gebhart/patrepeval huggingface dataset:
Vitamin D Endocrinology (1976)

Current status of our understanding of the metabolism of vitamin D and its implications in metabolic bone disease is reviewed. The details of metabolism of vitamin D3 to 25-hydroxyvitamin D3 in the liver and its further conversion in the kidneys to either 1,25-dihydroxyvitamin D3 or 24,25-dihydroxyvitamin D3 are presented. The latter conversions are regulated by the vitamin D status, serum calcium through the parathyroid gland system, and serum inorganic phosphorus concentration. The 1,25-dihydroxyvitamin D3 can now be regarded as a calcium- and a phosphate-mobilizing hormone and must be considered as one of the most important serum calcium-regulating hormones. Disruption of the vitamin D metabolic sequence or the signal system for 1,25-dihydroxyvitamin D3 results in several bone and calcium metabolism disorders such as renal osteodystrophy, hypoparathyroidism, pseudohypoparathyroidism, and vitamin D-dependency rickets. The use of the synthetic analogs of 1,25-dihydroxyvitamin D3 as well as 1,25-dihydroxyvitamin D3 itself in the management of these disease states is discussed.
Objective assessment of image quality III ROC metrics, ideal observers, and likelihood-generating functions (1998)

We continue the theme of previous papers [J. Opt. Soc. Am. A 7, 1266 (1990); 12, 834 (1995)] on objective (task-based) assessment of image quality. We concentrate on signal-detection tasks and figures of merit related to the ROC (receiver operating characteristic) curve. Many different expressions for the area under an ROC curve (AUC) are derived for an arbitrary discriminant function, with different assumptions on what information about the discriminant function is available. In particular, it is shown that AUC can be expressed by a principal-value integral that involves the characteristic functions of the discriminant. Then the discussion is specialized to the ideal observer, defined as one who uses the likelihood ratio (or some monotonic transformation of it, such as its logarithm) as the discriminant function. The properties of the ideal observer are examined from first principles. Several strong constraints on the moments of the likelihood ratio or the log likelihood are derived, and it is shown that the probability density functions for these test statistics are intimately related. In particular, some surprising results are presented for the case in which the log likelihood is normally distributed under one hypothesis. To unify these considerations, a new quantity called the likelihood-generating function is defined. It is shown that all moments of both the likelihood and the log likelihood under both hypotheses can be derived from this one function. Moreover, the AUC can be expressed, to an excellent approximation, in terms of the likelihood-generating function evaluated at the origin. This expression is the leading term in an asymptotic expansion of the AUC; it is exact whenever the likelihood-generating function behaves linearly near the origin. It is also shown that the likelihood-generating function at the origin sets a lower bound on the AUC in all cases.
Development of assay platforms forin vitroscreening of Treg modulating potential of pharmacological compounds (2014)

CD4 + CD25+ regulatory T cells (Tregs) are believed to be pivotal in controlling chronic inflammation as well as in opposing the effect of cancer immunotherapy. Therefore, identification of novel drug compounds that interfere with Treg function is of high priority together with research that investigates Treg modulation by current drugs. For such research as well as for novel cell based therapies based on Treg infusions, rapid in vitro assays as well as functional assays based on inhibitory capacity of Tregs are required. Here, we report on such assays using highly pure fluorescence-activated cell sorting (FACS) sorted CD4 + CD25(high)CD127(dim/-)CD45RA+ naïve Treg cells followed by in vitro expansion. We report on the use of these cells in a short-term assay based on Treg mediated inhibition of the early effector T cell activation markers CD69 and CD154. Additionally, we investigate the use of highly pure Tregs in a functional assay based on Treg mediated inhibition of effector T cell proliferation. We report highly reproducible Treg function in assays that test the effect of well-known model compounds such as CpG-A, anti-IL-6R (tocilizumab), anti-TNF-α (adalimumab) or a combination of IL-6 and TNF-α. In conclusion, these assays have the potential for use in pharmacological screening and discovery in relation to drug development in immunology.
Purification of a Phosphatidylinositol 4‐Phosphate Kinase from Bovine Brain Membranes (1990)

