gebhart/patrepeval huggingface dataset:
Ex vivo expansion of murine hematopoietic progenitor cells generates classes of expanded cells possessing different levels of bone marrow repopulating potential. (1996)

The objective of ex vivo expansion of primitive hematopoietic progenitor cells (HPC) is to increase the number of progeny cells possessing hematopoietic potential similar to the original HPC. In the context of bone marrow (BM) transplantation in mice, this implies that expanding a number of HPC sufficient for long-term rescue of one lethally irradiated animal should generate enough cells to rescue more than one lethally irradiated recipient. In the present study, Sca-1+Lin- cells from male C57Bl/6 mice were expanded in vitro with stem cell factor (SCF), interleukin-1alpha (IL-1alpha), IL-3, and IL-6 and used to transplant lethally irradiated syngeneic female recipients. Expanded cells were tracked in vitro with the fluorescent membrane dye PKH2, which becomes evenly distributed among dividing daughter cells, and fractionated on day 7 into Sca-1+ cells which did not divide (Sca-1+PKH2bright), those which had divided 1 to 2 times (Sca-1+PKH2moderate), or those which had divided four or more times (Sca-1+PKH2dim). Grafts of expanded cells consisted of either the same number of fresh cells proven to rescue lethally irradiated animals [3X10(3) cells; referred to as one repopulating dose (1 RD)] or the expansion equivalent (EE) of these cells. One EE of cells represented 3X10(3) multiplied by the fold increase in the number of cultured cells on day 7. All animals transplanted with 3X10(3) freshly isolated Sca-1+Lin- cells survived long-term. Only 53% of animals receiving 1 EE of all cultured day-7 cells survived. One RD from all three PKH2 fractions (bright, moderate, and dim) of day-7 cultured Sca-1+ cells failed to rescue more than 30% of lethally irradiated recipients. Comparable survival rates were obtained when 1 EE of Sca-1+PKH2dim or only 4 RD of Sca-1+PKH2bright cells were used as grafts, suggesting that a larger frequency of long-term repopulating cells may have been retained within the fraction of Sca-1+ cells undergoing minimal or no proliferation in culture. Engraftment of male ex vivo expanded cells in recipients was confirmed by polymerase chain reaction (PCR) analysis with Y chromosome-specific primers. When analyzed for their cell cycle status, Sca-1+PKH2bright cells were mostly quiescent, whereas a higher percentage of Sca-1+PKH2dim cells were in active phases of cell cycle. These data suggest that ex vivo expansion does not augment the number of BM repopulating HPC and that ex vivo expansion generates classes of progenitor cells with different BM repopulating potentials depending on their proliferative history. These studies also suggest that the cell cycle status of graft cells may affect the ability of these cells to engraft in myeloablated hosts.
A Simple Way of Accurately Calculating Average and Mean Square Flux Densities (1970)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. L. Wolfe, "A Simple Way of Accurately Calculating Average and Mean Square Flux Densities," Appl. Opt. 9, 2578-2579 (1970) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Accommodation of a highly symmetric core within a symmetric protein superfold (2003)

An alternative core packing group, involving a set of five positions, has been introduced into human acidic FGF-1. This alternative group was designed so as to constrain the primary structure within the core region to the same threefold symmetry present in the tertiary structure of the protein fold (the beta-trefoil superfold). The alternative core is essentially indistinguishable from the WT core with regard to structure, stability, and folding kinetics. The results show that the beta-trefoil superfold is compatible with a threefold symmetric constraint on the core region, as might be the case if the superfold arose as a result of gene duplication/fusion events. Furthermore, this new core arrangement can form the basis of a structural "building block" that can greatly simplify the de novo design of beta-trefoil proteins by using symmetric structural complementarity. Remaining asymmetry within the core appears to be related to asymmetry in the tertiary structure associated with receptor and heparin binding functionality of the growth factor.
Creation of RNA molecules that recognize the oxidative lesion 7,8-dihydro-8-hydroxy-2′-deoxyguanosine (8-oxodG) in DNA (1998)

