gebhart/patrepeval huggingface dataset:
Separation and Identification of Peptides from Gel-Isolated Membrane Proteins Using a Microfabricated Device for Combined Capillary Electrophoresis/Nanoelectrospray Mass Spectrometry (2000)

The coupling of microfabricated devices to nanoelectrospray mass spectrometers using both a triple quadrupole and a quadrupole time-of-flight mass spectrometer (QqTOF MS) is presented for the analysis of trace-level membrane proteins. Short disposable nanoelectrospray emitters were directly coupled to the chip device via a low dead volume connection. The analytical performance of this integrated device in terms of sensitivity and reproducibility was evaluated for standard peptide mixtures. A concentration detection limit ranging from 3.2 to 43.5 nM for different peptides was achieved in selected ion monitoring, thus representing a 10-fold improvement in sensitivity compared to that of microelectrospray using the same chip/mass spectrometer. Replicate injections indicated that reproducibility of migration time was typically less than 3.1% RSD whereas RSD values of 6-13% were observed on peak areas. Although complete resolution of individual components is not typically achieved for complex digests, the present chip capillary electrophoresis (chip-CE) device enabled proper sample cleanup and partial separation of multicomponent samples prior to mass spectral identification. Analyses of protein digests were typically achieved in less than 1.5 min with peak widths of 1.8-2.5 s (half-height definition) as indicated from individual reconstructed ion electropherograms. The application of this chip-CE/QqTOF MS system is further demonstrated for the identification of membrane proteins which form a subset of the Haemophilus influenzae proteome. Bands first separated by 1D-gel electrophoresis were excised and digested, and extracted tryptic peptides were loaded on the chip without any further sample cleanup or on-line adsorption preconcentration. Accurate molecular mass determination (< 5 ppm) in peptide-mapping experiments was obtained by introducing an internal standard via a postseparation channel. The analytical potential of this integrated device for the identification of trace-level proteins from different strains of H. influenzae is demonstrated using both peptide mass-fingerprint database searching and on-line tandem mass spectrometry.
Nucleophilic substitution reactions in m -nitrobenzylic substrates (1983)

The reaction of m -nitrobenzyl 2,4,6-trimethylbenzoate (11) with the salt (2) of 2-nitropropane, or the thiolate (16), gives moderate yields of substitution products [e.g.(3) or (17)]. However, the mechanism of formation of these products could not be definitively assigned. The m -nitrobenzyl chloride (12), on the other hand, was clearly demonstrated to undergo SRN1 substitution reactions with a variety of anions including the anion from the salt (2), thiolate ion from (16), azide from (22), the malononitrile anion from (20), and the malonic ester anion from (21). Inhibition and entrainment effects clearly rule out an alternative radical anion-radical process involving cage collapse. The occurrence of SRNl reactions in m -nitrobenzylic substrates adds support to a mechanism involving association of radicals with anions, and for dissociation of radical anions, which involves s* and p* radical anions.
Separating Microbes in the Manner of Molecules. 1. Capillary Electrokinetic Approaches (1999)

Selective, high-efficiency separations of intact bacteria may, in some cases, allow them to be identified and quantified in much the same way that molecules are done today. Two different capillary electrokinetic approaches were utilized. The first approach used a dissolved polymer-based CE separation that may be affected by size and shape considerations. Another approach uses capillary isoelectric focusing to separate bacteria by their surface charge or isoelectric point. Good peak shapes and extremely high efficiencies are observed (up to approximately 1,600,000 theoretical plates/m). Careful sample preparation and separation runs are essential in order to obtain reproducible separations. Expansion of these types of rapid, efficient microbial separations could have profound effects on many branches of science and technology.
Stereocontrolled Synthesis of (E,Z)-Dienals via Tandem Rh(I)-Catalyzed Rearrangement of Propargyl Vinyl Ethers (2013)

