gebhart/patrepeval huggingface dataset:
Synergy and Order Effects of Antibiotics and Phages in Killing Pseudomonas aeruginosa Biofilms (2017)

In contrast to planktonic cells, bacteria imbedded biofilms are notoriously refractory to treatment by antibiotics or bacteriophage (phage) used alone. Given that the mechanisms of killing differ profoundly between drugs and phages, an obvious question is whether killing is improved by combining antibiotic and phage therapy. However, this question has only recently begun to be explored. Here, in vitro biofilm populations of Pseudomonas aeruginosa PA14 were treated singly and with combinations of two phages and bactericidal antibiotics of five classes. By themselves, phages and drugs commonly had only modest effects in killing the bacteria. However some phage-drug combinations reduced bacterial densities to well below that of the best single treatment; in some cases, bacterial densities were reduced even below the level expected if both agents killed independently of each other (synergy). Furthermore, there was a profound order effect in some cases: treatment with phages before drugs achieved maximum killing. Combined treatment was particularly effective in killing in Pseudomonas biofilms grown on layers of cultured epithelial cells. Phages were also capable of limiting the extent to which minority populations of bacteria resistant to the treating antibiotic ascend. The potential of combined antibiotic and phage treatment of biofilm infections is discussed as a realistic way to evaluate and establish the use of bacteriophage for the treatment of humans.
Chloroquine and COVID-19, where do we stand? (2020)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destine au dpt et la diffusion de documents scientifiques de niveau recherche, publis ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.
Transient and persistent experimental infection of nonhuman primates with Helicobacter pylori: implications for human disease (1996)

Helicobacter pylori can establish chronic infection in the human gastric mucosa, and it is a major cause of peptic ulcer disease and a principal risk factor for gastric cancer. This creates a need for H. pylori infection models that mimic the human condition. To test the suitability of rhesus monkeys as infection models, H. pylori-free animals were inoculated intragastrically with mixtures of H. pylori strains, bacteria recovered from colonized animals were typed by arbitrarily primed PCR, and host inflammatory and immunologic responses were monitored. Among five H. pylori-free animals inoculated with a mixture of two human strains plus one monkey strain, one became persistently infected and one became only transiently infected. The recovered bacteria matched the monkey input strain in DNA fingerprint. A subsequent trial using two new human isolates and three animals that had resisted colonization by the monkey strain resulted in persistent infection in one animal and transient infection in two others. Antral gastritis, anti-H. pylori serum immunoglobulin G, and atrophy all increased, but with patterns that differed among animals. We conclude that (i) rhesus monkeys can be infected experimentally with H. pylori, (ii) individuals differ in susceptibility to particular bacterial strains, (iii) infections may be transient, and (iv) the fitness of a particular strain for a given host helps determine the consequences of exposure to that strain.
Transcriptomic Analysis of Colorectal Cancer Cells Treated with Oil Production Waste Products (OPWPs) Reveals Enrichment of Pathways of Mitochondrial Functionality (2022)

Oil production waste products (OPWPs) derive from olive mill and represent a crucial environmental problem due to their high polyphenolic content able to pollute the ground. One option to reduce the OPWPs' environmental impact is to exploit polyphenols' biological properties. We sought to analyze the transcriptomic variations of colorectal cancer cells exposed to the OPWPs extracts and hydroxytyrosol, the major component, to recognize unknown and ill-defined characteristics. Among the top affected pathways identified by GSEA, we focused on oxidative phosphorylation in an in vitro system. Colorectal cancer HCT116 and LoVo cells treated with hydroxytyrosol or OPWPs extracts showed enhancement of the respiratory chain complexes' protein levels, ATP production and membrane potential, suggesting stimulation of mitochondrial functions. The major proteins involved in mitochondrial biogenesis and fusion events of mitochondrial dynamics were positively affected, as by Western blot, fostering increase of the mitochondrial mass organized in a network of elongated organelles. Mechanistically, we proved that PPARγ mediates the effects as they are mimicked by a specific ligand and impaired by a specific inhibitor. OPWP extracts and hydroxytyrosol, thus, promote mitochondrial functionality via a feed-forward regulatory loop involving the PPARγ/PGC-1α axis. These results support their use in functional foods and as adjuvants in cancer therapy.
Illuminating the relationship between canopy light relations and fruit yield in apple planar cordon orchard systems (2020)

ISHS XXX International Horticultural Congress IHC2018: International Symposium on Cultivars, Rootstocks and Management Systems of Deciduous Fruit and Fruit Tree Behaviour in Dynamic Environments Illuminating the relationship between canopy light relations and fruit yield in apple planar cordon orchard systems
Organocatalyzed Asymmetric Vinylogous Allylic–Allylic Alkylation of Morita–Baylis–Hillman Carbonates with Olefinic Azlactones: Facile Access to Chiral Multifunctional α-Amino Acid Derivatives (2015)

