CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early-stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 10 datasets from previously-characterized cell lines as compared to previous short and long-read based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

ecDNA hubs drive cooperative intermolecular oncogene expression.

Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.

Lung Cancer Diagnosis on Virtual Histologically Stained Tissue Using Weakly Supervised Learning.

Lung adenocarcinoma (LUAD) is the most common primary lung cancer and accounts for 40% of all lung cancer cases. The current gold standard for lung cancer analysis is based on the pathologists' interpretation of hematoxylin and eosin (H&E)-stained tissue slices viewed under a brightfield microscope or a digital slide scanner. Computational pathology using deep learning has been proposed to detect lung cancer on histology images. However, the histological staining workflow to acquire the H&E-stained images and the subsequent cancer diagnosis procedures are labor-intensive and time-consuming with tedious sample preparation steps and repetitive manual interpretation, respectively. In this work, we propose a weakly supervised learning method for LUAD classification on label-free tissue slices with virtual histological staining. The autofluorescence images of label-free tissue with histopathological information can be converted into virtual H&E-stained images by a weakly supervised deep generative model. For the downstream LUAD classification task, we trained the attention-based multiple-instance learning model with different settings on the open-source LUAD H&E-stained whole-slide images (WSIs) dataset from the Cancer Genome Atlas (TCGA). The model was validated on the 150 H&E-stained WSIs collected from patients in Queen Mary Hospital and Prince of Wales Hospital with an average area under the curve (AUC) of 0.961. The model also achieved an average AUC of 0.973 on 58 virtual H&E-stained WSIs, comparable to the results on 58 standard H&E-stained WSIs with an average AUC of 0.977. The attention heatmaps of virtual H&E-stained WSIs and ground-truth H&E-stained WSIs can indicate tumor regions of LUAD tissue slices. In conclusion, the proposed diagnostic workflow on virtual H&E-stained WSIs of label-free tissue is a rapid, cost effective, and interpretable approach to assist clinicians in postoperative pathological examinations. The method could serve as a blueprint for other label-free imaging modalities and disease contexts.

Mailed Letter Versus Phone Call to Increase Diabetic-Related Retinopathy Screening Engagement by Patients in a Team-Based Primary Care Practice: Prospective, Single-Masked, Randomized Trial.

BACKGROUND: Vision loss from diabetic-related retinopathy (DR) is preventable through regular screening. OBJECTIVE: The purpose of this study was to test different patient engagement approaches to expand a teleophthalmology program at a primary care clinic in the city of Toronto, Canada. METHODS: A teleophthalmology program was set up in a large, urban, academic, team-based primary care practice. Patients older than 18 years with type 1 or type 2 diabetes were randomized to one of the following 4 engagement strategies: phone call, mail, mail plus phone call, or usual care. Outreach was conducted by administrative staff within the clinic. The primary outcome was booking an appointment for DR screening. RESULTS: A total of 23 patients in the phone, 28 in the mail, 32 in the mail plus phone call, and 27 in the control (usual care) group were included in the analysis. After the intervention and after excluding patients who said they were screened, 88% (15/17) of patients in the phone, 11% (2/18) in the mail, and 100% (21/21) in the mail and phone group booked an appointment with the teleophthalmology program compared to 0% (0/12) in the control group. Phoning patients positively predicted patients booking a teleophthalmology appointment (P<.001), whereas mailing a letter had no effect. CONCLUSIONS: Patient engagement to book DR screening via teleophthalmology in an urban, academic, team-based primary care practice using telephone calls was much more effective than patient engagement using letters or usual care. Practices that have access to a local DR screening program and have resources for such engagement strategies should consider using them as a means to improve their DR screening rates. TRIAL REGISTRATION: ClinicalTrials.gov NCT03927859; https://clinicaltrials.gov/ct2/show/NCT03927859.

Impact of virtual visits on primary care physician work flows.