A novel Rh(I)-catalyzed approach to functionalized (E,Z) dienals has been developed via tandem transformation where a stereoselective hydrogen transfer follows a propargyl Claisen rearrangement. Z-Stereochemistry of the first double bond suggests the involvement of a six-membered cyclic intermediate whereas the E-stereochemistry of the second double bond stems from the subsequent protodemetalation step giving an (E,Z)-dienal.
EFFECT OF REGIONAL GENE THERAPY WITH BONE MORPHOGENETIC PROTEIN-2-PRODUCING BONE MARROW CELLS ON SPINAL FUSION IN RATS (2003)

BMP-2-producing bone marrow cells, created by adenoviral gene transfer, produce sufficient BMP to induce an intertransverse fusion in the rat spine model.
Thyroid Function and Prevalence of Anti-Thyroperoxidase Antibodies in a Population with Borderline Sufficient Iodine Intake: Influences of Age and Sex (2005)

In inhabitants of the eastern part of The Netherlands, serum TSH gradually decreases with age, whereas after age 60, serum FT4 increases, possibly because of the development of thyroid autonomy after longstanding borderline sufficient iodine intake.
RNAi-mediated knockdown of Xist can rescue the impaired postimplantation development of cloned mouse embryos (2011)

Cloning mammals by somatic cell nuclear transfer (SCNT) is highly inefficient. Most SCNT-generated embryos die after implantation because of unidentified, complex epigenetic errors in the process of postimplantation embryonic development. Here we identify the most upstream level of dysfunction leading to impaired development of clones by using RNAi against Xist, a gene responsible for X chromosome inactivation (XCI). A prior injection of Xist-specific siRNA into reconstructed oocytes efficiently corrected SCNT-specific aberrant Xist expression at the morula stage, but failed to do so thereafter at the blastocyst stage. However, we found that shortly after implantation, this aberrant XCI status in cloned embryos had been corrected autonomously in both embryonic and extraembryonic tissues, probably through a newly established XCI control for postimplantation embryos. Embryo transfer experiments revealed that siRNA-treated embryos showed 10 times higher survival than controls as early as embryonic day 5.5 and this high survival persisted until term, resulting in a remarkable improvement in cloning efficiency (12% vs. 1% in controls). Importantly, unlike control clones, these Xist-siRNA clones at birth showed only a limited dysregulation of their gene expression, indicating that correction of Xist expression in preimplantation embryos had a long-term effect on their postnatal normality. Thus, contrary to the general assumption, our results suggest that the fate of cloned embryos is determined almost exclusively before implantation by their XCI status. Furthermore, our strategy provides a promising breakthrough for mammalian SCNT cloning, because RNAi treatment of oocytes is readily applicable to most mammal species.
Rapid Production of a Thin Electrode by Single Discharge Machining (2nd Report)-Dynamic behavior observation of thinning phenomenon- (2003)

In single discharge machining of a 0.1mm tungsten electrode with discharge current of between 30 to 50A and pulse duration of several hundreds microseconds, a needle of 20 to 35μm in diameter has been produced instantaneously. In the 1st report, we studied the effect of the discharge conditions on the shape of the formed electrode's tip. However, the forming mechanism could not be understood clearly from several experiments in the 1st report. To understand this phenomenon, a stroboscopic imaging system with a Q-switched Nd:YAG laser is used to observe the dynamical change of the electrode during and after the discharge pulse. Formation of the needle-shaped electrode occurs after a single discharge in an interval of 100 to 300μs. Therefore, the electrostatic or electromagnetic force may not be considered to have an effect on the thin electrode formation phenomenon. Air currents are suggested as one possible contributor to the formation mechanism and its effect on wear length for positive and negative electrode polarities is discussed.
Distinct subsets of human invariant NKT cells differentially regulate T helper responses via dendritic cells (2008)

