gebhart/patrepeval huggingface dataset:
Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement (2017)

Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.
A Novel Two-Step Silica-Coating Process for Engineering Magnetic Nanocomposites (1998)

A novel two-step silica-coating process, sol−gel followed by dense liquid coatings, is described. The maghemite surfaces coated with silica, using the two-step process, are characterized by X-ray photoelectron spectroscopy, electrokinetics, leaching test, and magnetization measurement. Compared with the single-step sol−gel or dense-liquid-coating process, the two-step process produces magnetic nanocomposites of the highest protection against acid attack at the lowest level of silica coatings with maximized magnetization.
Novel nanofibrous spiral scaffolds for neural tissue engineering (2008)

Due to several drawbacks associated with autografts and allografts, tissue-engineering approaches have been widely used to repair peripheral nerve injuries. Most of the traditional tissue-engineered scaffolds in use are either tubular (single or multi-lumen) or hydrogel-based cylindrical grafts, which provide limited surface area for cell attachment and regeneration. Here, we show a novel poly(lactide-co-glycotide) (PLGA) microsphere-based spiral scaffold design with a nanofibrous surface that has enhanced surface areas and possesses sufficient mechanical properties and porosities to support the nerve regeneration process. These scaffolds have an open architecture that goes evenly throughout the scaffolds hence leaving enough volume for media influx and deeper cell penetration into the scaffolds. The in vitro tests conducted using Schwann cells show that the nanofibrous spiral scaffolds promote higher cell attachment and proliferation when compared to contemporary tubular scaffolds or nanofiber-based tubular scaffolds. Also, the nanofiber coating on the surfaces enhances the surface area, mimics the extracellular matrix and provides unidirectional alignment of cells along its direction. Hence, we propose that these scaffolds could alleviate some drawbacks in current nerve grafts and could potentially be used in nerve regeneration.
Regulation of Human Leukocyte p21-Activated Kinases Through G Protein—Coupled Receptors (1995)

The Rac guanosine 5'-triphosphate (GTP)-binding proteins regulate oxidant production by phagocytic leukocytes. Two Ste20-related p21-activated kinases (PAKs) were identified as targets of Rac in human neutrophils. Activity of the approximately 65- and approximately 68-kilodalton PAKs was rapidly stimulated by chemoattractants acting through pertussis toxin-sensitive heterotrimeric GTP-binding proteins (G proteins). Native and recombinant PAKs phosphorylated the p47phox reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase component in a Rac-GTP-dependent manner. The action of PAKs during phagocyte activation by G protein-coupled pathways may contribute to regulation of NADPH oxidase activity.
The Etiology of Tuberculosis (1982)

These excerpts from the original are reprinted from Milestones in Microbiology, translated and edited by Thomas D. Brock, E. B. Fred Professor of Natural Science, Department of Bacteriology, University of Wisconsin; the book was originally published in 1961 by Prentice-Hall, Inc. and was reprinted in 1975 by the American Society for Microbiology, Washington, D.C.
Preparation and reactions of polyfunctional organozinc reagents in organic synthesis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and reactions of polyfunctional organozinc reagents in organic synthesisPaul. Knochel and Robert D. SingerCite this: Chem. Rev. 1993, 93, 6, 2117–2188Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/cr00022a008https://doi.org/10.1021/cr00022a008research-articleACS PublicationsRequest reuse permissionsArticle Views10359Altmetric-Citations950LEARN 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-Alertsclose Get e-Alerts
Enzyme replacement prevents neonatal death, liver damage, and osteoporosis in murine homocystinuria (2017)

