gebhart/patrepeval huggingface dataset:
An activated receptor tyrosine kinase, TEL/PDGFβR, cooperates with AML1/ETO to induce acute myeloid leukemia in mice (2003)

The t(8;21)(q22;q22) translocation, occurring in 40% of patients with acute myeloid leukemia (AML) of the FAB-M2 subtype (AML with maturation), results in expression of the RUNX1-CBF2T1 [AML1-ETO (AE)] fusion oncogene. AML/ETO may contribute to leukemogenesis by interacting with nuclear corepressor complexes that include histone deacetylases, which mediate the repression of target genes. However, expression of AE is not sufficient to transform primary hematopoietic cells or cause disease in animals, suggesting that additional mutations are required. Activating mutations in receptor tyrosine kinases (RTK) are present in at least 30% of patients with AML. To test the hypothesis that activating RTK mutations cooperate with AE to cause leukemia, we transplanted retrovirally transduced murine bone marrow coexpressing TEL-PDGFRB and AE into lethally irradiated syngeneic mice. These mice (19/19, 100%) developed AML resembling M2-AML that was transplantable in secondary recipients. In contrast, control mice coexpressing with TEL-PDGFRB and a DNA-binding-mutant of AE developed a nontransplantable myeloproliferative disease identical to that induced by TEL-PDGFRB alone. We used this unique model of AML to test the efficacy of pharmacological inhibition of histone deacetylase activity by using trichostatin A and suberoylanilide hydroxamic acid alone or in combination with the tyrosine kinase inhibitor, imatinib mesylate. We found that although imatinib prolonged the survival of treated mice, histone deacetylase inhibitors provided no additional survival benefit. These data demonstrate that an activated RTK can cooperate with AE to cause AML in mice, and that this system can be used to evaluate novel therapeutic strategies.
flowVS: channel-specific variance stabilization in flow cytometry (2016)

The homogeneity of variance in cell populations across FC samples is desirable when extracting features uniformly and comparing cell populations with different levels of marker expressions. The newly developed flowVS algorithm solves the variance-stabilization problem in FC and microarrays by optimally transforming data with the help of Bartlett's likelihood-ratio test. On two publicly available FC datasets, flowVS stabilizes within-population variances more evenly than the available transformation and normalization techniques. flowVS-based variance stabilization can help in performing comparison and alignment of phenotypically identical cell populations across different samples. flowVS and the datasets used in this paper are publicly available in Bioconductor.
Designer Cytokines: Targeting Actions to Cells of Choice (1995)

Some growth factors are therapeutically useful partly because restricted expression of their receptors limits their action to particular cell types. However, no unique stimulatory factor is known for many clinically relevant cell types, such as CD34 + hematopoietic stem cells. Here, soluble α receptor (Rα) components for interleukin-6 (IL-6) and ciliary neurotrophic factor (CNTF) were targeted in an active form to cells expressing surface markers such as CD34 or CD45, thereby rendering those cells responsive to IL-6 or CNTF. The targeting of Rα components may provide the means to create "designer" cytokines that activate a desired cell type expressing a specific cell surface marker.
A Thr357 to Ser Polymorphism in Homozygous and Compound Heterozygous Subjects Causes Absent or Reduced P2X7 Function and Impairs ATP-induced Mycobacterial Killing by Macrophages (2005)

The P2X(7) receptor is a ligand-gated cation channel that is highly expressed on mononuclear leukocytes and that mediates ATP-induced apoptosis and killing of intracellular pathogens. There is a wide variation in P2X(7) receptor function between subjects, explained in part by four loss-of-function polymorphisms (R307Q, E496A, I568N, and a 5'-intronic splice site polymorphism), as well as rare mutations. In this study, we report the allele frequencies of 11 non-synonymous P2X(7) polymorphisms and describe a fifth loss-of-function polymorphism in the gene (1096C --> G), which changes Thr(357) to Ser (T357S) with an allele frequency of 0.08 in the Caucasian population. P2X(7) function was measured by ATP-induced ethidium(+) influx into peripheral blood lymphocytes and monocytes and, when compared with wild-type subjects, was reduced to 10-65% in heterozygotes, 1-18% in homozygotes, and 0-10% in compound heterozygotes carrying T357S and a second loss-of-function polymorphism. Overexpression of the T357S mutant P2X(7) in either HEK-293 cells or Xenopus oocytes gave P2X(7) function of approximately 50% that of wild-type constructs. Differentiation of monocytes to macrophages, which also up-regulates P2X(7), restored P2X(7) function to near normal in cells heterozygous for T357S and to a value 50-65% of wild-type in cells homozygous for T357S or compound heterozygous for T357S/E496A. However, macrophages from subjects that are compound heterozygous for either T357S/R307Q or T357S/stop codon had near-to-absent P2X(7) function. These functional deficits induced by T357S were paralleled by impaired ATP-induced apoptosis and mycobacteria killing in macrophages from these subjects. Lymphocytes, monocytes, and macrophages from subjects homozygous for T357S or compound heterozygous for T357S and a second loss-of-function allele have reduced or absent P2X(7) receptor function.
Positive selection for loss of tetracycline resistance (1980)