Invariant natural killer T (iNKT) cells regulate the T helper (Th) 1/2 balance and elicit either enhancement or suppression of the immune responses. However, the exact mechanism by which iNKT cells exert these contrasting functions has remained elusive. We demonstrate herein that two major distinct subsets of human iNKT cells, CD4+CD8beta(-) (CD4+) and CD4(-)CD8beta(-) (double negative; DN) cells, express functional CD40 ligand (CD40L), but they differentially regulate the dendritic cell (DC) function by reciprocal NKT-DC interactions, thereby influencing the subsequent Th response. The CD4 subset stimulated by alpha-galactosylceramide (alpha-GalCer)-loaded DC immediately produced massive amounts of IL-4 and IL-13, which together with IFN-gamma enhanced CD40L-induced IL-12 production by DC. In contrast, the DN subset eliminated the DC by cytolysis and changed the living DC into a default subtype, in turn markedly down-regulating the levels of IL-12. Therefore, the DC stimulated by the CD4 subset preferentially induced Th1 responses, whereas the DC reacted with the DN subset induced a shift toward Th2 responses. These findings may provide an important insight into better understanding the contribution of iNKT-DC cross-talk governing the Th1/2 balance and the diverse influences of iNKT cells in various diseases.
Designing Cell-Compatible Hydrogels for Biomedical Applications (2012)

Designer Hydrogels Hydrogels, which consist of highly water swollen cross-linked polymer networks, can now be made with a range of chemistries and a combination of physical and chemical cross-links. They can also be designed to degrade gradually when exposed to chemical or biological signals and are thus finding use in a wide range of applications, including tissue engineering and drug delivery. Seliktar (p. 1124 ) reviews recent advances in tailoring hydrogels with specific properties and their applications to biology and medicine.
Regulation of the Pluripotency Marker Rex-1 by Nanog and Sox2 (2006)

Rex-1 (Zfp-42) is a known marker for undifferentiated embryonic stem cells and teratocarcinoma cells. However, the mechanism by which Rex-1 is regulated in pluripotent cells remains unresolved. Here we report that Nanog, an Nk-2 homeodomain protein known for its role in maintaining stem cell pluripotency, is a transcription activator for the Rex-1 promoter. Knockdown of Nanog in embryonic stem cells resulted in a reduction of Rex-1 expression, whereas forced expression of Nanog in P19 stimulated Rex-1 expression. Employing a Rex-1 reporter, we demonstrate that Nanog transactivates Rex-1 directly. Serial deletion studies mapped the Nanog-responsive element between -187 and -286 of the Rex-1 promoter. Although Oct-3/4 and Sox2 can both transactivate Rex-1 promoter, only Sox2 cooperates with Nanog in up-regulating Rex-1. Furthermore, we demonstrate that the C terminus of Nanog is responsible for transactivating the Rex-1 promoter, a function that can be substituted for by a viral transactivator Vp16 efficiently in NIH3T3 cells but less so in P19 cells. Taking these findings together, we conclude that Rex-1 is a direct target of Nanog, which is augmented by Sox2 and Oct-3/4.
Risk of Antigen Excess in Serum Free Light Chain Measurements (2007)

International audience
Efficient introduction of aryl bromide functionality into proteins in vivo (2000)

Artificial proteins can be engineered to exhibit interesting solid state, liquid crystal or interfacial properties and may ultimately serve as important alternatives to conventional polymeric materials. The utility of protein-based materials is limited, however, by the availability of just the 20 amino acids that are normally recognized and utilized by biological systems; many desirable functional groups cannot be incorporated directly into proteins by biosynthetic means. In this study, we incorporate para-bromophenylalanine (p-Br-phe) into a model target protein, mouse dihydrofolate reductase (DHFR), by using a bacterial phenylalanyl-tRNA synthetase (PheRS) variant with relaxed substrate specificity. Coexpression of the mutant PheRS and DHFR in a phenylalanine auxotrophic Escherichia coli host strain grown in p-Br-phe-supplemented minimal medium resulted in 88% replacement of phenylalanine residues by p-Br-phe; variation in the relative amounts of phe and p-Br-phe in the medium allows control of the degree of substitution by the analog. Protein expression yields of 20-25 mg/l were obtained from cultures supplemented with p-Br-phe; this corresponds to about two-thirds of the expression levels characteristic of cultures supplemented with phe. The aryl bromide function is stable under the conditions used to purify DHFR and creates new opportunities for post-translational derivatization of brominated proteins via metal-catalyzed coupling reactions. In addition, bromination may be useful in X-ray studies of proteins via the multiwavelength anomalous diffraction (MAD) technique.
Rapid Resolution of Suicidal Behavior and Depression With Single Low-Dose Ketamine Intravenous Push Even After 6 Months of Follow-Up (2014)