OBJECTIVE: To understand the impact of virtual visits on primary care physician (PCP) work flows. DESIGN: Qualitative semistructured interviews. SETTING: Primary care practices within 5 regions in southern Ontario. PARTICIPANTS: Physicians representing primary care practices of various sizes and remuneration models (eg, capitation and fee-for-service models). METHODS: Interviews were conducted with PCPs involved in a large-scale pilot project implementing virtual visits (via a Web-based application) into clinical practices. Convenience and purposive sampling were used to recruit PCPs between January 2018 and March 2019. To obtain a representative sample, participants were sought from a variety of practice types and geographic regions. High and low users of virtual visits were included. Interviews were audiorecorded and transcribed. An inductive thematic analysis was used to identify prominent themes and subthemes. MAIN FINDINGS: Twenty-six physicians were interviewed (n=15 using convenience sampling and n=11 through purposive sampling). Four themes were identified: PCPs employ diverse approaches to integrate virtual care into their work flow; PCPs recognize that implementing virtual visits requires upfront time and effort but have variable perceptions regarding long-term impact of virtual care on processes; asynchronous messaging is preferable to synchronous audio or video visits; and strategies were identified to improve the integration of virtual visits. CONCLUSION: The potential of virtual care to improve work flow is dependent on the way these visits are implemented and used. Dedicated time for implementation, emphasis on using asynchronous secure messaging, and access to clinical champions and structured change management support were associated with more seamless integration of virtual visits.

Redesigning primary care: Provider perspectives on the clinical utility of virtual visits.

OBJECTIVE: To explore primary care physician (PCP) perspectives on the clinical utility of virtual visits. DESIGN: Qualitative design involving semistructured interviews. SETTING: Primary care practices within 5 regions in southern Ontario. PARTICIPANTS: Primary care physicians representing different practice sizes and remuneration models. METHODS: Interviews were conducted with PCPs who were involved in a large-scale pilot implementation of virtual visits (patient-provider asynchronous messaging, or synchronous audio or video communication). The first phase involved a convenience sample of users in the first 2 regions where the pilot was initiated; after implementation in all 5 regions, purposive sampling was used to ensure diversity within the sample (eg, physicians representing different use frequencies of virtual visits, regions, and remuneration models). Interviews were audiorecorded and transcribed. An inductive thematic analysis was used to identify prominent themes and subthemes. MAIN FINDINGS: Twenty-six physicians were interviewed. Fifteen were recruited using convenience sampling and 11 through purposive sampling. Four themes regarding the clinical utility of virtual visits were identified: virtual visits can effectively resolve many patient concerns, with some variation in PCP comfort using virtual visits for specific conditions; virtual visits are beneficial for a range of patients but some patients might overuse or inappropriately use them; PCPs prefer to use asynchronous messaging (eg, text or online messaging) because of its convenience and flexibility; and virtual visits can provide value at the patient, provider, and health system levels. CONCLUSION: While participants believed that virtual visits can be appropriately used to resolve a variety of clinical concerns, they found in practice that virtual visits are fundamentally different from face-to-face encounters. Professional guidelines on appropriate use cases should be established to develop a standard framework for virtual care.

Plantar Pressure Variability and Asymmetry in Elderly Performing 60-Minute Treadmill Brisk-Walking: Paving the Way towards Fatigue-Induced Instability Assessment Using Wearable In-Shoe Pressure Sensors.

Evaluation of potential fatigue for the elderly could minimize their risk of injury and thus encourage them to do more physical exercises. Fatigue-related gait instability was often assessed by the changes of joint kinematics, whilst planar pressure variability and asymmetry parameters may complement and provide better estimation. We hypothesized that fatigue condition (induced by the treadmill brisk-walking task) would lead to instability and could be reflected by the variability and asymmetry of plantar pressure. Fifteen elderly adults participated in the 60-min brisk walking trial on a treadmill without a pause, which could ensure that the fatigue-inducing effect is continuous and participants will not recover halfway. The plantar pressure data were extracted at baseline, the 30th minute, and the 60th minute. The median of contact time, peak pressure, and pressure-time integrals in each plantar region was calculated, in addition to their asymmetry and variability. After 60 min of brisk walking, there were significant increases in peak pressure at the medial and lateral arch regions, and central metatarsal regions, in addition to their impulses (p < 0.05). In addition, the variability of plantar pressure at the medial arch was significantly increased (p < 0.05), but their asymmetry was decreased. On the other hand, the contact time was significantly increased at all plantar regions (p < 0.05). The weakened muscle control and shock absorption upon fatigue could be the reason for the increased peak pressure, impulse, and variability, while the improved symmetry and prolonged plantar contact time could be a compensatory mechanism to restore stability. The outcome of this study can facilitate the development of gait instability or fatigue assessment using wearable in-shoe pressure sensors.

