gebhart/patrepeval huggingface dataset:
Resources, standards and tools for systems biology (2007)

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation. In this review, we describe different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology.
Quantitation Of Gas Production In Laser Angiosurgery With An Optically-Shielded Laser Catheter (1987)

This study quantitates the amount of gas produced when firing an optically shielded argon ion laser into 0.9% saline solution and blood alone, and into atheromatous aorta in either a blood or 0.9% saline medium. Energies from 0.25 to 4 J were used at powers of 2, 5, and 8 watts. We found that total volume of gas produced is small not only at equilibrium (0.3 + 0.1 ul/J when firing in blood alone and also firing in aorta in blood or saline medium), but also at peak (2.5 + 0.2 ul/J firing in blood alone and 1.0 + 0.1 ul/J or 0.9 + 0.1 ul/J when ablating aorta in saline or aorta, respectively). The peak gas volume when firing in blood alone was significantly greater than the other chamber environments. This is thought to be due to increased absorption of argon laser light by hemoglobin. The gas volumes produced by lasing aorta in 0.9% saline or blood were not statistically different. This finding is attributed to the catheter design which has a quartz tip surrounding the optical fiber that acts to displace the media from the lasing field. This catheter design negates the effect the medium might have on the laser light/target interaction.
Nonruminant Nutrition : Effect of Dietary β-Mannanase Supplementation and Palm Kernel Meal Inclusion on Laying Performance and Egg Quality in 73 Weeks Old Hens (2013)

This study was conducted to evaluate the effect of dietary β-mannanase supplementation and palm kernel meal (PKM) inclusion (5%) on laying performance, egg quality and nutrient utilizability of laying hens with 73 weeks of age. A total of 240 Lohmann brown laying hens with average 77.5% egg production were randomly allocated with 60 hens per treatment, 4 replicates per treatment and 15 hens per replicate. Experimental design was a completely randomized design with 2 x 2 factorial arrangement, with the factors being (1) two levels of PKM (0 vs. 5%) and (2) with or without dietary β-mannanase (480 IU/㎏ of diet CTCzyme) supplementation. All hens were housed in cages (35 ㎝W ×35 ㎝H) with 2 hens per cage for six weeks feeding trial. Laying performance was recorded daily during feeding trial. Egg quality, nutrients utilizability and blood assays were done at the end of feeding trial. Egg production was improved (P<0.05) by both dietary PKM inclusion and β-mannanase combined supplementation. Either β-mannanase or PKM did not affect feed intakes and feed conversion ratio of all diets. Egg weight of hens fed diet containing 5% of PKM had heavier (P<0.05) eggs compared with hens fed without PKM. Albumen height was improved (P<0.05) by dietary mannanase supplementation. Crude fat utilization of 5% PKM diet was higher than that of no PKM diet regardless of β-mannanase supplementation. Both DM and total carbohydrate utilization were decreased (P<0.05) in hens fed 5% PKM diet. Serum IgG and yolk IgY contents of PKM groups were lower (P<0.05) than those of no PKM groups. This result showed that 5% PKM diet, independent of dietary β-mannanase supplementation, was able to improve egg production. In addition, dietary β-mannanasc supplementation could be used for improving the albumen height of eggs.
A 3.9 μs Settling-Time Fractional Spread-Spectrum Clock Generator Using a Dual-Charge-Pump Control Technique for Serial-ATA Applications (2015)

A low-jitter fractional spread-spectrum clock generator (SSCG) utilizing a fast-settling dual-charge-pump (CP) technique is developed for serial-advanced technology attachment (SATA) applications. The dual-CP architecture reduces a design area to 60% by shrinking an effective capacitance of a loop filter. Moreover, the settling-time is reduced by 4 μ s to charge a current to the capacitor by only main-CP in initial period in settling-time. The SSCG is fabricated in a 0.13 μ m CMOS and achieves settling time of 3.91 μ s faster than 8.11 μ s of a conventional SSCG. The random jitter and total jitter at 250 cycles at 1.5 GHz are less than 3.2 and 10.7 psrms, respectively. The triangular modulation signal frequency is 31.5 kHz and the modulation deviation is from −5000 ppm to 0 ppm at 1.5 GHz. The EMI reduction is 10.0 dB. The design area and power consumption are 300 × 700 μ m and 18 mW, respectively.
Supplementary Figure 6 from Activation of Hematopoietic Stem/Progenitor Cells Promotes Immunosuppression Within the Pre–metastatic Niche (2023)

