Application of the ERS/ATS Spirometry Standards and Race-Neutral Equations in the COPDGene Study.

RATIONALE: The European Respiratory Society (ERS) and the American Thoracic Society (ATS) recommend using z-scores, and the ATS has recommended using Global Lung Initiative (GLI)- "Global" race-neutral reference equations for spirometry interpretation. However, these recommendations have been variably implemented and the impact has not been widely assessed, both in clinical and research settings. OBJECTIVES: We evaluated the ERS/ATS airflow obstruction severity classification. METHODS: In the COPDGene Study (n = 10,108), airflow obstruction has been defined as a forced expiratory volume in one second to forced vital capacity (FEV1/FVC) ratio <0.70, with spirometry severity graded from class 1 to 4 based on race-specific percent predicted (pp) FEV1 cut-points as recommended by the Global Initiative for Chronic Obstructive Lung Disease (GOLD). We compared the GOLD approach, using NHANES III race-specific equations, to the application of GLI-Global equations using the ERS/ATS definition of airflow obstruction as FEV1/FVC ratio < lower limit of normal (LLN) and z-FEV1 cut-points of -1.645, -2.5, and -4 ("zGLI Global"). We tested the four-tier severity scheme for association with COPD outcomes. MEASUREMENTS AND MAIN RESULTS: The lowest agreement between ERS/ATS with zGLI Global and the GOLD classification was observed in individuals with milder disease (56.9% and 42.5% in GOLD 1 and 2) and race was a major determinant of redistribution. After adjustment for relevant covariates, zGLI Global distinguished all-cause mortality risk between normal spirometry and the first grade of COPD (Hazard Ratio 1.23, 95% CI 1.04-1.44, p=0.014), and showed a linear increase in exacerbation rates with increasing disease severity, in comparison to GOLD. CONCLUSIONS: The zGLI Global severity classification outperformed GOLD in the discrimination of survival, exacerbations, and imaging characteristics.

Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions.

The versatility of cellular response arises from the communication, or crosstalk, of signaling pathways in a complex network of signaling and transcriptional regulatory interactions. Understanding the various mechanisms underlying crosstalk on a global scale requires untargeted computational approaches. We present a network-based statistical approach, MuXTalk, that uses high-dimensional edges called multilinks to model the unique ways in which signaling and regulatory interactions can interface. We demonstrate that the signaling-regulatory interface is located primarily in the intermediary region between signaling pathways where crosstalk occurs, and that multilinks can differentiate between distinct signaling-transcriptional mechanisms. Using statistically over-represented multilinks as proxies of crosstalk, we infer crosstalk among 60 signaling pathways, expanding currently available crosstalk databases by more than five-fold. MuXTalk surpasses existing methods in terms of model performance metrics, identifies additions to manual curation efforts, and pinpoints potential mediators of crosstalk. Moreover, it accommodates the inherent context-dependence of crosstalk, allowing future applications to cell type- and disease-specific crosstalk.

Industrial Graphene Coating of Low-Voltage Copper Wires for Power Distribution.

Copper (Cu) is the electrical conductor of choice in many categories of electrical wiring, with household and building installation being the major market of this metal. This work demonstrates the coating of Cu wires-with diameters relevant for low-voltage (LV) applications-with graphene. The chemical vapor deposition (CVD) coating process is rapid, safe, scalable, and industrially compatible. Graphene-coated Cu wires display good oxidation resistance and increased electrical conductivity (up to 1% immediately after coating and up to 3% after 24 months), allowing for wire diameter reduction and thus significant savings in wire production costs. Combined spectroscopic and diffraction analysis indicates that the conductivity increase is due to a change in Cu crystallinity induced by the coating process conditions, while electrical testing of aged wires shows that graphene plays a major role in maintaining improved electrical performances over long periods of time. Finally, graphene coating of Cu wires using an ambient-pressure roll-to-roll (R2R) CVD reactor is demonstrated. This enables the in-line production of graphene-coated metallic wires as required for industrial scale-up.

Scalable High-Mobility Graphene/hBN Heterostructures.

Graphene-hexagonal boron nitride (hBN) scalable heterostructures are pivotal for the development of graphene-based high-tech applications. In this work, we demonstrate the realization of high-quality graphene-hBN heterostructures entirely obtained with scalable approaches. hBN continuous films were grown via ion beam-assisted physical vapor deposition directly on commercially available SiO2/Si and used as receiving substrates for graphene single-crystal matrixes grown by chemical vapor deposition on copper. The structural, chemical, and electronic properties of the heterostructure were investigated by atomic force microscopy, Raman spectroscopy, and electrical transport measurements. We demonstrate graphene carrier mobilities exceeding 10,000 cm2/Vs in ambient conditions, 30% higher than those directly measured on SiO2/Si. We prove the scalability of our approach by measuring more than 100 transfer length method devices over a centimeter scale, which present an average carrier mobility of 7500 ± 850 cm2/Vs. The reported high-quality all-scalable heterostructures are of relevance for the development of graphene-based high-performing electronic and optoelectronic applications.