We used in vitro evolution to obtain RNA molecules that specifically recognize and bind with high affinity to the oxidative lesion 7,8-dihydro-8-hydroxy-2′-deoxyguanosine (8-oxodG) in DNA. A pool of ≈10 15 RNA molecules containing a random insert of 45 nucleotides in length was subject to 10 successive rounds of chromatographic enrichment using an 8-oxodG affinity matrix, reverse transcription, PCR amplification, and RNA synthesis. Selected RNA molecules bind to 8-oxodG located at the 3′ terminus ( K d ≤ 270 nM) or in the center ( K d ≤ 2.8 μM) of a 19-nt strand of DNA, with no detectable affinity for the corresponding dG-containing DNA sequences. These 8-oxodG-binding RNAs will be used to monitor levels of 8-oxodG in DNA from biological sources and should provide a unique method for evaluating oxygen-mediated DNA damage. This approach should be applicable for the creation of RNA molecules that can bind to and identify the different modifications of DNA produced by a variety of environmental agents.
A quaternion-based unscented Kalman filter for orientation tracking (2003)

This paper describes a Kalman filter for the real-time estimation of a rigid body orientation from mea- surements of acceleration, angular velocity and magnetic field strength. A quaternion representation of the orienta- tion is computationally effective and avoids problems with singularities. The nonlinear relationship between estimated Orientation and expected measurement prevent the usage of a classical Kalman filter: This problem is solved by an Un- scented Kalman filter which allows nonlinear process and measurement models and is more accurate and less costly than the common Extended Kalman filter: Several exten- sions to the original Unscented Kalman filter are necessary to treat the inherent properties of unit quaternions. Results with simulated and measured data are discussed.
Remodelling the paternal chromatin at fertilization in mammals (2003)

At fertilization, the highly condensed and transcriptionally inert chromatin of the spermatozoa becomes remodelled into the decondensed and transcriptionally competent chromatin of the male pronucleus. The chromatin initially becomes dispersed and then transiently recondenses into a small mass upon entry into the ooplasm. This morphological change is coincident with and likely dependent on the replacement of the sperm-specific protamines by oocyte-supplied histones and the organization of the chromatin into nucleosomes. The chromatin then extensively decondenses within the male pronucleus and acquires many of the proteins that are associated with the maternal chromatin. Nonetheless, the paternal chromatin manifests distinct characteristics, including transient hyperacetylation of histone H4, increased transcription of endogenous and microinjected genes, and replication-independent demethylation of DNA. Sperm chromatin remodelling is controlled by an oocyte activity that appears during meiotic maturation and disappears approximately 3 h after activation (release from metaphase II arrest), and which requires factors associated with the germinal vesicle of the oocyte. The molecular components of this activity remain largely unknown. In frogs, nucleoplasmin is required to assemble histones H2A and H2B onto the paternal chromatin. Evidence is presented that related proteins may perform similar functions in mammals. Identifying the mechanisms that underlie sperm chromatin remodelling at fertilization may be relevant for understanding reprogramming of somatic cell nuclei after transfer into oocytes.
Preferential utilization of conserved immunoglobulin heavy chain variable gene segments during human fetal life. (1990)

The ability to respond to specific antigens develops in a programmed fashion. Although the antibody repertoire in adults is presumably generated by stochastic combinatorial joining of rearranged heavy variable, diversity, and joining (VH-DH-JH) and light (VL-JL) chains, experimental evidence in the mouse has shown nonrandom utilization of variable gene segments during ontogeny and in response to specific antigens. In this study, we have performed sequence analysis of 104-day human fetal liver-derived, randomly isolated constant region C+ mu transcripts and demonstrate a consistent preference during fetal life for a small subset of three highly conserved VH3 family gene segments. In addition, the data show that this preferential gene segment utilization extends to the DHQ52 and the JH3 and JH4 loci. Sequence analysis of two "sterile" DH-JH transcripts suggests that transcriptional activation of the JH-proximal DHQ52 element may precede initiation of DH-JH rearrangement and influence fetal DH utilization. Sequence comparisons reveal striking nucleotide polymorphism in allelic gene segments which is poorly reflected in the peptide sequence, implying considerable evolutionary selection pressure. Although vertebrate species utilize a variety of strategies to generate their antibody repertoire, preferential utilization of VH3 elements is consistently found during early development. These data support the hypothesis that VH3 gene segments play an essential role in the development of the immune response.
The c-kit tyrosine kinase inhibitor STI571 for colorectal cancer therapy. (2002)

