Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Gene Expression Changes Associated with the Airway Wall Response to Injury

Understanding the way in which the airway heals in response to injury is fundamental to dissecting the mechanisms underlying airway disease pathology. As only limited data is available in relation to the in vivo characterisation of the molecular features of repair in the airway we sought to characterise the dynamic changes in gene expression that are associated with the early response to physical injury in the airway wall.We profiled gene expression changes in the airway wall using a large animal model of physical injury comprising bronchial brush biopsy in anaesthetised sheep. The experimental design featured sequential studies in the same animals over the course of a week and yielded data relating to the response at 6 hours, and 1, 3 and 7 days after injury. Notable features of the transcriptional response included the early and sustained preponderance of down-regulated genes associated with angiogenesis and immune cell activation, selection and differentiation. Later features of the response included the up-regulation of cell cycle genes at d1 and d3, and the latter pronounced up-regulation of extracellular matrix-related genes at d3 and d7.It is possible to follow the airway wall response to physical injury in the same animal over the course of time. Transcriptional changes featured coordinate expression of functionally related genes in a reproducible manner both within and between animals. This characterisation will provide a foundation against which to assess the perturbations that accompany airway disease pathologies of comparative relevance

Reconstructing supply network

Theoretical Physic

Peptide and peptide-carbon nanotube hydrogels as scaffolds for tissue & 3D tumor engineering

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.actbio.2017.12.012 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/The use of hybrid self-assembling peptide (EFK8)-carbon nanotube (SWNT) hydrogels for tissue engineering and in vitro 3D cancer spheroid formation is reported. These hybrid hydrogels are shown to enhance the attachment, spreading, proliferation and movement of NIH-3T3 cells relative to that observed using EFK8-only hydrogels. After five days, ∼30% more cells are counted when the hydrogel contains SWNTs. Also, 3D encapsulation of these cells when injected in hydrogels does not adversely affect their behavior. Compressive modulus measurements and microscopic examination suggest that SWNTs have this beneficial effect by providing sites for cell anchorage, spreading and movement rather than by increasing hydrogel stiffness. This shows that the cells have a particular interaction with SWNTs not shared with EFK8 nanofibers despite a similar morphology. The effect of EFK8 and EFK8-SWNT hydrogels on A549 lung cancer cell behavior is also investigated. Increasing stiffness of EFK8-only hydrogels from about 44 Pa to 104 Pa promotes a change in A549 morphology from spheroidal to a stretched one similar to migratory phenotype. EFK8-SWNT hydrogels also promote a stretched morphology, but at lower stiffness. These results are discussed in terms of the roles of both microenvironment stiffness and cell-scaffold adhesion in cancer cell invasion. Overall, this study demonstrates that applications of peptide hydrogels in vitro can be expanded by incorporating SWNTs into their structure which further provides insight into cell-biomaterial interactions. Statement of significance For the first time we used hybrid self-assembling peptide-carbon nanotube hybrid hydrogels (that we have recently introduced briefly in the “Carbon” journal in 2014) for tissue engineering and 3D tumor engineering. We showed the potential of these hybrid hydrogels to enhance the efficiency of the peptide hydrogels for tissue engineering application in terms of cell behavior (cell attachment, spreading and migration). This opens up new rooms for the peptide hydrogels and can expand their applications. Also our system (peptide and peptide-CNT hydrogels) was used for cancer cell spheroid formation showing the effect of both tumor microenvironment stiffness and cell-scaffold adhesion on cancer cell invasion. This was only possible based on the presence of CNTs in the hydrogel while the stiffness kept constant. Finally it should be noted that these hybrid hydrogels expand applications of peptide hydrogels through enhancing their capabilities and/or adding new properties to them.Natural Sciences and Engineering Research Council of Canada (NSERC)Canada Foundation for Innovation (CFI)Canada Research Chairs (CRC) progra

CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer

The CDKN1B gene, encoding for the CDK inhibitor p27kip1, is mutated in defined human cancer subtypes, including breast, prostate carcinomas and small intestine neuroendocrine tumors. Lessons learned from small intestine neuroendocrine tumors suggest that CDKN1B mutations could be subclonal, raising the question of whether a deeper sequencing approach could lead to the identification of higher numbers of patients with mutations. Here, we addressed this question and analyzed human cancer biopsies from breast (n = 396), ovarian (n = 110) and head and neck squamous carcinoma (n = 202) patients, using an ultra-deep sequencing approach. Notwithstanding this effort, the mutation rate of CDKN1B remained substantially aligned with values from the literature, showing that essentially only hormone receptor-positive breast cancer displayed CDKN1B mutations in a relevant number of cases (3%). However, the analysis of copy number variation showed that another fraction of luminal breast cancer displayed loss (8%) or gain (6%) of the CDKN1B gene, further reinforcing the idea that the function of p27kip1 is important in this type of tumor. Intriguingly, an enrichment for CDKN1B alterations was found in samples from premenopausal luminal breast cancer patients (n = 227, 4%) and in circulating cell-free DNA from metastatic luminal breast cancer patients (n = 59, 8.5%), suggesting that CDKN1B alterations could correlate with tumor aggressiveness and/or occur later during disease progression. Notably, many of the identified somatic mutations resulted in p27kip1 protein truncation, leading to loss of most of the protein or of its C-terminal domain. Using a gene-editing approach in a luminal breast cancer cell line, MCF-7, we observed that the expression of p27kip1 truncating mutants that lose the C-terminal domains failed to rescue most of the phenotypes induced by CDKN1B gene knockout, indicating that the functions retained by the C-terminal portion are critical for its role as an oncosuppressor, at least in luminal breast cancer. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland

The Ratio 1660/1690 cm−1 Measured by Infrared Microspectroscopy Is Not Specific of Enzymatic Collagen Cross-Links in Bone Tissue

In postmenopausal osteoporosis, an impairment in enzymatic cross-links (ECL) occurs, leading in part to a decline in bone biomechanical properties. Biochemical methods by high performance liquid chromatography (HPLC) are currently used to measure ECL. Another method has been proposed, by Fourier Transform InfraRed Imaging (FTIRI), to measure a mature PYD/immature DHLNL cross-links ratio, using the 1660/1690 cm−1 area ratio in the amide I band. However, in bone, the amide I band composition is complex (collagens, non-collagenous proteins, water vibrations) and the 1660/1690 cm−1 by FTIRI has never been directly correlated with the PYD/DHLNL by HPLC. A study design using lathyritic rats, characterized by a decrease in the formation of ECL due to the inhibition of lysyl oxidase, was used in order to determine the evolution of 1660/1690 cm−1 by FTIR Microspectroscopy in bone tissue and compare to the ECL quantified by HPLC. The actual amount of ECL was quantified by HPLC on cortical bone from control and lathyritic rats. The lathyritic group exhibited a decrease of 78% of pyridinoline content compared to the control group. The 1660/1690 cm−1 area ratio was increased within center bone compared to inner bone, and this was also correlated with an increase in both mineral maturity and mineralization index. However, no difference in the 1660/1690 cm−1 ratio was found between control and lathyritic rats. Those results were confirmed by principal component analysis performed on multispectral infrared images. In bovine bone, in which PYD was physically destructed by UV-photolysis, the PYD/DHLNL (measured by HPLC) was strongly decreased, whereas the 1660/1690 cm−1 was unmodified. In conclusion, the 1660/1690 cm−1 is not related to the PYD/DHLNL ratio, but increased with age of bone mineral, suggesting that a modification of this ratio could be mainly due to a modification of the collagen secondary structure related to the mineralization process

Integrin α5β1 Function Is Regulated by XGIPC/kermit2 Mediated Endocytosis during Xenopus laevis Gastrulation

During Xenopus gastrulation α5β1 integrin function is modulated in a temporally and spatially restricted manner, however, the regulatory mechanisms behind this regulation remain uncharacterized. Here we report that XGIPC/kermit2 binds to the cytoplasmic domain of the α5 subunit and regulates the activity of α5β1 integrin. The interaction of kermit2 with α5β1 is essential for fibronectin (FN) matrix assembly during the early stages of gastrulation. We further demonstrate that kermit2 regulates α5β1 integrin endocytosis downstream of activin signaling. Inhibition of kermit2 function impairs cell migration but not adhesion to FN substrates indicating that integrin recycling is essential for mesoderm cell migration. Furthermore, we find that the α5β1 integrin is colocalized with kermit2 and Rab 21 in embryonic and XTC cells. These data support a model where region specific mesoderm induction acts through kermit2 to regulate the temporally and spatially restricted changes in adhesive properties of the α5β1 integrin through receptor endocytosis

Assessing generalizability of an AI-based visual test for cervical cancer screening

A number of challenges hinder artificial intelligence (AI) models from effective clinical translation. Foremost among these challenges is the lack of generalizability, which is defined as the ability of a model to perform well on datasets that have different characteristics from the training data. We recently investigated the development of an AI pipeline on digital images of the cervix, utilizing a multi-heterogeneous dataset of 9,462 women (17,013 images) and a multi-stage model selection and optimization approach, to generate a diagnostic classifier able to classify images of the cervix into “normal”, “indeterminate” and “precancer/cancer” (denoted as “precancer+”) categories. In this work, we investigate the performance of this multiclass classifier on external data not utilized in training and internal validation, to assess the generalizability of the classifier when moving to new settings. We assessed both the classification performance and repeatability of our classifier model across the two axes of heterogeneity present in our dataset: image capture device and geography, utilizing both out-of-the-box inference and retraining with external data. Our results demonstrate that device-level heterogeneity affects our model performance more than geography-level heterogeneity. Classification performance of our model is strong on images from a new geography without retraining, while incremental retraining with inclusion of images from a new device progressively improves classification performance on that device up to a point of saturation. Repeatability of our model is relatively unaffected by data heterogeneity and remains strong throughout. Our work supports the need for optimized retraining approaches that address data heterogeneity (e.g., when moving to a new device) to facilitate effective use of AI models in new settings

Search for heavy resonances decaying into a pair of Z bosons in the ℓ + ℓ - ℓ ′ + ℓ ′ - and ℓ + ℓ - ν ν ¯ final states using 139 fb - 1 of proton–proton collisions at s = 13 TeV with the ATLAS detector

Abstract: A search for heavy resonances decaying into a pair of Z bosons leading to ℓ+ℓ-ℓ′+ℓ′- and ℓ+ℓ-νν¯ final states, where ℓ stands for either an electron or a muon, is presented. The search uses proton–proton collision data at a centre-of-mass energy of 13 TeV collected from 2015 to 2018 that corresponds to the integrated luminosity of 139 fb-1 recorded by the ATLAS detector during Run 2 of the Large Hadron Collider. Different mass ranges spanning 200 GeV to 2000 GeV for the hypothetical resonances are considered, depending on the final state and model. In the absence of a significant observed excess, the results are interpreted as upper limits on the production cross section of a spin-0 or spin-2 resonance. The upper limits for the spin-0 resonance are translated to exclusion contours in the context of Type-I and Type-II two-Higgs-doublet models, and the limits for the spin-2 resonance are used to constrain the Randall–Sundrum model with an extra dimension giving rise to spin-2 graviton excitations