gebhart/patrepeval huggingface dataset:
From Egg to Embryo (1991)

The last ten years have shown a dramatic revolution in our understanding of early animal development. This new edition of the successful first edition describes the result of this revolution and explains how the body plan of an embryo emerges from the newly fertilised egg. The book starts with a critical discussion of embryological concepts and explains in simple terms the mathematics of cell states, morphogen gradients and threshold responses. The experimental evidence on the mechanism of regional specification in Xenopus, molluscs, annelids, ascidians as well as Caenorhabditis, the mouse, the chick and Drosophila is then discussed. The whole chapter devoted to the exciting developments in Drosophila provides a clear guide to the subject, including a new table outlining the developmentally important genes. The emphasis throughout is on conceptual clarity and unity: bringing together the mathematical models, embryological experiments and molecular biology into a single, comprehensive coherent account.
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets (2015)

Genome-wide expression profiling has revolutionized biomedical research; vast amounts of expression data from numerous studies of many diseases are now available. Making the best use of this resource in order to better understand disease processes and treatment remains an open challenge. In particular, disease biomarkers detected in case-control studies suffer from low reliability and are only weakly reproducible. Here, we present a systematic integrative analysis methodology to overcome these shortcomings. We assembled and manually curated more than 14,000 expression profiles spanning 48 diseases and 18 expression platforms. We show that when studying a particular disease, judicious utilization of profiles from other diseases and information on disease hierarchy improves classification quality, avoids overoptimistic evaluation of that quality, and enhances disease-specific biomarker discovery. This approach yielded specific biomarkers for 24 of the analyzed diseases. We demonstrate how to combine these biomarkers with large-scale interaction, mutation and drug target data, forming a highly valuable disease summary that suggests novel directions in disease understanding and drug repurposing. Our analysis also estimates the number of samples required to reach a desired level of biomarker stability. This methodology can greatly improve the exploitation of the mountain of expression profiles for better disease analysis.
Genome engineering via homologous recombination in mouse embryonic stem (ES) cells: an amazingly versatile tool for the study of mammalian biology (2001)

The ability to introduce genetic modifications in the germ line of complex organisms has been a long-standing goal of those who study developmental biology. In this regard, the mouse, a favorite model for the study of the mammals, is unique: indeed not only is it possible since the late seventies, to add genes to the mouse genome like in several other complex organisms but also to perform gene replacement and modification. This has been made possible via two technological breakthroughs: 1) the isolation and culture of embryonic stem cells (ES), which have the unique ability to colonize all the tissues of an host embryo including its germ line; 2) the development of methods allowing homologous recombination between an incoming DNA and its cognate chromosomal sequence (gene "targeting"). As a result, it has become possible to create mice bearing null mutations in any cloned gene (knock-out mice). Such a possibility has revolutionized the genetic approach of almost all aspects of the biology of the mouse. In recent years, the scope of gene targeting has been widened even more, due to the refinement of the knock-out technology: other types of genetic modifications may now be created, including subtle mutations (point mutations, micro deletions or insertions, etc.) and chromosomal rearrangements such as large deletions, duplications and translocations. Finally, methods have been devised which permit the creation of conditional mutations, allowing the study of gene function throughout the life of an animal, when gene inactivation entails embryonic lethality. In this paper, we present an overview of the methods and scenarios used for the programmed modification of mouse genome, and we underline their enormous interest for the study of mammalian biology.
Three-dimensional models of human and other mammalian microsomal P450s constructed from an alignment with P450102 (P450<sub>bm3</sub>) (1995)

1. A novel modelling alignment for P450s, utilizing NADPH-P450 reductase for electron transfer, is proposed on the basis of analysis of their amino acid sequences. 2. Information used to facilitate the alignment process includes: the recent X-ray crystal structure of P450102 (P450bm3), site-directed mutagenesis experiments, chemical modification of specific residues, and antibody recognition studies. 3. The alignment has been used to construct a number of microsomal P450s of relevance to xenobiotic and endogenous metabolism.
Fabrication of multimode polymer waveguides with integrated micro-mirrors using Deep Lithography with Protons (2004)