A simple technique has been devised that allows direct plate selection of tetracycline-sensitive clones from a predominantly tetracycline-resistant population. The technique is especially useful in genetic methodologies based on the use of tetracycline resistance transposons, such as Tn10. Potential uses of the method include selection of deletion mutants, fine-structure mapping, generalized mapping, construction of multiply marked strains, elimination of tetracycline resistance transposons and plasmids and cloning. The technique is based on our finding that tetracycline-resistant cells are hypersensitive to lipophilic chelating agents, such as fusaric acid. This finding supports the contention that certain metal ions critically facilitate tetracycline uptake and leads us to suggest possible molecular mechanisms for tetracycline resistance.
NHC‐Containing Manganese(I) Electrocatalysts for the Two‐Electron Reduction of CO2 (2014)

The synthesis and characterization of the first catalytic manganese N-heterocyclic carbene complexes are reported: MnBr(N-methyl-N'-2-pyridylbenzimidazol-2-ylidine)(CO)3 and MnBr(N-methyl-N'-2-pyridylimidazol-2-ylidine)(CO)3. Both new species mediate the reduction of CO2 to CO following two-electron reduction of the Mn(I) center, as observed with preparative scale electrolysis and verified with (13)CO2. The two-electron reduction of these species occurs at a single potential, rather than in two sequential steps separated by hundreds of millivolts, as is the case for previously reported MnBr(2,2'-bipyridine)(CO)3. Catalytic current enhancement is observed at voltages similar to MnBr(2,2'-bipyridine)(CO)3.
A niched Pareto genetic algorithm for multiobjective optimization (2002)

Many, if not most, optimization problems have multiple objectives. Historically, multiple objectives have been combined ad hoc to form a scalar objective function, usually through a linear combination (weighted sum) of the multiple attributes, or by turning objectives into constraints. The genetic algorithm (GA), however, is readily modified to deal with multiple objectives by incorporating the concept of Pareto domination in its selection operator, and applying a niching pressure to spread its population out along the Pareto optimal tradeoff surface. We introduce the Niched Pareto GA as an algorithm for finding the Pareto optimal set. We demonstrate its ability to find and maintain a diverse "Pareto optimal population" on two artificial problems and an open problem in hydrosystems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Computer Programs for Standardless Quantitative Analysis of Minerals Using the Full Powder Diffraction Profile (1991)

Abstract A Fortran 77 computer program has been developed for the quantitative analysis of minerals by multiphase profile analysis of the complete powder diffraction pattern. Featured are full-matrix least-squares refinement of 14 Rietveld “instrumental parameters” (phase scales, asymmetry, preferred orientations (March model), linewidths, instrument zero, lineshapes and unit cell dimensions), Brindley particle absorption contrast factors and amorphicity corrections. The program uses a crystal structure Databank, which contains information on absorption coefficients, unit cell data and crystal structures for some 90 common minerals. New minerals can be easily added. Structure parameters are also refinable by a profile decomposition method using a program called STRUCT. The sum of the calculated patterns, derived from the crystal structure data, is fitted to the observed pattern by a program called TRACSCAL which runs in singlepass multiphase mode and, after the above corrections have been applied, the weight percentages of the component phases are calculated from the Rietveld scaling factors. The program runs on an IBM-compatible AT computer with 640K of RAM, on an extended memory AT, or a mainframe system. Examples of its use are given with standard mixtures and naturally occurring specimens. On an AT computer with 20MHz clock speed a scaling run, including data input, reading of the pattern, processing of (hk l ) files, calculation of the profile and one cycle of least squares fitting takes about 30 seconds for binary standard mixtures and about 2.5 minutes for a 7-phase natural bauxite pattern containing 320 independent (hk l ) reflections.
Medical Consequences of Obesity (2004)