Assessment of community efforts to advance network-based prediction of protein-protein interactions.

Comprehensive understanding of the human protein-protein interaction (PPI) network, aka the human interactome, can provide important insights into the molecular mechanisms of complex biological processes and diseases. Despite the remarkable experimental efforts undertaken to date to determine the structure of the human interactome, many PPIs remain unmapped. Computational approaches, especially network-based methods, can facilitate the identification of previously uncharacterized PPIs. Many such methods have been proposed. Yet, a systematic evaluation of existing network-based methods in predicting PPIs is still lacking. Here, we report community efforts initiated by the International Network Medicine Consortium to benchmark the ability of 26 representative network-based methods to predict PPIs across six different interactomes of four different organisms: A. thaliana, C. elegans, S. cerevisiae, and H. sapiens. Through extensive computational and experimental validations, we found that advanced similarity-based methods, which leverage the underlying network characteristics of PPIs, show superior performance over other general link prediction methods in the interactomes we considered.

Biological Random Walks: multi-omics integration for disease gene prioritization.

MOTIVATION: Over the past decade, network-based approaches have proven useful in identifying disease modules within the human interactome, often providing insights into key mechanisms and guiding the quest for therapeutic targets. This is all the more important, since experimental investigation of potential gene candidates is an expensive task, thus not always a feasible option. On the other hand, many sources of biological information exist beyond the interactome and an important research direction is the design of effective techniques for their integration. RESULTS: In this work, we introduce the Biological Random Walks (BRW) approach for disease gene prioritization in the human interactome. The proposed framework leverages multiple biological sources within an integrated framework. We perform an extensive, comparative study of BRW's performance against well-established baselines. AVAILABILITY AND IMPLEMENTATION: All codes are publicly available and can be downloaded at https://github.com/LeoM93/BiologicalRandomWalks. We used publicly available datasets, details on their retrieval and preprocessing are provided in the Supplementary Material. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ultra-clean high-mobility graphene on technologically relevant substrates.

Graphene grown via chemical vapour deposition (CVD) on copper foil has emerged as a high-quality, scalable material, that can be easily integrated on technologically relevant platforms to develop promising applications in the fields of optoelectronics and photonics. Most of these applications require low-contaminated high-mobility graphene (i.e., approaching 10 000 cm2 V-1 s-1 at room temperature) to reduce device losses and implement compact device design. To date, these mobility values are only obtained when suspending or encapsulating graphene. Here, we demonstrate a rapid, facile, and scalable cleaning process, that yields high-mobility graphene directly on the most common technologically relevant substrate: silicon dioxide on silicon (SiO2/Si). Atomic force microscopy (AFM) and spatially-resolved X-ray photoelectron spectroscopy (XPS) demonstrate that this approach is instrumental to rapidly eliminate most of the polymeric residues which remain on graphene after transfer and fabrication and that have adverse effects on its electrical properties. Raman measurements show a significant reduction of graphene doping and strain. Transport measurements of 50 Hall bars (HBs) yield hole mobility µh up to ∼9000 cm2 V-1 s-1 and electron mobility µe up to ∼8000 cm2 V-1 s-1, with average values µh ∼ 7500 cm2 V-1 s-1 and µe ∼ 6300 cm2 V-1 s-1. The carrier mobility of ultraclean graphene reaches values nearly double than those measured in graphene processed with acetone cleaning, which is the method widely adopted in the field. Notably, these mobility values are obtained over large-scale and without encapsulation, thus paving the way to the adoption of graphene in optoelectronics and photonics.

Synthesis of Large-Scale Monolayer 1T'-MoTe2 and Its Stabilization via Scalable hBN Encapsulation.