&lt;p&gt;Ex vivo tumor-mediated bone marrow expansion&lt;/p&gt;
Packed‐bed reactor for short time gas phase olefin polymerization: Heat transfer study and reactor optimization (2011)

Abstract A specially conceived packed‐bed stopped flow minireactor (3 mL) suitable for short gas phase catalytic reactions has been used to study the start‐up of ethylene homopolymerization with a supported metallocene catalyst. Focus has been put on the heat transfer characteristics of the supported catalysts and on understanding the relationship between the initial rate and the relative gas/particle velocities and the influence of particle parameters in the packed bed. We performed a comprehensive study on the influence of various physical parameters on the heat transfer regime at start up conditions. The catalyst activity as well as the polymer morphology is shown to be dependent on heat transfer regime. The knowledge thus obtained is applicable to industrial problems like catalyst injection in fluidized beds and helps preventing experimental artifacts due to overheating in following studies. © 2011 American Institute of Chemical Engineers AIChE J, 2012
The anatomy of a Clustering Engine for Web Snippets (2004)

Recently there has been a surge of commercial interest about novel IR-tools, like Vivisimo or Groxis, that support the user of a search engine in his/her query formulation and query refinement. The basic idea is that the snippets returned by the search engine are grouped into clusters which are then organized in a hierarchy whose nodes are properly labeled via meaningful sentences. Each sentence must capture the "theme" of the snippets contained into the cluster it labels.&#13;\nThis way the user is provided with a small, but intelligible, picture of the query answers at various levels of details. &#13;\nDespite this commercial interest, we found just four scientific papers on this topic. None of them achieved results comparable to Vivisimo, that actually represents the state-of-the-art. In the present paper we address this problem in its full generality: labels of variable length &#13;\nfor denoting the clusters, labels drawn from the Web snippets as non contiguous sequences of terms, clusters possibly overlapping and organized within a hierarchy. We achieve this results by means of an algorithmic approach that exploits some innovative ideas, at least from the academic side!
Study of SiO2 Interfacial Layer Growth during Fabrication Process of Ferroelectric HfxZr1−XO2-Based Metal-Ferroelectric Semiconductor (2021)

We studied a SiO2 interfacial layer (SiO2-IL) growth between a ferroelectric HfxZr1−xO2 (HZO) film, which fabricated by atomic layer deposition (ALD) using a Hf/Zr cocktail precursor, and p-type Si substrate during the metal-ferroelectric-semiconductor (MFS) fabrication. For the annealing process, two types of a post-deposition annealing (PDA) and post-metallization annealing (PMA) were employed before and after the fabrication of the TiN top-electrodes, respectively. An ultra-thin SiO2-IL of one or two monolayers at the HZO/Si interface was achieved using a 300°C fabrication process of ALD, and PDA or PMA. In contrast, PDA and PMA processes at ≥ 400°C led to an unexpected SiO2-IL formation, which increased with the annealing temperature, regardless of the formation of TiN top-electrodes. Therefore, we found that a suppressed SiO2-IL of HZO-based MFS structures can be obtained using the 300°C fabrication process.
ERG Cooperates with Androgen Receptor in Regulating Trefoil Factor 3 in Prostate Cancer (2010)

To elucidate the role of ETS gene fusions in castration-resistant prostate cancer (CRPC), we characterized the transcriptome of 54 CRPC tumor samples from men with locally advanced or metastatic disease. Trefoil factor 3 (TFF3) emerged as the most highly differentially regulated gene with respect to ERG rearrangement status and resistance to hormoneablation therapy. Conventional chromatin immunoprecipitation (ChIP)–polymerasechain reaction andChIPfollowed by DNA sequencing (ChIP-seq) revealed direct binding of ERG to ETS binding sites in theTFF3promoter inERG-rearranged prostate cancer cell lines. These results were confirmed in ERG-rearranged hormone-naive prostate cancer (HNPC) and CRPC tissue samples. Functional studies demonstrated that ERG has an inhibitory effect on TFF3 expression in hormonenaive cancer but not in the castration-resistant state. In addition, we provide evidence suggesting an effect of androgen receptor signaling on ERG-regulated TFF3 expression. Furthermore, TFF3 overexpression enhances ERG-mediated cell invasion in CRPC prostate cancer cells. Taken together, our findings reveal a novel mechanism for enhanced tumor cell aggressiveness resulting from ERG rearrangement in the castration-resistant setting through TFF3 gene expression.
Abstract 583: Single Cell Analysis of Monocytes and Macrophages in the Infarcted Heart (2019)

