasters. In addition cholera cases have increased in the country, especially in urban settings such as in the capital city, Dhaka, where the number of hospitalized patients with more severe disease has tremendously increased. In the present observation, we have concentrated on determining the occurrence of diarrhoea caused by the two most common bacterial agents V. cholerae O1 and enterotoxigenic Escherichia coli (ETEC) in a densely populated, disease prone area Mirpur in Dhaka for two years from March 2008 to February 2010. Stool or rectal specimens from diarrheal patients coming to the ICDDR,B hospital from Mirpur were tested for the two bacterial pathogens. We found that V. cholerae O1 was the major bacterial pathogen and a cause of severe cholera disease in 23% of patients (2,647 of a total of 11,395 patients) from Mirpur. We surmise that cholera vaccines, as well as other public health tools that can target such high risk groups in the country, will be able to reduce the disease morbidity and the transmission of pathogens to improve the quality of life in urban settings

Lightfield hyperspectral imaging in neuro-oncology surgery: an IDEAL 0 and 1 study

IntroductionHyperspectral imaging (HSI) has shown promise in the field of intra-operative imaging and tissue differentiation as it carries the capability to provide real-time information invisible to the naked eye whilst remaining label free. Previous iterations of intra-operative HSI systems have shown limitations, either due to carrying a large footprint limiting ease of use within the confines of a neurosurgical theater environment, having a slow image acquisition time, or by compromising spatial/spectral resolution in favor of improvements to the surgical workflow. Lightfield hyperspectral imaging is a novel technique that has the potential to facilitate video rate image acquisition whilst maintaining a high spectral resolution. Our pre-clinical and first-in-human studies (IDEAL 0 and 1, respectively) demonstrate the necessary steps leading to the first in-vivo use of a real-time lightfield hyperspectral system in neuro-oncology surgery.MethodsA lightfield hyperspectral camera (Cubert Ultris ×50) was integrated in a bespoke imaging system setup so that it could be safely adopted into the open neurosurgical workflow whilst maintaining sterility. Our system allowed the surgeon to capture in-vivo hyperspectral data (155 bands, 350–1,000 nm) at 1.5 Hz. Following successful implementation in a pre-clinical setup (IDEAL 0), our system was evaluated during brain tumor surgery in a single patient to remove a posterior fossa meningioma (IDEAL 1). Feedback from the theater team was analyzed and incorporated in a follow-up design aimed at implementing an IDEAL 2a study.ResultsFocusing on our IDEAL 1 study results, hyperspectral information was acquired from the cerebellum and associated meningioma with minimal disruption to the neurosurgical workflow. To the best of our knowledge, this is the first demonstration of HSI acquisition with 100+ spectral bands at a frame rate over 1Hz in surgery.DiscussionThis work demonstrated that a lightfield hyperspectral imaging system not only meets the design criteria and specifications outlined in an IDEAL-0 (pre-clinical) study, but also that it can translate into clinical practice as illustrated by a successful first in human study (IDEAL 1). This opens doors for further development and optimisation, given the increasing evidence that hyperspectral imaging can provide live, wide-field, and label-free intra-operative imaging and tissue differentiation