Classical homocystinuria (HCU) is an inborn error of sulfur amino acid metabolism caused by deficient activity of cystathionine β-synthase (CBS), resulting in an accumulation of homocysteine and a concomitant decrease of cystathionine and cysteine in blood and tissues. In mice, the complete lack of CBS is neonatally lethal. In this study, newborn CBS-knockout (KO) mice were treated with recombinant polyethyleneglycolylated human truncated CBS (PEG-CBS). Full survival of the treated KO mice, along with a positive impact on metabolite levels in plasma, liver, brain, and kidneys, was observed. The PEG-CBS treatment prevented an otherwise fatal liver disease characterized by steatosis, death of hepatocytes, and ultrastructural abnormalities of endoplasmic reticulum and mitochondria. Furthermore, treatment of the KO mice for 5 mo maintained the plasma metabolite balance and completely prevented osteoporosis and changes in body composition that characterize both the KO model and human patients. These findings argue that early treatment of patients with HCU with PEG-CBS may prevent clinical symptoms of the disease possibly without the need of dietary protein restriction.-Majtan, T., Hůlková, H., Park, I., Krijt, J., Kožich, V., Bublil, E. M., Kraus, J. P. Enzyme replacement prevents neonatal death, liver damage, and osteoporosis in murine homocystinuria.
Eliminating Complement Factor D Reduces Photoreceptor Susceptibility to Light-Induced Damage (2007)

These results suggest that rod degeneration in the CL-damaged retina involves the activity of the alternative complement pathway and that eliminating the alternative pathway is neuroprotective. Thus, the light damage albino mouse model may be a good model to study complement-mediated photoreceptor degeneration.
Magnetic protein microspheres as dynamic contrast agents for magnetomotive optical coherence tomography (2008)

Optical coherence tomography (OCT) is an emerging biomedical imaging modality that has been developed over the last 15 years. More recently, OCT has been used for the intraoperative imaging of tumor margins in breast cancer and axillary lymph nodes providing a real time in-vivo assessment of the tissue morphology. Traditional OCT images are limited by only being able to observe morphological structures. As diagnostic medicine continues to push for earlier detection, one must develop functional imaging modalities that would detect molecular information in-vivo allowing a real-time microscopic analysis of the tissue specimen. A novel modality of OCT called magnetomotive-OCT (MMOCT) has been developed by our group, employing an induced modulated magnetic field with a magnetic contrast agent to create the added contrast to structural OCT images. Modified protein microspheres with a BSA protein shell functionalized with RGD peptide sequences for targeting and an oil core have been designed and synthesized. Magnetic nanoparticles (Fe3O4) and Nile Red dye have been encapsulated into its oil core. These microspheres have previously been demonstrated to target cancer cells by functionalizing them with a layer of RGD peptides and could be functionalized with monoclonal antibodies. Preliminary results show that these magnetic microspheres, which are 2.0- 5.0 microns in size, are readily detectable under MM-OCT when embedded in a 5% agarose gel, in a 3-D scaffold of macrophage cells previously incubated with the microspheres, and when injected in-vivo into a tumor from an NMUcarcinogen rat animal model for breast cancer.
Characterization of Proteoglycans of Human Placenta and Identification of Unique Chondroitin Sulfate Proteoglycans of the Intervillous Spaces That Mediate the Adherence ofPlasmodium falciparum-infected Erythrocytes to the Placenta (2000)

In pregnant women infected with Plasmodium falciparum, the infected red blood cells (IRBCs) selectively accumulate in the intervillous spaces of placenta, leading to poor fetal outcome and severe health complications in the mother. Although chondroitin 4-sulfate is known to mediate IRBC adherence to placenta, the natural receptor has not been identified. In the present study, the chondroitin sulfate proteoglycans (CSPGs) of human placenta were purified and structurally characterized, and adherence of IRBCs to these CSPGs investigated. The data indicate that the placenta contains three distinct types of CSPGs: significant quantities of uniquely low sulfated, extracellular CSPGs localized in the intervillous spaces, minor amounts of two cell-associated CSPGs, and major amounts of dermatan sulfate-like CSPGs of the fibrous tissue. Of the various CSPGs isolated from the placenta, the low sulfated CSPGs of the intervillous spaces most efficiently bind IRBCs. Based on IRBC adherence capacities and localization patterns of various CSPGs, we conclude that the CSPGs of the intervillous spaces are the receptors for placental IRBC adherence. The identification and characterization of these CSPGs provide a valuable tool for understanding the precise molecular interactions involved in placental IRBC adherence and for the development of therapeutic strategies for maternal malaria. In the accompanying paper (Alkhalil, A., Achur, R. N., Valiyaveettil, M., Ockenhouse, C. F., and Gowda, D. C. (2000) J. Biol. Chem. 275, 40357-40364), we report the structural requirements for the IRBC adherence.
Calcium‐Dependent Evoked Release of N[3H]Acetylaspartylglutamate from the Optic Pathway (1988)

