gebhart/patrepeval huggingface dataset:
Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes: FIGURE 1. (2004)

microRNAs (miRNAs) are 21-22-nucleotide noncoding RNAs that are widely believed to regulate complementary mRNA targets. However, due to the modest amount of pairing involved, only a few out of the hundreds of known animal miRNAs have thus far been connected to mRNA targets. Here, we considered the possibility that miRNAs might regulate non-mRNA targets, namely other miRNAs. To do so, we conducted a systematic assessment of the nearly complete catalogs of animal miRNAs for potential miRNA:miRNA complements. Our analysis uncovered several compelling examples that strongly suggest a function for miRNA duplexes, thus adding a potential layer of regulatory sophistication to the small RNA world. Interestingly, the most striking examples involve miRNAs complementary to members of the K-box family and Brd-box family, two classes of miRNAs previously implicated in regulation of Notch target genes. We emphasize that patterns of nucleotide constraint indicate that miRNA complementarity is not a simple consequence of miRNA:miRNA* complementarity; however, our findings do suggest that the potential regulatory consequences of the latter also deserve investigation.
Identification of NKG2A and NKp80 as specific natural killer cell markers in rhesus and pigtailed monkeys (2005)

Investigations of natural killer (NK) cells in simian models of disease have been hampered by a lack of appropriate phenotypic markers and by an inadequate understanding of the regulation of NK cell activities. In the present study, a panel of monoclonal antibodies (mAbs) specific for various human NK receptors was screened for cross-reactivity with NK cells from rhesus macaques and pigtailed macaques. Flow cytometric analyses using anti-human NKG2A and anti-human NKp80 mAbs individually, and particularly in combination with anti-CD16 mAb, allowed for the identification of the entire NK cell population in both species. NK cells in monkeys were generally identified by negative selection of peripheral blood mononuclear cells (PBMCs) for the absence of T-cell, B-cell, and monocyte markers. mAb-mediated ligation of NKp80 induced NK cell cytotoxicity, while in the case of NKG2A it displayed a clear capability to inhibit the lysis of target cells by NK cells from macaques, as well as from humans. This new phenotypic and functional characterization of NKG2A and NKp80 in rhesus and pigtailed macaque NK cells provides a new approach in the analysis of their innate immune system.
The First Practical and Efficient One-Pot Synthesis of 6-Substituted 7-Azaindoles via a Reissert-Henze Reaction (2008)

A variety of 6-substituted 7-azaindoles (30 examples) were obtained via selective O-methylation of 7-azaindole-N-oxide m-chlorobenzoic acid salt and subsequent, base-catalyzed one-pot reaction with a range of N-, O-, S-nucleophiles or cyanide.
Effects of unidirectional permeability in asymmetric poly(DL‐lactic acid‐co‐glycolic acid) conduits on peripheral nerve regeneration: An in vitro and in vivo study (2007)

The high outflow permeability of the nerve conduit used to emit the drained waste generated from the traumatized host nerve stump is critical in peripheral nerve regeneration. Our earlier studies have established that asymmetric conduits fulfill the basic requirements for use as nerve guide conduits. In this study, the inflow characteristics of optimal nerve conduits were further examined using in vivo and in vitro trials. Various asymmetric poly(DL-lactic acid-co-glycolic acid) (PLGA) conduits were controlled by modifying precipitation baths using 0, 20, and 95% isopropyl alcohol, with high-porosity (permeability), medium-porosity (high outflow and low inflow), and low-porosity (permeability), respectively. In the in vitro trial, the Schwann cells and fibroblasts were seeded on either side of the asymmetric PLGA films in a newly designed coculture system that simulated the repaired nerve conduit environment. The results of the directional permeable films indicated the statistically significant proliferation of Schwann cells and the inhibition of the division of fibroblasts in lactate dehydrogenase release and inhibition of 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl-tetrazolium bromide (MTT) reduction, compared with the other films. In the in vivo trial, the PLGA conduits seeded with Schwann cells were implanted into 10 mm right sciatic nerve defects in rats. After 6 weeks, implanted conduits were harvested. Histological examination verified that directional permeable conduits had markedly more A-type and B-type myelin fibers in the midconduit and distal nerve. In this work, the directional transport characteristics were established as an extremely important factor to the design and development of optimal nerve guide conduits in peripheral nerve regeneration.
Leukemia of early infancy: Early B-cell lineage associated with t(4:11) (1986)

