gebhart/patrepeval huggingface dataset:
Single-sided continuous optoelectrowetting (SCOEW) for droplet manipulation with light patterns (2010)

Electrowetting-on-dielectric (EWOD) promises to be an important lab-on-a-chip approach for effectively manipulating droplets with electric field-controlled surface tension. Droplets manipulated in electrowetting-based devices are typically sandwiched between two parallel plates and actuated by digital electrodes. The size of pixilated electrodes limits the minimum droplet size that can be manipulated. Here, we report on a single-sided continuous optoelectrowetting (SCOEW) mechanism that enables light-patterned electrowetting modulation for continuous droplet manipulation on an open, featureless, and photoconductive surface. SCOEW overcomes the size limitation of physical pixilated electrodes by utilizing dynamic and reconfigurable optical patterns and enables the continuous transport, splitting, merging, and mixing of droplets with volumes ranging from 50 microL to 250 pL, over 5-orders of magnitude. This single-sided open configuration provides a flexible interface for integration with other microfluidic components, such as sample reservoirs through simple tubing. Light-triggered, parallel, and volume-tunable droplet injection with volume variation less than 1% has been demonstrated with SCOEW. The unique lateral field-driven optoelectrowetting mechanism also enables extremely low light intensity actuation, and droplet manipulation can be achieved by directly positioning the SCOEW chip on a LCD screen used in a laptop or portable cellular phone.
Spin-On End-Functional Diblock Copolymers for Quantitative DNA Immobilization (2008)

We demonstrate a simple means to covalently bond DNA to both hard (i.e., glass and silicon wafers) and soft (i.e., polymeric) substrates that provides quantitative and precise control of the DNA areal density. The approach is based on spin coating an alkyne-end-functional diblock copolymer, alpha-alkyne-omega-Br-poly( tBA- b-MMA), that self-assembles on both types of substrates as an ordered monolayer and thereby directs alkyne groups to the surface. Azido-functionalized DNA is covalently linked to the alkyne functionalized substrates by means of a "click" reaction between azide and alkyne groups. The density of immobilized DNA can be quantitatively controlled by varying the parameters used for spin-coating the copolymer film, that is, solution concentration and rotational speed, or by varying the copolymer molecular weight. We find the yield of the DNA coupling reaction to be dependent on the nature of the polymer underlying the reactive alkyne functional groups, being higher for more hydrophilic polymers.
Plasmid-Determined AmpC-Type β-Lactamases (2002)

The predominant mechanism for resistance to β-lactam antibiotics in gram-negative bacteria is the synthesis of β-lactamase. To meet this challenge, β-lactams with greater β-lactamase stability, including cephalosporins, carbapenems, and monobactams, were introduced in the 1980s. Resistance
Adoptive immunotherapy for cancer: the next generation of gene‐engineered immune cells (2009)

Adoptive cellular immunotherapy involving transfer of tumor-reactive T cells has shown some notable antitumor responses in a minority of cancer patients. In particular, transfer of tumor-infiltrating lymphocytes has resulted in long-term objective responses in patients with advanced melanoma. However, the inability to isolate sufficient numbers of tumor-specific T cells from most malignancies has restricted the broad utility of this approach. An emerging approach to circumvent this limitation involves the genetic modification of effector cells with T cell receptor (TCR) transgenes or chimeric single-chain variable fragment (scFv) receptors that can specifically redirect T cells to tumor. There has been much progress in the design of TCR and scFv receptors to enhance the antigen-specific activation of effector cells and their trafficking and persistence in vivo. Considerable effort has been directed toward improving the safety of this approach and reducing the immunogenicity of the receptor. This review discusses the latest developments in the field of adoptive immunotherapy using genetically modified immune cells that have been transduced with either TCR or scFv receptor transgenes and used in preclinical and clinical settings as anticancer agents.
Osteopontin: Its Transglutaminase-Catalyzed Posttranslational Modifications and Cross-Linking to Fibronectin1 (1994)