N-Acetylaspartylglutamate (NAAG) is a neuropeptide localized to several putative glutamatergic neuronal systems, including the rodent optic pathway. To determine whether the peptide is released by depolarization, the superior colliculus of the rat was perfused with 2 microCi of [3H]NAAG, then with Krebs-bicarbonate buffer for 1 h, using a microdialysis system. Subsequently, 10-min fractions were collected and analyzed by HPLC for [3H]NAAG. Addition of 100 microM veratridine resulted in a several-fold increase in the evoked release of [3H]NAAG that was virtually abolished by coperfusion with Ca2+-free Krebs buffer containing 1 mM EGTA. When [3H]glutamate was used as the precursor, veratridine depolarization resulted in only an 80% increase in the release of [3H]NAAG. Prior enucleation of the right eye reduced the spontaneous release of [3H]NAAG by 50%, and the veratridine-evoked release by greater than 85%, from the left superior colliculus. These results suggest that NAAG is released upon depolarization and may serve as a neurotransmitter/neuromodulator in the optic tract.
A Necessary and Sufficient Determinant for Protein-selective Glycosylation in Vivo (2007)

A limited number of glycoproteins including luteinizing hormone and carbonic anhydrase-VI (CA6) bear N-linked oligosaccharides that are modified with beta1,4-linked N-acetylgalactosamine (GalNAc). The selective addition of GalNAc to these glycoproteins requires that the beta1,4-N-acetylgalactosaminyltransferase (betaGT) recognize both the oligosaccharide acceptor and a peptide recognition determinant on the substrate glycoprotein. We report here that two recently cloned betaGTs, betaGT3 and betaGT4, that are able to transfer GalNAc to GlcNAc in beta1,4-linkage display the necessary glycoprotein specificity in vivo. Both betaGTs transfer GalNAc to N-linked oligosaccharides on the luteinizing hormone alpha subunit and CA6 but not to those on transferrin (Trf). A single peptide recognition determinant encoded in the carboxyl-terminal 19-amino acid sequence of bovine CA6 mediates transfer of GalNAc to each of its two N-linked oligosaccharides. The addition of this 19-amino acid sequence to the carboxyl terminus of Trf confers full acceptor activity onto Trf for both betaGT3 and betaGT4 in vivo. The complete 19-amino acid sequence is required for optimal GalNAc addition in vivo, indicating that the peptide sequence is both necessary and sufficient for recognition by betaGT3 and betaGT4.
Second-Line Oxaliplatin, Folinic Acid, and Fluorouracil Versus Folinic Acid and Fluorouracil Alone for Gemcitabine-Refractory Pancreatic Cancer: Outcomes From the CONKO-003 Trial (2014)

Second-line OFF significantly extended the duration of overall survival when compared with FF alone in patients with advanced gemcitabine-refractory pancreatic cancer.
Promoters regulated by the glnG (ntrC) and nifA gene products share a heptameric consensus sequence in the -15 region. (1983)