Identifying Fatigue Indicators Using Gait Variability Measures: A Longitudinal Study on Elderly Brisk Walking.

Real-time detection of fatigue in the elderly during physical exercises can help identify the stability and thus falling risks which are commonly achieved by the investigation of kinematic parameters. In this study, we aimed to identify the change in gait variability parameters from inertial measurement units (IMU) during a course of 60 min brisk walking which could lay the foundation for the development of fatigue-detecting wearable sensors. Eighteen elderly people were invited to participate in the brisk walking trials for 60 min with a single IMU attached to the posterior heel region of the dominant side. Nine sets of signals, including the accelerations, angular velocities, and rotation angles of the heel in three anatomical axes, were measured and extracted at the three walking times (baseline, 30th min, and 60th min) of the trial for analysis. Sixteen of eighteen participants reported fatigue after walking, and there were significant differences in the median acceleration (p = 0.001), variability of angular velocity (p = 0.025), and range of angle rotation (p = 0.0011), in the medial-lateral direction. In addition, there were also significant differences in the heel pronation angle (p = 0.005) and variability and energy consumption of the angles in the anterior-posterior axis (p = 0.028, p = 0.028), medial-lateral axis (p = 0.014, p = 0.014), and vertical axis (p = 0.002, p < 0.001). Our study demonstrated that a single IMU on the posterior heel of the dominant side can address the variability of kinematics parameters for elderly performing prolonged brisk walking and could serve as an indicator for walking instability, and thus fatigue.

Overexpression of iASPP is required for autophagy in response to oxidative stress in choriocarcinoma.

BACKGROUND: Gestational trophoblastic disease (GTD) is a heterogeneous group of diseases developed from trophoblasts. ASPP (Ankyrin-repeat, SH3-domain and proline-rich region containing protein) family proteins, ASPP1 and ASPP2, have been reported to be dysregulated in GTD. They modulate p53 activities and are responsible for multiple cellular processes. Nevertheless, the functional role of the ASPP family inhibitory member, iASPP, is not well characterized in GTD. METHODS: To study the functional role of iASPP in GTD, trophoblastic tissues from normal placentas, hydatidiform mole (HM) and choriocarcinoma were used for immunohistochemistry, whereas siRNAs were used to manipulate iASPP expression in choriocarcinoma cell lines and study the subsequent molecular changes. RESULTS: We demonstrated that iASPP was overexpressed in both HM and choriocarcinoma when compared to normal placenta. Progressive increase in iASPP expression from HM to choriocarcinoma suggests that iASPP may be related to the development of trophoblastic malignancy. High iASPP expression in HM was also significantly associated with a high expression of autophagy-related protein LC3. Interestingly, iASPP silencing retarded the growth of choriocarcinoma through senescence instead of induction of apoptosis. LC3 expression decreased once iASPP was knocked down, suggesting a downregulation on autophagy. This may be due to iASPP downregulation rendered decrease in Atg5 expression and concomitantly hindered autophagy in choriocarcinoma cells. Autophagy inhibition per se had no effect on the growth of choriocarcinoma cells but increased the susceptibility of choriocarcinoma cells to oxidative stress, implying a protective role of iASPP against oxidative stress through autophagy in choriocarcinoma. CONCLUSIONS: iASPP regulates growth and the cellular responses towards oxidative stress in choriocarcinoma cells. Its overexpression is advantageous to the pathogenesis of GTD. (266 words).

A Web-Based Mental Health Platform for Individuals Seeking Specialized Mental Health Care Services: Multicenter Pragmatic Randomized Controlled Trial.