Out of the different structural phases of molybdenum ditelluride (MoTe2), the distorted octahedral 1T' possesses great interest for fundamental physics and is a promising candidate for the implementation of innovative devices such as topological transistors. Indeed, 1T'-MoTe2 is a semimetal with superconductivity, which has been predicted to be a Weyl semimetal and a quantum spin Hall insulator in bulk and monolayer form, respectively. Large instability of monolayer 1T'-MoTe2 in environmental conditions, however, has made its investigation extremely challenging so far. In this work, we demonstrate homogeneous growth of large single-crystal (up to 500 µm) monolayer 1T'-MoTe2 via chemical vapor deposition (CVD) and its stabilization in air with a scalable encapsulation approach. The encapsulant is obtained by electrochemically delaminating CVD hexagonal boron nitride (hBN) from copper foil, and it is applied on the freshly grown 1T'-MoTe2 via a top-down dry lamination step. The structural and electrical properties of encapsulated 1T'-MoTe2 have been monitored over several months to assess the degree of degradation of the material. We find that when encapsulated with hBN, the lifetime of monolayer 1T'-MoTe2 successfully increases from a few minutes to more than a month. Furthermore, the encapsulated monolayer can be subjected to transfer, device processing, and heating and cooling cycles without degradation of its properties. The potential of this scalable heterostack is confirmed by the observation of signatures of low-temperature phase transition in monolayer 1T'-MoTe2 by both Raman spectroscopy and electrical measurements. The growth and encapsulation methods reported in this work can be employed for further fundamental studies of this enticing material as well as facilitate the technological development of monolayer 1T'-MoTe2.

Ultrafast, Zero-Bias, Graphene Photodetectors with Polymeric Gate Dielectric on Passive Photonic Waveguides.

We report compact, scalable, high-performance, waveguide integrated graphene-based photodetectors (GPDs) for telecom and datacom applications, not affected by dark current. To exploit the photothermoelectric (PTE) effect, our devices rely on a graphene/polymer/graphene stack with static top split gates. The polymeric dielectric, poly(vinyl alcohol) (PVA), allows us to preserve graphene quality and to generate a controllable p-n junction. Both graphene layers are fabricated using aligned single-crystal graphene arrays grown by chemical vapor deposition. The use of PVA yields a low charge inhomogeneity ∼8 × 1010 cm-2 at the charge neutrality point, and a large Seebeck coefficient ∼140 µV K-1, enhancing the PTE effect. Our devices are the fastest GPDs operating with zero dark current, showing a flat frequency response up to 67 GHz without roll-off. This performance is achieved on a passive, low-cost, photonic platform, and does not rely on nanoscale plasmonic structures. This, combined with scalability and ease of integration, makes our GPDs a promising building block for next-generation optical communication devices.

Wafer-Scale Synthesis of Graphene on Sapphire: Toward Fab-Compatible Graphene.

The adoption of graphene in electronics, optoelectronics, and photonics is hindered by the difficulty in obtaining high-quality material on technologically relevant substrates, over wafer-scale sizes, and with metal contamination levels compatible with industrial requirements. To date, the direct growth of graphene on insulating substrates has proved to be challenging, usually requiring metal-catalysts or yielding defective graphene. In this work, a metal-free approach implemented in commercially available reactors to obtain high-quality monolayer graphene on c-plane sapphire substrates via chemical vapor deposition is demonstrated. Low energy electron diffraction, low energy electron microscopy, and scanning tunneling microscopy measurements identify the Al-rich reconstruction 31 × 31 R ± 9 ° of sapphire to be crucial for obtaining epitaxial graphene. Raman spectroscopy and electrical transport measurements reveal high-quality graphene with mobilities consistently above 2000 cm2 V-1 s-1 . The process is scaled up to 4 and 6 in. wafers sizes and metal contamination levels are retrieved to be within the limits for back-end-of-line integration. The growth process introduced here establishes a method for the synthesis of wafer-scale graphene films on a technologically viable basis.

The Games for Older Adults Active Life (GOAL) Project for People With Mild Cognitive Impairment and Vascular Cognitive Impairment: A Study Protocol for a Randomized Controlled Trial.

Background: People living with Mild Cognitive Impairment (MCI) and Vascular Cognitive Impairment (VCI) are persons who do not fulfill a diagnosis of dementia, but who have a high risk of progressing to a dementia disorder. The most recent guidelines to counteract cognitive decline in MCI/VCI subjects suggest a multidimensional and multi-domain interventions combining cognitive, physical, and social activities. The purpose of this study is to test an innovative service that provides a multi-dimensional tele-rehabilitation program through a user-friendly web application. The latter has been developed through a participatory design involving MCI specialists, patients, and their caregivers. Particularly, the proposed tele-rehabilitation program includes cognitive, physical, and caregiver-supported social activities. The goal is to promote and preserve an active life style and counteract cognitive decline in people living with MCI/VCI. Methods:The study is a randomized controlled trial. Sixty subjects will be randomly assigned to the experimental group, who will receive the tele-rehabilitation program, or the control group, who will not receive any treatment. The trial protocol comprises three steps of assessment for the experimental group: at the baseline (T_0), after tele-rehabilitation program (T_1) and at follow-up after 12-months (T_2). Differently, the control group will be assessed twice: at the baseline and at 12-months follow-up. Both the experimental and the control group will be assessed with a multidimensional evaluation battery, including cognitive functioning, behavioral, functional, and quality of life measures. The tele-rehabilitation program lasts 8 weeks and includes cognitive exercises 3 days a week, physical activities 2 days a week, and social activities once a week. In addition, group will be given an actigraph (GENEActiv, Activisinghts Ltd., Cambridgshire, UK) to track physical and sleep activity. Discussion:Results of this study will inform on the efficacy of the proposed tele-rehabilitation to prevent or delay further cognitive decline in MCI/VCI subjects. The expected outcome is to counteract cognitive decline and improve both physical functioning and quality of life. Ethics and Dissemination:The study is approved by the Local Ethics Committee and registered in https://clinicaltrials.gov (NCT03383549). Dissemination will include submission to a peer-reviewed journal, patients, and healthcare magazines and congress presentations. Trial Registration: ClinicalTrials.gov ID: NCT03383549 (registration date: 26/dec/2017) Trial Funding: Bando FAS Salute 2014 Regione Toscana Version Identifier: ver 5-16/11/2018.