Vinylogous reactivity of olefinic azlactones was realized through the development of a chiral amine-catalyzed highly stereoselective allylic-allylic alkylation with Morita-Baylis-Hillman carbonates. The Lewis base activation of electrophile and Brønsted base activation of nucleophile were efficiently combined, giving access to multifunctional acyclic α-amino acid derivatives in a highly stereocontrolled manner. The synthetic utility of these versatile synthons was further demonstrated by the facile synthesis of protected cyclic quaternary α-amino acids.
Depth Edge Guided CNNs for Sparse Depth Upsampling (2020)

Guided sparse depth upsampling aims to upsample an irregularly sampled sparse depth map when an aligned high-resolution color image is given as guidance. Many neural networks have been designed for this task. However, they often ignore the structural difference between the depth and the color image, resulting in obvious artifacts such as texture copy and depth blur at the upsampling depth. Inspired by the normalized convolution operation, we propose a guided convolutional layer to recover dense depth from sparse and irregular depth image with an depth edge image as guidance. Our novel guided network can prevent the depth value from crossing the depth edge to facilitate upsampling. We further design a convolution network based on proposed convolutional layer to combine the advantages of different algorithms and achieve better performance. We conduct comprehensive experiments to verify our method on real-world indoor and synthetic outdoor datasets. Our method produces strong results. It outperforms state-of-the-art methods on the Virtual KITTI dataset and the Middlebury dataset. It also presents strong generalization capability under different 3D point densities, various lighting and weather conditions.
Die allergische Inflammation der Lunge induziert pulmonalvaskuläre Hyperreagibilität (2006)

Hintergrund: Die pulmonalarterielle Vasokonstriktion ist eine wichtige frühe Komponente bei der Pulmonalen Hypertonie (PH). Inflammatorische Mechanismen spielen eine bedeutende Rolle in der Pathogenese der PH, die häufig mit Autoimmunerkrankungen, Infektionen und chronisch obstruktiven Lungenerkrankungen assoziiert ist. Wir haben den möglichen Einfluss allergischer Inflammation auf die pulmonale Hämodynamik untersucht. Methoden: BALB/c Mäuse wurden intraperitoneal mit Ovalbumin sensibilisiert und durch repetitive Ovalbumin-Inhalation provoziert. Anschließend wurden die Lungen dieser Tiere ex vivo ventiliert und perfundiert und der pulmonalarterielle Druck (Ppa) kontinuierlich registriert. Ergebnisse: Isoliert perfundierte Lungen allergen-sensibilisierter und -provozierter Mäuse zeigten eine deutlich erhöhte pulmonalarterielle Vasokonstriktion gegenüber Serotonin (5-HT) im Vergleich zu Kontrolltieren. Diese Ppa-Erhöhung wurde durch den 5-HT2A Rezeptor vermittelt, während der 5-HT1B Rezeptor unbeteiligt war. Die Vorbehandlung mit spezifischen Inhibitoren der PC-PLC (D609), der PKC (Bisindolylmaleimid) sowie der Rho-kinase (Y27632) reduzierten die Druckreaktion deutlich, während der Inositoltriphosphat-Inhibitor Xestospongin C keinen Effekt hatte. Neben 5-HT induzierte auch der Thromboxan Rezeptor Agonist U46619 eine deutlich höhere Druckreaktion in Lungen allergen-sensibilisierter und -provozierter Tiere im Vergleich zu Kontrolltieren. Schlussfolgerung: Die allergische Inflammation bewirkt eine ausgeprägte pulmonalvaskuläre Hyperreagibilität in der Mauslunge. Der durch 5-HT induzierte Ppa-Anstieg wird über den 5-HT2A Rezeptor, und durch PLC und PKC sowie Rho-kinase vermittelt. Diese Ergebnisse weisen auf eine mögliche Bedeutung der Mechanismen allergischer Inflammation für die Pathobiologie der PH hin.
Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails (2020)

Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly (A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development-and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
Paroxysmal Cranial Dyskinesia and Nail‐Patella Syndrome Caused by a Novel Variant in the LMX1B Gene (2020)

Paroxysmal dyskinesia is a heretofore unrecognized feature of the NPS spectrum. The pathogenic mechanism might relate to aberrant dopaminergic circuits. © 2020 International Parkinson and Movement Disorder Society.
High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery (2020)