Osteopontin (OP) is a component of extracellular, bone, and urinary stone matrices, but the mechanism by which it is stably incorporated into such matrices remains unknown. By SDS-PAGE analysis of [125I]OP, treated with a catalytic amount of TG, we first demonstrate both intra- and intermolecular covalent cross-linking of OP. Most importantly, the analysis of the products generated from reactions containing OP, Fn, and TG by SDS-PAGE, autoradiography, and Western blotting using either OP or Fn antibody, and quantitation of TG-catalyzed epsilon-(gamma-glutamyl)lysine isopeptide formation between OP and Fn demonstrate, for the first time, covalent cross-linking between these two proteins. Similar reactions in the presence of polyamine substrates of TG show OP-Fn intermolecular cross-linking via N,N-bis-(gamma-glutamyl)polyamine formation. Finally, immunoprecipitation of 125I-labeled NRK cell surface proteins with anti-OP and anti-Fn antibodies, SDS-PAGE analysis, and autoradiography provides critical evidence for nonreducible OP-Fn cross-linking in vivo. These results clearly suggest that TG-mediated cross-linking between OP and Fn represents one of the most likely mechanisms by which OP becomes covalently linked to bone matrix, urinary stone matrix, and to ECM.
Identification of Hematopoietic Stem Cell–Specific miRNAs Enables Gene Therapy of Globoid Cell Leukodystrophy (2010)

Globoid cell leukodystrophy (GLD; also known as Krabbe disease) is an invariably fatal lysosomal storage disorder caused by mutations in the galactocerebrosidase (GALC) gene. Hematopoietic stem cell (HSC)-based gene therapy is being explored for GLD; however, we found that forced GALC expression was toxic to HSCs and early progenitors, highlighting the need for improved regulation of vector expression. We used a genetic reporter strategy based on lentiviral vectors to detect microRNA activity in hematopoietic cells at single-cell resolution. We report that miR-126 and miR-130a were expressed in HSCs and early progenitors from both mice and humans, but not in differentiated progeny. Moreover, repopulating HSCs could be purified solely on the basis of miRNA expression, providing a new method relevant for human HSC isolation. By incorporating miR-126 target sequences into a GALC-expressing vector, we suppressed GALC expression in HSCs while maintaining robust expression in mature hematopoietic cells. This approach protected HSCs from GALC toxicity and allowed successful treatment of a mouse GLD model, providing a rationale to explore HSC-based gene therapy for GLD.
Long-distance charge transport in duplex DNA: The phonon-assisted polaron-like hopping mechanism (1999)

An anthraquinone-linked duplex DNA oligomer containing 60 base pairs was synthesized by PCR. The strand complementary to the quinone-containing strand has four isolated GG steps, which serve as traps for a migrating radical cation. Irradiation of the quinone leads to electron transfer from the DNA to the quinone forming the anthraquinone radical anion and a base radical cation. The radical cation migrates through the DNA, causing reaction at GG steps revealed as strand breaks. The efficiency of strand cleavage falls off exponentially with distance from the quinone (slope = -0.02 A(-1)). This finding necessitates reinterpretation of mechanisms proposed for radical cation migration in DNA. We propose that radical cations form self-trapped polarons that migrate by thermally activated hopping.
Mutations at specific atp6 codons which cause human mitochondrial diseases also lead to male sterility in a plant (1998)

Defects in the human mitochondrial genetic system result in some diseases. These disorders are the result of rearrangements or point mutations in mitochondrial genes. In higher plants mutations and rearrangements in the mitochondrial DNA are believed to cause cytoplasmic male sterility (CMS), a mitochondrially inherited inability to produce viable pollen. In sorghum, formation of CMS is strongly correlated with anther-specific loss of mitochondrial atp6 RNA editing. Here we show that this loss of atp6 RNA editing mimics point mutations at codons that cause severe disorders in humans. We conclude that (i) loss of RNA editing in sorghum anthers probably causes CMS, (ii) similarities exist in the onset of mitochondrial dysfunction in plant and human tissues, and (iii) the evolutionary appearance of RNA editing provided a mechanism to compensate for otherwise lethal point mutations.
Norepinephrine content in primary and secondary lymphoid organs is altered in rats with adjuvant-induced arthritis (1997)

