gebhart/patrepeval huggingface dataset:
Non-Gibbsian Markov random field models for contextual labelling of structured scenes (2007)

In this paper we propose a non-Gibbsian Markov random field to model the spatial and topological relationships between objects in s tructured scenes. The field is formulated in terms of conditional probabilities le arned from a set of training images. A locally consistent labelling of new scenes is achieved by relaxing the Markov random field directly using these condit ional probabilities. We evaluate our model on a varied collection of several hundred handsegmented images of buildings.
Increased IFN-γ Production by NK and NKT Cells From HIV-1-exposed But Uninfected Individuals (2005)

Background Innate immunity is very active at mucosal surfaces, that are the main port of viral entry; it is known that several components of the innate immune response have a direct anti-HIV-1 activity such IFNs and chemokines (1). Interestingly, a report (2) has indicated a high frequency of plasmocytoid dendritic cells and high production of IFNα in response to Herpex simplex virus infection in longterm non-progressors and long-term survivors, suggesting an important role of these innate mechanisms in the control of HIV-1 infection.
Accurate method to study static volume-pressure relationships in small fetal and neonatal animals (1994)

We designed an accurate method to study respiratory static volume-pressure relationships in small fetal and neonatal animals on the basis of Archimedes' principle. Our method eliminates the error caused by the compressibility of air (Boyle's law) and is sensitive to a volume change of as little as 1 microliters. Fetal and neonatal rats during the period of rapid lung development from day 19.5 of gestation (term = day 22) to day 3.5 postnatum were studied. The absolute lung volume at a transrespiratory pressure of 30-40 cmH2O increased 28-fold from 0.036 +/- 0.006 (SE) to 0.994 +/- 0.042 ml, the volume per gram of lung increased 14-fold from 0.39 +/- 0.07 to 5.59 +/- 0.66 ml/g, compliance increased 12-fold from 2.3 +/- 0.4 to 27.3 +/- 2.7 microliters/cmH2O, and specific compliance increased 6-fold from 24.9 +/- 4.5 to 152.3 +/- 22.8 microliters.cmH2O-1.g lung-1. This technique, which allowed us to compare changes during late gestation and the early neonatal period in small rodents, can be used to monitor and evaluate pulmonary functional changes after in utero pharmacological therapies in experimentally induced abnormalities such as pulmonary hypoplasia, surfactant deficiency, and congenital diaphragmatic hernia.
Modulatory effect of myricitrin against chromosome instability and cytostasis induced by bleomycin and oxaliplatin in CHO-K1 cells (2022)

Myricitrin (MYR), a flavonol consumed in the leaves and fruits of plants of the <i>Myrtaceae</i> family, presents anti-proliferative, anti-inflammatory, anti-diabetic, and antioxidant properties in humans. However, there are few studies regarding the cyto-genotoxicity and the chemopreventive potential of MYR. Using the <i>in vitro</i> Micronucleus test, the cytostasis, mutagenicity, and modulatory effect of MYR in CHO-K1 cells were assessed. The concentrations of 39 and 78 µg/mL (<i>p</i> < 0.001.) of MYR decrease the cytokinesis-block proliferation index (CBPI) in the short exposure treatment (4 h), while in the extended treatment (24 h), concentrations of 4.8, 9.7, 19.5, 39 and 78 µg/mL (<i>p</i> < 0.001.) decreased the CBPI. MYR associated with oxaliplatin decreased CBPI at all tested concentrations in the pre-(<i>p</i> < 0.001) and post-treatments (<i>p</i> < 0.001), but there was no decrease when associated with bleomycin. As for chromosome instability, MYR did not increase the frequency of micronuclei (MNi), nucleoplasmic bridges (NPBs), or nuclear buds (NBUDs) in the 4 h exposure time, however, in the 24 h treatment, MYR increased the frequency of MNi and NPBs at concentration 19.5 µg/mL (<i>p</i> < 0.001). As for the modulatory effect, MYR associated with bleomycin decreased the frequency of MNi, NPBs, and NBUDs at all concentrations in the pretreatment (MNi and NPBs <i>p</i> < 0.001, NBUDs <i>p</i> < 0.05) and simultaneously (MNi, NPBs and NBUDs <i>p</i> < 0.001). When associated with oxaliplatin, the simultaneous treatment decreased the frequency of MNi (<i>p</i> < 0.001) and NBUDs (<i>p</i> < 0.01) at all concentrations, however, in the post-treatment, MYR increased MNi (<i>p</i> < 0.001) and NPBs <i>p</i> < 0.05) in CHO-K1 cells, when compared to oxaliplatin alone. The results demonstrated that MYR could modulate the mutagenic and cytostatic actions of bleomycin and oxaliplatin, demonstrating distinct behaviors, depending on the mechanism of action of the chemotherapeutic agent.
Research on Polymers as Sizing Agents—Laboratory to Loom (1984)