A case of infantile acute leukemia associated with translocation t(4:11)(q21:q23) is reported. This leukemia has a very poor prognosis, and this patient survived for only 9 months. The blast cell morphology was L1/L2 according to the FAB classification and showed a lymphoid appearance on transmission electron microscopy. The histochemical stains showed a pattern of periodic acid-Schiff positivity and variable alpha-naphtyl acetate staining. The cells were TdT-positive and surface-marker phenotyping was positive for Ia-like and B4 antigens but negative for CALLA, T-cell markers, myelocyte and monocyte markers. The leukemic cells represent a frozen state of a very early precursor, corresponding to the earliest recognizable stage of the B-cell lineage. This observation may contribute to the controversion regarding the cell origin of this unique leukemia associated with t(4:11), lymphatic versus null cell, early myeloid, or mixed, and points to the possibility of a very early B-cell lineage leukemia.
Mechanical properties of the upper airway (1998)

Abnormalities of upper airway mechanical properties are a well-recognized and important feature of the pathophysiology of the obstructive sleep apnea hypopnea syndrome (OSAHS). Recently, investigations enhanced our understanding of the factors that promote upper airway obstruction. In patients with OSAHS, anatomic narrowing of the pharyngeal airway, particularly in the lateral dimension with thickening of the lateral pharyngeal walls, is present. In addition, the passive upper airway (absent muscle activity) demonstrates increased collapsibility, which is modulated by caudal tracheal traction, mucosal surface forces, route of breathing, and the balance of intraluminal airway and extraluminal tissue pressures. In patients with OSAHS, pharyngeal dilator muscles (including the genioglossus and soft palate muscles) demonstrate a coordinated pattern of increased muscle activity while awake compared with normals. This is thought to represent a neuromuscular compensatory mechanism for the anatomically narrow, more collapsible upper airway. With the onset of sleep, the reflexes that drive this muscular compensation are diminished, leading to reduced muscle activity and predisposing the OSAHS patient to pharyngeal collapse. Better understanding of the mechanical properties of the upper airway in normals and patients with OSAHS should help in the development of new therapeutic strategies.
S‐Layers as a basic building block in a molecular construction kit (2006)

Crystalline arrays of protein or glycoprotein subunits forming surface layers (S-layers) are the most common outermost envelope components of prokaryotic organisms (archaea and bacteria). The wealth of information on the structure, chemistry, genetics, morphogenesis, and function of S-layers has revealed a broad application potential. As S-layers are periodic structures, they exhibit identical physicochemical properties for each molecular unit down to the subnanometer level and possess pores of identical size and morphology. Many applications of S-layers in nanobiotechnology depend on the ability of isolated subunits to recrystallize into monomolecular lattices in suspension or on suitable surfaces and interfaces. S-Layer lattices can be exploited as scaffolding and patterning elements for generating more complex supramolecular assemblies and structures, as required for life and nonlife science applications.
New developments in optical coherence tomography for glaucoma (2008)

The next generation optical coherence tomography is around the corner. By understanding the current strengths and limitations of this advancing technology, one can better assess its use in clinical practice.
Mutants of Arabidopsis thaliana defective in the acquisition of tolerance to high temperature stress (2000)

The ability of organisms to acquire thermotolerance to normally lethal high temperatures is an ancient and conserved adaptive response. However, knowledge of cellular factors essential to this response is limited. Acquisition of thermotolerance is likely to be of particular importance to plants that experience daily temperature fluctuations and are unable to escape to more favorable environments. We developed a screen, based on hypocotyl elongation, for mutants of Arabidopsis thaliana that are unable to acquire thermotolerance to high-temperature stress and have defined four separate genetic loci, hot1-4, required for this process. hot1 was found to have a mutation in the heat shock protein 101 (Hsp101) gene, converting a conserved Glu residue in the second ATP-binding domain to a Lys residue, a mutation that is predicted to compromise Hsp101 ATPase activity. In addition to exhibiting a thermotolerance defect as assayed by hypocotyl elongation, 10-day-old hot1 seedlings were also unable to acquire thermotolerance, and hot1 seeds had greatly reduced basal thermotolerance. Complementation of hot1 plants by transformation with wild-type Hsp101 genomic DNA restored hot1 plants to the wild-type phenotype. The hot mutants are the first mutants defective in thermotolerance that have been isolated in a higher eukaryote, and hot1 represents the first mutation in an Hsp in any higher plant. The phenotype of hot1 also provides direct evidence that Hsp101, which is required for thermotolerance in bacteria and yeast, is also essential for thermotolerance in a complex eukaryote.
Lowering oxygen tension enhances the differentiation of mouse embryonic stem cells into neuronal cells (2009)