The c-kit tyrosine kinase inhibitor STI571 exhibits a substantial therapeutic activity in patients with chronic myeloid leukemia and gastrointestinal stromal tumors respectively associated with constitutive activation of the BCR-ABL and c-kit tyrosine kinases. Human colorectal tumors also express the c-kit proto-oncogene. The present study focuses on the anticancer activity of STI571 in human colorectal tumor cells in vitro and in vivo. The c-kit receptor was identified as a M(r) 145,000 immunoreactive band in human colon cancer cells HT29, HCT8/S11, and HCT116. Cellular invasion induced by 10 ng/ml stem cell factor (EC(50) = 3 ng/ml) in HT29 cells was blocked by 1 micro M STI571 (IC(50) = 56 nM) and pharmacological inhibitors of several oncogenic signaling pathways, namely, phosphatidylinositol 3-kinase (LY294002), Rho GTPases (Clostridium botulinum exoenzyme C3 transferase), and Rho-kinase (Y27632). STI571 inhibited HT29 cell proliferation (IC(50) = 6 micro M) and induced apoptosis in vitro. These cellular effects were associated with a decrease in tumor growth. We also demonstrated that stem cell factor is a proangiogenic factor in vivo and in vitro. These encouraging results warrant further preclinical investigations and clinical trials on the use of the c-kit inhibitor STI571 as a chemotherapeutic agent in colon cancer prevention and in treatment of advanced colorectal cancers associated with liver metastases.
Deaths: leading causes for 1999. (2001)

In 1999 the 10 leading causes of death were (in rank order) Diseases of heart; Malignant neoplasms; Cerebrovascular diseases; Chronic lower respiratory diseases; Accidents; Diabetes mellitus; Influenza and pneumonia; Alzheimer's disease; Nephritis, nephrotic syndrome, and nephrosis; and Septicemia and accounted for nearly 80 percent of all deaths occurring in the United States. Differences in the rankings are evident by age, sex, race, and Hispanic origin. Leading causes of infant death for 1999 were (in rank order) Congenital malformations, deformations and chromosomal abnormalities; Disorders related to short gestation and low birthweight, not elsewhere classified; Sudden infant death syndrome; newborn affected by maternal complications of pregnancy; Respiratory distress of newborn; Newborn affected by complications of placenta, cord, and membranes; Accidents; Bacterial sepsis of newborn; Diseases of the circulatory system; and Atelectasis. Important variation in the leading causes of infant death is noted for the neonatal and postneonatal periods.
Recombinant hormones from fragments of human growth hormone and human placental lactogen. (1981)

Peptide fragments generated by limited plasmin digestion and reduction of human growth hormone (hGH) and human placental lactogen (hPL) were recombined to produce biologically active molecules consisting of the NH2-terminal two-thirds of one hormone molecule linked to the COOH-terminal one-third of the other. Plasmin-cleaved hPL and hGH each consist of an NH2-terminal fragment (1-134) connected to a COOH-terminal fragment (141-191) through a Cys53-Cys165 disulfide bond. The plasmin-cleaved hormones were reduced, the fragments isolated, and then recombined in equimolar quantities to prepared recombinant hormones. On sodium dodecyl sulfate disc gel electrophoresis the recombinants migrated as a single band in the position of native hormone when they were not reduced and as two bands in the positions of the fragments when they were reduced. This indicated that the recombinants had re-formed a disulfide bond. The derivatives were tested for immunologic activity in hPL and hGH radioimmunoassays, for lactogenic and growth-promoting activity by the radioreceptor assays using membranes from mammary gland and liver of lactating rabbits, and for secondary and tertiary structure by circular dichroism measurements in the near and far UV regions. The recombinant with NH2-terminal hGH had hGH immunologic activity, hGH structure and lactogenic and growth-promoting activity, while the hybrid with NH2-terminal hPL had hPL immunologic activity, hPL structure, and lactogenic activity alone. Therefore the immunologic activity, biologic activity, and structure of each of the covalently linked derivatives was characteristic of the hormone's NH2-terminal 1-134 fragment. The COOH-terminal 141-191 sequence maintains overall conformation but appears to have little, if any, role in determining biologic specificity.
Comparison of three bacterial detection methods under routine conditions (2006)