Obesity is an epidemic disease that threatens to inundate health care resources by increasing the incidence of diabetes, heart disease, hypertension, and cancer. These effects of obesity result from two factors: the increased mass of adipose tissue and the increased secretion of pathogenetic products from enlarged fat cells. This concept of the pathogenesis of obesity as a disease allows an easy division of disadvantages of obesity into those produced by the mass of fat and those produced by the metabolic effects of fat cells. In the former category are the social disabilities resulting from the stigma associated with obesity, sleep apnea that results in part from increased parapharyngeal fat deposits, and osteoarthritis resulting from the wear and tear on joints from carrying an increased mass of fat. The second category includes the metabolic factors associated with distant effects of products released from enlarged fat cells. The insulin-resistant state that is so common in obesity probably reflects the effects of increased release of fatty acids from fat cells that are then stored in the liver or muscle. When the secretory capacity of the pancreas is overwhelmed by battling insulin resistance, diabetes develops. The strong association of increased fat, especially visceral fat, with diabetes makes this consequence particularly ominous for health care costs. The release of cytokines, particularly IL-6, from the fat cell may stimulate the proinflammatory state that characterizes obesity. The increased secretion of prothrombin activator inhibitor-1 from fat cells may play a role in the procoagulant state of obesity and, along with changes in endothelial function, may be responsible for the increased risk of cardiovascular disease and hypertension. For cancer, the production of estrogens by the enlarged stromal mass plays a role in the risk for breast cancer. Increased cytokine release may play a role in other forms of proliferative growth. The combined effect of these pathogenetic consequences of increased fat stores is an increased risk of shortened life expectancy.
Efficient activation of nucleoside phosphoramidites with 4,5- dicyanoimidazole during oligonucleotide synthesis (1998)

A new activator for the coupling of phosphoramidites to the 5'-hydroxyl group during oligonucleotide synthesis is introduced. The observed time to complete coupling is twice as fast with 4, 5-dicyanoimidazole (DCI) as the activator, compared with 1 H -tetrazole. The effectiveness of DCI is thought to be based on its nucleophilicity. DCI is soluble in acetonitrile up to 1.1 M at room temperature and can be used as the sole coupling activator during routine automated solid phase synthesis of oligonucleotides. The addition of 0.1 M N -methylimidazole to 0.45 M 1 H -tetrazole also results in higher product yields during oligonucleotide synthesis than observed with 1 H -tetrazole alone.
Use of transgenic mice to study the routing of secretory proteins in intestinal epithelial cells: analysis of human growth hormone compartmentalization as a function of cell type and differentiation. (1989)

The intestinal epithelium is a heterogeneous cell monolayer that undergoes continuous renewal and differentiation along the crypt-villus axis. We have used transgenic mice to examine the compartmentalization of a regulated endocrine secretory protein, human growth hormone (hGH), in the four exocrine cells of the mouse intestinal epithelium (Paneth cells, intermediate cells, typical goblet cells, and granular goblet cells), as well as in its enteroendocrine and absorptive (enterocyte) cell populations. Nucleotides -596 to +21 of the rat liver fatty acid binding protein gene, when linked to the hGH gene (beginning at nucleotide +3) direct efficient synthesis of hGH in the gastrointestinal epithelium of transgenic animals (Sweetser, D. A., D. W. McKeel, E. F. Birkenmeier, P. C. Hoppe, and J. I. Gordon. 1988. Genes & Dev. 2:1318-1332). This provides a powerful in vivo model for analyzing protein sorting in diverse, differentiating, and polarized epithelial cells. Using EM immunocytochemical techniques, we demonstrated that this foreign polypeptide hormone entered the regulated basal granules of enteroendocrine cells as well as the apical secretory granules of exocrine Paneth cells, intermediate cells, and granular goblet cells. This suggests that common signals are recognized by the "sorting mechanisms" in regulated endocrine and exocrine cells. hGH was targeted to the electron-dense cores of secretory granules in granular goblet and intermediate cells, along with endogenous cell products. Thus, this polypeptide hormone contains domains that promote its segregation within certain exocrine granules. No expression of hGH was noted in typical goblet cells, suggesting that differences exist in the regulatory environments of granular and typical goblet cells. In enterocytes, hGH accumulated in dense-core granules located near apical and lateral cell surfaces, raising the possibility that these cells, which are known to conduct constitutive vesicular transport toward both apical and basolateral surfaces, also contain a previously unrecognized regulated pathway. Together our studies indicate that transgenic mice represent a valuable system for analyzing trafficking pathways and sorting mechanisms of secretory proteins in vivo.
Prolongation of murine islet allograft survival by pretreatment of islets with antibody directed to Ia determinants. (1981)

Islets of Langerhans treated with donor-specific anti-Ia serum and complement were transplanted across a major histocompatibility barrier into nonimmunosuppressed diabetic mice. The allografts survived in all recipients for at least 200 days after transplantation. Rejection of an established allograft could be induced by intravenous injection of donor splenocytes. This demonstrates that allografts can serve as targets for immune rejection and supports the possible role of Ia-positive passenger lymphoid cells in initiation of immune rejection. The results show that immunosuppression of the recipient is not a prerequisite for successful transplantation.
Therapeutic Effects of Psychological Autopsies (2009)

We recommend that interviewers receive preparatory training and ongoing supervision while conducting interviews, to assure a reflective and professional stance.
Rapamycin Ameliorates Kidney Fibrosis by Inhibiting the Activation of mTOR Signaling in Interstitial Macrophages and Myofibroblasts (2012)

