gebhart/patrepeval huggingface dataset:
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure (2011)

Elevated temperatures resulting from climate change pose a clear threat to reef-building corals; however, the traits that might influence corals' survival and dispersal during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits. Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-building coral Acropora millepora. This analysis of a single full-sibling family revealed contrasting responses between short- (4-h) and long-term (5-day) exposures to elevated temperatures. Heat shock proteins were up-regulated only in the short-term treatment, while the long-term treatment induced the down-regulation of ribosomal proteins and up-regulation of genes associated with ion transport and metabolism (Ca(2+) and CO(3)(2-)). We also profiled responses to settlement cues using a natural cue (crustose coralline algae, CCA) and a synthetic neuropeptide (GLW-amide). Both cues resulted in metamorphosis, accompanied by differential expression of genes with known developmental roles. Some genes were regulated only by the natural cue, which may correspond to the recruitment-associated behaviour and morphology changes that precede metamorphosis under CCA treatment, but are bypassed under GLW-amide treatment. Validation of these expression profiles using qPCR confirmed the quantitative accuracy of our RNA-Seq approach. Importantly, qPCR analysis of different larval families revealed extensive variation in these responses depending on genetic background, including qualitative differences (i.e. up-regulation in one family and down-regulation in another). Future studies of gene expression in corals will have to address this genetic variation, which could have important adaptive consequences for corals during global climate change.
Aspergillus fumigatus tryptophan metabolic route differently affects host immunity (2021)

Indoleamine 2,3-dioxygenases (IDOs) degrade l-tryptophan to kynurenines and drive the de novo synthesis of nicotinamide adenine dinucleotide. Unsurprisingly, various invertebrates, vertebrates, and even fungi produce IDO. In mammals, IDO1 also serves as a homeostatic regulator, modulating immune response to infection via local tryptophan deprivation, active catabolite production, and non-enzymatic cell signaling. Whether fungal Idos have pleiotropic functions that impact on host-fungal physiology is unclear. Here, we show that Aspergillus fumigatus possesses three ido genes that are expressed under conditions of hypoxia or tryptophan abundance. Loss of these genes results in increased fungal pathogenicity and inflammation in a mouse model of aspergillosis, driven by an alternative tryptophan degradation pathway to indole derivatives and the host aryl hydrocarbon receptor. Fungal tryptophan metabolic pathways thus cooperate with the host xenobiotic response to shape host-microbe interactions in local tissue microenvironments.
Bcr-TMP, a Novel Nanomolar-Active Compound That Exhibits Both MYB- and Microtubule-Inhibitory Activity (2021)

Studies of the role of MYB in human malignancies have highlighted MYB as a potential drug target for acute myeloid leukemia (AML) and adenoid cystic carcinoma (ACC). Here, we present the initial characterization of 2-amino-4-(3,4,5-trimethoxyphenyl)-4<i>H</i>-naphtho[1,2-<i>b</i>]pyran-3-carbonitrile (Bcr-TMP), a nanomolar-active MYB-inhibitory compound identified in a screen for novel MYB inhibitors. Bcr-TMP affects MYB function in a dual manner by inducing its degradation and suppressing its transactivation potential by disrupting its cooperation with co-activator p300. Bcr-TMP also interferes with the p300-dependent stimulation of C/EBPβ, a transcription factor co-operating with MYB in myeloid cells, indicating that Bcr-TMP is a p300-inhibitor. Bcr-TMP reduces the viability of AML cell lines at nanomolar concentrations and induces cell-death and expression of myeloid differentiation markers. It also down-regulates the expression of MYB target genes and exerts stronger anti-proliferative effects on MYB-addicted primary murine AML cells and patient-derived ACC cells than on their non-oncogenic counterparts. Surprisingly, we observed that Bcr-TMP also has microtubule-disrupting activity, pointing to a possible link between MYB-activity and microtubule stability. Overall, Bcr-TMP is a highly potent multifunctional MYB-inhibitory agent that warrants further investigation of its therapeutic potential and mechanism(s) of action.
Potent human broadly SARS-CoV-2–neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2 (2022)

Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
Impaired Sphingolipid Synthesis in the Respiratory Tract Induces Airway Hyperreactivity (2013)