Adult Psychiatry Program Department of Psychiatry School of Medicine The University of Texas Health Science Center at San Antonio San Antonio, TX Department of Psychiatry and Behavioral Medicine The University of Texas Health Science Center at San Antonio San Antonio, TX Department of Psychiatry and Behavioral Medicine The University of Texas Health Science Center at San Antonio San Antonio, TX [email protected]
Diversification of C-Function Activity in Maize Flower Development (1996)

The Arabidopsis gene AGAMOUS is required for male and female reproductive organ development and for floral determinacy. Reverse genetics allowed the isolation of a transposon-induced mutation in ZAG1, the maize homolog of AGAMOUS. ZAG1 mutants exhibited a loss of determinacy, but the identity of reproductive organs was largely unaffected. This suggested a redundancy in maize sex organ specification that led to the identification and cloning of a second AGAMOUS homolog, ZMM2, that has a pattern of expression distinct from that of ZAG1. C-function organ identity in maize (as defined by the A, B, C model of floral organ development) may therefore be orchestrated by two closely related genes, ZAG1 and ZMM2, with overlapping but nonidentical activities.
The Reorganization of Somatosensory Cortex Following Peripheral Nerve Damage in Adult and Developing Mammals (1983)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
THC exposure of human iPSC neurons impacts genes associated with neuropsychiatric disorders (2018)

There is a strong association between cannabis use and schizophrenia but the underlying cellular links are poorly understood. Neurons derived from human-induced pluripotent stem cells (hiPSCs) offer a platform for investigating both baseline and dynamic changes in human neural cells. Here, we exposed neurons derived from hiPSCs to Δ<sup>9</sup>-tetrahydrocannabinol (THC), and identified diagnosis-specific differences not detectable in vehicle-controls. RNA transcriptomic analyses revealed that THC administration, either by acute or chronic exposure, dampened the neuronal transcriptional response following potassium chloride (KCl)-induced neuronal depolarization. THC-treated neurons displayed significant synaptic, mitochondrial, and glutamate signaling alterations that may underlie their failure to activate appropriately; this blunted response resembles effects previously observed in schizophrenia hiPSC- derived neurons. Furthermore, we show a significant alteration in THC-related genes associated with autism and intellectual disability, suggesting shared molecular pathways perturbed in neuropsychiatric disorders that are exacerbated by THC.
Enhancement of Protein Crystal Nucleation by Critical Density Fluctuations (1997)

Numerical simulations of homogeneous crystal nucleation with a model for globular proteins with short-range attractive interactions showed that the presence of a metastable fluid-fluid critical point drastically changes the pathway for the formation of a crystal nucleus. Close to this critical point, the free-energy barrier for crystal nucleation is strongly reduced and hence, the crystal nucleation rate increases by many orders of magnitude. Because the location of the metastable critical point can be controlled by changing the composition of the solvent, the present work suggests a systematic approach to promote protein crystallization.
Robot Vision (1986)