A phosphatidylinositol 4-phosphate (PIP) kinase (EC 2.7.1.68) was purified from bovine brain membranes in a six-step procedure involving solubilization of the enzyme with 170 mM NaCl followed by chromatography on diethylaminoethyl-cellulose, phosphocellulose, Ultrogel AcA44, hydroxylapatite, and ATP-agarose. The enzyme preparation was nearly homogeneous and was purified 5,600-fold with a final specific activity of 85 nmol/min/mg of protein and a yield of 20%. Its molecular mass was 110 kilodaltons, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme was specific for PIP; phosphorylation of phosphatidylinositol and diacylglycerol was not observed.
Structure-activity studies of the carcinogenicities in the mouse and rat of some naturally occurring and synthetic alkenylbenzene derivatives related to safrole and estragole. (1983)

Twenty-three naturally occurring and synthetic alkenylbenzene derivatives structurally related to the hepatocarcinogen safrole (1-allyl-3,4-methylenedioxybenzene) were assayed for their hepatocarcinogenicity in mice. Some of these compounds (safrole, estragole, eugenol, anethole, methyleugenol, myristicin, elemicin, and dill and parsley apiols) may be ingested in very small amounts by human as natural components of certain spices, essential oils, or vegetables. Estragole (1-allyl-4-methoxybenzene) and its proximate carcinogenic metabolite 1'-hydroxyestragole, previously shown to induce hepatic tumors when administered to male CD-1 mice only during the preweaning period, also induced hepatic tumors on administration for 12 months in the diet of female CD-1 mice. Eugenol (1-allyl-4-hydroxy-3-methoxybenzene) and anethole (trans-4-methoxy-1-propenylbenzene) were inactive in this assay; they were also inactive when administered i.p. during the preweaning period at total doses of up to 9.45 mumol/mouse to male CD-1 or C57BL/6 x C3H F1 (hereafter called B6C3F1) mice. Methyleugenol (1-ally-3,4-dimethoxybenzene) and its 1'-hydroxy metabolite had activities similar to those of estragole and its 1'-hydroxy metabolite for the induction of hepatic tumors in male B6C3F1 mice treated prior to weaning; 1-allyl-1'-hydroxy-4-methoxynaphthalene was somewhat less active. At the levels tested, myristicin (1-allyl-5-methoxy-3,4-methylenedioxybenzene), elemicin (1-allyl-3,4,5-trimethoxybenzene) and its 1'-hydroxy metabolite, dill apiol (1-allyl-2,3-dimethoxy-4,5-methylenedioxybenzene), parsley apiol (1-allyl-2,5-dimethoxy-3,4-methylenedioxybenzene), 1'-hydroxyallybenzene, 3'-hydroxyanethole, and benzyl and anisyl alcohols had no detectable activity for the initiation of hepatic tumors on administration to male mice prior to weaning. The acetylenic derivative 1'-hydroxy-2',3'-dehydroestragole was much more active than either 1'-hydroxysafrole or 1'-hydroxyestragole when administered to preweanling mice. The 2',3'-oxides of safrole, estragole, eugenol, and 1'-hydroxysafrole, which are metabolites of these alkenylbenzenes, had little or no activity in this test. The 2',3'-oxides of safrole and estragole and their 1'-hydroxy derivatives likewise had little or no activity for the induction of lung adenomas in female A/J mice or for the induction of tumors on repetitive injections s.c. in male Fischer rats. However, the 2',3'-oxides of safrole, estragole, eugenol, 1'-hydroxysafrole, and 1'-hydroxyestragole, when administered topically to female CD-1 mice at relatively high doses, initiated benign skin tumors that could be promoted with croton oil.
Strategies in quantitative LC‐MS/MS analysis of unstable small molecules in biological matrices (2010)

Stability is an important pre-analytical variable for quantitative LC-MS/MS analysis of drug molecules and/or their metabolites in biological matrices. Instability of an analyte in any stage of the bioanalytical process, including sample collection, processing, storage, extraction and LC-MS/MS analysis, can result in under-/over-estimation if an adequate preventive procedure is not in place. In the current review on practical strategies in quantitative LC-MS/MS bioanalysis of unstable small molecules, the common causes of analyte instability were examined. The instability of some analytes is readily predictable because of the presence of certain chemically or biologically labile moieties in the molecules or because the compounds are in an inter-convertible form, e.g. lactone vs hydroxyl carboxylic acid. However, the instability of many other analytes is not readily predictable. Necessary evaluation needs to be conducted to identify the possible instability issues. The current review highlighted some general considerations and specific approaches for developing a robust LC-MS/MS method. In particular, incurred samples should be used as part of routine short-term stability assessment of any unstable analyte during the early stages of method development and validation. This can help unveil any 'hidden' instability issues that, if left unaddressed, could lead to the invalidation of a 'validated' method.
Detection of bacteriuria and pyuria by URISCREEN a rapid enzymatic screening test (1992)

