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Abstract Background The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. Results Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. Conclusions We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.

BACKGROUND: Mechanical thrombectomy (MT) has revolutionized the treatment of acute ischemic stroke (AIS) due to large vessel occlusion (LVO), but its efficacy and safety in medium vessel occlusion (MeVO) remain less explored. This multicenter, retrospective study aims to investigate the incidence and clinical outcomes of vessel perforations (confirmed by extravasation during an angiographic series) during MT for AIS caused by MeVO. METHODS: Data were collected from 37 academic centers across North America, Asia, and Europe between September 2017 and July 2021. A total of 1373 AIS patients with MeVO underwent MT. Baseline characteristics, procedural details, and clinical outcomes were analyzed. RESULTS: The incidence of vessel perforation was 4.8% (66/1373). Notably, our analysis indicates variations in perforation rates across different arterial segments: 8.9% in M3 segments, 4.3% in M2 segments, and 8.3% in A2 segments (p = 0.612). Patients with perforation had significantly worse outcomes, with lower rates of favorable angiographic outcomes (TICI 2c-3: 23% vs 58.9%, p

INTRODUCTION: First pass effect (FPE), achievement of complete recanalization (mTICI 2c/3) with a single pass, is a significant predictor of favorable outcomes for endovascular treatment (EVT) in large vessel occlusion stroke (LVO). However, data concerning the impact on functional outcomes and predictors of FPE in medium vessel occlusions (MeVO) are scarce. PATIENTS AND METHODS: We conducted an international retrospective study on MeVO cases. Multivariable logistic modeling was used to establish independent predictors of FPE. Clinical and safety outcomes were compared between the two study groups (FPE vs non-FPE) using logistic regression models. Good outcome was defined as modified Rankin Scale 0-2 at 3 months. RESULTS: Eight hundred thirty-six patients with a final mTICI ⩾ 2b were included in this analysis. FPE was observed in 302 patients (36.1%). In multivariable analysis, hypertension (aOR 1.55, 95% CI 1.10-2.20) and lower baseline NIHSS score (aOR 0.95, 95% CI 0.93-0.97) were independently associated with an FPE. Good outcomes were more common in the FPE versus non-FPE group (72.8% vs 52.8%), and FPE was independently associated with favorable outcome (aOR 2.20, 95% CI 1.59-3.05). 90-day mortality and intracranial hemorrhage (ICH) were significantly lower in the FPE group, 0.43 (95% CI, 0.25-0.72) and 0.55 (95% CI, 0.39-0.77), respectively. CONCLUSION: Over 2/3 of patients with MeVOs and FPE in our cohort had a favorable outcome at 90 days. FPE is independently associated with favorable outcomes, it may reduce the risk of any intracranial hemorrhage, and 3-month mortality.

Convolutional neural networks (CNNs) are deep learning architectures used for image classification that have been improved in recent years to increase their accuracies and reduce their computation times. Hierarchical approaches are based on a step-by-step strategy and aim to optimize performance on difficult tasks by solving successive subtasks. The gain provided by these solutions must be relativized with the explosion in the number of parameters they imply, which makes their implementation on embedded systems difficult. New constraints also appear in the choice of the architectures of the branches when one seeks to have a global network providing predictions at different levels. We propose a strategy that allows the merging of heterogeneous CNNs by following a hierarchical approach in which the information extracted by first-level networks can be fed back at any location into second-level networks. Despite the differences in the number and size of the feature maps, such grafting can be done by using clustering, dimension reduction, and interpolation techniques. This strategy eliminates the computational redundancy induced by the recalculation of low-level features. The proposed grafting approach significantly reduces the inference time of the second network without impacting the accuracy. Tests performed on MNIST, CIFAR-10, and PlantVillage datasets with several CNNs illustrate the possibility of implementation in various situations. Our solution allows us to consider in an innovative way the implementation of hierarchical solutions on devices with limited capacities.