Introduction: Ischemic Heart Disease (IHD), the leading cause of death in the world, is often initiated by myocardial infarction (MI). In mice, death typically occurs on day 4 after acute MI is induced by coronary artery ligation. At this time the interferon regulatory factor 3 (IRF3)/type I interferon (IFN) pathway is activated almost exclusively in mononuclear cells in the infarct. We have shown that the genetic or pharmacologic disruption of critical components of this innate immune pathway reduces inflammation, limits ventricular dilation and contractile dysfunction, and improves survival. Hypothesis: Treatment with the IFNAR neutralizing antibody will bias the differentiation of cardiac macrophages and in doing so establish a cardioprotective environment in the infarct. Methods: We conducted single cell RNA-sequencing analysis of mononuclear cells isolated from infarct tissue collected on day 4 after MI from mice that had been treated with an IFNAR neutralizing antibody (Ab) as well as untreated mice. Results: Analyses demonstrate the presence of 3 core cell populations in the untreated sample: monocytes expressing Plac8 and Ms4a4c , phagocytic macrophages expressing Mrc1 and Ccl8 , and reparative macrophages expressing Arg1 and Fn1 . In addition, the dramatic co-expression of related genes in response to environmental stimuli, such as secreted type I IFNs or reactive oxygen species (ROS), resulted in the formation of two more clusters of cells. One cluster was marked by the expression of interferon stimulated genes. The other was marked by the expression of an established anti-oxidant transcriptional program. Anti-interferon therapy with IFNAR Ab inhibited both the interferon stimulated genes and the anti-oxidative transcriptional program. Conclusion: We have defined the differentiation patterns of monocytes and macrophages within the infarcted heart on day 4 after MI. Treatment with the IFNAR Ab after MI alters the composition of macrophage subsets.
A model of catheter‐associated urinary tract infection initiated by bacterial contamination of the catheter tip (2008)

The present results are consistent with the hypothesis that contamination of the tip of the catheter while it is being inserted is a possible means by which bacteria gain access to the bladder.
Magnetic Neurosurgery (1996)

Because of the complex shape of many brain structures, the ideal brain probe would be highly flexible and give the neurosurgeon the ability to independently and precisely control movement of the probe tip. A magnetic surgery system has been developed that implements this concept. Flexible brain probes with small permanent magnetic tips are placed on the brain surface through a small burr hole and then magnetically manipulated within the brain. Drive forces are produced by an array of six superconducting magnets suspended within a cryostatic helmet. They produce a maximum force of 3 times the threshold needed to move the probe through the parenchymal tissues at its normal speed of 1 mm/s. Computer-controlled magnetic impulses precisely direct the probe movement in any direction desired with movement accuracy of 0.47 mm in phantom gels. Probe position is monitored 3 times per second with orthogonally oriented microchannel plate X-ray systems, X-ray dose from a 3-hour simulated procedure is comparable to that of a chest X-ray. In vivo and in vitro feasibility studies have been carried out in dog and pig brains. Preclinical trials are planned for clinical applications including implantation of flexible brachytherapy threads.
G-104 The Helicobacter pylori adhesin protein HopQ exploits the dimer interface of human CEACAMs for oncoprotein translocation (2018)