We have determined the nucleotide sequences of the Klebsiella pneumoniae nifL (regulation of N2 fixation genes) and the Escherichia coli glnA (glutamine synthetase) promoters. We compared these sequences with the published sequences of three other promoters that, like the nifL and glnA promoters, are activated by the general nitrogen regulators glnF (ntrA) and glnG (ntrC). The three promoters are the argTr (arginine transport) and dhuA (histidine transport) promoters of Salmonella typhimurium and the nifH (nitrogenase) promoter of Rhizobium meliloti. All five sequences (with at most one mismatch) contain the heptameric consensus sequence T-T-T-T-G-C-A. In the R. meliloti nifH and K. pneumoniae nifL promoters, in which the transcription initiation sites have been determined, the consensus sequence is situated in the -15 region. We recently reported that the K. pneumoniae nifA product, which activates nif genes, can substitute for the glnG (ntrC) product in activating promoters of several genes involved in nitrogen assimilation, including the nifL, the glnA, and the R. meliloti nifH promoters. It is likely that nifA also activates the S. typhimurium argTr and dhuA promoters. In contrast, the glnG product cannot substitute for the nifA product in the activation of the K. pneumoniae nifH (nitrogenase) promoter. Consistent with this latter observation, and supporting the conclusion that the T-T-T-T-G-C-A sequence is a regulatory site for glnG product activation, the K. pneumoniae nifH promoter (C-C-C-T-G-C-A) has only partial similarity with the T-T-T-T-G-C-A consensus sequence in the -15 region.
Diffractive elements for annular laser beam transformation (1992)

A diffractive optical system for the transformation of an annular laser beam to a uniform circular beam is presented. It is composed of two diffractive elements which are recorded as surface relief transmission gratings with multilevel discrete binary steps. Our experiments with CO2 laser radiation show that high diffraction efficiencies and good uniformity of the output beam can be achieved.
Structure and stability range of a hexanuclear Th(iv)–glycine complex (2012)

A hexanuclear Th(IV)-glycine complex was observed by Th L(3)-edge EXAFS measurements in an aqueous solution. Within the stability range of this complex the positively charged hexanuclear species [Th(6)(μ(3)-O)(4)(μ(3)-OH)(4)(H(2)O)(6)(Gly)(6)(HGly)(6)](6+) was preserved in a crystal with the composition [Th(6)(μ(3)-O)(4)(μ(3)-OH)(4)(H(2)O)(6)(Gly)(6)(HGly)(6)]·(NO(3))(3)(ClO(4))(3)(H(2)O)(3). This complex appears as a result of a competing reaction between hydrolysis and ligation by glycine. At a pH value below the stability range of the hexanuclear complex, crystals with the composition [Th(H(2)O)(3)(HGly)(3)]·(ClO(4))(4)H(2)O were obtained from the solution. Three water molecules in the thorium coordination sphere indicate that this complex occurs prior to the onset of Th(IV) hydrolysis.
Epoxomicin, a potent and selective proteasome inhibitor, exhibitsin vivoantiinflammatory activity (1999)

The proteasome regulates cellular processes as diverse as cell cycle progression and NF-kappaB activation. In this study, we show that the potent antitumor natural product epoxomicin specifically targets the proteasome. Utilizing biotinylated-epoxomicin as a molecular probe, we demonstrate that epoxomicin covalently binds to the LMP7, X, MECL1, and Z catalytic subunits of the proteasome. Enzymatic analyses with purified bovine erythrocyte proteasome reveal that epoxomicin potently inhibits primarily the chymotrypsin-like activity. The trypsin-like and peptidyl-glutamyl peptide hydrolyzing catalytic activities also are inhibited at 100- and 1,000-fold slower rates, respectively. In contrast to peptide aldehyde proteasome inhibitors, epoxomicin does not inhibit nonproteasomal proteases such trypsin, chymotrypsin, papain, calpain, and cathepsin B at concentrations of up to 50 microM. In addition, epoxomicin is a more potent inhibitor of the chymotrypsin-like activity than lactacystin and the peptide vinyl sulfone NLVS. Epoxomicin also effectively inhibits NF-kappaB activation in vitro and potently blocks in vivo inflammation in the murine ear edema assay. These results thus define epoxomicin as a novel proteasome inhibitor that likely will prove useful in exploring the role of the proteasome in various in vivo and in vitro systems.
The partial retro–inverso modification: A road traveled together (2005)