Asthma is a clinically heterogeneous genetic disease, and its pathogenesis is incompletely understood. Genome-wide association studies link ORM (yeast)-Like protein isoform 3 [corrected] (ORMDL3), a member of the ORM gene family, to nonallergic childhood-onset asthma. Orm proteins negatively regulate sphingolipid (SL) synthesis by acting as homeostatic regulators of serine palmitoyl-CoA transferase (SPT), the rate-limiting enzyme of de novo SL synthesis, but it is not known how SPT activity or SL synthesis is related to asthma. The present study analyzes the effect of decreased de novo SL synthesis in the lung on airway reactivity after administration of myriocin, an inhibitor of SPT, and in SPT heterozygous knockout mice. We show that, in both models, decreased de novo SL synthesis increases bronchial reactivity in the absence of inflammation. Decreased SPT activity affected intracellular magnesium homeostasis and altered the bronchial sensitivity to magnesium. This functionally links decreased de novo SL synthesis to asthma and so identifies this metabolic pathway as a potential target for therapeutic interventions.
Novelty Enhancements in Memory Are Dependent on Lateral Prefrontal Cortex (2009)

Physiological evidence indicates that several brain regions, including the medial temporal lobes and prefrontal cortex (PFC), are involved in processing events that are novel or distinctive in their immediate context. However, behavioral studies that investigate whether these regions are critical for producing stimulus novelty advantages in memory are limited. For example, evidence from an animal lesion study indicated that the PFC is involved in stimulus novelty effects, but this has not been examined in humans. In the current study, we used a von Restorff novelty paradigm to test a large cohort of lateral PFC patients (<i>n</i> = 16). We found that patients with lateral PFC damage were impaired in recollection- and familiarity-based recognition, and they did not exhibit a normal memory advantage for novel compared with non-novel items. These results provide neuropsychological evidence supporting a key role for the lateral PFC in producing stimulus novelty advantages in memory.
Conversion of Lignocellulosic Material into Fermentable Sugars (2012)

Die Umwandlung von Lignocellulose-Biomasse zu Biokraftstoffen ist eine vielversprechende Technologie, um diese einzigartige und nachhaltige Ressource zur Bereitstellung von umweltfreundlichen, organischen Brennstoffen und Chemikalien zu nutzen. Die meisten Projektionen zur globalen Energienutzung gehen davon aus, dass Biomasse eine wichtige Komponente der primären Energieversorgung in Zukunft sein wird. Hierbei stellt Agrarholz die primäre Quelle von Biomasse. Kurzumtrieb-Weidenholz (Salix sp.) gilt als vielversprechende Quelle von Bioenergie, denn Weidenholz besitzt mehrere Eigenschaften, die es ideal für für den agrarwirtschaftlichen Anbau machen. Zu diesen Eigenschaften gehören hohe Jahreserträge, eine breite genetische Basis, ein kurzer Fortpflanzungszyklus und die Fähigkeit, nach mehreren Ernten wieder austreiben zu erleichtern. Leider hat sich gezeigt, dass die enzymatische Hydrolyse von Lignocellulose-Biomasse zu Chemikalien und Kraftstoffe ein limitierender Faktor bei der Umwandlung von Biomasse ist. Diese Einschränkung ist bedingt durch innere strukturelle Merkmale (dh Acetylgehalt, Ligningehalt, Kristallinität Oberfläche, Teilchengröße und Porenvolumens) der Biomasse. Diese strukturellen Merkmale sind Barrieren, die eine vollständige Hydrolyse zu verhindern. Daher sind Vorbehandlung notwendigen, um die Biomasse weiter verarbeitbar zu machen. Bei der kurzeitigen, oxidativen Vorbehandlung mit Kalk wird Weidenholz mit einem Überschuß von Calciumhydroxid (0,4 g Ca (OH) 2 / g rohen Biomasse) gemischt und in Wasser suspendiert (15 g / g rohen Biomasse). Die Vorbehandlung mit Kalk wurde mit unterschiedlichen Verweilzeiten durchgeführt (1, 2, 3,5, 5, 6) Stunden, bei unterschiedlichen Temperaturen (100, 113, 130, 147, 160 ) und unterschiedlichen Drücken mit Sauerstoff als Oxidationsmittel (6, 9, 13.5, 17.8, 21 bar (absolut)). Optimierungsziel war eine maximale Gesamtausbeute von Glucan (g Glucan hydrolysiert / 100 g ursprünglichen glukan) und Xylan (g Xylan hydrolysiert / 100 g ursprünglichen Xylan) unter Verwendung einer Cellulose-Beladung von 0,1 g Enzym / g Glucan in Rohbiomasse, bei Substrattemperaturen Konzentration 50 g / L während 72 h von enzymatischen Hydrolyse. Die optimalen Bedingungen für kurzzeitige, oxidative Vorbehandlung mit Kalk von Weidenholz warden wie folgt: (1) 1,33 h, 147 , 17,8 bar absolut, 0,26 g Ca (OH) 2 / g rohen Biomasse und (2) 1,25 h, 155 und 21 bar absolut, 0,26 Ca (OH) 2 / g rohen Biomasse. In diesen beiden Fällen war die Reaktivität nahezu identisch, weshalb die ausgewählte Bedingungen einen wirtschaftlichen Kompromiss zwischen Druck und Temperatur darstellen. Die optimale Teilchengröße betrug weniger als 3 mm. Die Ergebnisse der enzymatische Hydrolyse unter diesen empfohlenen Bedingungen waren wie folgt: 96,00 g Glucan / 100 g von Glucan in rohen Biomasse und 65,00 g Xylan / 100 g Xylan in roher Biomasse
Recent Developments in Schlieren and Shadowgraphy (2010)

