Multi-Cancer Computational Analysis Reveals Metastasis-Associated Variant of Desmoplastic Reaction Involving INHBA and THBS2

Despite extensive research, the details of the metastasis-associated biological mechanisms are largely unknown. Here, we analyze data from multiple cancers using a novel computational method identifying sets of genes whose coordinated overexpression indicates the presence of a particular phenotype. We conclude that there is one shared “core” metastasis-associated gene expression signature corresponding to a specific variant of desmoplastic reaction, present in a large subset of samples that have exceeded a threshold of invasive transition specific to each cancer, indicating that the biological mechanism is triggered at that point. For example this threshold is reached at stage IIIc in ovarian cancer and at stage II in colorectal cancer. It has several features, such as coordinated expression of particular collagens, mainly COL11A1 and other genes, mainly THBS2 and INHBA. The universally prominent presence of INHBA in all cancers strongly suggests a biological mechanism centered on activin A induced TGF-β signaling, because activin A is a member of the TGF-β superfamily consisting of an INHBA homodimer. It is accompanied by the expression of several transcription factors related to epithelial-mesenchymal transition, but not of SNAI1, and expression of E-cadherin is not downregulated. It is reversible, as evidenced by its absence in many matched metastasized samples, but its presence indicates that metastasis has occurred. Therefore, these results can be used for developing high-specificity biomarkers, as well as potential multi-cancer metastasis-inhibiting therapeutics targeting the corresponding biological mechanism

A comparison of rotary- and stationary-head tape recorders

Digital recording may take advantage of many types of media, but usually a preferred type of drive or transport emerges for each. In magnetic tape recording, two approaches have emerged in which essentially the same medium is tracked in two radically different ways. This paper compares the characteristics of Rotary- and Stationary-Head transports in an attempt to establish which approach might be considered for a given application. The conclusion is that in many cases there is no obvious choice based on recording physics and that often the choice will be made on the experimental knowledge of the designer

A haplotype inference algorithm for trios based on deterministic sampling

In genome-wide association studies, thousands of individuals are genotyped in hundreds of thousands of single nucleotide polymorphisms (SNPs). Statistical power can be increased when haplotypes, rather than three-valued genotypes, are used in analysis, so the problem of haplotype phase inference (phasing) is particularly relevant. Several phasing algorithms have been developed for data from unrelated individuals, based on different models, some of which have been extended to father-mother-child "trio" data. We introduce a technique for phasing trio datasets using a tree-based deterministic sampling scheme. We have compared our method with publicly available algorithms PHASE v2.1, BEAGLE v3.0.2 and 2SNP v1.7 on datasets of varying number of markers and trios. We have found that the computational complexity of PHASE makes it prohibitive for routine use; on the other hand 2SNP, though the fastest method for small datasets, was significantly inaccurate. We have shown that our method outperforms BEAGLE in terms of speed and accuracy for small to intermediate dataset sizes in terms of number of trios for all marker sizes examined. Our method is implemented in the "Tree-Based Deterministic Sampling" (TDS) package, available for download at http://www.ee.columbia.edu/~anastas/tds Using a Tree-Based Deterministic sampling technique, we present an intuitive and conceptually simple phasing algorithm for trio data. The trade off between speed and accuracy achieved by our algorithm makes it a strong candidate for routine use on trio datasets

On the Winds of Change: Repositories, Researchers and Technologies: The 18th Health Sciences Lively Lunch Discussion

This year’s sponsored but no holds barred health sciences lively lunchtime gathering again was open to all. Moderator Jean Gudenas introduced this year’s three presentations: a report on a survey, a report on a research study, and a technology update. Ramune Kubilius provided a brief annual traditional update on developments in the health sciences publishing world. She then segued to highlighting some findings from a survey she and two co-authors conducted in December 2017-January 2018 of AAHSL (Association of Academic Health Sciences Libraries) members on medical school institutional repositories (IRs). She focused on responses to questions about IR collections and management. Are early career researchers the harbingers of change? Anthony Watkinson shared some findings from a three year (2015-2018) worldwide CIBER longitudinal research study of early career researchers that was commissioned by the Publishing Research Consortium. He focused on highlighting what medical researchers in countries, including the U.S., where surveys were conducted, think about scholarly communications and scholarly publishing. Does the RA21 project hold promise for keeping access secure in the future? John Felts began with a background and a review of some current technologies. He then provided some insights as to what expectations we can have from initiatives such as RA21, with its mission: “to align and simplify pathways to subscribed content across participating scientific platforms…