Helicobacter pylori infects half of the world's population and strains that encode the cag type IV secretion system for injection of the oncoprotein CagA into host gastric epithelial cells are associated with elevated levels of cancer. CagA translocation into host cells is dependent on interactions between the H. pylori adhesin protein HopQ and human CEACAMs. Here, we present high-resolution structures of numerous HopQ-CEACAM complexes and CEACAMs in their monomeric and dimeric forms establishing that HopQ uses a coupled folding and binding mechanism to engage the canonical CEACAM dimerization interface for CEACAM recognition. By combining mutagenesis with biophysical and functional analyses, we show that the modes of CEACAM recognition by HopQ and CEACAMs themselves are starkly different. Our data describe precise molecular mechanisms by which microbes exploit host CEACAMs for infection and enable future development of novel oncoprotein translocation inhibitors and H. pylori-specific antimicrobial agents.
Detection of TNT and Picric Acid on Surfaces and in Seawater by Using Photoluminescent Polysiloles (2001)

Nitroaromatic explosives can be detected in a simple and rapid method by the quenching of the photoluminescence of fluorescent polysiloles. Quenching is achieved by electron transfer from the conduction band of the polysiloles to electron-poor molecules such as picric acid, nitrobenzene, 2,4-dinitrotoluene (DNT), and 2,4,6-trinitrotoluene (TNT). Dilute polymer solutions can also be employed as a forensic spray-on reagent to visualize TNT or picric acid residues under a UV lamp (see picture of the print of a nitrile-gloved hand that had been in contact with TNT).
Supplementary Figure 2 from Temporal Dissection of Tumorigenesis in Primary Cancers (2023)

Supplementary Figure 2 from Temporal Dissection of Tumorigenesis in Primary Cancers
ChemInform Abstract: Synthesis of Enantiopure Substituted Piperidines via an Aziridinium Ring Expansion. (2011)

Abstract The ring expansion of chiral pyrrolinols proceeds via intermediate aziridine formation which is followed by treatment with various C‐, N‐, O‐ and S‐nucleophiles.
Thirteen-channel wavelength division demultiplexer based on polymer waveguide holograms (1994)

We present a thirteen-channel infrared wavelength division demultiplexer based on multiplexed phase-matched volume holograms recorded in a graded index (GRIN) polymer thin film waveguide. Channel center wavelengths ranged from 844 to 976 nm (11 nm channel separation), with corresponding output diffraction angles of 22 degree(s) to 70 degree(s) (4 degree(s) between channels). The device demonstrated diffraction efficiencies from 40% to 65% with an average channel crosstalk of -17.2 dB, which is largely attributable to the spectral width of the Ti:Al<SUB>2</SUB>O<SUB>3</SUB> laser source. The optical power requirements of the system are evaluated and shown to be well within practical limits.
Purification and characterization of glucosidase II involved in N-linked glycoprotein processing in bovine mammary gland (1987)

Glucosidase I, the first enzyme involved in the post-translational processing of N-linked glycoproteins, was purified to homogeneity from the lactating bovine mammary tissue. The enzyme was extracted by differential treatment of the microsomal fraction with Triton X-100 and Lubrol PX. The solubilized enzyme was subjected to affinity chromatography on Affi-Gel 102 with N-5-carboxypentyldeoxynojirimycin as ligand and DEAE-Sepharose CL-6B chromatography. Purified glucosidase I shows a molecular mass of 320-330 kDa by gel filtration on Sephacryl S-300. SDS/polyacrylamide-gel electrophoresis under reducing conditions indicates a single band of approx. 85 kDa, indicating that the native enzyme is probably a tetrameric protein. Several criteria, including pH optimum of 6.6-7.0, specific hydrolytic action towards Glc3Man9GlcNAc2, to release the terminally alpha-1,2-linked glucosyl residue, and total lack of activity towards Glc1Man9GlcNAc2 and Glc2Man9GlcNAc2 saccharides, which are the biological substrates for processing glucosidase II, and 4-methylumbelliferyl alpha-D-glucopyranoside show the non-lysosomal origin and the processing-specific role of the purified enzyme. The enzyme does not require any metal ions for its activity. Hg2+, Ag+ and Cu2+ are potent inhibitors of the enzyme; this inhibition can be reversed by adding an excess of dithiothreitol. Among the saccharides tested, kojibiose (Glc alpha 1----2Glc) was inhibitory to the enzyme. Polyclonal antibodies raised against the enzyme in rabbit were found to be specific for glucosidase I, as revealed by Western-blot analysis and by immunoadsorption with Protein A-Sepharose. Anti-(glucosidase I) antibodies were cross-reactive towards a similar antigen in solubilized microsomal preparations from liver, mammary gland and heart from the bovine, guinea pig, rat and mouse.
Analytical Platform for Glycomic Characterization of Recombinant Erythropoietin Biotherapeutics and Biosimilars by MS (2013)