Sensitivity was best for BacT/ALERT, whereas specificity was enhanced for Pall eBDS and Scansystem. Scansystem required specially trained staff, whereas BacT/ALERT and Pall eBDS were easy, quick, user-friendly and objective methods.
Magnetic Levitation and Noncoalescence of Liquid Helium (1996)

We describe experiments in which drops of liquid helium-4, as large as 2 cm in diameter, are magnetically levitated. We have found that, when two or more drops are levitated in the same magnetic trap, the drops often remain in a state of apparent contact without coalescing. It appears that this effect is caused by the slow evaporation of liquid from the drops.
Anti-Ma2 antibody related paraneoplastic limbic/brain stem encephalitis associated with breast cancer expressing Ma1, Ma2, and Ma3 mRNAs (2003)

A 69 year old woman presented with cognitive impairment and supranuclear gaze palsy caused by paraneoplastic limbic/brain stem encephalitis associated with atypical medullary breast carcinoma. The cerebrospinal fluid from the patient harboured an anti-neuronal cell antibody against Ma2 antigen, but not against Ma1 or Ma3 antigen. Despite the antibody being restricted to the Ma2 antigen, the patient's cancer tissue expressed Ma1, Ma2, and Ma3 mRNAs. These results, and the expression of Ma2 mRNA in an atypical medullar breast carcinoma in another patient without paraneoplastic encephalitis, indicate that the induction of anti-Ma2 antibody depends on host immunoreponsiveness and not on the presence of the antigen itself in the cancer.
Adeno-Associated Virus Vector-Mediated Transgene Integration into Neurons and Other Nondividing Cell Targets (1998)

The site-specific integration of wild-type adeno-associated virus (wtAAV) into the human genome is a very attractive feature for the development of AAV-based gene therapy vectors. However, knowledge about integration of wtAAV, as well as currently configured recombinant AAV (rAAV) vectors, is limited. By using a modified Alu-PCR technique to amplify and sequence the vector-cellular junctions, we provide the first direct evidence both in vitro and in vivo of rAAV-mediated transgene integration in several types of nondividing cells, including neurons. This novel technique will be highly useful for further delineating the mechanisms underlying AAV-mediated integration, including issues of frequency, site preference, and DNA rearrangement in human as well as animal cells. Results from these studies should be beneficial for the development of the next generation of gene delivery vectors.
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates (1993)

Metabolic by-product secretion is commonly observed in oxygen-limited cultures. Oxygen limitations occur because of limits in the capacity of the respiratory system or because of the oxygenation limits of the cultivation method used. The latter restriction is of considerable practical importance since it results in a critical cell concentration above which oxygenation is insufficient, leading to by-product secretion. In this study we used a flux balance approach to determine optimal metabolic performance of Escherichia coli under variable oxygen limitations. This method uses linear optimization to find optimal metabolic flux patterns with respect to cell growth. Cell growth was defined as precursor requirements on the basis of a composition analysis. A growth-associated maintenance requirement of 23 mmol of ATP per g of biomass and a non-growth-associated maintenance value of 5.87 mmol at ATP per g (dry weight)-h were incorporated on the basis of a comparison with experimental data. From computations of optimal growth increased oxygen limitations were found to result in the secretion of acetate, formate, and ethanol in that order. Consistent with the experimental data in the literature, by-product secretion rates increased linearly with the growth rate. The computed optimal growth under increasing oxygen limitation revealed four critical growth rates at which changes in the by-product secretion pattern were observed. Concomitant with by-product secretion under oxygen limitations were changes in metabolic pathway utilization. The shifts in metabolism were characterized by changes in the metabolic values (computed as shadow prices) of the various redox carriers. The redox potential was thus identified as a likely trigger that leads to metabolic shifts.2+ ă
Virus membrane fusion (2007)