Building of European data economy is an integral part of Digital Single Market strategy in the European Union. Digital data is recognised as an essential resource for economic growth, competitiveness, innovation, job creation and societal progress in general. Estimation on possible data economy benefits on European Union scale are well known. At the same time, there is no quantifiable evidence on the state and perspectives of the data driven economy in Western Balkans. In this paper, we provide an overview and elaborate on the emerging opportunities for the establishment of data-driven innovation and data economies in Western Balkans, where National Spatial Data Infrastructures implementation and Open data initiatives could be seen as main drivers. In February 2018, European Commission also adopted strategy for Western Balkans, thus, confirming the European future of the region.

Cold stimulations during egg incubation were reported to limit the occurrence of ascites in broilers subjected to cold temperature after 14 d of age. However, data are lacking on the impacts of such strategy in case of cold temperature conditions at start. This study aimed to evaluate the effects of incubation and posthatch cold challenge on performance, breast muscle integrity, and meat processing quality in broiler chickens. Ross 308 eggs were incubated under control temperature (I0, 37.6°C) or subjected to 15°C during 30 min on day 18 and 19 of incubation (I1). Chicks from each group were reared in floor pens either at standard rearing temperature (T0), from 32°C at 0 d to 21°C at 21 d of age, or exposed to colder rearing temperature (T1), from 29°C at 0 to 21°C at 21 d of age. All birds were then kept at 21°C until slaughter (day 40), when body weights (BW), feed conversion ratio (FCR), breast muscle yield, meat processing quality, and the occurrences of meat defects, hock burns, and pododermatitis were recorded. No significant impact of incubation conditions on hatchability was observed. At day 40, BW was more under T1 than under T0 conditions, with T0 females (but not males) presenting more BW after I1 than after I0 conditions. In the whole period, T1 chickens presented lower FCR than T0 chickens and higher breast meat yields at day 40. The occurrence of white striping was more in I1T1 males than in all other groups, except for the I0T1 males. Hock burns were more frequent in I1T1 males than in all females and I0T0 males, whereas the occurrence of pododermatitis was lower in T0 males than in other groups. Despite some positive effects of I1 incubation on growth after starting under low ambient temperature, this study reveals the limits of such strategy concerning chicken health and welfare, demonstrating that early thermal environment is a major component of the quality and sustainability of chicken meat production.

Abstract Background Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3′ untranslated regions (3’UTRs). Given the increasing importance of UTRs in the understanding of RNA metabolism, and the growing interest in alternative polyadenylation especially in the nervous system, we aimed at identifying the alternative isoforms of odorant receptor mRNAs generated through 3’UTR variation. Results We implemented a dedicated pipeline using IsoSCM instead of Cufflinks to analyze RNA-Seq data from whole olfactory mucosa of adult mice and obtained an extensive description of the 3’UTR isoforms of odorant receptor mRNAs. To validate our bioinformatics approach, we exhaustively analyzed the 3’UTR isoforms produced from 2 pilot genes, using molecular approaches including northern blot and RNA ligation mediated polyadenylation test. Comparison between datasets further validated the pipeline and confirmed the alternative polyadenylation patterns of odorant receptors. Qualitative and quantitative analyses of the annotated 3′ regions demonstrate that 1) Odorant receptor 3’UTRs are longer than previously described in the literature; 2) More than 77% of odorant receptor mRNAs are subject to alternative polyadenylation, hence generating at least 2 detectable 3’UTR isoforms; 3) Splicing events in 3’UTRs are restricted to a limited subset of odorant receptor genes; and 4) Comparison between male and female data shows no sex-specific differences in odorant receptor 3’UTR isoforms. Conclusions We demonstrated for the first time that odorant receptor genes are extensively subject to alternative polyadenylation. This ground-breaking change to the landscape of 3’UTR isoforms of Olfr mRNAs opens new avenues for investigating their respective functions, especially during the differentiation of olfactory sensory neurons.