A multicenter study was performed to evaluate the ability of the URISCREEN (Analytab Products, Plainview, N.Y.), a 2-min catalase tube test, to detect bacteriuria and pyuria. This test was compared with the Chemstrip LN (BioDynamics, Division of Boehringer Mannheim Diagnostics, Indianapolis, Ind.), a 2-min enzyme dipstick test; a semiquantitative plate culture method was used as the reference test for bacteriuria, and the Gram stain or a quantitative chamber count method was used as the reference test for pyuria. Each test was evaluated for its ability to detect probable pathogens at greater than or equal to 10(2) CFU/ml and/or greater than or equal to 1 leukocyte per oil immersion field, as determined by the Gram stain method, or greater than 10 leukocytes per microliter, as determined by the quantitative count method. A total of 1,500 urine specimens were included in this evaluation. There were 298 specimens with greater than or equal 10(2) CFU/ml and 451 specimens with pyuria. Of the 298 specimens with probable pathogens isolated at various colony counts, 219 specimens had colony counts of greater than or equal to 10(5) CFU/ml, 51 specimens had between 10(4) and 10(5) CFU/ml, and 28 specimens had between 10(2) and less than 10(4) CFU/ml. Both the URISCREEN and the Chemstrip LN detected 93% (204 of 219) of the specimens with probable pathogens at greater than or equal to 10(5) CFU/ml. For the specimens with probable pathogens at greater than or equal to 10(2) CFU/ml, the sensitivities of the URISCREEN and the Chemstrip LN were 86% (256 of 298) and 81% (241 of 298), respectively. Of the 451 specimens with pyuria, the URISCREEN detected 88% (398 of 451) and Chemstrip LN detected 78% (350 if 451). There were 204 specimens with both greater than or equal to 10(2) CFU/ml and pyuria; the sensitivities of both methods were 95% (193 of 204) for these specimens. Overall, there were 545 specimens with probable pathogens at greater than or equal to 10(2) CFU/ml and/or pyuria. The URISCREEN detected 85% (461 of 545), and the Chemstrip LN detected 73% (398 of 545). A majority (76%) of the false-negative results obtained with either method were for specimens without leukocytes in the urine. There were 955 specimens with no probable pathogens or leukocytes. Of these, 28% (270 of 955) were found positive by the URISCREEN and 13% (122 of 955) were found positive by the Chemstrip LN. A majority of the false-positive results were probably due, in part, to the detection of enzymes present in both bacterial and somatic cells by each of the test systems. Overall, the URISCREEN is rapid, manual, easy-to-perform enzymatic test that yields findings similar to those yielded by the Chemstrip LN for specimens with both greater than or equal to 10(2) CFU/ml and pyuria or for specimens with greater than or equal to 10(5) CFU/ml and with or without pyuria. However, when the data were analyzed for either probable pathogens at less 10(5) CFU/ml or pyuria, the sensitivity of the URISCREEN was higher (P less than 0.05).
Fluorescence lifetime biosensing with DNA microarrays and a CMOS-SPAD imager (2010)

Fluorescence lifetime of dye molecules is a sensitive reporter on local microenvironment which is generally independent of fluorophores concentration and can be used as a means of discrimination between molecules with spectrally overlapping emission. It is therefore a potentially powerful multiplexed detection modality in biosensing but requires extremely low light level operation typical of biological analyte concentrations, long data acquisition periods and on-chip processing capability to realize these advantages. We report here fluorescence lifetime data obtained using a CMOS-SPAD imager in conjunction with DNA microarrays and TIRF excitation geometry. This enables acquisition of single photon arrival time histograms for a 320 pixel FLIM map within less than 26 seconds exposure time. From this, we resolve distinct lifetime signatures corresponding to dye-labelled HCV and quantum-dot-labelled HCMV nucleic acid targets at concentrations as low as 10 nM.
Recombinant Respiratory Syncytial Virus (RSV) Bearing a Set of Mutations from Cold-Passaged RSV Is Attenuated in Chimpanzees (1998)