Esophageal adenocarcinoma (EAC) is a highly heterogeneous disease, dominated by large-scale genomic rearrangements and copy number alterations. Such characteristics have hampered conventional target-directed drug discovery and personalized medicine strategies, contributing to poor outcomes for patients. We describe the application of a high-content Cell Painting assay to profile the phenotypic response of 19,555 compounds across a panel of six EAC cell lines and two tissue-matched control lines. We built an automated high-content image analysis pipeline to identify compounds that selectively modified the phenotype of EAC cell lines. We further trained a machine-learning model to predict the mechanism of action of EAC selective compounds using phenotypic fingerprints from a library of reference compounds. We identified a number of phenotypic clusters enriched with similar pharmacological classes, including methotrexate and three other antimetabolites that are highly selective for EAC cell lines. We further identify a small number of hits from our diverse chemical library that show potent and selective activity for EAC cell lines and that do not cluster with the reference library of compounds, indicating they may be selectively targeting novel esophageal cancer biology. Overall, our results demonstrate that our EAC phenotypic screening platform can identify existing pharmacologic classes and novel compounds with selective activity for EAC cell phenotypes.
Multi-Paced Dictionary Learning for cross-domain retrieval and recognition (2016)

Several applications benefit from learning coupled representations able to describe data from multiple sources. For instance, cross-domain dictionary learning methods demonstrated to be particularly effective. In this paper we introduce Multi-Paced Dictionary Learning (MPDL) and propose an instantiation of it under the framework of cross-domain dictionary learning. MPDL is inspired by previous works on self-paced learning, a framework able to enhance the accuracy of conventional learning models by presenting the training data in a meaningful order, i.e. easy samples are provided first. However, most of existing self-paced learning methods only consider a single modality, while MPDL is specifically designed to assess the learning pace when data from multiple sources are available. We present the model and propose an efficient algorithm to learn the dictionaries and codes. The approach is validated via experiments on two different tasks, namely cross-media retrieval and sketch-to-photo face recognition, using publicly available datasets.
The Company You Keep: Mobile Malware Infection Rates and Inexpensive Risk Indicators (2013)

There is little information from independent sources in the public domain about mobile malware infection rates. The only previous independent estimate (0.0009%) [12], was based on indirect measurements obtained from domain name resolution traces. In this paper, we present the first independent study of malware infection rates and associated risk factors using data collected directly from over 55,000 Android devices. We find that the malware infection rates in Android devices estimated using two malware datasets (0.28% and 0.26%), though small, are significantly higher than the previous independent estimate. Using our datasets, we investigate how indicators extracted inexpensively from the devices correlate with malware infection. Based on the hypothesis that some application stores have a greater density of malicious applications and that advertising within applications and cross-promotional deals may act as infection vectors, we investigate whether the set of applications used on a device can serve as an indicator for infection of that device. Our analysis indicates that this alone is not an accurate indicator for pinpointing infection. However, it is a very inexpensive but surprisingly useful way for significantly narrowing down the pool of devices on which expensive monitoring and analysis mechanisms must be deployed. Using our two malware datasets we show that this indicator performs 4.8 and 4.6 times (respectively) better at identifying infected devices than the baseline of random checks. Such indicators can be used, for example, in the search for new or previously undetected malware. It is therefore a technique that can complement standard malware scanning by anti-malware tools. Our analysis also demonstrates a marginally significant difference in battery use between infected and clean devices.
MEASURING THE DYNAMIC RESPONSE OF A LIVELY FOOTBRIDGE TO AMBIENT AND WALKING EXCITATION (2020)

The paper presents selected results of a first experimental campaign on a footbridge over-passing the Lambro River near Milano (Italy). The 3-span footbridge, for a bicycle-pedestrian mixed use, has a reinforced concrete deck supported by a steel structure. The footbridge, 107 m long and with a constant width of 4.4m, is roughly symmetric about both mid-span and the longitudinal axis. As a part of proof tests performed in March 2016, ambient vibration tests identified the footbridge modal properties, detecting at 1.75 Hz the fundamental bending mode with the maximum amplitude recorded at mid-span, a finding confirmed by an ANSYS FE model of the footbridge. A series of forced vibration tests, performed in July 2017, investigated the response of the bridge under different loading conditions. Groups of pedestrians, in number of 1, 2, 3, 4, 6, 8 and 12, crossed the bridge, walking with a step frequency as close as possible to the first fundamental frequency. Different spatial configurations were explored for each number of pedestrians, investigating the spread in data related to different walking people/groups and their formation. Pedestrians followed straight trajectories and their spatial configuration was symmetric about the longitudinal axis of the bridge; single pedestrians walked along the footbridge axis. This paper focuses on a few results related to: (a) single pedestrians; (b) groups of multiple pedestrians in the same configuration, a longitudinal row; (c) 12 pedestrians in different spatial configurations. Experimental results highlight the effect of both intra-subject and inter-subject variability and the influence of spatial configuration on the maximum measured acceleration. The bridge performance is discussed by comparison between experimental results and limit values of the vertical acceleration according to HiVoSS guideline.
Comparing alternative approaches for networking of named objects in the future Internet (2012)