Chemical sympathectomy of secondary lymphoid organs with sparing of the hind limbs exacerbates adjuvant-induced arthritis (AA) in Lewis rats supporting a role for noradrenergic (NA) innervation of the immune system in AA pathology. The present study examines sympathetic innervation of lymphoid organs from Lewis rats 32 days after treatment with complete Freund's adjuvant (CFA) or vehicle using fluorescence histochemistry for localization of catecholamines (CA) and high-performance liquid chromatography with electrochemical detection (LCEC) for measurement for norepinephrine. The thymus from AA rats was significantly reduced in size, while secondary lymphoid organs, i.e., spleen and draining lymph nodes (DLN), were significantly enlarged compared with that seen in vehicle-treated controls. Fluorescence histochemistry revealed no apparent differences in the density of NA innervation, or the intensity of staining in sympathetic nerves in any of the secondary lymphoid organs from AA rats compared with that observed in control animals. However, there was an apparent increase in the density of NA nerve fibers in the thymus of AA rats. Norepinephrine (NE) concentration (pmol NE per g or mg wet weight), in the thymus from AA rats was significantly increased. Conversely, a significant decrease in splenic and lymph node NE concentration was measured in adjuvant-treated animals compared with that seen in vehicle-treated rats. Total NE content (pmol NE per whole organ weight) in lymphoid organs was not altered, except in popliteal lymph nodes (PLN), where it was increased. Collectively, our findings suggest that changes in NA innervation of lymphoid organs from AA rats result largely from increases or decreases in organ mass. Since NE released from NA nerves acts in a paracrine fashion, changes in lymphoid tissue volume that result from enhanced proliferation, migration, or cell death can make a significant difference in the availability of NE for interaction with immune target cells in these organs, even in the absence of a change in NE metabolism. Decreased thymic weight and increased spleen and lymph node weight should increase and decrease NE availability for interaction with target cells, respectively. Additionally, in PLN (a site where the highest concentration of antigen is encountered) an increase in total NE content suggests compensatory changes in NE metabolism.
Coumarin-Based Inhibitors of HIV Integrase (1997)

The structures of a large number of HIV-1 integrase inhibitors have in common two aryl units separated by a central linker. Frequently at least one of these aryl moieties must contain 1,2-dihydroxy substituents in order to exhibit high inhibitory potency. The ability of o-dihydroxy-containing species to undergo in situ oxidation to reactive quinones presents a potential limitation to the utility of such compounds. The recent report of tetrameric 4-hydroxycoumarin-derived inhibitor 5 provided a lead example of an inhibitor which does not contain the catechol moiety. Compound 5 represents a large, highly complex yet symmetrical molecule. It was the purpose of the present study to determine the critical components of 5 and if possible to simplify its structure while maintaining potency. In the present study, dissection of tetrameric 5 (IC50 = 1.5 microM) into its constituent parts showed that the minimum active pharmacophore consisted of a coumarin dimer containing an aryl substituent on the central linker methylene. However, in the simplest case in which the central linker aryl unit consisted of a phenyl ring (compound 8, IC50 = 43 microM), a significant reduction in potency resulted by removing two of the original four coumarin units. Replacement of this central phenyl ring by more extended aromatic systems having higher lipophilicity improved potency, as did the addition of 7-hydroxy substituents to the coumarin rings. Combining these latter two modifications resulted in compounds such as 3,3'-(2-naphthalenomethylene)bis[4,7-dihydroxycoumarin] (34, IC50 = 4.2 microM) which exhibited nearly the full potency of the parent tetramer 5 yet were structurally much simpler.
Controlling Structure from the Bottom-Up:  Structural and Optical Properties of Layer-by-Layer Assembled Palladium Coordination-Based Multilayers (2006)