We present Deep Lithography with Protons (DLP) as a promising, fast prototyping technology to fabricate multimode polymer waveguides to transfer optical signals between in-plane emitters and receivers. A free-standing waveguide, with a 500 µm by 500 µm cross-section, was realized in Poly(Methyl MethAcrylate) (PMMA). We have characterized the surface roughness by means of an optical non-contact surface profiler and experimentally measured the optical transmission efficiency of the micro-optical component using a Hexapod six-axis parallel-kinematics robot. The results are compared with non-sequential ray-tracing simulations.
Synthesis of a Novel Lysophosphatidylcholine (2000)

The novel lysophosphatidylcholine (1), which naturally occurs in the marine sponge Spirastrella abata and was reported to inhibit cholesterol biosynthesis in the Chang liver cell, has been synthesized in four steps from methyl cis-11-octadecenoate (2).
Mechanical force promotes dimethylarginine dimethylaminohydrolase 1-mediated hydrolysis of the metabolite asymmetric dimethylarginine to enhance bone formation (2022)

Mechanical force is critical for the development and remodeling of bone. Here we report that mechanical force regulates the production of the metabolite asymmetric dimethylarginine (ADMA) via regulating the hydrolytic enzyme dimethylarginine dimethylaminohydrolase 1 (Ddah1) expression in osteoblasts. The presence of -394 4 N del/ins polymorphism of Ddah1 and higher serum ADMA concentration are negatively associated with bone mineral density. Global or osteoblast-specific deletion of Ddah1 leads to increased ADMA level but reduced bone formation. Further molecular study unveils that mechanical stimulation enhances TAZ/SMAD4-induced Ddah1 transcription. Deletion of Ddah1 in osteoblast-lineage cells fails to respond to mechanical stimulus-associated bone formation. Taken together, the study reveals mechanical force is capable of down-regulating ADMA to enhance bone formation.
Effect of γ-Aminobutyric Acid-enriched Tempeh-like Fermented Soybean (GABA-Tempeh) on the Blood Pressure of Spontaneously Hypertensive Rats (2003)

GABA-enriched tempeh-like fermented soybean (GABA-tempeh) was supplemented to the AIN-76 diet and fed for 2 months to spontaneously hypertensive rats (SHRs), an animal model of spontaneously developed hypertension, to compare the antihypertensive activity with that of authentic GABA. The elevation of systolic blood pressure in SHRs was significantly retarded in the GABA-tempeh group as well as that with authentic GABA when compared with the controls, and the effect lasted for two months of the feeding period. The blood urea nitrogen level tended to be higher in the control group than in the GABA-supplemented groups. On the other hand, no effect was apparent on the plasma levels of cholesterol, triacylglycerol and glucose, or on the urinary excretion of Na and K.
[Is free plasmatic cortisol measurement useful in intensive care unit?]. (2008)

Serum cortisol free fraction is responsible for its physiological function. Determination of serum total cortisol concentration does not allow accurate evaluation of hypothalamic pituitary adrenal axis when there is a quantitative variation in serum transcortin. Although free cortisol can be assayed by salivary or urinary cortisol measurements, these methods can not be easily applied in intensive care units. Free plasmatic cortisol measurement could provide a better reflect of circulating cortisol in patients with critical illness whom have a decreased concentration of binding proteins and whom adrenal status is an important prognostic factor. Free cortisol can be measured after separation from bound cortisol, calculated with equation based on equilibrium binding or evaluated by cortisol/CBG ratio. In various studies, free plasmatic cortisol allows in critical care patients a better appreciation of adrenal status than total cortisol and be more differential than total cortisol increment after stimulation with synacthen used to diagnose "relative adrenal insufficiency".
Control of charging in resonant tunneling through InAs nanocrystal quantum dots (2001)

