gebhart/patrepeval huggingface dataset:
Human Amniotic Membrane as a Physiologic Wound Dressing (1974)

In 65 patients, split-thickness donor sites were covered with amniotic membrane. Amniotic membrane was used to dress partialthickness burns in 42 patients. In rats, open wounds were covered with amnion and in others it was placed in a subcutaneous pocket. The amnion acted as a comfortable and effective wound dressing. None of the biopsy specimens, however, showed vascularization of the amnion by the host.
Cloning and Characterization of the Gene for a New Epithelial β-Defensin (1999)

Mammalian beta-defensins are endogenous cysteine-rich peptide antibiotics that are produced either by epithelial cells lining the respiratory, digestive, and urogenital tracts or by granulocytes and macrophages. A growing body of evidence has implicated these peptides in host defense, particularly mucosal innate immunity. We previously reported the cloning of the full-length cDNA for a porcine beta-defensin (pBD-1), which was found to be expressed throughout the airway and oral mucosa. Here, we provide the structural organization of the pBD-1 gene, showing that the entire gene spans approximately 1.9 kilobases with two short exons separated by a 1.5-kilobase intron. Fluorescence in situ hybridization mapped the pBD-1 gene to porcine chromosome 15q14-q15. 1 within a region of conserved synteny to the chromosomal locations of human and mouse alpha- and beta-defensins. We also provide several independent lines of evidence showing that the pBD-1 gene is expressed constitutively during inflammation and infection, despite its resemblance to many inducible epithelial beta-defensins in amino acid sequence, genomic structure, and sites of expression. First, stimulation of primary porcine tongue epithelial cells with lipopolysaccharide, tumor necrosis factor-alpha, and interleukin (IL)-1beta failed to up-regulate the expression of pBD-1 mRNA. Second, pBD-1 gene expression was not enhanced in either digestive or respiratory mucosa of pigs following a 2-day infection with Salmonella typhimurium or Actinobacillus pleuropneumoniae. Last, direct transfection of the pBD-1 gene promoter into NIH/3T3 cells showed no difference in reporter gene activity in response to stimulation by lipopolysaccharide and IL-1beta. The constitutive expression of pBD-1 in airway and oral mucosa, which is consistent with a lack of consensus binding sites for nuclear factor-kappaB or NF-IL-6 in its promoter region, suggests that it may play a surveillance role in maintaining the steady state of microflora on mucosal surfaces.
Malignant mesothelioma. The eastern cooperative oncology group (ECOG) experience (1983)

The Eastern Cooperative Oncology Group has conducted a retrospective review of their experience of 96 patients with a tissue diagnosis of malignant mesothelioma treated between 1972 and 1980 on four separate sarcoma chemotherapy protocols. Thirty-two of the 96 patients were diagnosed and treated in South Africa. There were 75 males and 21 females with an age range of 27 to 78 with a median of 58.1 years. All, except for 28 patients, had some form of prior therapy. The median time from the onset of symptoms to diagnosis was 12 weeks; from the diagnosis to randomization was 15.1 weeks. Only 12 of the 96 patients demonstrated an objective regression. The responses were 7/51 on Adriamycin with 2 complete responses (complete responses--38 weeks and 52 weeks), 2/24 on Adriamycin combinations, 2/7 on cycloleucine, 1/3 on bleomycin, and 0/10 on non-Adriamycin combinations. Only 1/28 responded to a cross-over therapy (Adriamycin). The median survival from the start of protocol chemotherapy was 7.4 months and 7.5 months for Adriamycin treated patients. The median survival for responders was 29.9 months, compared to 6.3 months for nonresponders. The median survival for this entire series from the time of first symptoms was 15.2 months. The median survival for the 7 patients with abdominal mesothelioma was 12 weeks. There was a slight improvement in survival for the South Africans as compared to the Americans. Malignant mesothelioma in this series, was a rapidly lethal, nonresponsive disease whose treatment will require new therapies.
Energy-Transfer Modeling for the Rational Design of Multiporphyrin Light-Harvesting Arrays (1998)

