Bordered Floer homology and the spectral sequence of a branched double cover I

Given a link in the three-sphere, Z. Szab\'o and the second author constructed a spectral sequence starting at the Khovanov homology of the link and converging to the Heegaard Floer homology of its branched double-cover. The aim of this paper and its sequel is to explicitly calculate this spectral sequence, using bordered Floer homology. There are two primary ingredients in this computation: an explicit calculation of filtered bimodules associated to Dehn twists and a pairing theorem for polygons. In this paper we give the first ingredient, and so obtain a combinatorial spectral sequence from Khovanov homology to Heegaard Floer homology; in the sequel we show that this spectral sequence agrees with the previously known one.Comment: 45 pages, 16 figures. v2: Published versio

Evaluation of deep convolutional neural networks for automatic classification of common maternal fetal ultrasound planes

The goal of this study was to evaluate the maturity of current Deep Learning classification techniques for their application in a real maternal-fetal clinical environment. A large dataset of routinely acquired maternal-fetal screening ultrasound images (which will be made publicly available) was collected from two different hospitals by several operators and ultrasound machines. All images were manually labeled by an expert maternal fetal clinician. Images were divided into 6 classes: four of the most widely used fetal anatomical planes (Abdomen, Brain, Femur and Thorax), the mother's cervix (widely used for prematurity screening) and a general category to include any other less common image plane. Fetal brain images were further categorized into the 3 most common fetal brain planes (Trans-thalamic, Trans-cerebellum, Trans-ventricular) to judge fine grain categorization performance. The final dataset is comprised of over 12,400 images from 1,792 patients, making it the largest ultrasound dataset to date. We then evaluated a wide variety of state-of-the-art deep Convolutional Neural Networks on this dataset and analyzed results in depth, comparing the computational models to research technicians, which are the ones currently performing the task daily. Results indicate for the first time that computational models have similar performance compared to humans when classifying common planes in human fetal examination. However, the dataset leaves the door open on future research to further improve results, especially on fine-grained plane categorization

Population structure, antimicrobial resistance and virulence-associated genes in Campylobacter jejuni isolated from three ecological niches: gastroenteritis patients, broilers, and wild birds

Campylobacter jejuni is the causal agent of the food-borne infection with the highest incidence in Europe. Both poultry and wild birds are a major reservoir. To gain insight into the population structure, virulence potential, and antimicrobial resistance (AMR), a collection of 150 isolates from three different ecological niches (broilers, wild birds, and human patients) was studied. Despite the high genetic diversity found, the population structure defined two distinct clusters, one formed mostly by broiler and human isolates and another one by most wild bird isolates. The ST-21 complex exhibits highest prevalence (in humans and broilers), followed by ST-1275 complex (only in wild birds). The ST-48, -45, and -354 complexes were found in all three niches, but represent only 22 out of 150 studied strains. A higher occurrence of AMR and multidrug resistance was detected among broiler and human isolates. Moreover, significant differences were found in the distribution of certain putative virulence genes. Remarkably, many wild bird strains were negative for either cdtA, cdtB, or cdtC from the canonical strain 81-176, whereas all broiler and human strains were positive. These data suggest that the different variants of the cdt genes might be relevant for the efficient colonization of certain hosts by C. jejuni. Our study contributes to the understanding of the role of the diverse Campylobacter reservoirs in the transmission of campylobacteriosis to humans

Convergence of decreasing male and increasing female incidence rates in major tobacco-related cancers in Europe in 1988-2010

Introduction: Smoking prevalence has been declining in men all over Europe, while the trend varies in European regions among women. To study the impact of past smoking prevalence, we present a comprehensive overview of the most recent trends in incidence, during 1988-2010, in 26 countries, of four of the major cancers in the respiratory and upper gastro-intestinal tract associated with tobacco smoking. Methods: Data from 47 population-based cancer registries for lung, laryngeal, oral cavity and pharyngeal, and oesophageal cancer cases were obtained from the newly developed data repository within the European Cancer Observatory (http://eco.iarc.fr/). Truncated age-standardised incidence rates (35-74 years) by calendar year, average annual percentage change in incidence over 1998-2007 were calculated. Smoking prevalence in selected countries was extracted from the Organisation for Economic Co-operation and Development and the World Health Organization databases. Results:

RiboTag : Ribosomal tagging strategy to analyze cell type specific mRNA expression in vivo

Ribosome tagging has become a very useful in vivo approach for analyzing gene expression and mRNA translation in specific cell types that are difficult and time consuming to isolate by conventional methods. The approach is based on selectively expressing an HA-tagged ribosomal protein in a target cell type and then using antibodies against HA to purify the polysomes and associated mRNAs from the target cell. The original approach makes use of a mouse line (RiboTag) harboring a modified allele of Rpl22 (Rpl22-HA) that is induced by the action of Cre recombinase. The Rpl22-HA gene can also be introduced into the animal by stereotaxic injections of an AAV-DIO-Rpl22-HA that is then activated in Cre-expressing cells. Both methods for tagging ribosomes facilitate the immunoprecipitation of ribosome bound mRNAs and their analysis by qRT-PCR or RNA-Seq. This protocol will discuss the technical procedures and describe important considerations relevant to the analysis of the data