A set of five missense mutations previously identified by nucleotide sequence analysis of subgroup A cold-passaged (cp) respiratory syncytial virus (RSV) has been introduced into a recombinant wild-type strain of RSV. This recombinant virus, designated rA2cp, appears to replicate less efficiently in the upper and lower respiratory tracts of seronegative chimpanzees than either biologically derived or recombinant wild-type RSV. Infection with rA2cp also resulted in significantly less rhinorrhea and cough than infection with wild-type RSV. These findings confirm the role of the cp mutations in attenuation of RSV and identify their usefulness for inclusion in future live attenuated recombinant RSV vaccine candidates.
Overexpression of Branched O-Linked Oligosaccharides on T Cell Surface Glycoproteins Impairs Humoral Immune Responses in Transgenic Mice (1998)

The aberrant expression of core 2 O-glycans on T cell surface glycoproteins has been associated with various immunodeficient syndromes such as Wiskott-Aldrich syndrome and AIDS. To determine the effect of this aberrant expression of core 2 O-glycans on immune responses, we previously generated transgenic mice overexpressing core 2 beta-1,6-N-acetylglucosaminyltransferase (C2GnT) in T cells, and demonstrated that T cell primary immune responses mediated through interaction between T cells and antigen-presenting cells are impaired in the transgenic mice (Tsuboi, S., and Fukuda, M. (1997) EMBO J. 16, 6364-6373). In this study, we determined whether overexpression of core 2 oligosaccharides on T cells leads to impaired humoral immune responses by B cells using the same transgenic mice. When T cells were activated, both T and B cells from the transgenic and control mice expressed an equivalent amount of CD40L and CD40, which are, respectively, the receptor and counter-receptor for the interaction between T and B cells. However, activated T cells from the transgenic mice induced B cell proliferation less efficiently than those from control mice, regardless of whether B cells were isolated from control or the transgenic mice. This suggests that overexpression of core 2 O-glycans on T cell surface glycoproteins renders T cell-B cell interaction inefficient. Moreover, in the transgenic mice both immunoglobulin isotype switching and germinal center formation were also impaired. Taken together, these results indicate that aberrant expression of core 2 O-glycans on T cell surface glycoproteins results in impaired humoral immune responses due to an impaired interaction between T and B cells.
Invited review: Frontotemporal dementia caused by microtubule‐associated protein tau gene (MAPT) mutations: a chameleon for neuropathology and neuroimaging (2014)

Hereditary frontotemporal dementia associated with mutations in the microtubule-associated protein tau gene (MAPT) is a protean disorder. Three neuropathologic subtypes can be recognized, based on the presence of inclusions made of tau isoforms with three and four repeats, predominantly three repeats and mostly four repeats. This is relevant for establishing a correlation between structural magnetic resonance imaging and positron emission tomography using tracers specific for aggregated tau. Longitudinal studies will be essential to determine the evolution of anatomical alterations from the asymptomatic stage to the various phases of disease following the onset of symptoms.
Effects of a 1‐year exercise and lifestyle intervention on irisin, adipokines, and inflammatory markers in obese children (2014)

A 1-year long lifestyle intervention program is associated with improvement in anthropometric and metabolic parameters and leads to an elevation in irisin levels in obese children.
Oral administration of antigens from intestinal flora anaerobic bacteria reduces the severity of experimental acute colitis in BALB/c mice (2000)

Homeostasis between indigenous intestinal flora and host response may be broken in inflammatory bowel disease. The present study explores whether repeated oral administration of intestinal flora antigens can protect mice against dextran sodium sulphate (DSS)-induced colitis. Sonicates of Gram-positive, Gram-negative, or anaerobic resident bacteria isolated from mouse intestinal flora were fed to BALB/c mice by gastric gavage, with or without cholera toxin. After four weekly doses of 1 mg of these antigen preparations (or of PBS as control), DSS colitis was induced. One week later colitis was evaluated by clinical scores and histology. Mice fed a pool of the three sonicates had decreased inflammation scores (5 (1-14); median (range)) compared with PBS-fed control animals (15 (7-19); P < 0.05). Decreased inflammation was observed in mice fed anaerobic bacteria antigens (7 (6-11); P < 0.05 versus control), but not in mice fed a pool of Gram-positive and -negative sonicates (16 (12-16)). Inflammation scores of mice fed antigens with cholera toxin were similar to those of PBS-fed control animals. DSS-induced colitis can be suppressed by oral administration of normal intestinal flora antigens containing anaerobes.
The stepwise specification of embryonic stem cells to hematopoietic fate is driven by sequential exposure to Bmp4, activin A, bFGF and VEGF (2008)