This platform may be applied to QC and batch analysis of not only recombinant erythropoietin, but also other complex, glycosylated biotherapeutics and biosimilars.
Simultaneous Red/Green Dual Fluorescence Detection of Both the Nuclear and Nucleolar Compartments of Live Cells (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
N-butyl cyanoacrylate embolization of cerebral arteriovenous malformations: results of a prospective, randomized, multi-center trial. (2002)

This prospective, randomized trial showed that n-BCA is equivalent to PVA as a preoperative embolic agent for treatment of cerebral AVM as determined by percent of nidus reduction and number of feeding pedicles embolized.
Measurement of the elliptic anisotropy of charged particles produced in PbPb collisions at √sNN=2.76 TeV (2013)

Artículo escrito por un elevado número de autores, sólo se referencian el primero, los autores que firman como Universidad Autónoma de Madrid y el grupo de colaboración en el caso de que aparezca en el artículo
Immunohistochemical analysis of tissue remodelling during the anagen-catagen transition of the human hair follicle (1997)

The transition from the growth phase (anagen) to the involution phase (catagen) involves profound morphological changes in the human hair follicle. Club hair and epithelial column formation, for example, are key features of the catagen phase, which result in the disruption of physical interaction between the bulb and the dermal papilla. However, the dynamics and tissue remodelling that occur during this involution process remain largely unknown. Using monoclonal antibodies directed against K14 keratin, trichohyalin, transglutaminase I, desmoglein and Ki67 antigen, we followed the movements of each of the main hair follicle compartments during the onset of catagen. Our results indicate that the inner root sheath is an early target in this process, suggesting a key role for this compartment in the maintenance of hair follicle homeostasis.
Density Functional Study of Oxygen Insertion into Niobium–Phosphorus Bonds: Novel Mechanism for Liberating P3– Synthons (2016)

We explore the mechanism of oxygen insertion into niobium–phosphorus bonds to liberate synthetically relevant, phosphorus-containing molecules. Oxygen insertion mechanisms generally proceed through either direct oxygen insertion from an oxo ligand, M═O (oxy-insertion), or an insertion of an oxygen atom from an external oxidant, OY (Baeyer–Villiger, BV). Computational methods were employed to elucidate the preferred mechanism for the liberation of the phosphorus moiety from [(η2-P3)Nb(ODipp)3] (Dipp = 2,6-iPr2C6H3, P3 = P3-SnPh3) when treated with pyridine-N-oxide as an external oxidant. Careful analysis of conformational isomers and energies clearly suggests that the BV mechanism is the preferred pathway toward phosphorus liberation. Once free, the P3 moiety can react with 1,3-cyclohexadiene to form the Diels–Alder product, which is also modeled in the computational study.
Mining the web to predict future events (2013)

We describe and evaluate methods for learning to forecast forthcoming events of interest from a corpus containing 22 years of news stories. We consider the examples of identifying significant increases in the likelihood of disease outbreaks, deaths, and riots in advance of the occurrence of these events in the world. We provide details of methods and studies, including the automated extraction and generalization of sequences of events from news corpora and multiple web resources. We evaluate the predictive power of the approach on real-world events withheld from the system.
FDM 3D printed coffee glove embedded with flexible electronic (2017)

With the advances in 3D printing technology, Flexible Electronics can now be exploited to form the so-called “Embedded Electronics”. This paper describes experiences learned from a research project which ran during summer 2016 at KAUST, in collaboration with the Electrical and Computer Engineering Department at Effat University, and aimed at creating a heating coffee glove product operating on double alkaline batteries using Kapton© as a flexible substrate for the circuit. The circuit and its batteries are encapsulated in a 3D printed glove, designed using SolidWorks©. The proposed methodology and techniques applied during this work could be further used in implementing other technologies, such as thermoelectric coolers head patches, smart garments, and flexible smartphones. Limitation and recommendation of the present methodology are also discussed.