Tunneling spectroscopy of InAs nanocrystals deposited on graphite was measured using scanning tunneling microscopy, in a double-barrier tunnel-junction configuration. The effect of the junction symmetry on the tunneling spectra is studied experimentally and modeled theoretically. When the tip is retracted, we observe resonant tunneling through the nanocrystal states without charging. Charging is regained upon reducing the tip–nanocrystal distance, making the junction more symmetric. The effect of voltage distribution between the junctions on the measured spectra is also discussed.
Equilibrium segregation of phosphorus at grain boundaries of Fe–P, Fe–C–P, Fe–Cr–P, and Fe–Cr–C–P alloys (1981)

AbstractThe equilibrium grain-boundary segregation of phosphorus was investigated in Fe–P, Fe–C–P, Fe–Cr–P, and Fe–Cr–C–P alloys after annealing at temperatures in the range 400–800°C. The grain-boundary concentrations were determined by Auger electron spectroscopy on intergranular fracture surfaces. The phosphorus segregation in Fe–P alloys with 0·003–0·3%P can be described by the McLean equation, the free energy of segregation is ∆G° = −34 300–21·5T (J mol−1). The percentage of intergranular fracture is increased by the presence of phosphorus at grain boundaries. In Fe–C–P alloys grain-boundary segregation is affected by site competition. Increasing carbon content of the samples causes an increase of the carbon concentration and a decrease of the phosphorus concentration at the grain boundaries; the intergranular part of fracture is simultaneously lowered. The addition of chromium causes an increase of phosphorus segregation in Fe–C–P alloys but no change in Fe–P alloys. The behaviour in carbon-containing alloys is explained by the decrease of carbon activity by chromium which allows enhanced phosphorus segregation. As chromium does not affect phosphorus segregation in carbon-free alloys, there is no ‘synergistic cosegregation’ of chromium and phosphorus. The results lead to a new understanding of the influence of phosphorus on temper embrittlement of unalloyed and low-alloyed steels.
Single-Crystal Matrix Isolation of Biopolymers (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSingle-Crystal Matrix Isolation of BiopolymersJean Chmielewski, Jerry J. Lewis, Scott Lovell, Reena Zutshi, Phil Savickas, Christine A. Mitchell, J. Anand Subramony, and Bart KahrView Author Information Department of Chemistry, Purdue University West Lafayette, Indiana 47907 Biopharmaceutical Technology Development, Eli Lilly Indianapolis, Indiana 46285 Analytical Sciences Laboratory, Dow Chemical Company Midland, Michigan 48667 Cite this: J. Am. Chem. Soc. 1997, 119, 43, 10565–10566Publication Date (Web):October 29, 1997Publication History Received30 April 1997Published online29 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/ja971370zhttps://doi.org/10.1021/ja971370zrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views270Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Biopolymers,Crystal structure,Crystallization,Crystals,Peptides and proteins Get e-Alerts
Intention-aware risk estimation: Field results (2015)

This paper tackles the risk estimation problem from a new perspective: a framework is proposed for reasoning about traffic situations and collision risk at a semantic level, while classic approaches typically reason at a trajectory level. Risk is assessed by estimating the intentions of drivers and detecting conflicts between them, rather than by predicting the future trajectories of the vehicles and detecting collisions between them. More specifically, dangerous situations are identified by comparing what drivers intend to do with what they are expected to do according to the traffic rules. The reasoning is performed in a probabilistic manner, in order to take into account sensor uncertainties and interpretation ambiguities. This framework can in theory be applied to any type of traffic situation; here we present its application to road intersections. The approach was validated with field trials using passenger vehicles equipped with Vehicle-to-Vehicle wireless communication modems. The results demonstrate that the algorithm is able to detect dangerous situations early and complies with real-time constraints.
Benzo[<i>c</i>,<i>d</i>]indole‐Containing Aza‐BODIPY Dyes: Asymmetrization‐Induced Solid‐State Emission and Aggregation‐Induced Emission Enhancement as New Properties of a Well‐Known Chromophore (2015)