The differentiation of embryonic stem (ES) cells offers a powerful approach to study mechanisms implicated in cell fate decision. A major hurdle, however, is to promote the directed and efficient differentiation of ES cells toward a specific lineage. Here, we define in serum-free media the minimal factor requirement controlling each step of the differentiation process, resulting in the production of highly enriched hematopoietic progenitors. Four factors - Bmp4, activin A, bFGF (Fgf2) and VEGF (VegfA) - are sufficient to drive the selective and efficient differentiation of mouse ES cells to hematopoiesis. Each of these factors appears to regulate a step of the process: Bmp4 promotes the very efficient formation of mesoderm; bFGF and activin A induce the differentiation of these mesodermal precursors to the hemangioblast fate; and VEGF is required for the production of fully committed hematopoietic progenitors. The stimulation of mesodermal precursors by bFGF and activin A switches on very rapidly the hematopoietic program, allowing us to dissect the molecular events leading to the formation of the hemangioblast. Runx1, Scl (Tal1) and Hhex expression is upregulated within 3 hours of stimulation, whereas upregulation of Lmo2 and Fli1 is observed later. Interestingly, increased expression levels of genes such as cMyb, Pu.1 (Sfpi1), Gata1 and Gata2 are not observed at the onset of hemangioblast commitment. This stepwise control of differentiation is extremely efficient, giving rise to a very high frequency of hematopoietic precursors, and provides an optimal system for understanding the molecular machineries involved in blood progenitor commitment.
B7 Expression on T Cells Down-Regulates Immune Responses through CTLA-4 Ligation via R-T Interactions (2004)

Although B7 on APCs has a well-recognized role in T cell costimulation, little is known about the functional significance of constitutive and activation-induced B7 expression that also occurs on T cells. To analyze the role of B7 on T cells, B7-1/B7-2-deficient mice (B7 double knockout) and mice overexpressing B7-2 exclusively on T cells (B7-2 transgenic) were used as T cell donors for allogeneic transplant recipients, and graft-vs-host disease (GVHD) was assessed. B7 double-knockout T cells resulted in significant GVHD acceleration compared with wild-type T cells. Conversely, B7-2 transgenic donor T cells mediated reduced GVHD mortality compared with wild-type T cells. Data indicated that B7 expression on T cells down-regulated alloresponses through CTLA-4 ligation. This study is the first to provide definitive in vivo data illustrating the importance of T cell-associated B7 as a negative regulator of immune responses in a clinically relevant murine model of GVHD. The up-regulation of B7 on T cells may be an important component of normal immune homeostasis.
Target silencing of disease-associated B-lymphocytes by chimeric molecules in SCID model of pristane-induced autoimmunity (2010)

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the generation of autoantibodies against a diverse array of self-antigens. The B cells producing immunoglobulin G (IgG) antibodies to double-stranded DNA appear to play a main role in the disease progression. Their specific elimination is a reasonable mechanism for effective therapy of SLE. The presently used approaches for silencing autoreactive disease-associated B cells are nonspecific and more precise therapies are needed. We have previously constructed a chimeric protein molecule consisting of several DNA-mimotope peptides coupled to a rat monoclonal anti-mouse CD32 (FcγRIIb) antibody. The mineral oil pristane induces a lupus-like syndrome in non-autoimmune mice leading to the development of glomerulonephritis and lupus-associated autoantibodies. In the present paper, using a pristane-induced autoimmune model in SCID mice, we analyzed the ability of the chimeric antibody to suppress selectively the autoreactive B lymphocytes by cross-linking B-cell surface immunoglobulin receptors with the inhibitory IgG FcγRIIb receptors. Treatment with DNA-like chimeric molecules inhibited B- and T-cell proliferation, restricted the number of anti-DNA antibody-producing cells and suppressed the generation of IgG anti-DNA antibodies. In contrast, phosphate buffered saline (PBS)-injected control mice experienced an increase of disease-associated antibody levels and developed glomerulonephritis similar to pristane-treated donor Balb/c mice.