In the mid-1970s, Dr. Murray Goodman was interested in a reversed peptide bond as a surrogate to understand the functional role of the amide bond in aspartame, a dipeptide sweetener. Very soon, realizing the breath and potential of this modification, Murray expanded this activity into a full program and I was fortunate to be part of it. Together we formulated new concepts such as the partially modified retro-inverso and end-group modified retro-inverso transformations, tested hypotheses, generated novel nomenclature, developed synthetic routes, characterized the preferred conformations of the unique building blocks employed in this modification, the gem-diaminoalkyl and the C2-substituted malonyl residues, and studied the biological activity of retro-inverso isomers of bioactive peptides. In the early 1980s several laboratories initiated extensive research targeted at the retro-inverso modification. The revival of this field led to new applications, new methods of synthesis, and new insights on the conformational and topological properties of the retro-inverso modification. Among the fields that embraced the retro-inverso concept were immunology as pertains to subjects such as synthetic vaccines, immunomodulators, and diagnostic tools, and drug delivery field as pertains to targeted and nontargeted cell permeation vectors loaded with bioactive cargo. Doctor Murray Goodman's sudden death leaves behind not only family, friends, and colleagues, but also an impressive record of scientific achievements among which is the revival of the modern era of the retro-inverso transformation. Murray's numerous contributions, excellent leadership, enthusiastic promotion, and outstanding teachings in this field will carry and illuminate his memory far into the future.
Combined evaluation of mucin antigen and E-cadherin expression may help select patients with gastric cancer suitable for minimally invasive therapy (2003)

A normal E-cadherin/MUC1-negative expression pattern in gastric cancer is a favourable marker. Preoperative estimation of the E-cadherin and MUC1 status of an endoscopic biopsy specimen may help select appropriate patients for minimally invasive treatment of gastric cancer.
Sclera-Choroid-RPE Transport of Eight β-Blockers in Human, Bovine, Porcine, Rabbit, and Rat Models (2011)

Owing to the presence of pigment and drug binding, choroid-RPE is the principal barrier to transscleral β-blocker transport, with the barrier being more significant for lipophilic β-blockers. Although different in magnitude between species, sclera/SCRPE transport can be correlated between species. Tissue thickness accounts for the species differences in scleral transport. Differences in tissue thickness and melanin content largely account for the species differences in SCRPE transport.
Upper and lower extremity robotic devices for rehabilitation and for studying motor control (2003)

Purpose of review The successful motor rehabilitation of stroke, traumatic brain-injured and spinal cord-injured patients requires an intensive and task-specific therapy approach. Budget constraints limit a hand-to-hand therapy approach, so that intelligent machines may offer a solution to promote motor recovery and obtain a better understanding of motor control. This new field of automated or robot-assisted motor rehabilitation has emerged since the 1990s. Recent findings This article will present clinically viable devices for upper and lower extremity rehabilitation. The MIT-Manus and the Mirror-Image Motion Enabler robot, which enable unrestricted unilateral or bilateral shoulder and elbow movement, consistently proved superior on the motor impairment level. The ARM guide, which assisted reaching in a straight-line trajectory, and the Bi-Manu-Track, which enabled the bilateral practice of a forearm and wrist movement, are currently being tested. For gait rehabilitation after stroke, the electromechanical gait trainer, GT I, has proved effective compared with treadmill training with body weight support. The Lokomat, consisting of a treadmill and a powered exoskeleton, lessened the therapeutic effort compared with manually assisted treadmill training in spinal cord-injured patients. Future developments will see more degrees of freedom, improved man-machine interaction and the implementation of virtual reality. Summary Technical possibilities are one aspect, but multi-centre trials and a consideration of the unsubstantiated fears among therapists of being replaced by machines will decide on the successful implementation of this most promising field to the benefit of patients.