Mona Ahmed,1 Roland Baumgartner,2 Silvia Aldi,3 Philip Dusart,4 Ulf Hedin,1 Björn Gustafsson,1 Kenneth Caidahl1,51Department of Molecular Medicine and Surgery, Karolinska Institutet, SE 17176, Stockholm, Sweden; 2Department of Medicine Solna, Karolinska Institutet, SE 17176, Stockholm, Sweden; 3Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 17177, Stockholm, Sweden; 4Department of Cellular and Clinical Proteomics, Science for Life Laboratory, Kungliga Tekniska Högskolan (KTH), SE 17165, Stockholm, Sweden; 5Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE 41345, Gothenburg, SwedenBackground: Inflammation and accumulation of macrophages are key features of unstable atherosclerotic plaques. The ability of macrophages to take up molecular probes can be exploited in new clinical imaging methods for the detection of unstable atherosclerotic lesions. We investigated whether modifications of human serum albumin (HSA) could be used to target macrophages efficiently in vitro.Materials and methods: Maleylated and aconitylated HSA were compared with unmodified HSA. Fluorescent or radiolabeled (89Zr) modified HSA was used in in vitro experiments to study cellular uptake by differentiated THP-1 cells and primary human macrophages. The time course of uptake was evaluated by flow cytometry, confocal microscopy, real-time microscopy and radioactivity measurements. The involvement of scavenger receptors (SR-A1, SR-B2, LOX-1) was assessed by knockdown experiments using RNA interference, by blocking experiments and by assays of competition by modified low-density lipoprotein.Results: Modified HSA was readily taken up by different macrophages. Uptake was mediated nonexclusively via the scavenger receptor SR-A1 (encoded by the MSR1 gene). Knockdown of CD36 and ORL1 had no influence on the uptake. Modified HSA was preferentially taken up by human macrophages compared with other vascular cell types such as endothelial cells and smooth muscle cells.Conclusions: Modified 89Zr-labeled HSA probes were recognized by different subsets of polarized macrophages, and maleylated HSA may be a promising radiotracer for radionuclide imaging of macrophage-rich inflammatory vascular diseases.Keywords: atherosclerosis, inflammation, macrophage, molecular imaging, scavenger receptor, zirconium

Feed production is the main contributor to several environmental impacts of livestock. To decrease environmental impacts of feed, those of feedstuffs should be considered during formulation. In particular, multiobjective feed formulation (MOF) can help reduce several environmental impacts simultaneously while keeping any increase in feed price moderate. The objective of this study was to assess environmental benefits of MOF at the farm gate for fattening pigs and broilers. For pigs, three feeding strategies were tested: classic 2-phase (2P), 2-phase with lower net energy content (2P−), and multiphase (MP). For broilers, two strategies were tested: classic 3-phase (3P) and 3-phase with higher digestible amino acid contents and lower metabolisable energy content (3P+). Diets were formulated using both least-cost formulation (LCF) and MOF, yielding six pig scenarios and four broiler scenarios. Environmental impacts at the farm gate were estimated using a modelling approach based on life cycle assessment. Indicators for six impact categories were then calculated: climate change (CC), cumulative non-renewable energy demand (CEDNR), acidification (AC), eutrophication (EU), land occupation (LO), and phosphorus demand (PD). As expected, MOF had lower farm-gate impacts than LCF (as much as −13%), but the degree of decrease varied by feeding strategy and impact. For pigs, MOF was equally effective in all strategies at reducing PD (−6 to −9%) and AC (−2%). In contrast, MOF was more effective in 2P and 2P− at decreasing CC (−5% to −7%), LO (−9% to −13%) and EU (−6% to −8%) than in MP (CC: −2%; LO: −4%; EU: −3%). The benefit of MOF was found greater in 2P (−7%) than in other pig strategies for CEDNR (−3 to +0%). For broilers, MOF was equally effective in both strategies tested at decreasing PD (−12%), AC (−2%), and EU (−4%). For CC and CEDNR, MOF was more effective in 3P (CC: −9%; CEDNR: −11%) than 3P+ (−6% for both impacts), but not for LO (+3% in 3P vs −1% in 3P+). These differences were due mainly to differences in animal performance (especially feed conversion ratio) among the strategies tested. Finally, in all scenarios, gross margin at the farm gate decreased with MOF comparatively to LCF (pigs: −3% to −11%); broilers: −7% to −11%). These results demonstrate the importance of comprehensive economic and environmental optimisation of feeding strategies by simultaneously considering feed impacts, animal performance, and manure management. To do so, further research is therefore required to develop new modelling tools.