Membrane fusion of enveloped viruses with cellular membranes is mediated by viral glycoproteins (GP). Interaction of GP with cellular receptors alone or coupled to exposure to the acidic environment of endosomes induces extensive conformational changes in the fusion protein which pull two membranes into close enough proximity to trigger bilayer fusion. The refolding process provides the energy for fusion and repositions both membrane anchors, the transmembrane and the fusion peptide regions, at the same end of an elongated hairpin structure in all fusion protein structures known to date. The fusion process follows several lipidic intermediate states, which are generated by the refolding process. Although the major principles of viral fusion are understood, the structures of fusion protein intermediates and their mode of lipid bilayer interaction, the structures and functions of the membrane anchors and the number of fusion proteins required for fusion, necessitate further investigations.
Tumour Antigens Recognized by Antibodies (2001)

Abstract Antigens are frequently overexpressed on tumours, and the recognition of these antigens by antibodies can be used for tumour characterization, and for potential diagnostic and therapeutic purposes.
Combining Membrane Potential Imaging with l-Glutamate or GABA Photorelease (2011)

Combining membrane potential imaging using voltage sensitive dyes with photolysis of L-glutamate or GABA allows the monitoring of electrical activity elicited by the neurotransmitter at different sub-cellular sites. Here we describe a simple system and some basic experimental protocols to achieve these measurements. We show how to apply the neurotransmitter and how to vary the dimension of the area of photolysis. We assess the localisation of photolysis and of the recorded membrane potential changes by depolarising the dendrites of cerebellar Purkinje neurons with L-glutamate photorelease using different experimental protocols. We further show in the apical dendrites of CA1 hippocampal pyramidal neurons how L-glutamate photorelease can be used to calibrate fluorescence changes from voltage sensitive dyes in terms of membrane potential changes (in mV) and how GABA photorelease can be used to investigate the phenomenon of shunting inhibition. We also show how GABA photorelease can be used to measure chloride-mediated changes of membrane potential under physiological conditions originating from different regions of a neuron, providing important information on the local intracellular chloride concentrations. The method and the proof of principle reported here open the gateway to a variety of important applications where the advantages of this approach are necessary.
Interaction of water with titania and zirconia surfaces (2006)

Abstract Isotopic exchange of water on the surface of monoclinic zirconia and the anatase form of titania was studied experimentally using an ordinary gas chromatograph/mass spectrometer (GC/MS) as a pulse microreactor. Interaction of water with these surfaces was modeled by first principles calculations for periodic structures within density functional theory. Experimental data support computational results showing dissociation of water on monoclinic zirconia's most stable surfaces ( 1 ¯ 1 1 ), ( 1 ¯ 0 1 ) and (1 1 1). Water is adsorbed molecularly on the anatase (1 0 1) surface and dissociatively on the anatase (1 0 0) surface. Interaction of water with the anatase (0 0 1) surface proceeds through insertion into a Ti O bond. By monitoring the concentration of the mixed water isotope, DHO, during the isotopic exchange of surface water with D2O, it was found that exchange of water on anatase surfaces at 200–400 °C proceeds by whole molecules from 30% to 70% depending on the temperature and the surface coverage. In contrast, water exchanges on zirconia by single hydrogen atoms with a complete scrambling of hydrogens, at least 99%, under the same conditions. The proposed mechanism of water exchange on zirconia surface includes interaction through hydrogen bonding between hydroxyl groups adsorbed on neighboring sites. The observed anomaly on anatase is in agreement with the preferential molecular adsorption on a (1 0 1) surface and with the insertion of water into Ti O bonds on a (0 0 1) surface. This study contributes to the understanding of the atomic structure of acid–base catalytic sites on anatase titania and monoclinic zirconia surfaces.
B CELL IMMUNOBIOLOGY IN DISEASE: Evolving Concepts from the Clinic (2006)

The pathogenic roles of B cells in autoimmune diseases occur through several mechanistic pathways that include autoantibodies, immune complexes, dendritic and T cell activation, cytokine synthesis, chemokine-mediated functions, and ectopic neolymphogenesis. Each of these pathways participate to different degrees in autoimmune diseases. The use of B cell-targeted and B cell subset-targeted therapies in humans is illuminating the mechanisms at work in a variety of human autoimmune diseases. In this review, we highlight some of these recent findings that provide insights into both murine models of autoimmunity and human autoimmune diseases.