gebhart/patrepeval huggingface dataset:
Development expression of Hox11 and specification of splenic cell fate. (1995)

Hox11 is the first member of a novel class of orphan homeobox genes. We report that Hox11 is expressed in a discrete temporal and spatially segmented pattern during embryonic development and appears critical for the specification of splenic cell fate. Expression is first observed in the developing muscle plates of branchial arches 1, 2, 3 and 4/6, and subsequently within motor neurons of cranial nerves V, VII, IX, and X, which innervate these muscles. Hox11 serves as a molecular maker distinguishing branchial from somatic motor nuclei. Additionally, Hox11 is expressed in the surface ectoderm of the first branchial arch in the region destined to become the tongue and teeth and then in ganglia innervating this area. However, Hox11-deficient mice have no apparent morphological of functional defects within these structures. Notably the closely related homeobox genes, Hox11L.1 and Hox1L1.2, were not expressed in a redundant pattern. Neither Hox11L1 nor Hox11L2 was expressed in the branchial arches or their motor nuclei within wild-type or Hox11-/- mice. Beginning at E11.5, Hox11 is normally expressed at a single site in the abdomen within splanchnic mesoderm destined to form the spleen, and Hox11-/- mice have no spleen. We noted no increase in cell death within the dorsal mesogastrium of Hox11-deficient mice. Instead the dorsal mesogastrium fails to separate from the stomach. Hox11-/- mice display a larger stomach and possibly pancreas, suggesting that these mesodermal cells now contribute to other organs.
Femtosecond laser machining and lamination for large-area flexible organic microfluidic chips (2009)

A hybrid process compatible with reel-to-reel manufacturing is developed for ultra low-cost large-scale manufacture of disposable microfluidic chips. It combines ultra-short laser microstructuring and lamination technology. Microchannels in polyester foils were formed using focused, high-intensity femtosecond laser pulses. Lamination using a commercial SU8-epoxy resist layer was used to seal the microchannel layer and cover foil. This hybrid process also enables heterogeneous material structuration and integration.
Antibody localization to B-cell lymphoma xenografts in immunodeficient mice: importance of using residualizing radiolabels. (2002)

Antibody (Ab) localization to Raji B-cell lymphoma xenografts in severe combined immunodeficient (SCID) mice was investigated using three Abs: anti-CD20; anti-CD147; and anti-MHC class II. These antigens are all high-density cell surface antigens, and the Abs are all considered to be slowly internalized and catabolized, with catabolism primarily due to the basal turnover rate of cell surface constituents. Unexpectedly, specific Ab uptake was demonstrated only when residualizing labels were used. The residualizing labels tested were 111In-benzyl-diethylenetriaminepentaacetic acid and [125I]iodo-dilactitol-tyramine, whereas the nonresidualizing label was a conventional iodine label. In contrast, in vitro experiments demonstrated very slow catabolism of the same Abs. These data strongly suggest that Ab catabolism is much more rapid in vivo than in vitro and has a strong impact on Ab accumulation in the tumor. If autologous human tumors are similar to these xenografts, then there should be a large advantage in the use of residualizing radiolabels for radioimmunotherapy.
ASSIMILATION OF NUTRIENTS BY CULTURED HYBRID LOBSTERS (Homarussp.) FED EXPERIMENTAL DIETS1 (1983)

ABSTRACT Indirect calorimetry and the chromic oxide indicator method were employed to investigate the digestibility and assimilation of nutrients by cultured lobsters ( Homarus sp.) growing on experimental diets. Starved and fed lobsters were compared by observing food and oxygen consumption and fecal and urinary excretions in a closed, recirculating metabolic chamber. Apparent digestible and metabolizable energy and nitrogen were determined for 2 diets, which differed in the type and level of protein and carbohydrate. The apparent digestibility of diet 79F, a purified ration containing 46.8% crude protein, was 68.8% on an as‐fed basis, with an apparent digestibility of energy of 88.1%. For diet SM25B, which contained 61.1% crude protein including shrimp meal, apparent digestibility was 66.2% as‐fed and the apparent digestibility of energy was 91.3%. Metabolizable energy values of 4.59 and 4.65 kcal/g dry weight were obtained for diets 79F and SM25B respectively. Growth on the two diets was similar but lobsters fed 79F consumed and excreted significantly more than those fed SM25B. For both diets protein and lipid were better than 90% digested, but the carbohydrate fraction was only about 65% digestible. The apparent higher nutritive value of SM25B for lobsters may be related to protein quality and improved efficiency of utilization.
Stimulation of Human γδ T Cells by Nonpeptidic Mycobacterial Ligands (1994)