Embryonic stem cells (ESC) are capable of proliferating indefinitely in vitro whilst retaining their ability to differentiate into cells of every adult lineage. Efficient, high yield processes, which direct differentiation of ESC to specific lineages, will underpin the development of cost-effective drug screening and cell therapy products. The aim of this study was to investigate whether laboratory oxygen tension currently used for the neuronal differentiation of ESC was suboptimal resulting in inefficient process yields. An adherent monolayer protocol for the neuronal differentiation of mouse ESC (mESC) was performed in oxygen controlled chambers using a chemically defined media over an 8 day period of culture. When exposed to oxygen tensions more appropriate to in vivo neuronal development (2% O(2)), there was a 34-fold increase in the yield of viable cells from the differentiation process. Low oxygen tension inhibited cell death during an early phase (48 to 96 h) and toward the end (120 to 192 h) of the process. The percentage of cells expressing neuronal markers was determined by flow cytometry, revealing a small rise in the betaIII tubulin and a threefold increase in the MAP2 populations at 2% O(2). The total increase in the yield of viable cells expressing neuronal markers was shown to be 55-fold for betaIII tubulin and 114-fold for MAP2. In conclusion, this study revealed that low oxygen tension can be used to enhance the yield of neuronal cells derived from ESCs and has implications for the development of efficient, cost-effective production processes.
Lung-Derived Mesenchymal Stromal Cell Post-Transplantation Survival, Persistence, Paracrine Expression, and Repair of Elastase-Injured Lung (2011)

While multipotent mesenchymal stromal cells have been recently isolated from adult lung (L-MSCs), there is very limited data on their biological properties and therapeutic potential in vivo. How L-MSCs compare with bone marrow-derived MSCs (BM-MSCs) is also unclear. In this study, we characterized L-MSC phenotype, clonogenicity, and differentiation potential, and compared L-MSCs to BM-MSCs in vivo survival, retention, paracrine gene expression, and repair or elastase injury after transplantation. L-MSCs were highly clonogenic, frequently expressed aldehyde dehydrogenase activity, and differentiated into osteocytes, chondrocytes, adipocytes, myofibroblasts, and smooth muscle cells. After intravenous injection (2 h), L-MSCs showed greater survival than BM-MSCs; similarly, L-MSCs were significantly more resistant than BM-MSCs to anchorage independent culture (4 h) in vitro. Long after transplantation (4 or 32 days), a significantly higher number of CD45(neg) L-MSCs were retained than BM-MSCs. By flow cytometry, L-MSCs expressed more intercellular adhesion molecule-1 (ICAM-1), platelet derived growth factor receptor alpha (PDGFRα), and integrin α2 than BM-MSCs; these proteins were found to modulate endothelial adherence, directional migration, and migration across Matrigel in L-MSCs. Further, L-MSCs with low ICAM-1 showed poorer lung retention and higher phagocytosis in vivo. Compared with BM-MSCs, L-MSCs expressed higher levels of several transcripts (e.g., Ccl2, Cxcl2, Cxcl10, IL-6, IL-11, Hgf, and Igf2) in vitro, although gene expression in vivo was increased by L-MSCs and BM-MSCs equivalently. Accordingly, both L-MSCs and BM-MSCs reduced elastase injury to the same extent. This study demonstrates that tissue-specific L-MSCs possess mechanisms that enhance their lung retention after intravenous transplantation, and produce substantial healing of elastase injury comparable to BM-MSCs.
Induction of T-Cell Immunity Against Ras Oncoproteins by Soluble Protein or Ras-Expressing Escherichia coli (1995)