Continuous positive airway pressure (CPAP) telemonitoring (TMg) has become widely implemented in routine clinical care. Objective measures of CPAP compliance, residual respiratory events, and leaks can be easily monitored, but limitations exist. This review aims to assess the role of TMg in CPAP-treated obstructive sleep apnea (OSA) patients. We report recent data related to the accuracy of parameters measured by CPAP and try to determine the role of TMg in CPAP treatment follow-up, from the perspective of both healthcare professionals and patients. Measurement and accuracy of CPAP-recorded data, clinical management of these data, and impacts of TMg on therapy are reviewed in light of the current literature. Moreover, the crucial questions of who and how to monitor are discussed. TMg is a useful tool to support, fine-tune, adapt, and control both CPAP efficacy and compliance in newly-diagnosed OSA patients. However, clinicians should be aware of the limits of the accuracy of CPAP devices to measure residual respiratory events and leaks and issues such as privacy and cost-effectiveness are still a matter of concern. The best methods to focus our efforts on the patients who need TMg support should be properly defined in future long-term studies.

EUPATI Belgium (EUPATI.be) is an informal gathering of local partners who are interested in improving patient involvement in healthcare innovation and medicines research and development. EUPATI.be brings together various stakeholders from different areas related to healthcare including patients, academia and industry. In doing so, we create an innovative collaborative approach where actors from different backgrounds work toward improving patient involvement in medical research, and putting the patient at the center of the Belgian healthcare system. Previously, we performed in-depth interviews with a small group of stakeholders on patient involvement. Here, we elaborate on our previous findings by using a nation-wide survey to inquire into Belgian stakeholders' perception on patient involvement. To this end, an electronic survey was available in French, Dutch and English, and accessible for 11 months. Twelve questions were asked, including 11 multiple choice questions and 1 open question. The latter was thematically analyzed according to the framework method. A total of 117 responses were registered and descriptive statistics were performed. The majority of respondents could be categorized into patient, academia and industry, whereas policy makers, payers, and healthcare professionals were underrepresented. We identified several barriers that hamper patient involvement, which were sometimes more reported by specific stakeholder groups. Next, we found that various stakeholders still consider patient involvement as a passive role, i.e., medical subject in a clinical trial. Respondents also reported that the role of the various stakeholders needed more clarification; this was also confirmed by the level of trust amongst the various stakeholders. Existing and the wish for more collaboration with the various stakeholders was reported by almost all respondents. Based on this survey, we can define the potential of involving patients in the medical research and development in the Belgian landscape. Our results will help to understand and tackle the various barriers that currently hamper patient involvement, whilst highlighting the need for a collaborative landscape from the multi-stakeholder perspective.

Building of European data economy is an integral part of Digital Single Market strategy in the European Union. Digital data is recognised as an essential resource for economic growth, competitiveness, innovation, job creation and societal progress in general. Estimation on possible data economy benefits on European Union scale are well known. At the same time, there is no quantifiable evidence on the state and perspectives of the data driven economy in Western Balkans. In this paper, we provide an overview and elaborate on the emerging opportunities for the establishment of data-driven innovation and data economies in Western Balkans, where National Spatial Data Infrastructures implementation and Open data initiatives could be seen as main drivers. In February 2018, European Commission also adopted strategy for Western Balkans, thus, confirming the European future of the region.