Excited-state energy migration among a collection of pigments forms the basis for natural light-harvesting processes and synthetic molecular photonic devices. The rational design of efficient energy-transfer devices requires the ability to analyze the expected performance characteristics of target molecular architectures comprised of various pigments. Toward that goal, we present a general tool for modeling the kinetics of energy migration in weakly coupled multipigment arrays. A matrix-formulated eigenvalue/eigenvector approach has been implemented, using empirical data from a small set of prototypical molecules, to predict the quantum efficiency (QE) of energy migration in a variety of arrays as a function of rate, competitive processes, and architecture. Trends in the results point to useful design strategies including the following: (1) The QE for energy transfer to a terminal acceptor upon random excitation within a linear array of isoenergetic pigments decreases rapidly as the length of the array is increased. (2) Increasing the rate of transfer and/or the lifetime of the competitive deactivation processes significantly improves QE. (3) Qualitatively similar results are obtained in simulations of linear molecular photonic wires in which excitation and trapping occur at opposite ends of the array. (4) Branched and cyclic array architectures exhibit higher QEs than linear architectures with equal numbers of pigments. (5) Dramatic improvements in QE are achieved when energy transfer is directed by a progressive downward cascade in excited-state energy. (6) The most effective light-harvesting architectures are those where isolated pools of donors each have independent paths directly to the terminal acceptor. Collectively, these results provide valuable insight into the types of molecular designs that are expected to exhibit high efficiency in overall energy transfer.
Mass transfer limitation in PAH-contaminated soil remediation (1998)

Batch experiments were conducted to determine the effects of Triton X-100, a nonionic phenolic ethoxylate surfactant, on the biodegradation of soil-bound naphthalene and phenanthrene. Two different types of soils, one contaminated with polynuclear aromatic hydrocarbons (PAHs) for different lengths of time, 2 days to 10 months, in the laboratory and the other, a field-contaminated soil from a manufactured gas plant (MGP) site, were used. Biodegradation of PAHs was measured by monitoring the 14CO2 production for the artificially contaminated soils and the residual PAHs in soil phase for the MGP soil. Without adding surfactant, the mineralization rate of phenanthrene was significantly smaller in the 1 0-month contaminated soil compared to that in the 2-day contaminated soil. Presumably, mineralization was mass-transfer limited in the soil with longer contamination period. Triton X-100 significantly enhanced mineralization in the 10 month-old soil but none in the 2-day old soil. The MGP soil, weathered over 2-3 decades, exhibited even greater enhancement of mineralization. Mineralization of PAHs in aged soils appears to be controlled by mass transfer rather than the rate of biodegradation. Surfactants increase the rate of release of soil-bound contaminant and thus help promote biodegradation.
HIV models to inform health policy (2011)

Several modeling studies published recently intend to provide information to decision makers to support the development of policies and strategies. These models include a study on male circumcision that provides a consensus among modeling groups on key issues relating to impact and targeting, a study proposing a new approach to treatment and prevention and explorations of the potential impacts of two new technologies (pre-exposure prophylaxis and HIV vaccines) and the conditions under which they will be most beneficial.
Establishment and characterization of a mantle cell lymphoma cell line (1998)

A mantle cell lymphoma (MCL) cell line (JeKo-1) was established from peripheral blood mononuclear cells of a patient with a large cell variant of MCL showing leukaemic conversion. JeKo-1 cells were Epstein-Barr virus negative and showed a B-cell phenotype with IgM+, IgD+, CD3-, CD5+, CD10-, CD19+, CD20+ and CD23-; they overexpressed cyclin D1, Bcl-2, c-Myc and Rb proteins. Bcl-1/J(H) gene rearrangement was confirmed by polymerase chain reaction, although karyotypic analysis showed 40/41 chromosomes devoid of apparent t(11;14)(q13;q32) translocation. JeKo-1 cells were highly tumourigenic in SCID mice.
Stem Cells in Sepsis (2009)