Most human peripheral blood γδ T lymphocytes respond to hitherto unidentified mycobacterial antigens. Four ligands from Mycobacterium tuberculosis strain H37Rv that stimulated proliferation of a major human γδ T cell subset were isolated and partially characterized. One of these ligands, TUBag4, is a 5′ triphosphorylated thymidine-containing compound, to which the three other stimulatory molecules are structurally related. These findings support the hypothesis that some γδ T cells recognize nonpeptidic ligands.
Two-Photon Imaging with Thermal Light (2005)

We report the first experimental demonstration of two-photon imaging with a pseudothermal source. Similarly to the case of entangled states, a two-photon Gaussian thin lens equation is observed, indicating EPR type correlation in position. We introduce the concepts of two-photon coherent and two-photon incoherent imaging. The differences between the entangled and the thermal cases are explained in terms of these concepts.
Changes in Mumps Virus Gene Sequence Associated with Variability in Neurovirulent Phenotype (2003)

Mumps virus is highly neurotropic and, prior to widespread vaccination programs, was the major cause of viral meningitis in the United States. Nonetheless, the genetic basis of mumps virus neurotropism and neurovirulence was until recently not understood, largely due to the lack of an animal model. Here, nonneurovirulent (Jeryl Lynn vaccine) and highly neurovirulent (88-1961 wild type) mumps virus strains were passaged in human neural cells or in chicken fibroblast cells with the goal of neuroadapting or neuroattenuating the viruses, respectively. When tested in our rat neurovirulence assay against the respective parental strains, a Jeryl Lynn virus variant with an enhanced propensity for replication (neurotropism) and damage (neurovirulence) in the brain and an 88-1961 wild-type virus variant with decreased neurotropic and neurovirulent properties were recovered. To determine the molecular basis for the observed differences in neurovirulence and neuroattenuation, the complete genomes of the parental strains and their variants were fully sequenced. A comparison at the nucleotide level associated three amino acid changes with enhanced neurovirulence of the neuroadapted vaccine strain: one each in the nucleoprotein, matrix protein, and polymerase and three amino acid changes with reduced neurovirulence of the neuroattenuated wild-type strain: one each in the fusion protein, hemagglutinin-neuraminidase protein, and polymerase. The potential role of these amino acid changes in neurotropism, neurovirulence, and neuroattenuation is discussed.
Mutagenesis and Mapping of a Mouse Gene, Clock , Essential for Circadian Behavior (1994)

In a search for genes that regulate circadian rhythms in mammals, the progeny of mice treated with N-ethyl-N-nitrosourea (ENU) were screened for circadian clock mutations. A semidominant mutation, Clock, that lengthens circadian period and abolishes persistence of rhythmicity was identified. Clock segregated as a single gene that mapped to the midportion of mouse chromosome 5, a region syntenic to human chromosome 4. The power of ENU mutagenesis combined with the ability to clone murine genes by map position provides a generally applicable approach to study complex behavior in mammals.
Localization of 125I-Labeled Antigen in Germinal Centers of Mouse Spleen: Histologic and Ultrastructural Autoradiographic Studies of the Secondary Immune Reaction (1968)

Summary Histologic and ultrastructural studies were carried out on the process of the localization of antigen in splenic germinal centers during the secondary immune reaction in mice. The magnitude and regularity of the developed plasma membrane infoldings of antigen-retaining reticular cells in germinal centers are described. The key finding was that these specifically developed plasma membrane infoldings are degraded during the early intervals of the secondary response. This response occurred in conjunction with a loss of label and an apparent loss of function of the existing antigen-trapping mechanism in splenic germinal centers. We suggest that the described cytotoxic sequelae could be a result of complement fixation and that such a regulatory mechanism would be essential to prevent further contact of immunologically competent cells with antigen, while clearing the centers for their development against other antigens. A conformity of vesicles was observed in the cytoplasm of the parenchymal cells of the germinal centers and in the plasma membrane infoldings of the antigen-retaining reticular cells.
Hydraulic Response and Nitrogen Retention in Bioretention Mesocosms with Regulated Outlets: Part II—Nitrogen Retention (2011)