Schlieren and shadowgraph techniques are hundreds of years old, yet several important developments have occurred in the last decade, as summarized in this paper. Progress has been made in using the turbulent eddies of a refractive flow as “particle” tracers for seedless velocimetry. This approach will never supplant standard PIV, but “schlieren PIV” can be useful, for example, in cases where particles cannot be seeded in a turbulent flow under study. Background-oriented schlieren (BOS) has become very popular in just a few years. Given modern image-processing software for PIV or digital image correlation, a digital camera and a proper background, schlieren-like images of all sorts are easy to make without parabolic mirrors or even a knife-edge. “Rainbow schlieren” is the name for a quantitative schlieren instrument that uses color to make density, temperature, or species measurements in steady and unsteady planar or axisymmetric flows. Data acquisition and reduction are highly automated and the range of applications is very broad. Finally, shadowgraphy has not been forgotten: it is the simplest of all the optical flow visualization methods, but is often the best choice for imaging shock waves and turbulence. The addition of a retroreflective screen and a high-speed camera makes direct shadowgraphy a robust tool for the study of large-scale events in harsh environments.
Automated segmentation based upon remitted scatter spectra from pathologically distinct tumor regions (2009)

Multi-spectral scatter visualization of tissue ultra-structure <i>in situ</i> can provide a unique tool for guiding surgical resection, but since changes are subtle and the data is multi-parametric, an automated methodology was sought to interpret these data, in order to classify their tissue sub-type. Tissue types observed across AsPC-1 pancreatic tumor samples were pathologically classified under three major groups (epithelium, fibrosis and necrosis) and the variations in scattering parameters, i.e. scattering power, scattering amplitude and average scattered intensity, across these groups were analyzed. The proposed scheme uses statistical pre-processing of the scattering parameter images to create additional data features followed by a k-nearest neighbors (kNN) based algorithm for tissue type classification. The classification accuracy inside some predefined regions of interest was determined and the mean region values of scattering parameters turned out to be stronger data sets for classification, rather than the individual pixel values. This presumably indicates that pixel-to-pixel variations in the remitted spectra need to be minimized for reliable classification approaches. Results show a strong correlation between the automated and expert-based classification within the predefined regions of interest.
Hepatitis C Virus-Induced Cytoplasmic Organelles Use the Nuclear Transport Machinery to Establish an Environment Conducive to Virus Replication (2013)