Experimental evidence indicates that stem cells are immunologically responsive cells that home to sites of inflammation and tissue injury. Stem cells also secrete growth factors in response to lipopolysaccharide and tumor necrosis factor that may limit apoptosis and organ injury. Stem cells represent an endogenous therapeutic strategy that may be enhanced for maximum clinical benefit.
Acute pulmonary hypertension in infants and children: cGMP-related drugs (2010)

Pharmacologic strategies to reduce pulmonary vascular tone and to treat pulmonary hypertension originally aimed to enrich vascular smooth muscle cyclic adenosine monophosphate levels. Alternatively, increasing cyclic guanosine monophosphate (cGMP) also reduces pulmonary vascular tone. Inhaled nitric oxide is extremely efficacious in increasing cGMP and selectively reducing mean pulmonary arterial pressure in pediatric cardiac patients. It is considered standard treatment in most centers. However, not all patients respond to inhaled nitric oxide and withdrawal is sometimes problematic. This has prompted investigation of alternative methods to increase intracellular vascular smooth muscle cGMP. Phosphodiesterase type 5 is particularly abundant in the lung vasculature of patients with severe pulmonary hypertension. Its inhibition with the sildenafil class of drugs is now commonplace. Drugs that affect cGMP metabolism in children with acute pulmonary hypertension are the subject of this review and consensus statement. Oral sildenafil is recommended in postoperative pulmonary hypertension after failed withdrawal of inhaled NO (class I, level of evidence B). The effectiveness of prolonged treatment with sildenafil in documented postoperative pulmonary hypertension is not well established (class IIb, level of evidence C). Sildenafil is indicated in idiopathic pulmonary hypertension, although data have been extrapolated mainly from adult trial (class I, level of evidence A, extrapolated). Recently, completed pediatric trials have seemed to support this recommendation. Longer-acting and intravenous forms of phosphodiesterase type 5 inhibitors, brain natriuretic peptides, and direct soluble guanylate cyclise activators all have appeal, but there is insufficient experience in children with acute pulmonary hypertensive disorders for recommendations on treatment.
Space-time coding with maximum diversity gains over frequency-selective fading channels (2001)

We study space-time (ST) block coding for single carrier zero-padded (ZP) block transmissions through finite impulse response (FIR) multipath fading channels of order L. We prove that the maximum diversity of order 2(L+1) is achieved with two transmit and one receive antenna. Simulations demonstrate that joint exploitation of multi-antenna diversity and multipath diversity leads to significantly enhanced performance.
Triplet luminescent dinuclear-gold(I) complex-based light-emitting diodes with low turn-on voltage (1999)

The electroluminescence (EL) from a dinuclear-gold(I)-chlorate compound containing bridging phosphine ligands [Au2(dppm)Cl2] as emitting layer is reported. Devices with a structure Al/Au2(dppm)Cl2/indium–tin–oxide demonstrated a uniform emission under the driving voltage below 1 V. The EL emission was from triplet excited state and the emission color of the device was found to depend on the deposition rate of Au2(dppm)Cl2, which can be explained as the different aggregation forms of the stacking compound in the deposition process.
O2Consumption by Isolated Pancreatic Islets, as Measured in a Microincubation System with a Clark-Type Electrode* (1982)

The role of B-cell respiration in fuel-induced insulin secretion has not been clarified. Therefore, a new method for the measurement of O2 uptake in islets of Langerhans was developed. An all-glass microincubation chamber was equipped with a Clark-type electrode, a stirring bar, and a special channel for loading the chamber with islets, media, and test compounds. The sensitivity of the system was sufficient for convenient determination of O2 consumption by less than 100 islets. Using DNA as reference value, the exactness of the method was scaled up considerably. Basal O2 uptake in mouse islets amounted to 5.6 +/- 0.2 nmol/h/micrograms DNA. alpha-Ketoisocaproic acid (2.5-20 mM) enhanced O2 consumption by 63-207%. The rate of O2 uptake as well as those of insulin secretion and oxidation of alpha-ketoisocaproic acid in incubated mouse islets were maximal at about 10 mM alpha-ketoisocaproic acid. 14CO2 production from U-14C-labeled alpha-ketoisocaproic acid was up to 36% lower than the corresponding increase in O2 uptake. However, the differences were partly caused by insufficient mixing of media in the oxidation studies. D-Glucose (20 mM) released more than twice the amount of insulin than 5 mM alpha-ketoisocaproic acid, although O2 uptake in the islets did not differ. The results are consistent with the view that an increase in the production of metabolic energy is necessary for recognizing insulin-releasing fuels by B-cells.
The major histocompatibility complex class I heavy chain as a structural subunit of the human cell membrane insulin receptor: implications for the range of biological functions of histocompatibility antigens. (1986)