Earlier research on the development of durable polymeric sizing agents for room temperature application to cotton yarns has been expanded to full warp slashing and weaving evaluation. Weaving of yarns treated with high concentra tions of a low-temperature-cure polyacrylate, with a glass transition temperature of 0°C, were unsuccessful. Trials using a similar polyacrylate with Tg, 33°C and/or a polyurethane with film forming temperature of 28°C have been much more en couraging. Film properties of various formulations have been described and treated yams have been evaluated for breaking strength, elongation, and abrasion resistance.
Characterizing the hydraulic properties of paper coating layer using FIB-SEM tomography and 3D pore-scale modeling (2016)

Paper used in the printing industry generally contains a relatively thin porous coating covering a thicker fibrous base layer. The three-dimensional pore structure of coatings has a major effect on fluid flow patterns inside the paper medium. Understanding and quantifying the flow properties of thin coating layers is hence crucial. Pore spaces within the coating have an average size of about 180 nm. We used scanning electron microscopy combined with focused ion beam (FIB-SEM) to visualize the nano-scale pore structure of the paper coating layer. Post-processing of the FIB-SEM images allowed us to reconstruct the three-dimensional pore space of the coating. The 3D FIB-SEM images were analyzed in detail to obtain pore size distribution and porosity value. The permeability was estimated using the GeoDict software, based on solutions of the Stokes equation. By determining the porosity and permeability of increasingly larger domain sizes, we estimated the size of a representative elementary volume (REV) for the coating layer to be 60 µm3, which is well within the volume analyzed using FIB-SEM. The estimated porosity and permeability of the REV domain were 0.34 and 0.09 mDarcy, respectively. Using the pore morphology method, capillary pressure-saturation (Pc-S) and relative permeability curves of the REV domain could be constructed next. The Pc-S curves showed that the coating had a high air entry suction, which is very favorable for printing in that ink will invade the coating as soon as it is applied to the coating. Our results are essential for macroscale modelling of ink penetration into a coating layer during inkjet printing. Macroscopic models can be valuable tools for optimization of the penetration depth and the spreading of ink on and within paper substrates.
Author response: Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions (2021)

Through interactions with both ubiquitin units that emanate from a branch point in polyubiquitin, UCH37 recognizes and hydrolyzes branched chains to promote proteasome-mediated degradation upon proteolytic stresses.
Cationic Donor–Two-Acceptor Dye–Graphene Quantum Dot Nanoconjugate for the Ratiometric Detection of Bisulfite Ions and Monitoring of SO2 Levels in Heat-Stressed Cells (2023)