This paper describes and compares alternative architectures for achieving the functional goals of name oriented networking. The CCN (content-centric network) scheme proposed by Van Jacobson is contrasted with hybrid name and address based routing proposed in conjunction with the MobilityFirst (MF) future Internet architecture. In a CCN network, routers forward data directly on content names (such as URNs), achieving elegant and efficient retrieval of content files; the framework can also be extended to other communications services such as VoIP. The MF scheme supports name-based communication services by introducing the concept of a flat `globally unique identifier (GUID)', which is used as the authoritative header for routing. Further, the GUID is dynamically mapped to one or more topological network addresses using a global name resolution service (GNRS). This leads to a hybrid GUID and network address based routing (HGN) scheme in which routers operate with both flat names (GUIDs) and network addresses, reducing routing table size and overhead at the cost of a fast distributed service for dynamic mapping of names to addresses. Protocol operations for both CCN and HGN are outlined in context of specific services including content retrieval, unicast and mobility. Preliminary evaluations of scalability and performance for both schemes are given using simple analytical models and selected results from Internet-scale simulations for GNRS and BGP.
Disseminated Herpes Simplex Virus Type 1 Primary Infection in a Healthy Individual (2009)

Use of polymerase chain reaction detection techniques for HSV may identify viremic patients in the absence of obvious immunosuppression.
Analytical investigation of spin-transfer dynamics using a perpendicular-to-plane polarizer (2005)

We studied current-induced magnetic switching and excitations in structures comprising a free layer with in-plane magnetization traversed by a current with perpendicular-to-plane spin polarization. We derived analytical solutions from the Landau–Lifshitz–Gilbert equation including the spin-torque term, and compared them to numerical simulations within the single domain assumption. Taking into account the criterion of thermal stability, the magnetization switching in nanostructures of typical size below 100nm comprising a perpendicular polarizer is found to require larger current density but to be much faster than with a longitudinal polarizer. Furthermore, a steady precession of magnetization can be generated in this geometry; those frequencies can be tuned from about 1 to 20GHz by only changing the current without applying any external field. This opens a promising application as microwave sources.
Primary Tissue Culture of Normal Adult Human Decapsulated Adrenal Cortex: Radioautographic Studies on the Metabolic Effects of ACTH<sub>1-2</sub><sub>4</sub> (1975)

ACTH-deprived primary normal adult human adrenocortical cells on the 23rd day in vitro were found to lack any DNA synthetic and proliferative activity, but incorporated uridine-3H and 1-leucine-3H actively. In cortical cells of the same age treated for 2 and 7 days with ACTH1-24 (3 X 10(-6) M) the incorporation of the precursors for RNA and DNA synthesis and the cell proliferation were found to be markedly stimulated. The apparent uptake of leucine-3H was instead reduced in 2-day and, less still, in 7-day treated cells. In parallel with ultrastructural studies, these data suggest that ACTH orderly activates the template activity of chromatin while eliciting the differentiation and hypertrophy of human adrenocortical cells.
Role of Sp1 transcription factor in the pathogenesis of diabetic retinopathy (2012)

Abstract Purpose Proangiogenic factors, VEGF and Cyr61, drive aberrant retinal neovascularization in diabetic retinopathy (DR). Their expression is regulated by the transcription factor Sp1. Several layers of the retina participate in the secretion of these factors; however, the contribution of the retinal pigment epithelium (RPE) to the pathogenesis of diabetic retinopathy has remained largely overlooked. Our objective was to characterize the Sp1‐dependent production of VEGF and Cyr61 in models of the diabetic retina, specifically focusing on the RPE, with the ultimate goal of identifying potential novel therapeutic targets for the treatment of DR. Methods Glucose‐treated ARPE‐19 (human retinal pigment epithelial cells) and TR‐iBRB (rat retinal microendothelial cells) were assayed for levels of VEGF and Cyr61 by qPCR, Western blot, and tubule formation assays. RNAi was used to deplete cells of Sp1. Binding of Sp1 to VEGF and Cyr61 promoters was monitored by chromatin immunoprecipitation (ChIP). Immunohistochemistry for VEGF and Cyr61 was done in diabetic mouse retinas. Results Glucose treatment caused increased VEGF and Cyr61 transcript and protein, and Sp1 depletion abrogated these changes in both cell types. ChIP analysis showed glucose‐induced increase in the Sp1 binding to VEGF and Cyr61 promoters. Additionally, expression of both factors was increased in the RPE of diabetic mice. Conclusion VEGF and Cyr61 are upregulated in ARPE‐19 and TR‐iBRB in hyperglycemia, which coincides with elevated Sp1 binding at their promoters. Depletion of Sp1 significantly reduced their aberrant expression. Sp1 may participate in the pathogenesis of diabetic retinopathy via upregulation of these proangiogenic genes in the RPE as well as in the vascular retina.