Hepatitis C virus (HCV) infection induces formation of a membranous web structure in the host cell cytoplasm where the viral genome replicates and virions assemble. The membranous web is thought to concentrate viral components and hide viral RNA from pattern recognition receptors. We have uncovered a role for nuclear pore complex proteins (Nups) and nuclear transport factors (NTFs) in the membranous web. We show that HCV infection leads to increased levels of cytoplasmic Nups that accumulate at sites enriched for HCV proteins. Moreover, we detected interactions between specific HCV proteins and both Nups and NTFs. We hypothesize that cytoplasmically positioned Nups facilitate formation of the membranous web and contribute to the compartmentalization of viral replication. Accordingly, we show that transport cargo proteins normally targeted to the nucleus are capable of entering regions of the membranous web, and that depletion of specific Nups or Kaps inhibits HCV replication and assembly.
Dynamic rate‐based model for multicomponent batch distillation (1999)

Abstract Dynamic rate‐based approach for modeling and simulating batch distillation is presented. To predict separation efficiencies, mass transfer was considered explicitly using the Maxwell‐Stefan. Process dynamics were modeled by considering all relevant dynamic changes in the system, including the column periphery. The model, implemented at the large‐scale ABACUSS modeling environment, addresses implications of the dynamic and multicomponent nature of the process for its mathematical representation, the use of mass‐transfer coefficients, and the need for further experimental correlations. To validate the model, a series of separations of the highly nonideal quaternary system of methyl acetate, methanol, acetic acid, and water in a pilot‐plant batch‐distillation column with structured packings were conducted. The results show that a rate‐based approach can predict the column operation within the experimental error over the entire operation time without fitting of any kind. For the first time the use of a rate‐based approach on the ground of the Maxwell‐Stefan equations for a multicomponent batch‐distillation process was validated experimentally. Comparison of predictions of the rate‐based approach with simulations based on an equally tailored equilibrium‐stage model shows that the largest differences between the two approaches occur in short periods of very significant changes in the column profile. The additional effort of rate‐based modeling can be justified for the design of operating policies of multicomponent batch‐distillation processes.
An automated and efficient substrate noise analysis tool (2006)

This paper presents a methodology for the efficient modeling of substrate noise coupling. A closed-form Green's function for nonuniformly doped substrates is employed with the correct singular characteristics. A novel global surface impedance matrix scheme is introduced to efficiently model nonuniformly doped wells, channel stop implants, and buried layers. Layout, device, and netlist extractors are developed so as to integrate our boundary element method (BEM) solver with commercial layout and circuit simulation tools.
An Aldol-Based Build/Couple/Pair Strategy for the Synthesis of Medium- and Large-Sized Rings: Discovery of Macrocyclic Histone Deacetylase Inhibitors (2010)

An aldol-based build/couple/pair (B/C/P) strategy was applied to generate a collection of stereochemically and skeletally diverse small molecules. In the build phase, a series of asymmetric syn- and anti-aldol reactions were performed to produce four stereoisomers of a Boc-protected γ-amino acid. In addition, both stereoisomers of O-PMB-protected alaninol were generated to provide a chiral amine coupling partner. In the couple step, eight stereoisomeric amides were synthesized by coupling the chiral acid and amine building blocks. The amides were subsequently reduced to generate the corresponding secondary amines. In the pair phase, three different reactions were employed to enable intramolecular ring-forming processes: nucleophilic aromatic substitution (S(N)Ar), Huisgen [3+2] cycloaddition, and ring-closing metathesis (RCM). Despite some stereochemical dependencies, the ring-forming reactions were optimized to proceed with good to excellent yields, providing a variety of skeletons ranging in size from 8- to 14-membered rings. Scaffolds resulting from the RCM pairing reaction were diversified on the solid phase to yield a 14 400-membered library of macrolactams. Screening of this library led to the discovery of a novel class of histone deacetylase inhibitors, which display mixed enzyme inhibition, and led to increased levels of acetylation in a primary mouse neuron culture. The development of stereo-structure/activity relationships was made possible by screening all 16 stereoisomers of the macrolactams produced through the aldol-based B/C/P strategy.
SiC Foams Produced by Gel Casting: Synthesis and Characterization (2004)