BACKGROUND: Web-based self-directed mental health applications are rapidly emerging to address health service gaps and unmet needs for information and support. OBJECTIVE: The aim of this study was to determine if a multicomponent, moderated Web-based mental health application could benefit individuals with mental health symptoms severe enough to warrant specialized mental health care. METHODS: A multicenter, pragmatic randomized controlled trial was conducted across several outpatient mental health programs affiliated with 3 hospital programs in Ontario, Canada. Individuals referred to or receiving treatment, aged 16 years or older, with access to the internet and an email address, and having the ability to navigate a Web-based mental health application were eligible. A total of 812 participants were randomized 2:1 to receive immediate (immediate treatment group, ITG) or delayed (delayed treatment group, DTG) access for 3 months to the Big White Wall (BWW), a multicomponent Web-based mental health intervention based in the United Kingdom and New Zealand. The primary outcome was the total score on the Recovery Assessment Scale, revised (RAS-r) which measures mental health recovery. Secondary outcomes were total scores on the Patient Health Questionnaire-9 item (PHQ-9), the Generalized Anxiety Disorder Questionnaire-7 item (GAD-7), the EuroQOL 5-dimension quality of life questionnaire (EQ-5D-5L), and the Community Integration Questionnaire. An exploratory analysis examined the association between actual BWW use (categorized into quartiles) and outcomes among study completers. RESULTS: Intervention participants achieved small, statistically significant increases in adjusted RAS-r score (4.97 points, 95% CI 2.90 to 7.05), and decreases in PHQ-9 score (-1.83 points, 95% CI -2.85 to -0.82) and GAD-7 score (-1.55 points, 95% CI -2.42 to -0.70). Follow-up was achieved for 55% (446/812) at 3 months, 48% (260/542) of ITG participants and 69% (186/270) of DTG participants. Only 58% (312/542) of ITG participants logged on more than once. Some higher BWW user groups had significantly greater improvements in PHQ-9 and GAD-7 relative to the lowest use group. CONCLUSIONS: The Web-based application may be beneficial; however, many participants did not engage in an ongoing way. This has implications for patient selection and engagement as well as delivery and funding structures for similar Web-based interventions. TRIAL REGISTRATION: ClinicalTrials.gov NCT02896894; https://clinicaltrials.gov/ct2/show/NCT02896894 (Archived by WebCite at http://www.webcitation.org/78LIpnuRO).

Exploring the utility and scalability of a telehomecare intervention for patients with chronic kidney disease undergoing peritoneal dialysis-a study protocol.

BACKGROUND: Chronic Kidney Disease (CKD) is a pressing global health concern that is placing increased strain on health care resources. CKD patients regularly receive peritoneal dialysis as a common CKD treatment. An emerging technological solution is telehomecare as way to support patients receiving PD in their homes. This study protocol outlines a mixed methods evaluation exploring a telehomecare developed to enhance CKD patients' outcomes and experiences. The study aims to assess the usability, acceptability and scalability of this virtual care application. METHODS: A realist evaluation using an embedded case study design will be used to understand the usability, acceptability and scalability of a telehomecare application for patients with CKD undergoing PD. The realist evaluation that is further described in this paper is part of a larger evaluation of the eQ Connect™ intervention that includes a randomized, parallel-arm control trial aimed at determining if utilizing eQ Connect improves selected clinical outcomes for PD patients (CONNECT Trial). DISCUSSION: Potential implications of this study include elucidating which components of the intervention are most effective and under what conditions with a focus on the contextual influences. Collectively, our multi-method design will yield knowledge around how best to implement, sustain and spread the telehomecare application that will be useful to guide the development, implementation and evaluation of future virtual care applications aimed at improving the quality of care outcomes and experiences of patients. TRIAL REGISTRATION: NCT02670512 . Registered: January 18, 2016.

Principles for Health System Capacity Planning: Insights for Healthcare Leaders.

Jurisdictions across Canada and around the world face the challenge of planning high-performing and sustainable health systems in response to growing healthcare demands. In this paper, we report on the process of developing principles for health system capacity planning by the Ministry of Health and Long-Term Care in Ontario. Integrating the results of a literature review on health system planning and a symposium with representatives from local health integration networks, we describe the following six principles in detail: (1) develop an aspirational vision, (2) establish clear leadership, (3) commit to stakeholder engagement, (4) engage patients and the public, (5) build analytics infrastructure and (6) revise policy when necessary.