A series of symmetric and asymmetric benzo[c,d]indole-containing aza boron dipyrromethene (aza-BODIPY) compounds was synthesized by a titanium tetrachloride-mediated Schiff-base formation reaction of commercially available benzo[c,d]indole-2(1H)-one and heteroaromatic amines. These aza-BODIPY analogues show different electronic structures from those of regular aza-BODIPYs, with hypsochromic shifts of the main absorption compared to their BODIPY counterparts. In addition to the intense fluorescence in solution, asymmetric compounds exhibited solid-state fluorescence due to significant contribution of the vibronic bands to both absorption and fluorescence as well as reduced fluorescence quenching in the aggregates. Finally, aggregation-induced emission enhancement, which is rare in BODIPY chromophores, was achieved by introducing a nonconjugated moiety into the core structure.
High efficiency bifacial n-PERT cells with co-plated Ni/Ag contacts for multi-wire interconnection (2017)

In this paper we present bifacial n-type PERT cells (n-PERT+) with ultra-thin (< 3 μm) and narrow (< 20 μm) Ni/Ag plated contacts on both the n+ and p+ side of the cell. This cell architecture is designed for multi-wire interconnection and has the potential to deliver low cost of ownership at module level (< 0.30 $/Wp), as it can profit from bifacial gain, a low cost metallization (~ 0.07 $/cell) and reduced shadowing and recombination losses. A self-aligned, fully plated metallization sequence, able to form Ni/Ag electrodes simultaneously on both polarities of the cell with a low specific contact resistance, is demonstrated. We benchmark this novel process to a seed-and-plate sequence where the plating seed is obtained by physical vapor deposition (PVD) of Ni and we show comparable efficiency results. Efficiencies of up to 22.8% for cells featuring this fully plated Ni/Ag metallization sequence have been obtained (Cz, 239 cm2, GridTOUCH measurement). We also report 1-cell laminates assembled using multi-wire foils reaching maximum power of about 5 W (256 cm2 aperture area), which shows that the proposed metallization sequence is well suited for integration with such interconnection technology, despite small finger section and the absence of a highly conductive Cu inter-layer. The 1-cell laminates also exhibit less than 4% power degradation after 400 thermal cycles (-40 ºC to +85 ºC).
Atmospheric Turbulence (1992)

The field of fluid mechanics is rapidly advancing, driven by unprecedented volumes of data from experiments, field measurements, and large-scale simulations at multiple spatiotemporal scales. Machine learning (ML) offers a wealth of techniques to extract ...Read More
Motion adaption - the everyday solution to varispeed disk playback (1995)

The paper discusses the implementation of a varispeed playback system for digital disk recorders used as post production image stores and computer graphics image storage devices. The digital disk recorder is almost tailor made for varispeed play, it has huge bandwidth allowing random access to any frame of video, therefore the problem of selecting a pre-set number of frames from contiguous video streams, a constant problem for tape machines, is almost non-existent. (8 pages)
Sequence homologies between nucleotide binding regions of CFTR and G‐proteins suggest structural and functional similarities (1995)

Sequence homology between the alpha-subunits of G-proteins and other GTP-binding proteins and certain regions within the nucleotide binding domains (NBDs) of cystic fibrosis transmembrane conductance regulator (CFTR) indicates that these protein structures may be similar. A sequence alignment of the NBDs of CFTR and NBDs from other membrane transporters, forms the basis of a structural model. This model predicts that one of the conserved sequences GGQR, within which a number of CF mutations occur, forms part of the nucleotide binding pocket and serves as an ON/OFF conformational switch as observed in GTP binding proteins. Furthermore, based on subtle sequence differences between the first and second NBDs of CFTR and from structure-activity data, we suggest that the nucleotide binding site environments of the two NBDs are different.
Government Turns Its Back on Students (2006)

The Higher Education Support Amendment (Abolition of Compulsory Up-Front Student Union Fees) Bills 2005 is passed without amendment despite a number of proposed amendments put forward in the final weeks of Parliament. The passage of this legislation would be a major loss for students, universities, and communities.
Molecular cloning and characterization of a novel anti-TLR9 intrabody (2013)