Monoclonal antibodies against some of the monomorphic determinants of major histocompatibility complex (MHC) class I molecules reduce insulin binding and precipitate 125I-labeled insulin receptor preparations. A monoclonal antibody with specificity for the insulin binding site on the cell membrane insulin receptor of human cells was used to precipitate insulin receptors from human cell lines and resulted in distinct bands of Mr approximately 130,000, 90,000, and 45,000. The Mr 45,000 molecules thus precipitated were subjected to NaDodSO4/PAGE, eluted from the gels, and found to react with monoclonal antibodies against monomorphic and a polymorphic MHC class I determinant known to be expressed on the cell line used as receptor source. Moreover, a murine thymoma line (RI) with MHC class I expression bound significant amounts of insulin, whereas a MHC class I-negative variant had low insulin binding capacity. Reduction in the density on human cells of the MHC class I heavy chain was obtained by capping with antibodies to beta 2-microglobulin or to the MHC class I heavy chain and resulted in decreased insulin binding, whereas down-regulation of insulin receptors induced increased density of MHC class I molecules. It is concluded that the MHC class I heavy chain and the tetrameric insulin receptor are structurally associated in the cell membrane and suggested that this association may occur by displacement of beta 2-microglobulin by the insulin receptor.
Cover Picture: Angew. Chem. Int. Ed. 19/2002 (2002)

The cover picture shows a novel hierarchic endohedral clusterization of H2O molecules in the form of a dodecahedron ((H2O)20, red), a further “mounted” dodecahedron (green), and a rhombicosidodecahedron ((H2O)60, yellow). The shell/host (Mo atoms blue, O red) is built up by 12 pentagonal {(Mo)Mo5} type building blocks (one is highlighted as a blue ring),which are connected by 30 MoV2 linkers with the consequence that 20 nanosized Mo9O9 pores/rings of classical crown ether quality are formed in which 20 guanidinium cations are encapsulated (C black, N green). The MoV2 type linkers are stabilized by PO2H2−/SO42− ligands (P/S purple). As the clusterization in the cavity takes place after filling the receptors/pores at the cluster surface with guests, a process is modeled by which a cell converts an extracellular molecular signal into a response. The representative red ring below the blue ring is marked out by the 60 H2O ligands coordinated to the pentagonal Mo units, which altogether form a rhombicosidodecahedron (not shown completely). As the geometric forms described are those of Platonic and Archimedean solids Plato and Archimedes feel involved. Further details are reported by A. Müller et al. on p. 3604 ff.
BAC Transgenesis in Human Embryonic Stem Cells as a Novel Tool to Define the Human Neural Lineage (2008)

Human embryonic stem cells (hESCs) have enormous potential for applications in basic biology and regenerative medicine. However, harnessing the potential of hESCs toward generating homogeneous populations of specialized cells remains challenging. Here we describe a novel technology for the genetic identification of defined hESC-derived neural cell types using bacterial artificial chromosome (BAC) transgenesis. We generated hESC lines stably expressing Hes5::GFP, Dll1::GFP, and HB9::GFP BACs that yield green fluorescent protein (GFP)(+) neural stem cells, neuroblasts, and motor neurons, respectively. Faithful reporter expression was confirmed by cell fate analysis and appropriate transgene regulation. Prospective isolation of HB9::GFP(+) cells yielded purified human motor neurons with proper marker expression and electrophysiological activity. Global mRNA and microRNA analyses of Hes5::GFP(+) and HB9::GFP(+) populations revealed highly specific expression signatures, suggesting that BAC transgenesis will be a powerful tool for establishing expression libraries that define the human neural lineage and for accessing defined cell types in applications of human disease.
A Constitutive Heat Shock Element-binding Factor Is Immunologically Identical to the Ku Autoantigen (1995)