Layer-by-layer assembly of two palladium coordination-based multilayers on silicon and glass substrates is presented. The new assemblies consist of rigid-rod chromophores connected by terminal pyridine moieties to palladium centers. Both colloidal palladium and PdCl2(PhCN)2 were used in order to determine the effect of the metal complex precursor on multilayer structure and optical properties. The multilayers were formed by an iterative wet-chemical deposition process at room temperature in air on a siloxane-based template layer. Twelve consecutive deposition steps have been demonstrated resulting in structurally regular assemblies with an equal amount of chromophore and palladium added in each molecular bilayer. The optical intensity characteristics of the metal-organic films are clearly a function of the palladium precursor employed. The colloid-based system has a UV-vis absorption maximum an order of magnitude stronger than that of the PdCl2-based multilayer. The absorption maximum of the PdCl2-based film exhibits a significant red shift of 23 nm with the addition of 12 layers. Remarkably, the structure and physiochemical properties of the submicron scale PdCl2-based structures are determined by the configuration of the approximately 15 angstroms thick template layer. The refractive index of the PdCl2-based film was determined by spectroscopic ellipsometry. Well-defined three-dimensional structures, with a dimension of 5 microm, were obtained using photopatterned template monolayers. The properties and microstructure of the films were studied by UV-vis spectroscopy, spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray reflectivity (XRR), scanning electron microscopy (SEM), and aqueous contact angle measurements (CA).
The orderly allocation of mesodermal cells to the extraembryonic structures and the anteroposterior axis during gastrulation of the mouse embryo (1999)

The prospective fate of cells in the primitive streak was examined at early, mid and late stages of mouse gastrula development to determine the order of allocation of primitive streak cells to the mesoderm of the extraembryonic membranes and to the fetal tissues. At the early-streak stage, primitive streak cells contribute predominantly to tissues of the extraembryonic mesoderm as previously found. However, a surprising observation is that the erythropoietic precursors of the yolk sac emerge earlier than the bulk of the vitelline endothelium, which is formed continuously throughout gastrula development. This may suggest that the erythropoietic and the endothelial cell lineages may arise independently of one another. Furthermore, the extraembryonic mesoderm that is localized to the anterior and chorionic side of the yolk sac is recruited ahead of that destined for the posterior and amnionic side. For the mesodermal derivatives in the embryo, those destined for the rostral structures such as heart and forebrain mesoderm ingress through the primitive streak early during a narrow window of development. They are then followed by those for the rest of the cranial mesoderm and lastly the paraxial and lateral mesoderm of the trunk. Results of this study, which represent snapshots of the types of precursor cells in the primitive streak, have provided a better delineation of the timing of allocation of the various mesodermal lineages to specific compartments in the extraembryonic membranes and different locations in the embryonic anteroposterior axis.
The Protein Quality, Digestibility, and Composition of Algae, Chlorella 71105 a (1963)

SUMMARY Freeze‐dried Chlorella 71105 was found to contain 55.5% crude protein; 7.5% crude fat; 8.25% ash; 7.0% moisture; 17.8% total carbohydrate; 3.1% crude fiber; 2.68% chlorophyll; and .08% urea. The digestibility of the protein was 86%; of crude fat, 93%; of total carbohydrate, 72%; and of crude fiber, 15%. The protein efficiency ratio (PER) was 2.19, which compares favorably with soy protein. The PER of Chlorella with 0.2% L‐methionine was 2.90, which compares favorably with casein values in the literature. The PER of casein was 3.30; that of defatted egg protein, 4.01, in these studies. The rats were fed at 10% protein levels. In addition, Chlorella 71105 contained all essential amino acids as well as having a high carotene content. Available energy value was 3.3 kcal/g.
Exploitation of cyclostationarity for identifying the Volterra kernels of nonlinear systems (1993)