A pragmatic randomized control trial and realist evaluation on the implementation and effectiveness of an internet application to support self-management among individuals seeking specialized mental health care: a study protocol.

BACKGROUND: Mental illness is a substantial and rising contributor to the global burden of disease. Access to and utilization of mental health care, however, is limited by structural barriers such as specialist availability, time, out-of-pocket costs, and attitudinal barriers including stigma. Innovative solutions like virtual care are rapidly entering the health care domain. The advancement and adoption of virtual care for mental health, however, often occurs in the absence of rigorous evaluation and adequate planning for sustainability and spread. METHODS: A pragmatic randomized controlled trial with a nested comparative effectiveness arm, and concurrent realist process evaluation to examine acceptability, effectiveness, and cost-effectiveness of the Big White Wall (BWW) online platform for mental health self-management and peer support among individuals aged 16 and older who are accessing mental health services in Ontario, Canada. Participants will be randomized to 3 months of BWW or treatment as usual. At the end of the 3 months, participants in the intervention group will have the opportunity to opt-in to an intervention extension arm. Those who opt-in will be randomized to receive an additional 3 months of BWW or no additional intervention. The primary outcome is recovery at 3 months as measured by the Recovery Assessment Scale-revised (RAS-r). Secondary outcomes include symptoms of depression and anxiety measured with the Personal Health Questionnaire-9 item (PHQ-9) and the Generalized Anxiety Disorder Questionnaire-7 item (GAD-7) respectively, quality of life measured with the EQ-5D-5L, and community integration assessed with the Community Integration Questionnaire. Cost-effectiveness evaluations will account for the cost of the intervention and direct health care costs. Qualitative interviews with participants and stakeholders will be conducted throughout. DISCUSSION: Understanding the impact of virtual strategies, such as BWW, on patient outcomes and experience, and health system costs is essential for informing whether and how health system decision-makers can support these strategies system-wide. This requires clear evidence of effectiveness and an understanding of how the intervention works, for whom, and under what circumstances. This study will produce such effectiveness data for BWW, while simultaneously exploring the characteristics and experiences of users for whom this and similar online interventions could be helpful. TRIAL REGISTRATION: Clinicaltrials.gov NCT02896894 . Registered on 31 August 2016 (retrospectively registered).

Screening Algorithm for BK Virus-Associated Nephropathy Using Sequential Testing of Urinary Cytology: A Probabilistic Model Analysis.

BACKGROUND: Incorporating urinary cytology in BK virus (BKV) screening algorithm potentially reduces the screening cost for BK viral nephropathy. We aimed to evaluate the test performances and screening cost of sequential 2-stage screening consisting of urine cytology followed by BKV serum quantitative polymerase chain reaction (PCR). METHODS: Ninety-five kidney transplant recipients who had BKV serum quantitative PCR/urine cytology tested and verified with histopathology (the reference gold standard) were included. A probabilistic model was constructed to evaluate the test performance and screening cost of 2-stage screening, and was compared with screening with urine cytology or serum viral load alone. RESULTS: At a viral load threshold of ≥104 copies/ml, the sensitivity and specificity of quantitative PCR alone were 83% (95% CI 69-96) and 91% (95% CI 83-97), respectively. The sensitivity and specificity of urine cytology alone were 91% (95% CI 79-100) and 74% (95% CI 60-91), respectively. Sequential 2-stage screening resulted in loss in sensitivity but a net gain in specificity (viral load threshold ≥104 copies/ml - sensitivity, 75% (95% CI 60-91); specificity, 98% (95% CI 95-99)). Two-stage screening also had superior positive predictive value and is cost effective when BKV-associated nephropathy prevalence is below 94%. CONCLUSIONS: Our study had demonstrated a favorable test performance and cost efficiency of 2-stage BKV screening.

Exceeding the limit for microscopic image translation with a deep learning-based unified framework.