Abstract DCC, a NETRIN-1 receptor, is considered as a cell-autonomous regulator for midline guidance of many commissural populations in the central nervous system. The corticospinal tract (CST), the principal motor pathway for voluntary movements, crosses the anatomic midline at the pyramidal decussation. CST fails to cross the midline in Kanga mice expressing a truncated DCC protein. Humans with heterozygous DCC mutations have congenital mirror movements (CMM). As CMM has been associated, in some cases, with malformations of the pyramidal decussation, DCC might also be involved in this process in human. Here, we investigated the role of DCC in CST midline crossing both in human and mice. First, we demonstrate by multimodal approaches, that patients with CMM due to DCC mutations have an increased proportion of ipsilateral CST projections. Second, we show that in contrast to Kanga mice, the anatomy of the CST is not altered in mice with a deletion of DCC in the CST. Altogether, these results indicate that DCC controls CST midline crossing in both humans and mice, and that this process is non cell-autonomous in mice. Our data unravel a new level of complexity in the role of DCC in CST guidance at the midline.

Oligodendrocyte and myelin deficits have been reported in mental/psychiatric diseases. The p21-activated kinase 3 (PAK3), a serine/threonine kinase, whose activity is stimulated by the binding of active Rac and Cdc42 GTPases is affected in these pathologies. Indeed, many mutations of Pak3 gene have been described in non-syndromic intellectual disability diseases. Pak3 is expressed mainly in the brain where its role has been investigated in neurons but not in glial cells. Here, we showed that PAK3 is highly expressed in oligodendrocyte precursors (OPCs) and its expression decreases in mature oligodendrocytes. In the developing white matter of the Pak3 knockout mice, we found defects of oligodendrocyte differentiation in the corpus callosum and to a lesser extent in the anterior commissure, which were compensated at the adult stage. In vitro experiments in OPC cultures, derived from Pak3 knockout and wild type brains, support a developmental and cell-autonomous role for PAK3 in regulating OPC differentiation into mature oligodendrocytes. Moreover, we did not detect any obvious alterations of the proliferation or migration of Pak3 null OPCs compared to wild type. Overall, our data highlight PAK3 as a new regulator of OPC differentiation.

Summary: Changes in the endothelium of the cerebral vasculature can contribute to inflammatory, thrombotic, and malignant disorders. The importance of defining cell-type-specific genes and their modification in disease is increasingly recognized. Here, we develop a bioinformatics-based approach to identify normal brain cell-enriched genes, using bulk RNA sequencing (RNA-seq) data from 238 normal human cortex samples from 2 independent cohorts. We compare endothelial cell-enriched gene profiles with astrocyte, oligodendrocyte, neuron, and microglial cell profiles. Endothelial changes in malignant disease are explored using RNA-seq data from 516 lower-grade gliomas and 401 glioblastomas. Lower-grade gliomas appear to be an “endothelial intermediate” between normal brain and glioblastoma. We apply our method for the prediction of glioblastoma-specific endothelial biomarkers, providing potential diagnostic or therapeutic targets. In summary, we provide a roadmap of endothelial cell identity in normal and malignant brain, using a method developed to resolve bulk RNA-seq into constituent cell-type-enriched profiles. : Dusart et al. use a correlation-based bulk RNA-seq analysis method to identify cell-type-enriched transcriptomes in human brain. The endothelial transcriptome in glioblastoma is profiled and compared to normal brain to predict tumor-specific endothelial markers. A web-based portal is provided to allow exploration of cell-type enrichment profiles. Keywords: endothelial cells, brain, RNA-seq, gene expression, cell identity, glioblastoma, tumor vasculature

The correct integration of the detoxification processes in a risk assessment model for ozone damage on plants remains challenging. In particular, the intracellular compartmentation of antioxidant metabolites could play a role, since each compartment presents its own sensitivity to ROS and metabolite set. For each compartment, we tried to provide both qualitative and quantitative information on the metabolites present as well as the putative transporters implied. When they are known, the modifications caused by O3 or oxidative stress are presented. Clearly, under O3 exposure, integrative data which would allow to improve predictive models for O3 risk assessment are missing.