Detection of cytomegalovirus in bronchoalveolar lavage fluid from immunocompromised patients with pneumonitis by viral culture and DNA quantification

Altres ajuts: acords transformatius de la UABTo compare the detection of human cytomegalovirus (HCMV) in bronchoalveolar lavage (BAL) fluid by viral culture and quantitative polymerase chain reaction (qPCR), and to establish a viral load threshold that can identify cases of HCMV replication indicative of pneumonitis. There is currently no universal viral load cut-off to differentiate between patients with and without pneumonitis, and the interpretation of qPCR results is challenging. 176 consecutive BAL samples from immunosuppressed hosts with signs and/or symptoms of respiratory infection were prospectively studied by viral culture and qPCR. Concordant results were obtained in 81.25% of the BAL samples. The rest were discordant, as only 34% of the qPCR-positive BAL samples were positive by culture. The median HCMV load was significantly higher in culture-positive than in culture-negative BAL samples (5038 vs 178 IU/mL). Using a cut-off value of 1258 IU/mL of HCMV in BAL, pneumonia was diagnosed with a sensitivity of 76%, a specificity of 100%, a VPP of 100% and VPN of 98%, and HCMV was isolated in 100% of the BAL cultures. We found that a qPCR-negative was a quick and reliable way of ruling out HCMV pneumonitis, but a positive result did not always indicate clinically significant replication in the lung. However, an HCMV load in BAL fluid of ≥ 1258 IU/mL was always associated with disease, whereas < 200 IU/mL rarely so

PALB2 chromatin recruitment restores homologous recombination in BRCA1-deficient cells depleted of 53BP1

Abstract: Loss of functional BRCA1 protein leads to defects in DNA double-strand break (DSB) repair by homologous recombination (HR) and renders cells hypersensitive to poly (ADP-ribose) polymerase (PARP) inhibitors used to treat BRCA1/2-deficient cancers. However, upon chronic treatment of BRCA1-mutant cells with PARP inhibitors, resistant clones can arise via several mechanisms, including loss of 53BP1 or its downstream co-factors. Defects in the 53BP1 axis partially restore the ability of a BRCA1-deficient cell to form RAD51 filaments at resected DSBs in a PALB2- and BRCA2-dependent manner, and thereby repair DSBs by HR. Here we show that depleting 53BP1 in BRCA1-null cells restores PALB2 accrual at resected DSBs. Moreover, we demonstrate that PALB2 DSB recruitment in BRCA1/53BP1-deficient cells is mediated by an interaction between PALB2’s chromatin associated motif (ChAM) and the nucleosome acidic patch region, which in 53BP1-expressing cells is bound by 53BP1’s ubiquitin-directed recruitment (UDR) domain

Circuit reliability prediction: Challenges and solutions for the device time-dependent variability characterization roadblock

Copyright IEEEThe characterization of the MOSFET Time-Dependent Variability (TDV) can be a showstopper for reliability-Aware circuit design in advanced CMOS nodes. In this work, a complete MOSFET characterization flow is presented, in the context of a physics-based TDV compact model, that addresses the main TDV characterization challenges for accurate circuit reliability prediction at design time. The pillars of this approach are described and illustrated through examples.This work was supported by the VIGILANT Project (PID2019-103869RB / AEI / 10.13039/501100011033) and the TEC2016-75151-C3-R Project (AEI/FEDER, UE).Peer reviewe

The long-term outcomes of CIS patients in the Barcelona inception cohort : Looking back to recognize aggressive MS

Altres ajuts: This study has been funded by European Regional Development Fund and co-funded by Instituto Carlos III. It has also received support by a grant from Genzyme foundation (GENZYME-2015-01) granted to M.T. and from the 'Red Española de Esclerosis Múltiple (REEM)', which is sponsored by FIS, the Instituto de Salud Carlos III, the Ministry of Economy and Competitiveness in Spain, and the 'Ajuts per donar Suport als Grups de Recerca de Catalunya', which is sponsored by the 'Agència de Gestió d'Ajuts Universitaris i de Recerca' (AGAUR) of the Generalitat de Catalunya in Spain.To explore the long-term outcomes of patients with clinically isolated syndromes from the Barcelona cohort. We selected patients with a follow-up longer than 10 years to (1) estimate the risks of multiple sclerosis (MS) and disability accumulation according to the baseline number of T2 lesions and to compare treated versus untreated patients and early versus delayed treatment, and (2) to study baseline features of patients with aggressive MS (Expanded Disability Status Scale (EDSS) ⩾6.0 at 10 years). In all, 401 patients were included (mean follow-up of 14.4 (standard deviation of 2.9) years). A higher number of T2 lesions was associated with an earlier MS diagnosis and an earlier risk of irreversible disability. Early treatment was associated with a decreased risk of EDSS of 3.0: adjusted hazard ratio = 0.4, 95% confidence interval = (0.2, 0.7). Patients with aggressive MS differed in their baseline brain magnetic resonance images: The median (interquartile range) number of T2 lesions and contrast-enhancing lesions (CEL) was 71 (28-95) versus 7 (1-19) and 3 (1-24) versus 0 (0-1), respectively. The cut-offs that better classified patients with aggressive MS were 20 for T2 lesions and 2 for CEL. Although MS natural history is changing, a high lesion load at onset is helpful to identify patients at risk of presenting an aggressive MS