A class of random time-series inputs for nonlinear time-invariant systems that permit the analytical specification of a set of operators on the input that are orthonormal over all time to the Volterra operators for all orders and all lag sets is introduced. The time series in this class are cyclostationary and complex valued. The orthonormal operators are used to obtain an input-output type of cross-correlation formula for identifying the individual Volterra kernels of arbitrary order for a nonlinear system of possibly infinite order and possibly infinite memory. The real parts of the complex-valued inputs in this class comprise a class of real-valued inputs for which the same sets of specified operators apply. However, the orthogonality for different orders holds for these real inputs only for Volterra operators of order less than the order of the specified operator. Thus, these real inputs can be used to identify Volterra kernels only for finite-order systems. Frequency-domain counterparts of the time-domain methods that can utilize an FFT algorithm are developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells (2012)

We recently showed that defined sets of transcription factors are sufficient to convert mouse and human fibroblasts directly into cells resembling functional neurons, referred to as "induced neuronal" (iN) cells. For some applications however, it would be desirable to convert fibroblasts into proliferative neural precursor cells (NPCs) instead of neurons. We hypothesized that NPC-like cells may be induced using the same principal approach used for generating iN cells. Toward this goal, we infected mouse embryonic fibroblasts derived from Sox2-EGFP mice with a set of 11 transcription factors highly expressed in NPCs. Twenty-four days after transgene induction, Sox2-EGFP(+) colonies emerged that expressed NPC-specific genes and differentiated into neuronal and astrocytic cells. Using stepwise elimination, we found that Sox2 and FoxG1 are capable of generating clonal self-renewing, bipotent induced NPCs that gave rise to astrocytes and functional neurons. When we added the Pou and Homeobox domain-containing transcription factor Brn2 to Sox2 and FoxG1, we were able to induce tripotent NPCs that could be differentiated not only into neurons and astrocytes but also into oligodendrocytes. The transcription factors FoxG1 and Brn2 alone also were capable of inducing NPC-like cells; however, these cells generated less mature neurons, although they did produce astrocytes and even oligodendrocytes capable of integration into dysmyelinated Shiverer brain. Our data demonstrate that direct lineage reprogramming using target cell-type-specific transcription factors can be used to induce NPC-like cells that potentially could be used for autologous cell transplantation-based therapies in the brain or spinal cord.
Solid-phase synthesis of serine-based glycosphingolipid analogues for preparation of glycoconjugate arrays (2004)

Synthetic glycolipids with defined structures are important tools in the study of glycolipid biology. In this paper we describe a solid-phase synthesis of three galactosylated serine-based glycosphingolipid analogues using the novel linker 2-fluoro-4-(hydroxymethyl)-phenoxyacetic acid. Gel-phase (19)F-NMR spectroscopy was used to measure the yield and stereochemical outcome of the solid-phase glycosylations. Under NIS-TfOH promotion, alpha- and beta-selective glycosylations were performed at room temperature with thioglycoside donors carrying fluorine labelled protective groups. Finally, the glycolipids were covalently linked to microtiter plates and labelled lectins with different selectivity for alpha- and beta-galactosides could bind to the glycolipid arrays.
De Novo Formation of Insulin-Producing “Neo-β Cell Islets” from Intestinal Crypts (2014)

SUMMARY The ability to interconvert terminally differentiated cells could serve as a powerful tool for cell-based treatment of degenerative diseases, including diabetes mellitus. To determine which, if any, adult tissues are competent to activate an islet β cell program, we performed an in vivo screen by expressing three β cell “reprogramming factors” in a wide spectrum of tissues. We report that transient intestinal expression of these factors—Pdx1, MafA, and Ngn3 (PMN)—promotes rapid conversion of intestinal crypt cells into endocrine cells, which coalesce into “neoislets” below the crypt base. Neoislet cells express insulin and show ultrastructural features of β cells. Importantly, intestinal neoislets are glucose-responsive and able to ameliorate hyperglycemia in diabetic mice. Moreover, PMN expression in human intestinal “organoids” stimulates the conversion of intestinal epithelial cells into β-like cells. Our results thus demonstrate that the intestine is an accessible and abundant source of functional insulin-producing cells.