Synthesis of Graphene Nanoribbons by Ambient-Pressure Chemical Vapor Deposition and Device Integration.

Graphene nanoribbons (GNRs), quasi-one-dimensional graphene strips, have shown great potential for nanoscale electronics, optoelectronics, and photonics. Atomically precise GNRs can be "bottom-up" synthesized by surface-assisted assembly of molecular building blocks under ultra-high-vacuum conditions. However, large-scale and efficient synthesis of such GNRs at low cost remains a significant challenge. Here we report an efficient "bottom-up" chemical vapor deposition (CVD) process for inexpensive and high-throughput growth of structurally defined GNRs with varying structures under ambient-pressure conditions. The high quality of our CVD-grown GNRs is validated by a combination of different spectroscopic and microscopic characterizations. Facile, large-area transfer of GNRs onto insulating substrates and subsequent device fabrication demonstrate their promising potential as semiconducting materials, exhibiting high current on/off ratios up to 6000 in field-effect transistor devices. This value is 3 orders of magnitude higher than values reported so far for other thin-film transistors of structurally defined GNRs. Notably, on-surface mass spectrometry analyses of polymer precursors provide unprecedented evidence for the chemical structures of the resulting GNRs, especially the heteroatom doping and heterojunctions. These results pave the way toward the scalable and controllable growth of GNRs for future applications.

Evaluation of HER2 and p53 expression in predicting response to docetaxel-based first-line chemotherapy in advanced breast cancer.

BACKGROUND: The human epidermal growth factor receptor 2 (HER2) and p53 pathways may be involved in chemotherapy sensitivity and/or resistance. We explore the value of HER2 and p53 status to foretell docetaxel sensitivity in advanced breast cancer. METHODS: HER2 and p53 expression was analysed in 36 (median age 55 yrs; range 37-87) metastatic breast cancer patients receiving docetaxel-based first-line chemotherapy. HER2 was determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), p53 was tested by IHC. We correlate the expression of study parameters with pathologic parameters, RECIST response and survival. The standard cut-off value of 2 was used to determine HER2 overexpression while p53 mean expression level was used to divide low/high expressors tumors. RESULTS: Median time to progression and overall survival were 9 (range 2-54) and 20 (range 3-101) months. Overall response rate was 41.6%. Nine cases showed HER2 overexpression. HER2 was more frequently overexpressed in less differentiated (p=0.05) and higher stage (p=0.003) disease. Mean FISH-HER2 values were significantly higher in responder than in non-responder pts (8.53±10.21 vs 2.50±4.12, p=0.027). Moreover, HER2 overexpression correlates with treatment response at cross-tabulation analysis (p=0.046). p53 expression was only associated with higher stage disease (p=0.02) but lack of any significant association with HER status or docetaxel response. No significant relation with survival was observed for any parameter. CONCLUSION: Our data seem to indicate that FISH-determined HER2 status but not p53 is associated with docetaxel sensitivity in metastatic breast cancer.

Ipsilateral right testicular metastasis from renal cell carcinoma in a responder patient to interleukine-2 treatment.

We present a case of metastatic spreading to the testicle in a 46-year-old patient with renal cell carcinoma, "clear-cell" type, during interleukin-2 combined subcutaneous plus aerosol treatment. Testicular metastasis occurred while the patient showed a response to the treatment with disappearance of lung lesions and reduction of lymph-nodes lesions. After orchiectomy with spermatic cord resection and disease re-evaluation confirming the previous response, the patient re-started immunotherapy. The contrast between systemic disease response to treatment and disease testicular progression might be explained by a relative insensitivity of the testicle to interleukin-2 immunotherapy as a result of a possible establishment of an immunosuppressive microenvironment. We believe that the rarity of this metastatic site and the intriguing possible mechanisms at its base, makes an interesting case for clinicians.