We observed dissolved nitrogen retention in vegetated bioretention mesocosms using different media with varying hydraulic conductivities. Elevated outlets were installed to regulate hydraulic response, with one treatment left free draining. The treatments (three replicates each) were loaded weekly with 50 cm of effluent averaging 2.47 mg/L nitrogen oxides (NOx) and 4.67 mg/L total nitrogen for 1 year. The NOx and total nitrogen retention by the outlet regulated treatments was significantly greater than the unregulated treatment. The systems then were dosed 6 times with 53 cm of synthetic stormwater averaging 0.77 mg/ L NOx and 1.46 mg/L total nitrogen, applied over 90 minutes. The outlet regulated treatment retained 68% NOx and 60% total nitrogen, while the corresponding free draining treatment retained 25% NOx and 27% total nitrogen. Over the following winter, the outlet regulated treatment retained 50% NOx and 73% total nitrogen, while the corresponding free draining treatment exported 17% more NOx, while retaining 50% total nitrogen.
Rituximab treatment induces the expression of genes involved in healing processes in the rheumatoid arthritis synovium (2011)

Rituximab displays unique effects on global gene expression profiles in the synovial tissue of RA patients. These observations open new perspectives in the understanding of the biologic effects of the drug and in the selection of patients likely to benefit from this therapy.
Uphill Photooxidation of NADH Analogues by Hexyl Viologen Catalyzed by Zinc Porphyrin-Linked Fullerenes (2001)

In the absence of oxygen, the photolytically generated C60•- moiety in ZnP•+−C60•- and ZnP•+−H2P−C60•- radical ion pairs undergoes one-electron oxidation by hexyl viologen (HV2+), whereas the ZnP•+ moiety is reduced by NADH analogues (1-benzyl-1,4-dihydronicotinamide and 10-methyl-9,10-dihydroacridine). Thus, both ZnP−C60 and ZnP−H2P−C60 donor−acceptor ensembles act in benzonitrile as efficient photocatalysts for the uphill oxidation of NADH analogues by HV2+. In the case of ZnP−C60, the quantum yield of the photocatalytic reaction increases with increasing concentration of HV2+ or an NADH analogue to reach a limiting value of 0.99. The limiting quantum yields of ZnP−C60 and ZnP−H2P−C60 agree well with the quantum yields of radical ion pair formation, ZnP•+−C60•- and ZnP•+−H2P−C60•-, respectively. In the presence of oxygen, the lifetimes of the radical ion pairs are, however, markedly reduced because of an oxygen-catalyzed back electron transfer process between C60•- and ZnP•+. Such an impact on the radical ion pair lifetime consequences a significant decrease in the photocatalytic reactivity of the dyad (i.e., ZnP−C60) in the overall photooxidation of an NADH analogue by HV2+. By contrast, the reactivity of the triad (i.e., ZnP−H2P−C60) shows little effects upon admitting O2.
Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2 (2006)

Using a comparative genomics approach, a copper resistance gene cluster has been identified in multiple archaeal genomes. The cop cluster is predicted to encode a metallochaperone (CopM), a P-type copper-exporting ATPase (CopA) and a novel, archaea-specific transcriptional regulator (CopT) which might control the expression of the cop genes. Sequence analysis revealed that CopT has an N-terminal DNA-binding helix-turn-helix domain and a C-terminal TRASH domain; TRASH is a novel domain which has recently been proposed to be uniquely involved in metal-binding in sensors, transporters and trafficking proteins in prokaryotes. The present study describes the molecular characterization of the cop gene cluster in the thermoacidophilic crenarchaeon Sulfolobus solfataricus. The polycistronic copMA transcript was found to accumulate in response to growth-inhibiting copper concentrations, whereas copT transcript abundance appeared to be constitutive. DNA-binding assays revealed that CopT binds to the copMA promoter at multiple sites, both upstream and downstream of the predicted TATA-BRE site. Copper was found to specifically modulate the affinity of DNA binding by CopT. This study describes a copper-responsive operon in archaea, a new family of archaeal DNA-binding proteins, and supports the idea that this domain plays a prominent role in the archaeal copper response. A model is proposed for copper-responsive transcriptional regulation of the copMA gene cluster.
Effect of capsaicin and analogues on potassium and calcium currents and vanilloid receptors in Xenopus embryo spinal neurones (1996)