Immunization as described here leads to Ras mutation-specific antitumor immunity in vitro and in vivo, with therapeutic efficacy in an established tumor model.
The gene 4 protein of bacteriophage T7. Characterization of helicase activity. (1983)

Gene 4 protein of bacteriophage T7 is a multifunctional enzyme that both stimulates T7 DNA polymerase during leading strand synthesis, and synthesizes RNA primers that initiate lagging strand synthesis. Both activities are dependent on the ability of the gene 4 protein to translocate unidirectionally (5' to 3') along single-stranded DNA (Tabor, S., and Richardson, C.C. (1981) Proc. Natl. Acad. Sci. U. S. A. 78, 205-209), a reaction that is coupled to the hydrolysis of nucleoside 5'-triphosphates. In this paper, we show that gene 4 protein, in the absence of other proteins, is a helicase, an activity previously inferred from its ability to stimulate T7 DNA polymerase on duplex DNA. We have designed a DNA substrate for use in characterizing the helicase activity which consists of a short DNA fragment bearing a single-stranded 3'-tail when annealed to circular, single-stranded M13 DNA. With such a DNA substrate, the gene 4 protein can disrupt the helical structure of a 96-nucleotide-long fragment, resulting in its displacement from the circle. Helicase activity requires a long stretch of at least 17 nucleotides of single-stranded DNA on the 5'-side of the duplex to be unwound. In addition, helicase activity is not observed unless a short (greater than 6 nucleotides) single-stranded 3'-tail is present. The helicase activity has an absolute requirement for hydrolysis of a nucleoside 5'-triphosphate. The inhibitor of nucleoside triphosphate hydrolysis, beta, gamma-methylene dTTP, is an effective inhibitor of helicase activity. Based on these results, we propose a model for the action of the gene 4 protein at a replication fork.
Eradication of established tumors by a fully human monoclonal antibody to the epidermal growth factor receptor without concomitant chemotherapy. (1999)

A fully human IgG2kappa monoclonal antibody (MAb), E7.6.3, specific to the human epidermal growth factor (EGF) receptor (EGFr) was generated from human antibody-producing XenoMouse strains engineered to be deficient in mouse antibody production and to contain the majority of the human antibody gene repertoire on megabase-sized fragments from the human heavy and kappa light chain loci. The E7.6.3 MAb exhibits high affinity (KD = 5 x 10(-11) M) to the receptor, blocks completely the binding of both EGF and transforming growth factor alpha (TGF-a) to various EGFr-expressing human carcinoma cell lines, and abolishes EGF-dependent cell activation, including EGFr tyrosine phosphorylation, increased extracellular acidification rate, and cell proliferation. The antibody (0.2 mg i.p. twice a week for 3 weeks) prevents completely the formation of human epidermoid carcinoma A431 xenografts in athymic mice. More importantly, the administration of E7.6.3 without concomitant chemotherapy results in complete eradication of established tumors as large as 1.2 cm3. Tumor eradication of A431 xenografts was achieved in nearly all of the mice treated with total E7.6.3 doses as low as 3 mg, administered over the course of 3 weeks, and a total dose of 0.6 mg led to tumor elimination in 65% of the mice. No tumor recurrence was observed for more than 8 months after the last antibody injection, which further indicated complete tumor cell elimination by the antibody. The potency of E7.6.3 in eradicating well-established tumors without concomitant chemotherapy indicates its potential as a monotherapeutic agent for the treatment of multiple EGFr-expressing human solid tumors, including those for which no effective chemotherapy is available. Being a fully human antibody, E7.6.3 is expected to exhibit minimal immunogenicity and a longer half-life as compared with mouse or mouse-derivatized MAbs, thus allowing repeated antibody administration, including in immunocompetent patients. These results suggest E7.6.3 as a good candidate for assessing the full therapeutic potential of anti-EGFr antibody in the therapy of multiple patient populations with EGFr-expressing solid tumors.
In vivo Real-Time Mass Spectrometry for Guided Surgery Application (2016)