Interstitial fibrosis is an inevitable outcome of all kinds of progressive chronic kidney disease (CKD). Emerging data indicate that rapamycin can ameliorate kidney fibrosis by reducing the interstitial infiltrates and accumulation of extra cellular matrix (ECM). However, the cellular mechanism that regulates those changes has not been well understood yet. In this study, we revealed the persistent activation of mammalian target of rapamycin (mTOR) signaling in the interstitial macrophages and myofibroblasts, but rarely in injured proximal epithelial cells, CD4+ T cells, neutrophils, or endothelial cells, during the development of kidney fibrosis. Administration of rapamycin to unilateral ureteral obstruction (UUO) mice significantly suppressed the immunoreactivity of mTOR signaling, which decreased the inflammatory responses and ECM accumulation in the obstructed kidneys. Isolated macrophages from rapamycin-treated obstructed kidneys presented less inflammatory activity than vehicle groups. In vitro study confirmed that rapamycin significantly inhibited the fibrogenic activation of cultured fibroblasts (NIH3T3 cells), which was induced by the stimulation of TGF-β(1). Further experiment revealed that rapamycin did not directly inhibit the fibrogenesis of HK2 cells with aristolochic acid treatment. Our findings clarified that rapamycin can ameliorate kidney fibrosis by blocking the mTOR signaling in interstitial macrophages and myofibroblasts.
Infantile Colic and Food Hypersensitivity (2000)

In this article, some aspects of the phenomenon of infantile colic or fussing and crying behavior in early infancy are reviewed. The major points addressed are as follows: 1) evidence that infants with colic differ significantly in their pattern of distressed behavior from noncolicky infants; 2) the evidence of colic in children with known food allergy; 3) the incidence of food allergy in children with colic; 4) the outcome of trials focusing on the dietary management of colic; 5) the outcome of studies involving behavior modification in colic; 6) the outcome of a preliminary trial of modification of maternal diet in very young infants with colic; and 7) findings of a systematic review of different treatments for colic.
A Blue-Blocking Intraocular Lens Should Be Used in Cataract Surgery (2005)

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The microsoft 2016 conversational speech recognition system (2017)

We describe Microsoft's conversational speech recognition system, in which we combine recent developments in neural-network-based acoustic and language modeling to advance the state of the art on the Switchboard recognition task. Inspired by machine learning ensemble techniques, the system uses a range of convolutional and recurrent neural networks. I-vector modeling and lattice-free MMI training provide significant gains for all acoustic model architectures. Language model rescoring with multiple forward and backward running RNNLMs, and word posterior-based system combination provide a 20% boost. The best single system uses a ResNet architecture acoustic model with RNNLM rescoring, and achieves a word error rate of 6.9% on the NIST 2000 Switchboard task. The combined system has an error rate of 6.2%, representing an improvement over previously reported results on this benchmark task.
Novel B cell population producing functional IgG in the absence of membrane IgM expression (2002)

Surface expression of IgM is a characteristic feature of the development of most B cells. Only pre-B cells bearing functional IgM heavy chains mu chains) are selected for clonal expansion and differentiation. Cells lacking mu chains are normally eliminated. muMT mice carrying a deletion of the first exon coding for the transmembrane domain of the immunoglobulin mu chain gene were described as mice deficient for mature B cells, plasma cells and immunoglobulins in serum. In this study, we describe in muMT/BALB/c mice the presence of a novel B cell population, producing IgG, IgA and IgE in the absence of IgM membrane expression. Moreover, this small population of B cells is able to recognize antigens and to differentiate into plasma cells. These "non-conventional" mu(- / -) B cells produce functional immunoglobulins after immunization, undergo germinal center reactions, and maintain B cell memory. Our findings support the concept, that a small percentage of mu -non-expressing pre-B cells can escape elimination, switch to downstream immunoglobulin heavy chains and respond to antigens. It remains an open question how the reactivity of these B cells is regulated and in which extent such B cells play a role in physiological and pathological processes such as autoantibody production and autoimmunity.
Inhibition of cytotoxic T-cell clonal expansion by cyclophosphamide and the recovery of cytotoxic T-lymphocyte precursors by supernatants from mixed-lymphocyte cultures. (1981)

Spleen cells from mice treated with cyclophosphamide (150 mg/kg) and cultured at suboptimal concentrations do not generate a cytotoxic T-lymphocyte (CTL) response to allogeneic tumor cells. The reduced response of spleen cells from cyclophosphamide-treated mice is not due to the elimination of CTL precursors because normal responses are obtained by the addition of a helper factor(s) derived from mixed lymphocyte culture supernatants. The results indicate that helper cells, required for development of CTL responses to tumor alloantigens, are eliminated by cyclophosphamide in the absence of evident toxicity to CTL precursors.