Analysis of the heat shock element (HSE)-binding proteins in extracts of rodent cells, during heat shock and their post-heat shock recovery, indicates that the regulation of heat shock response involves a constitutive HSE-binding factor (CHBF), in addition to the heat-inducible heat shock factor HSF1. We purified the CHBF to apparent homogeneity from HeLa cells using column chromatographic techniques including an HSE oligonucleotide affinity column. The purified CHBF consists of two polypeptides with apparent molecular masses of 70 and 86 kDa. Immunoblot and gel mobility shift analysis verify that CHBF is identical or closely related to the Ku autoantigen. The DNA binding characteristics of CHBF to double-stranded or single-stranded DNA are similar to that of Ku autoantigen. In gel mobility shift analysis using purified CHBF and recombinant human HSF1, CHBF competes with HSF1 for the binding of DNA sequences containing HSEs in vitro. Furthermore, when Rat-1 cells were co-transfected with human Ku expression vectors and the hsp70-promoter-driven luciferase reporter gene, thermal induction of luciferase is significantly suppressed relative to cells transfected with only the hsp70-luciferase construct. These data suggest a role of CHBF (or Ku protein) in the regulation of heat response in vivo.
The homeobox gene Hex is required in definitive endodermal tissues for normal forebrain, liver and thyroid formation (2000)

The homeobox gene Hex is expressed in the anterior visceral endoderm (AVE) and rostral definitive endoderm of early mouse embryos. Later, Hex transcripts are detected in liver, thyroid and endothelial precursor cells. A null mutation was introduced into the Hex locus by homologous recombination in embryonic stem cells. Hex mutant embryos exhibit varying degrees of anterior truncation as well as liver and thyroid dysplasia. The liver diverticulum is formed but migration of hepatocytes into the septum transversum fails to occur. Development of the thyroid is arrested at the thyroid bud stage at 9.5 dpc. Brain defects are restricted to the rostral forebrain and have a caudal limit at the zona limitans intrathalamica, the boundary between dorsal and ventral thalamus. Analysis of Hex(-/-) mutants at early stages shows that the prospective forebrain ectoderm is correctly induced and patterned at 7.5 days post coitum (dpc), but subsequently fails to develop. AVE markers are expressed and correctly positioned but development of rostral definitive endoderm is greatly disturbed in Hex(-/-) embryos. Chimeric embryos composed of Hex(-/-) cells developing within a wild-type visceral endoderm show forebrain defects indicating that Hex is required in the definitive endoderm. All together, these results demonstrate that Hex function is essential in definitive endoderm for normal development of the forebrain, liver and thyroid gland.
Cell-free fetal DNA in maternal blood: kinetics, source and structure (2004)

The kinetics and structure of cell-free fetal DNA in maternal plasma is currently under investigation. Plasma fetal DNA seems quite stable albeit cleared rapidly following birth, suggesting continuous fetal DNA release into the maternal circulation during pregnancy. However, to understand better the kinetics of circulating DNA, studies to determine the biological (structural) form in which fetal and maternal DNA exist and the mechanisms underlying variation in plasma are warranted to ensure quantitative diagnostic reliability. It is likely that circulating fetal DNA is released from fetal and/or placental cells undergoing apoptosis. Thus, the majority of fetal DNA is proposed to circulate in membrane-bound vesicles (apoptotic bodies). This review summarizes the latest reports in this field.
Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities (2012)

BackgroundSamples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues.MethodsMicrobial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.ResultsContaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status.ConclusionsMicrobial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.