How can healthcare organisations improve the social determinants of health for their local communities? Findings from realist-informed case studies among secondary healthcare organisations in England

Objectives Increasingly, healthcare and public health strategists invite us to look at healthcare organisations as not just care providers but as anchor institutions (ie, large community-rooted organisations with significant impact in the local economy, social fabric and overall community well-being). In response, this study explores the mechanisms through which healthcare organisations can impact social determinants of health and communities in their local areas.Design We conducted case studies with interviews and synthesised the findings using a realist approach to produce a set of explanations (programme theory) of how healthcare organisations can have a positive impact on the overall well-being of local communities by operating as anchor institutions.Setting Secondary healthcare organisations in England, including mental health and community services.Participants Staff from case study sites which were directly employed or actively engaged in the organisation’s anchor institution strategy. Data collection took place from early June to the end of August 2023.Results We found four building blocks for effective anchor activity including employment, spending, estates and sustainability. Healthcare organisations—as anchor institutions—can improve the social determinants of health for their local communities through enabling accessible paths for local community recruitment and career progression; empowering local businesses to join supply chains boosting income and wealth; transforming organisational spaces into community assets; and supporting local innovation and technology to achieve their sustainability goals. These blocks need to be integrated across organisations on the basis of a population health approach promoted by supportive leadership, and in collaboration with a diverse range of local partners.Conclusions Healthcare organisations have the potential for a positive impact on the overall well-being of local communities. Policymakers should support healthcare organisations to leverage employment, spending, estates and sustainability to help address the unequal distribution of the social determinants of health

Research to support the British Library's work on emerging formats

A report for the British Library examining the issues around the legal deposit and preservation of apps, interactive narratives and databases

Audio Guidance to Enable Vision-Impaired Individuals to Move Independently

At present, when an individual who is blind or has low-vision runs or walks for exercise, they might use a treadmill, rely on a guide dog, or use a tethered human guide. Independent and safe exercise, whether walking or running, is one way to increase personal agency and improve the quality of life for vision-impaired persons. This disclosure describes techniques that use on-device machine learning to enable a vision-impaired individual to independently walk or run, e.g., for exercise. A tape or guideline is painted along the running path. A mobile device camera detects the guideline. An app on the phone estimates the user\u27s position to the left or to the right of the guideline. The app provides audio cues in stereo to direct the person to stay in close proximity to the guideline while walking or running

Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype

Summary:We present a visualization tool applied on genome-wide association data, revealing disease-associated haplotypes, epistatically interacting loci, as well as providing visual signatures of multivariate correlations of genetic markers with respect to a phenotype

SenseMaker: Co-creating Sensors for Journalism

SenseMaker started with a simple question: what happens when journalists, engineers and communities come together to design and build sensors for storytelling? The project was underpinned by the desire to create new ‘sensing’ devices. These sensors would have a tangible benefit for journalists and storytellers who seek to capture data to reveal, drive or enhance stories in their communities. The core enquiry sought to understand how open collaborations, centred on research and development, can create new editorial opportunities, particularly when data, sensors and narratives combine. In short, the core to SenseMaker was: • To co-design journalism sensors • To use them to create, prompt, underpin and develop content • To provoke, prompt or challenge public debate Partners included the Media Innovation Studio and Engineering Innovation Centre teams at the University of Central Lancashire (UCLan) and Reach PLC, specifically with the involvement of the Manchester Evening News (MEN). This is our final project report

Organizational Alignment

There are many players in the scholarly communications space including librarians (current service/collections models), the academic institution (campus administration, research centers, colleges and departments), researchers (the professional field/discipline), and publishers of all stripes (commercial publishers, scholarly societies, university presses). What kinds of interactions do library publishers have with these various groups as they strive for organizational alignment and where are the most promising opportunities for future collaborations? This panel provides an overview of the variety of relationships library publishers engage in on and beyond their campuses to help move scholarly communications forward