1. The potassium current in embryo spinal neurones of Xenopus consists of at least two kinetically distinct components with overlapping voltage-dependencies of activation. We investigated whether capsaicin might specifically block these components in acutely dissociated neurones from stage 37/38 embryos by use of standard patch clamp techniques. 2. Capsaicin caused a time-dependent block of both the slow and fast components of the potassium current. The concentration-dependence was described by the Hill equation with a KD of 21 microM and a coefficient of 1.5 (n = 9-11 at each concentration). Differences between the observed and fitted values were not significant at the 5% level (chi(2) = 2.80, 6 degrees of freedom). 3. Capsaicin did not affect the time course or voltage-sensitivity of activation, but the steady-state block was voltage-dependent. The block could be relieved by hyperpolarization, and the rate of the removal of block was voltage- and time-dependent. The time constant for the blocking reaction was also voltage-dependent for voltage steps below +30 mV, but above this level it was voltage-independent. These results suggest that capsaicin blocks potassium channels by an open channel mechanism. 4. Other derivatives of vanillin, such as capsazepine, resiniferatoxin, and piperine also blocked potassium channels. Capsazepine and resiniferatoxin caused a greater block than similar concentrations of capsaicin, and in the case of capsazepine, the block was also clearly time-dependent. 5. Capsaicin and capsazepine also blocked calcium currents in a time-dependent manner. Fitting the Hill equation to the averaged data gave a KD of 43.5 microM, and a coefficient of 1.35 (n = 11 at each concentration). The fitted values were not significantly different from the observed means at the 5% level (chi(2) = 12.1, 6 degrees of freedom). 6. Six out of 29 Rohon-Beard sensory neurones responded to capsaicin with an inward current that appeared to be similar to the capsaicin activation of mammalian C sensory neurones. This response saturated at 10 microM capsaicin.
Multiple Interferon Subtypes: The Phenomenon and Its Relevance (1987)

Over the last 10 years the structure of various human interferon-alpha (IFN-alpha) and interferon-gamma (IFN-gamma) subtypes was elucidated by combining protein chemistry and molecular biology. In this article some key studies related to the interferon structure are reviewed. The significance of the multiplicity of IFN-alpha and IFN-gamma subtypes is discussed in view of some current results.
Selective Perfluoro- and Polyfluoroarylation of Meldrum’s Acid (2014)

This work describes the facile and mono-selective per- and polyfluoroarylation of Meldrum's acid to generate a versatile synthon for highly fluorinated α-phenyl acetic acid derivatives, which provide straightforward access to fluorinated building blocks. The reaction takes place quickly, and most products were isolated without the need for chromatography. Importantly, this method provides an alternative strategy to access α-arylated Meldrum's acids, which avoids the need for aryl-Pb(IV) salts or diaryliodonium salts. Furthermore, we demonstrate the synthetic versatility and utility of the Meldrum's acid products by subjecting our products to several derivatizations of the Meldrum's acid products as well as photocatalytic hydrodefluorination.
Analysis of late graft failure after allogeneic bone marrow transplantation: detection of residual host cells using amplification of variable number of tandem repeats loci. (1992)

In an attempt to gain insight into the etiology of late graft failure, we analysed the origin of bone marrow mononuclear cells (BMMC) and peripheral blood leukocytes in patients with this syndrome by taking advantage of DNA fragment length polymorphisms in variable number of tandem repeats (VNTR) loci. Amplification of the VNTR loci in DNA from BMMC using the polymerase chain reaction revealed the persistence of host cells in two of four patients studied. One of the patients, whose cultured lymphocytes inhibited in vitro growth of donor-derived hemopoietic progenitor cells, responded to immunosuppressive therapy and donor-derived hemopoiesis was restored. In the other patient, host-derived polymorphonuclear leukocytes (PMN) appeared together with donor-derived PMN from the early post-transplant period, and he proceeded to relapse with myelodysplastic syndrome. In the other two patients in whom host cells were not detectable, the marrow hypoplasia was associated with chronic graft-versus-host disease (GVHD). The hypoplasia improved significantly as the chronic GVHD improved in response to immunosuppressive therapy. We conclude that detecting minimal residual host cells by means of amplification of VNTR loci is valuable for understanding the etiology of late graft failure in marrow transplant recipients, and could prove helpful for choosing appropriate therapy for this syndrome.
Shewanella putrefaciens Adhesion and Biofilm Formation on Food Processing Surfaces (2001)