When the body temperature rises above 40.6 °C, heat stress in the cells causes mitochondrial damage. This damage can lead to apoptosis, multiple organ failure, and even death. The dysregulation of SO2 levels in the mitochondria is linked to this heat stress, and its detection may act as an early indicator of heat stroke. Graphene quantum dots (GQDs), a common class of zero-dimensional carbon-based fluorescent nanomaterials, have shown immense potential as sensory probes, and it is a prospective candidate for monitoring SO2 levels in living cells. Herein, we report a combination of a donor–two acceptor (D2A) red-emissive di-picolinium salt (PPy-Br) and hydroxy-functionalized graphene quantum dots (GQDs-OH) as the fluorescence resonance energy transfer (FRET)-based ratiometric sensor for bisulfite ions detection in aqueous media. The dye-GQD nanoconjugate displays excellent photostability and good aqueous dispersibility allowing the monitoring of SO2 levels in living cells during heat stress. The PPy-Br:GQD nanoconjugate is indifferent to a large number of cations, anions, or biologically relevant species and displays a detection limit of 36 nM for the solution phase detection of bisulfite. PPy-Br is biocompatible with human cell lines and endocytoses into the cells to ensure monitoring of SO2 levels in the mitochondrial milieu. PPy-Br-treated human breast cancer cells displayed a gradual decrease in fluorescence at temperatures above 40 °C, indicating an increase in SO2 levels in heat-stressed cells. The PPy-Br:GQDs sensing conjugate is efficient in the real-time monitoring of intracellular SO2 levels and demonstrates enough prospects for further explorations as a diagnostic kit for heat stroke monitoring.
ChemInform Abstract: A Short Route to Malto‐trisaccharide Synthons: Synthesis of the Branched Nonasaccharide, 6′′‐α‐Maltotriosyl‐maltohexaose. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
68Ga- and 177Lu-Labeled PSMA I&T: Optimization of a PSMA-Targeted Theranostic Concept and First Proof-of-Concept Human Studies (2015)

(68)Ga-PSMA I&T shows potential for high-contrast PET imaging of metastatic PC, whereas its (177)Lu-labeled counterpart exhibits suitable targeting and retention characteristics for successful endoradiotherapeutic treatment. Prospective studies on larger cohorts of patients are warranted and planned.
EWS–FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex (2019)

Connections between epigenetic reprogramming and transcription or splicing create novel mechanistic networks that can be targeted with tailored therapies. Multiple subunits of the chromatin remodeling BAF complex, including ARID1A, play a role in oncogenesis, either as tumor suppressors or oncogenes. Recent work demonstrated that EWS-FLI1, the oncogenic driver of Ewing sarcoma (ES), plays a role in chromatin regulation through interactions with the BAF complex. However, the specific BAF subunits that interact with EWS-FLI1 and the precise role of the BAF complex in ES oncogenesis remain unknown. In addition to regulating transcription, EWS-FLI1 also alters the splicing of many mRNA isoforms, but the role of splicing modulation in ES oncogenesis is not well understood. We have identified a direct connection between the EWS-FLI1 protein and ARID1A isoform protein variant ARID1A-L. We demonstrate here that ARID1A-L is critical for ES maintenance and supports oncogenic transformation. We further report a novel feed-forward cycle in which EWS-FLI1 leads to preferential splicing of ARID1A-L, promoting ES growth, and ARID1A-L reciprocally promotes EWS-FLI1 protein stability. Dissecting this interaction may lead to improved cancer-specific drug targeting.
Interpreting Embedding Spaces by Conceptualization (2022)

One of the main methods for computational interpretation of a text is mapping it into a vector in some embedding space. Such vectors can then be used for a variety of textual processing tasks. Recently, most embedding spaces are a product of training large language models (LLMs). One major drawback of this type of representation is their incomprehensibility to humans. Understanding the embedding space is crucial for several important needs, including the need to debug the embedding method and compare it to alternatives, and the need to detect biases hidden in the model. In this paper, we present a novel method of understanding embeddings by transforming a latent embedding space into a comprehensible conceptual space. We present an algorithm for deriving a conceptual space with dynamic on-demand granularity. We devise a new evaluation method, using either human rater or LLM-based raters, to show that the conceptualized vectors indeed represent the semantics of the original latent ones. We show the use of our method for various tasks, including comparing the semantics of alternative models and tracing the layers of the LLM. The code is available online https://github.com/adiSimhi/Interpreting-Embedding-Spaces-by-Conceptualization.
DTS Measurements in Oil and Gas Production and Storage Wells (2017)