Here we describe a new instrument (SpiderMass) designed for in vivo and real-time analysis. In this instrument ion production is performed remotely from the MS instrument and the generated ions are transported in real-time to the MS analyzer. Ion production is promoted by Resonant Infrared Laser Ablation (RIR-LA) based on the highly effective excitation of O-H bonds in water molecules naturally present in most biological samples. The retrieved molecular patterns are specific to the cell phenotypes and benign versus cancer regions of patient biopsies can be easily differentiated. We also demonstrate by analysis of human skin that SpiderMass can be used under in vivo conditions with minimal damage and pain. Furthermore SpiderMass can also be used for real-time drug metabolism and pharmacokinetic (DMPK) analysis or food safety topics. SpiderMass is thus the first MS based system designed for in vivo real-time analysis under minimally invasive conditions.
A review of infectious bovine rhinotracheitis, shipping fever pneumonia and viral-bacterial synergism in respiratory disease of cattle. (1982)

Unanswered questions on the etiology and prevention of shipping fever pneumonia have allowed this disease to remain one of the most costly to the North American cattle industry. Research in this area has indirected that while Pasteurella haemolytica and, to a lesser extent, P. multocida are involved in most cases, they seem to require additional factors to help initiate the disease process. Bovine herpes virus 1 has been shown experimentally to be one such factor. This review examines in some detail the topics of infectious bovine rhinotracheitis, shipping fever, and viral-bacterial interactions in the production of respiratory disease in various species. It deals with history, definitions, etiologies, clinical signs and lesions, and considers exposure levels, transmission and various pathogenetic mechanisms that are postulated or known to occur.
Electronic Structure and Reactivity of Isomeric Oxo-Mn(V) Porphyrins:  Effects of Spin-State Crossing and pKa Modulation (2006)

The reactivity of the isomeric oxo-Mn(V)-2-tetra-N-methylpyridyl (2-TMPyP) and oxo-Mn(V)-4-tetra-N-methylpyridyl (4-TMPyP) porphyrins has been investigated by a combined experimental and theoretical approach based on density functional theory. The unusual higher reactivity of the more electron-rich 4-TMPyP species appears to be related to both the higher basicity of its oxo ligand, compared to that of the 2-TMPyP isomer, and the smaller low-spin-high-spin promotion energy of 4-TMPyP, compared to that of 2-TMPyP, because of the stabilization of the A2u orbital in the latter isomer. Therefore, in a two-state energy profile involving crossing of the initial singlet and final quintet potential energy surfaces, the 4-TMPyP isomer should be kinetically favored. The calculated differences in the singlet-quintet gaps for the 2-TMPyP and 4-TMPyP systems compare well with the measured differences in the activation energies for two isomeric porphyrins. Both effects, proton affinity and electron-promotion energy, contribute to reduce the reactivity of the more electrophilic oxidant when electron-withdrawing groups are closer to the active site, contrary to the usual expectations based on simple chemical reactivity correlations. These theoretical results are in accord with new experimental data showing O=Mn(V)-O-H pK(a)s of 7.5 and 8.6 for the isomeric 2-TMPyP and 4-TMPyP systems, respectively.
Graphene-Wrapped Fe3O4 Anode Material with Improved Reversible Capacity and Cyclic Stability for Lithium Ion Batteries (2010)

A well-organized flexible interleaved composite of graphene nanosheets (GNSs) decorated with Fe3O4 particles was synthesized through in situ reduction of iron hydroxide between GNSs. The GNS/Fe3O4 composite shows a reversible specific capacity approaching 1026 mA h g−1 after 30 cycles at 35 mA g−1 and 580 mAh g−1 after 100 cycles at 700 mA g−1as well as improved cyclic stability and excellent rate capability. The multifunctional features of the GNS/Fe3O4 composite are considered as follows: (i) GNSs play a "flexible confinement" function to enwrap Fe3O4 particles, which can compensate for the volume change of Fe3O4 and prevent the detachment and agglomeration of pulverized Fe3O4, thus extending the cycling life of the electrode; (ii) GNSs provide a large contact surface for individual dispersion of well-adhered Fe3O4 particles and act as an excellent conductive agent to provide a highway for electron transport, improving the accessible capacity; (iii) Fe3O4 particles separate GNSs and prevent their restacking thus improving the adsorption and immersion of electrolyte on the surface of electroactive material; and (iv) the porosity formed by lateral GNSs and Fe3O4 particles facilitates ion transportation. As a result, this unique laterally confined GNS/Fe3O4 composite can dramatically improve the cycling stability and the rate capability of Fe3O4 as an anode material for lithium ion batteries.