SiC foams were fabricated by gelcasting with a commercially available powder and agar as gelling agent. Ceramic foams processed by gel casting have dense struts and are therefore mechanically stronger than foams produced by the conventional poly‐urethane replica method. First, special attention was given to the preparation and characterization of the powder suspension using silicon carbide powders which has been recognized as a high performance material.
Literatura e educação para os valores ambientais: Os Contos da Mata dos Medos , de Álvaro Magalhães (2013)

A afirmação da grandeza de tudo o que constitui a natureza, e a necessidade de nos concebermos numa relação de igualdade e respeito em relação a ela, é o tema dos Contos da Mata dos Medos . Nesta série de quatro narrativas, publicada entre 2003 e 2010, Álvaro Magalhães concilia o seu modo de ver a infância com ética animal, ecologia e consciência ambiental. O autor, partindo de personagens-animais que ilustram a biodiversidade de uma área do litoral do concelho de Almada (distrito de Lisboa), celebra a natureza e convida-nos a assumir perspectivas e comportamentos ecocêntricos. O Coelho, o Ouriço, o Chapim, a Toupeira, a Coruja ou o Caracol não têm como única função explicar o Homem. Estes animais aparecem-nos como seres que têm a sua dignidade própria e direito à vida como qualquer ser humano. Dotados de características próprias, eles procuram sobreviver num ambiente natural que lhes satisfaz todas as necessidades biológicas e oferece todos os bens materiais e espirituais, mas que, por ação do Homem, pode ser profundamente hostil.
Interoperable Grid Scheduling Strategies (2008)

The increasing demand for resources of the high performance computing systems has led to new forms of collaboration of distributed systems such as interoperable grid systems that contain and manage their own resources. While with a single domain one of the most important tasks is the selection of the most appropriate set of resources to d ispatch a job, in an interoperable grid environment this problem shifts to selecting the most ap propriate domain containing the requiring resources for the job. In the Latin American Grid initiative, our model consists of multiple domains. Each domain has its domain broker, and the task of scheduling on top of brokers can be called meta-brokering or broker selection. In this paper, we describe and evaluate our broker selection strategies. In particular, we present and evaluate the “bestBrokerRank” policy and two different variants. The first one uses the resource information in aggregated forms as input, and the second one also uses the brokers average bounded slowdown as a dynamic performance metric. From our evaluations performed with simulation tools, we firstly state that the interoperable grid sc enario is better compared to the independent brokering one in terms of execution time and resource utilization. We also show that the proposed resource aggregation algorithms are scalable for an interoperable grid environment. Moreover, we show that the best performance results are obtained with our coordinated policy. Therefore, we conclude that delegating part of the scheduling responsibilities to the underlying scheduling layers promote s separation of concerns and is a good way to balance the performance among the different brokers and schedulers.
Bromopyrrole Alkaloids from the Jamaican Sponge Didiscus Oxeata (2005)

Three bromopyrrole alkaloids (1–3) were isolated from the acetone extracts of Didiscus oxeata during chemical and biological investigation of Caribbean and Indo-Pacific marine sponges. The structures were established by spectroscopic methods. Mukanadin D (3) was obtained for the first time as a naturally-occurring C 11 bromopyrrole alkaloid.
Aptamer-Phage Reporters for Ultrasensitive Lateral Flow Assays (2015)

We introduce the modification of bacteriophage particles with aptamers for use as bioanalytical reporters, and demonstrate the use of these particles in ultrasensitive lateral flow assays. M13 phage displaying an in vivo biotinylatable peptide (AviTag) genetically fused to the phage tail protein pIII were used as reporter particle scaffolds, with biotinylated aptamers attached via avidin-biotin linkages, and horseradish peroxidase (HRP) reporter enzymes covalently attached to the pVIII coat protein. These modified viral nanoparticles were used in immunochromatographic sandwich assays for the direct detection of IgE and of the penicillin-binding protein from Staphylococcus aureus (PBP2a). We also developed an additional lateral flow assay for IgE, in which the analyte is sandwiched between immobilized anti-IgE antibodies and aptamer-bearing reporter phage modified with HRP. The limit of detection of this LFA was 0.13 ng/mL IgE, ∼100 times lower than those of previously reported IgE assays.