From the Publisher:
This book presents a coherent approach to the fast-moving field of computer vision, using a consistent notation based on a detailed understanding of the image formation process. It covers even the most recent research and will provide a useful and current reference for professionals working in the fields of machine vision, image processing, and pattern recognition. 
An outgrowth of the author's course at MIT, Robot Vision presents a solid framework for understanding existing work and planning future research. Its coverage includes a great deal of material that is important to engineers applying machine vision methods in the real world. The chapters on binary image processing, for example, help explain and suggest how to improve the many commercial devices now available. And the material on photometric stereo and the extended Gaussian image points the way to what may be the next thrust in commercialization of the results in this area. 
Chapters in the first part of the book emphasize the development of simple symbolic descriptions from images, while the remaining chapters deal with methods that exploit these descriptions. The final chapter offers a detailed description of how to integrate a vision system into an overall robotics system, in this case one designed to pick parts out of a bin. 
The many exercises complement and extend the material in the text, and an extensive bibliography will serve as a useful guide to current research. 
Errata (164k PDF)
Cheap solar energy (2004)

ADVERTISEMENT RETURN TO ISSUEPREVNewsNEXTCheap solar energyKellyn BettsCite this: Environ. Sci. Technol. 2004, 38, 4, 70APublication Date (Web):February 15, 2004Publication History Published online15 February 2004Published inissue 1 February 2004https://doi.org/10.1021/es040373qRIGHTS & PERMISSIONSArticle Views473Altmetric-Citations-LEARN 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 InReddit PDF (57 KB) Get e-AlertsSUBJECTS:Solar energy Get e-Alerts
Bone morphogenetic protein 7 is widely overexpressed in primary breast cancer (2006)

Bone morphogenetic proteins (BMP) make up a family of extracellular signaling molecules that play a critical role in vertebrate development and both inhibit and stimulate growth in cancer cells. BMP7 was recently identified in our genomewide copy number and expression survey as being activated through amplification in breast cancer cell lines. In the present study, we further explored BMP7 gene copy number and expression changes in 22 breast cancer cell lines and 146 primary breast tumors. FISH analysis revealed that BMP7 copy number varied greatly from one cell line to another, with three cell lines showing extremely high-level amplification. Among primary tumors, BMP7 copy number was increased in 16% of the cases. BMP7 mRNA expression was determined in the cell lines and in a subset of 44 tumor samples by RT-PCR or quantitative real-time RT-PCR, respectively. Despite elevated mRNA levels in cancer cells, there was no significant association between copy number increase and mRNA expression, even though the highest expression was seen in cell lines and tumors with increased BMP7 copy number. Most interestingly, immunohistochemical analysis revealed BMP7 protein staining in all 11 breast cancer cell lines examined and strongly elevated BMP7 protein expression in 71.4% of the tumor samples as compared to normal mammary epithelium. Our results illustrate the frequent involvement of BMP7 alterations in breast cancer and especially highlight overexpression of the BMP7 protein in a very large fraction of primary breast tumors, thus suggesting a possible functional role for BMP7 in breast cancer development.
Trastuzumab emtansine (T-DM1) renders HER2 + breast cancer highly susceptible to CTLA-4/PD-1 blockade (2015)

Targeted drug delivery with antibody-drug conjugates such as the HER2-directed ado-trastuzumab emtansine (T-DM1) has emerged as a powerful strategy for cancer therapy. We show that T-DM1 is particularly effective in eliciting antitumor immunity in patients with early breast cancer (WSG-ADAPT trial) and in a HER2-expressing orthotopic tumor model. In the latter, despite primary resistance to immunotherapy, combined treatment with T-DM1 and anti-CTLA-4/PD-1 (cytotoxic T lymphocyte-associated protein-4/programmed cell death protein-1) was curative because it triggered innate and adaptive immunity. Tumor rejection was accompanied by massive T cell infiltration, TH1 (T helper 1) cell polarization, and, notably, a substantial increase in regulatory T cells. Depletion of regulatory T cells resulted in inflammation and tissue damage, implying their essential role in protecting the host during therapy. This study provides insights into the mechanisms of T-DM1's therapeutic activity and a rationale for potential therapeutic combination strategies with immunotherapy.