Deep learning algorithms have been widely used in microscopic image translation. The corresponding data-driven models can be trained by supervised or unsupervised learning depending on the availability of paired data. However, general cases are where the data are only roughly paired such that supervised learning could be invalid due to data unalignment, and unsupervised learning would be less ideal as the roughly paired information is not utilized. In this work, we propose a unified framework (U-Frame) that unifies supervised and unsupervised learning by introducing a tolerance size that can be adjusted automatically according to the degree of data misalignment. Together with the implementation of a global sampling rule, we demonstrate that U-Frame consistently outperforms both supervised and unsupervised learning in all levels of data misalignments (even for perfectly aligned image pairs) in a myriad of image translation applications, including pseudo-optical sectioning, virtual histological staining (with clinical evaluations for cancer diagnosis), improvement of signal-to-noise ratio or resolution, and prediction of fluorescent labels, potentially serving as new standard for image translation.

Deep learning-assisted low-cost autofluorescence microscopy for rapid slide-free imaging with virtual histological staining.

Slide-free imaging techniques have shown great promise in improving the histological workflow. For example, computational high-throughput autofluorescence microscopy by pattern illumination (CHAMP) has achieved high resolution with a long depth of field, which, however, requires a costly ultraviolet laser. Here, simply using a low-cost light-emitting diode (LED), we propose a deep learning-assisted framework of enhanced widefield microscopy, termed EW-LED, to generate results similar to CHAMP (the learning target). Comparing EW-LED and CHAMP, EW-LED reduces the cost by 85×, shortening the image acquisition time and computation time by 36× and 17×, respectively. This framework can be applied to other imaging modalities, enhancing widefield images for better virtual histology.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss.

Synaptic plasticity is obstructed by pathogenic tau in the brain, representing a key mechanism that underlies memory loss in Alzheimer's disease (AD) and related tauopathies. Here, we found that reduced levels of the memory-associated protein KIdney/BRAin (KIBRA) in the brain and increased KIBRA protein levels in cerebrospinal fluid are associated with cognitive impairment and pathological tau levels in disease. We next defined a mechanism for plasticity repair in vulnerable neurons using the C-terminus of the KIBRA protein (CT-KIBRA). We showed that CT-KIBRA restored plasticity and memory in transgenic mice expressing pathogenic human tau; however, CT-KIBRA did not alter tau levels or prevent tau-induced synapse loss. Instead, we found that CT-KIBRA stabilized the protein kinase Mζ (PKMζ) to maintain synaptic plasticity and memory despite tau-mediated pathogenesis. Thus, our results distinguished KIBRA both as a biomarker of synapse dysfunction and as the foundation for a synapse repair mechanism to reverse cognitive impairment in tauopathy.

A review on the effectiveness of repetitive transcranial magnetic stimulation (rTMS) on post-stroke aphasia.

BACKGROUND: This evidence-based review reports an updated evaluation and critical appraisal of available studies that investigated the effectiveness of repetitive transcranial magnetic stimulation (rTMS) on post-stroke aphasia rehabilitation. METHODS: A literature search was performed to identify studies that investigated the therapeutic effects of rTMS on post-stroke aphasia in various electronic databases, from their inception to 2011. The selected studies were classified according to the types of participants, types of interventions, outcome measures, and results. The methodological qualities of the selected studies were evaluated using the Physiotherapy Evidence Database scale. RESULTS: The current review was based on 12 studies, including open-label designs and controlled trials, that showed a positive effect of rTMS, with or without conventional rehabilitation, on post-stroke aphasia compared with sham or conventional rehabilitation alone. About 41% of the selected studies reported the long-term effect of rTMS on aphasia recovery. No adverse effect was reported. CONCLUSIONS: The current review reveals that rTMS with or without conventional rehabilitation has positive effects on post-stroke aphasia. The studies also contributed to the plausible mechanisms of stroke recovery. However, with the concerns over the methodology of the selected studies in this review, a larger-scale, multicenter, well-designed randomized controlled trial involving different phases and types of aphasia needs to be carried out before recommending rTMS as a complementary treatment for post-stroke aphasia.

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.