Laboratory model systems were developed for studying Shewanella putrefaciens adhesion and biofilm formation under batch and flow conditions. S. putrefaciens plays a major role in food spoilage and may cause microbially induced corrosion on steel surfaces. S. putrefaciens bacteria suspended in buffer adhered readily to stainless steel surfaces. Maximum numbers of adherent bacteria per square centimeter were reached in 8 h at 25 degrees C and reflected the cell density in suspension. Numbers of adhering bacteria from a suspension containing 10(8) CFU/ml were much lower in a laminar flow system (modified Robbins device) (reaching 10(2) CFU/cm(2)) than in a batch system (reaching 10(7) CFU/cm(2)), and maximum numbers were reached after 24 h. When nutrients were supplied, S. putrefaciens grew in biofilms with layers of bacteria. The rate of biofilm formation and the thickness of the film were not dependent on the availability of carbohydrate (lactate or glucose) or on iron starvation. The number of S. putrefaciens bacteria on the surface was partly influenced by the presence of other bacteria (Pseudomonas fluorescens) which reduced the numbers of S. putrefaciens bacteria in the biofilm. Numbers of bacteria on the surface must be quantified to evaluate the influence of environmental factors on adhesion and biofilm formation. We used a combination of fluorescence microscopy (4',6'-diamidino-2-phenylindole staining and in situ hybridization, for mixed-culture studies), ultrasonic removal of bacteria from surfaces, and indirect conductometry and found this combination sufficient to quantify bacteria on surfaces.
A new anti-CEA-SN-38 antibody-drug conjugate (ADC), IMMU-130, is active in controlling metastatic colorectal cancer (mCRC) in patients (pts) refractory or relapsing after irinotecan-containing chemotherapies: Initial results of a phase I/II study. (2015)

2505 Background: Combination chemotherapies with 5-FU, irinotecan, oxaliplatin, anti-VEGF, and anti-EGFR agents have improved the outcome of mCRC pts. However, there is still an urgent need for better therapies to control this disease. IMMU-130 (labetuzumab govitecan), a conjugate of a humanized anti-CEACAM5 antibody, coupled site-specifically to SN-38 (7.6 moles SN-38/IgG) using a proprietary linker, is an attractive therapeutic option for mCRC pts. Methods: A phase I/II clinical trial (NCT01605318) was initiated in irinotecan- refractory/relapsed mCRC pts with an elevated CEA ( > 5 ng/mL), treated with IMMU-130 once- or twice-weekly at escalating 4-10 mg/kg dosages on weeks 1 and 2 of 3-week cycles. The primary objective of the study was determination of MTD, with secondary objectives of efficacy (by RECIST 1.1), PK and immunogenicity. Treatment was continued until disease progression or intolerance. Results: Between Feb 2013 and Nov 2014, 66 patients were enrolled. Median age was 57 years [39-82]. Median prior therapies were 5 [1-9], with 76% and 36% pts receiving prior bevacizumab and an EGFR inhibitor, respectively. Median number of cycles per pt was 2 [1-15]. Fifty-eight patients were evaluable for toxicity, with 3 DLTs (G3 typhlitis, G4 neutropenia and G3 nausea/vomiting > 48h) in all pts. Grade 3/4 drug-related toxicities were found in 25% pts, including neutropenia (G3, 7%; G4, 3%), diarrhea (G3, 2%), anemia (G3, 3%) and lymphopenia (G3, 3%). The dose selected for further study was 10 mg/kg weekly or 6 mg/kg biw. No pt developed antibodies to the conjugate. Tumor reductions were seen in 23/66 (35%) pts, including one PR with 88% best tumor shrinkage still being treated for 52+ weeks, 6 pts with 20-30% tumor reductions, and 16 pts with 0-20% tumor reductions. Conclusions: Repeated cycles of IMMU-130 monotherapy had an acceptable toxicity profile. Tumor reductions were noted in 35% of patients despite prior relapse to irinotecan-containing therapies. These results encourage further evaluation of IMMU-130 in combination with other agents in mCRC. Clinical trial information: NCT01605318.