The temperature distribution inside a production well or inside a storage facility and its variation with time and depth are key parameters for assessing operating conditions. In combination with geological and petrophysical data, long-term temperature monitoring of underground storage facilities can provide thermodynamic information on reservoir dynamics. The storage capacity (gas volume and injection/withdrawal rates) strongly depends on temperature. The same is true for the dew point, the vapour pressure and chemical reactions. Knowing exactly about temperature vs. depth and time in a production well of a cavern or aquifer storage facility is crucial when it comes to optimizing the methanol inhibition regime (methanol/glycol) and the operating conditions. From a known well head pressure and the thermodynamic equation of state one can derive the pressure profile based on the temperature profile. Moreover, the temperature dependence of pressure opens the chance to measure and survey fluid levels in aquifer boreholes.
The Biochemistry of Neoplastic Tissue (1952)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Completing the puzzle of aurachinbiosynthesis in Stigmatella aurantiaca Sg a15 (2011)

The aurachins are a family of secondary metabolites, with the main members aurachin A, B, C, and D, produced by the myxobacterium Stigmatella aurantiaca Sg a15. These isoprenoid quinoline alkaloids are classified as A-type or C-type aurachins according to the position of the farnesyl residue either at C4 or C3 of the quinoline core, respectively. Previous feeding studies revealed that the C-type aurachins are converted to A-type aurachins by late stage tailoring reactions. While the core gene cluster coding for the functionalities required for the biosynthesis of the basic structure aurachin D is known, neither of the genes encoding for the successively acting tailoring enzymes was known up to date, which was assumed to be due to a split cluster organisation. Here we describe the identification of a total of five genes, located upstream of the aurachin core cluster and at additional two loci elsewhere in the genome, encoding for the aforementioned functionalities. The generation and evaluation of respective inactivation mutants of S. aurantiaca Sg a15 allowed for the first time to propose an exhaustive model for aurachin biosynthesis. One of the deduced biosynthetic transformations corresponds to a pinacol rearrangement, an unprecedented tailoring reaction in secondary metabolite biosynthesis.
Ground mapping using active and passive UHF-band SAR (2020)

Synthetic-aperture radar (SAR) is normally used in an active mode for ground surveillance. Passive SAR has also been demonstrated using DVB-T (Digital Video Broadcasting – Terrestrial) signals from TV-broadcasting masts as illuminators of opportunity. However, simultaneous active and passive SAR have not yet been demonstrated. In this paper, we compare active and passive SAR and describe a system which can perform acquisition of both active and passive UHF-band SAR-data onboard an airborne platform. We also show, for the first time, active and passive SAR images processed from data acquired during the same flight.
Novel Online Sensorless Dual-Axis Sun Tracker (2016)

In this study, a novel online sensorless dual-axis sun tracker regulated by the maximum power point tracking (MPPT) unit is proposed. The MPPT controller continuously calculates the maximum output power of the photovoltaic module/panel/array, and uses the altitude and azimuth angles deviations to find the sun direction where the greatest value of the maximum output power is extracted. Unlike all the other sensorless sun trackers that operate as open-loop systems, the proposed sun tracker is a closed-loop system, which uses the actual direction of the sun at any time to track the sun direction and this is the contribution of this study. The proposed sun tracker has the advantages of both sensor-based and sensorless dual-axis sun trackers, but it does not have their disadvantages. A photovoltaic system has been constructed, and it is experimentally verified that the proposed sun tracker finds the sun direction with the tracking error of only 0.11° which is less than the tracking errors of other both sensor-based and sensorless trackers. An increase of 28.8%-43.6% in the captured solar energy depending on the seasons is the main advantage of utilizing the proposed sun tracker.
High-contrast reflection modulation at normal incidence in asymmetric multiple quantum well Fabry-Perot structure (1989)

We have modelled the properties of a multiple quantum well pin diode optical modulator with the natural semiconductor reflectivity (R ≈ 0.3) at its front surface and a high reflector (R ≈ 0.95), such as an integrated semiconductor quarterwave stack, at the back. By using resonant electroabsorption, rather than electrorefraction, our calculations show that it is possible to achieve contrast ratios of over 200, with less than 3dB insertion loss.
Correlations of oral bacterial arginine and urea catabolism with caries experience (2009)

This study supports the theory that increased caries risk is associated with reduced alkali-generating capacity of the bacteria colonizing the oral cavity; providing compelling evidence to further our understanding of oral alkali-generation in health and disease.
STEREOSELECTIVE HYDROLYSIS OF AMINO ACID ESTERS IN MODIFIED LINEAR POLY(ETHYLENIMINE) DOMAINS (1984)