Toll-like receptor 9 (TLR9) is a component of the innate immune system, which recognizes the DNA of both pathogens and hosts. Thus, it can drive autoimmune diseases. Intracellular antibodies expressed inside the ER block transitory protein functions by inhibiting the translocation of the protein from the ER to its subcellular destination. Here, we describe the construction and characterization of an anti-TLR9 ER intrabody (αT9ib). The respective single-chain Fv comprises the variable domains of the heavy and light chain of a monoclonal antibody (mAb; 5G5) towards human and murine TLR9. Co-expression of αT9ib and mouse TLR9 in HEK293 cells resulted in co-localization of both molecules with the ER marker calnexin. Co-immunoprecipitation of mouse TLR9 with αT9ib indicated that αT9ib interacts with its cognate antigen. The expression of αT9ib inhibited NF-κB-driven reporter gene activation upon CpG DNA challenge but not the activation of TLR3 or TLR4. Consequently, TLR9-driven TNFα production was inhibited in RAW264.7 macrophages upon transfection with the αT9ib expression plasmid. The αT9ib-encoding open reading frame was integrated into an adenoviral cosmid vector to produce the recombinant adenovirus (AdV)-αT9ib. Transduction with AdVαT9ib specifically inhibited TLR9-driven cellular TNFα release. These data strongly indicate that αT9ib is a very promising experimental tool to block TLR9 signaling.
Short and long latency reflex responses elicited by electrical and mechanical stimulation in human hand muscle (1986)

The relationship between electrically and mechanically induced reflex responses in the rectified, averaged surface electromyogram of the first interosseus dorsalis muscle was examined in 18 healthy human subjects. Both methods evoked identifiable short and long latency reflex responses. The onset latencies for short latency reflexes with electrical and mechanical stimulations were 30.6 ms (+/- 2.2 ms) and 28.9 ms (+/- 2.2 ms) and for long latency reflexes 50.0 ms (+/- 2.8 ms) and 51.2 ms (+/- 5.2 ms), respectively. The correlation of the onset latencies of the reflexes revealed significant correspondence between the electrical and mechanical methods implying at least partly mutual mechanisms.
A New Class of Low Compressibility Materials: Clathrates of Silicon and Related Materials (2002)

We discuss the high pressure properties of different silicon clathrate structures that we have investigated by means of X-ray diffraction and ab initio calculations. Compressibility, transition pressures or phase transformations are interpreted as a function of the nature of the guest atom intercalation. The compressibility of the clathrate structure is in all cases close to that of silicon diamond whereas transition pressures or the high pressure phases are extremely depending on the nature of the guest atom. We address the implications for obtaining a metallic material as hard as diamond.
Current Status and Future Prospects for Satraplatin, an Oral Platinum Analogue (2008)

Platinum drugs are major chemotherapeutic agents that are used alone or in combination with other systemic agents and/or radiation therapy in the management of many human malignancies. All three platinum drugs approved by the Food and Drug Administration, cisplatin, carboplatin, and oxaliplatin, are administrated intravenously. Satraplatin is the first orally administered platinum drug under active clinical investigation. Satraplatin and its major metabolite, JM118, have shown antineoplastic activity in in vitro, in vivo, and in clinical settings. Use of satraplatin as an alternative platinum cytotoxic agent is particularly attractive because of the convenience of administration, milder toxicity profile, lack of cross-resistance with cisplatin, theoretical advantage as a radiosensitizer, and activity in cancers historically nonresponsive to platinum drugs. The most mature clinical data for satraplatin come from the recently completed phase III trial that investigated the efficacy of satraplatin and prednisone on hormone-refractory prostate cancer patients who had failed a course of other chemotherapy agents. Preliminary reports show that the combination is statistically superior to placebo and prednisone in multiple end points, including progression-free survival, prostate-specific antigen response, objective tumor response, pain response, and duration of pain response. The difference in overall survival, however, did not reach statistical significance.