Background: Autosomal dominant congenital mirror movements (CMM) is a neurodevelopmental disorder characterized by early onset involuntary movements of one side of the body that mirror intentional movements on the contralateral side; these persist throughout life in the absence of other neurological symptoms. The main culprit genes responsible for this condition are RAD51 and DCC. This condition has only been reported in a few families, and the molecular mechanisms linking RAD51 mutations and mirror movements (MM) are poorly understood. Methods: We collected demographic, clinical, and genetic data of a new family with CMM due to a truncating mutation of RAD51. We reviewed the literature to identify all reported patients with CMM due to RAD51 mutations. Results: We identified a heterozygous nonsense mutation c.760C>T (p.Arg254∗) in eight subjects: four with obvious and disabling MM, and four with a mild phenotype. Including our new family, we identified 32 patients from 6 families with CMM linked to RAD51 variants. Discussion: Our findings further support the involvement of RAD51 in CMM pathogenesis. Possible molecular mechanisms involved in CMM pathogenesis are discussed.

Limiting the development of secondary damage represents one of the major goals of neuroprotective therapies after spinal cord injury. Here, we demonstrate that specific JNK inhibition via a single intraperitoneal injection of the cell permeable peptide D-JNKI1 6 h after lesion improves locomotor recovery assessed by both the footprint and the BMS tests up to 4 months post-injury in mice. JNK inhibition prevents c-jun phosphorylation and caspase-3 cleavage, has neuroprotective effects and results in an increased sparing of white matter at the lesion site. Lastly, D-JNKI1 treated animals show a lower increase of erythrocyte extravasation and blood brain barrier permeability, thus indicating protection of the vascular system. In total, these results clearly point out JNK inhibition as a promising neuroprotective strategy for preventing the evolution of secondary damage after spinal cord injury.

Oligodendrocyte differentiation is temporally regulated during development by multiple factors. Here, we investigated whether the timing of oligodendrocyte differentiation might be controlled by neuronal differentiation in cerebellar organotypic cultures. In these cultures, the slices taken from newborn mice show very few oligodendrocytes during the first week of culture (immature slices) whereas their number increases importantly during the second week (mature slices). First, we showed that mature cerebellar slices or their conditioned media stimulated oligodendrocyte differentiation in immature slices thus demonstrating the existence of diffusible factors controlling oligodendrocyte differentiation. Using conditioned media from different models of slice culture in which the number of Purkinje cells varies drastically, we showed that the effects of these differentiating factors were proportional to the number of Purkinje cells. To identify these diffusible factors, we first performed a transcriptome analysis with an Affymetrix array for cerebellar cortex and then real-time quantitative PCR on mRNAs extracted from fluorescent flow cytometry sorted (FACS) Purkinje cells of L7-GFP transgenic mice at different ages. These analyses revealed that during postnatal maturation, Purkinje cells down-regulate Sonic Hedgehog and up-regulate vitronectin. Then, we showed that Sonic Hedgehog stimulates the proliferation of oligodendrocyte precursor cells and inhibits their differentiation. In contrast, vitronectin stimulates oligodendrocyte differentiation, whereas its inhibition with blocking antibodies abolishes the conditioned media effects. Altogether, these results suggest that Purkinje cells participate in controlling the timing of oligodendrocyte differentiation in the cerebellum through the developmentally regulated expression of diffusible molecules such as Sonic Hedgehog and vitronectin.