Abstract A large rate enhancement and a stereoselective preference are exhibited in the hydrolysis catalysed by N-decanoyl-l-histidine(2a) and a dipeptide containing l-histidyl residue (2b) in the domain of linear poly(ethylenimine) derivatives.
Transluminal Aortic Valve Placement (1996)

Percutaneous stents are used in vascular applications in conjunction with angioplasly and in combination with graft material for repair of abdominal aneurysms. The authors have designed a collapsible bioprosthetic aortic valve for placement by a transluminal catheter technique. This trileaflet stent valve is composed of stainless steel and bovine pericardium. Stent valves, 23 and 29 mm, were tested in a pulse duplicator system with rigid rings from 21 to 31 mm in 2 mm increments. At a mean flow of 3.1 L/min ($$0.7), normal systemic aortic pressure was generated with a transvalvular gradient of 14.9 ± 7 mmHg (mean$$ SD). Regurgitation fraction ranged from 10 to 18% (mean 13.8 ± 3%) in the best ring size. Valves with the best hemodynamic profile were used for implantation in three 70 kg pigs in an open chest model. The valve was collapsed in a 24 Fr catheter designed to allow slow, controlled release. After resection of the native leaflets, the new valve was placed in the subcoronary position. No additional sutures were used for securing the valve. Two animals were successfully weaned from cardiopulmonary bypass and maintained systemic pressures of 100/45 ($$10) and 116/70 ($$15) mmHg, respectively, Intraoperative color echocardiography revealed minimal regurgitation, central flow, full apposition of all leaflets, and no interference with coronary blood flow. Both animals were sacrificed after being off bypass for 2 hr. Postmortem examination revealed the valves to be securely anchored. The third animal was weaned from cardiopulmonary bypass but developed refractory ventricular fibrillation because of valve dislodgment due to structural failure. Although long term survival data are needed, development of a hemodynamically acceptable prosthetic aortic valve for transluminal placement is feasible.
Expression profiles of phosphatidylinositol phosphate kinase genes during normal human in vitro erythropoiesis (2012)

Phosphatidylinositol phosphate kinases (PIPKs) are enzymes that participate in diverse intracellular signaling pathways. They are classified into 3 functionally distinct subfamilies - PIPKI (α, β, γ), PIPKII (α, β, γ), and PIPKIII - located in various subcellular compartments. Recently, the PIPKIIα and β-globin genes were found to be overexpressed in reticulocytes from 2 siblings with hemoglobin H disease, suggesting a possible relationship between PIPKIIa and the production of globins. The main aim of this study was to determine the expression profiles of PIPK genes in healthy individuals during in vitro erythropoiesis using quantitative real-time polymerase chain reaction and to compare these profiles with profiles of globin genes. Our results showed that expression of all PIPKs increases as the cells differentiate, coinciding with the expression profiles of globins. Analysis of the effects of globins on PIPK genes revealed that they varied significantly between the globins, the most noticeable being the effect of α-globin on PIPKIIα (P < 0.0001) and γ-globin on PIPKIIγ (P < 0.0001). The relationship between the expression of PIPKs and globin genes was statistically significant, particularly between PIPKIIα and α-globin (P = 0.0002) and PIPKIIγ and β-globin (P < 0.0001). Linear correlation analysis revealed a strong relationship between PIPKIIα and α-globin genes. This study is the first to establish the expression profiles of PIPK genes during in vitro erythropoiesis in healthy individuals and suggests a parallel between the expression of PIPK and globin genes, reinforcing the hypothesis that they may be related.
Direct estimation of musical pitch contour from audio data (2004)

The increasing amount of music being stored in digital formats calls for increasingly more creative methods for music information retrieval. One subset of music retrieval methods relies on storing a melody in a pitch contour representation. Most often, this contour information is generated either from symbolic format (MIDI) or from raw audio after a pitch transcription step. We propose a method of extracting pitch contour information from musical audio without an intermediate transcription step by combining a musically-tuned constant Q transform with crosscorrelation. When tested on a database of 520 monophonic music recordings, our method generates pitch contours from raw audio data with up to 98% accuracy.