gebhart/patrepeval huggingface dataset:
Apoptotic Cell Death and Amyloid Precursor Protein Signaling in Neuroblastoma SH‐SY5Y Cells (2004)

We have recently shown that the amyloid precursor protein (APP) and a subset of its C-terminal fragments (CTFs) are tyrosine phosphorylated in human brain and in cultured cells. Tyrosine phosphorylation generates a substrate that is sequentially bound by the adaptor proteins ShcA and Grb2, and this interaction is significantly enhanced in Alzheimer's disease brains. Here we have studied the APP/CTFs phosphorylation and ShcA activation in a human neuroblastoma cell line, SH-SY5Y, under basal and apoptotic conditions. To commit these cells to apoptosis, we used staurosporin, a well-known apoptotic inducer and protein kinase C blocker. Our data suggest the following: (1) in normally proliferating SH-SY5Y cells, full-length APP is complexed with Grb2[Q3], likely through its SH2 domain; (2) upon induction of apoptosis, APP is degraded and ShcA-Grb2 coimmunoprecipitates with CTFs recognized by anti-APP antibodies; and (3) caspase inhibitors partially block the degradation of APP and the coprecipitation of CTFs with ShcA-Grb2 adaptors. In summary, our data suggest that in SH-SY5Y cells, tyrosine-phosphorylated APP is involved in a complex with ShcA-Grb2 adaptors that is disrupted during apoptosis. The abnormal degradation of APP and consequent increased levels of CTFs (as has been observed in Alzheimer's disease and Down's syndrome) generate a complex between tyrosine-phosphorylated CTFs and intracellular adaptors. The signaling through APP and its CTFs may have significant relevance for apoptotic cell death in Alzheimer's disease.
BMP signaling pathway is required for commitment of C3H10T1/2 pluripotent stem cells to the adipocyte lineage (2009)

Obesity is accompanied by an increase in both adipocyte number and size. The increase in adipocyte number is the result of recruitment to the adipocyte lineage of pluripotent stem cells present in the vascular stroma of adipose tissue. These pluripotent cells have the potential to undergo commitment and then differentiate into adipocytes, as well as myocytes, osteocytes, and chondrocytes. In this article, we show that both bone morphogenetic protein (BMP)2 and BMP4 can induce commitment of C3H10T1/2 pluripotent stem cells into adipocytes. After treatment of C3H10T1/2 stem cells with these BMPs during proliferation followed by exposure to differentiation inducers at growth arrest, nearly all cells enter the adipose development pathway, express specific adipocyte markers, and acquire the adipocyte phenotype. Overexpression of constitutively active BMP receptor (CA)-BMPr1A or CA-BMPr1B induces commitment in the absence of BMP2/4, whereas overexpression of a dominant-negative receptor dominant-negative-BMPr1A suppresses commitment induced by BMP. Also, knockdown of the expression of Smad4 (coregulator in the BMP/Smad signaling pathway) with RNAi disrupts commitment by the BMPs. However, knockdown of expression of p38 MAPK (an intermediary in the BMP/MAPK signaling pathway) with RNAi had little effect on BMP-induced commitment. Together, these findings indicate that the BMP/Smad signaling pathway has a dominant role in adipocyte lineage determination. Proteomic analysis identified lysyl oxidase (LOX), a bona fide downstream target gene of the BMP signaling pathway. Expression of LOX is induced by BMP2/4 during adipocyte lineage commitment, and knockdown of its expression disrupts the commitment process.
Acute Pancreatitis (2009)

Our data raised the hypothesis that a sequence of HTS lung protection events increases HSP70 and HSP90, inhibiting infiltration of neutrophils and their protease actions in the lung.
Direct selection of human bone marrow mesenchymal stem cells using an anti‐CD49a antibody reveals their CD45med,low phenotype (2003)

Human bone marrow mesenchymal stem cells (MSC) generate, via a fibroblast colony-forming unit (CFU-F), osteo-chondroblastic cells as well as adipocytes and stromacytes. To date, these stem cells are isolated indirectly using a cell culture method and phenotyped as CD45 negative while the in vivo counterparts are undetermined. Our aim was to develop a direct selection method and to determine the phenotype of the MSC isolated in this way. Mesenchymal cells were selected with anti-CD49a and/or anti-CD45 antibodies using either flow cytometry or a magnetic beads method. All CFU-F were always detected in the small population of CD49a-positive cells. These CFU retained their differentiation potential and gave rise to osteo-chondroblastic cells, adipocytes and stromacytes. Phenotypic studies on uncultured cells revealed a CD45med,low, CD34low, HLA-II- cell population. Flow cytometry cell sorting showed that MSC with CFU-F potential were obtained only from a CD49a+/CD45med,low population. In addition, when cultured, they clearly became CD45-, CD34-, HLA-II-, CD49a+. These results confirmed that MSC can be directly selected easily from human bone marrow using magnetic beads without altering their differentiation potential. These cells expressed mildly the haematopoietic marker CD45, which was dramatically downregulated by in vitro culture. The expression of CD45 coupled to CD49a thus enabled direct selection of the MSC.
REL proto-oncogene is frequently amplified in extranodal diffuse large cell lymphoma (1996)

Comparative genomic hybridization (CGH) analysis of DNA extracted from a diffuse lymphoma with a large cell component (DLLC) that displayed double minute chromosomes upon conventional karyotypic analysis indicated overt amplification of DNA sequences derived from the 2p13-15 region. Southern blot analysis of this tumor DNA with a cDNA probe for the proto-oncogene REL, previously mapped to 2p14-15, indicated a greater than 35-fold amplification of REL. To determine the incidence of REL amplification and possible clinical or histologic association with DLLC, a panel of 111 tumor DNAs from DLLC specimens was screened for REL amplification by Southern blot analysis. A copy number of > or = 4 was noted in 26 cases (23%). Southern blot analysis of these 26 tumor DNAs with a cDNA probe for TGFA, mapped to 2p13, indicated lack of coamplification except in one case. Another member of the Rel/NF-kappa B family of transcriptional activators, RELA/p65 mapped to 11q13, was amplified in five cases as determined by Southern blot analysis using a cDNA probe. Nineteen of the 26 DLLC (73%) with REL amplification were primary extranodal lymphomas. As a group, the tumors with REL amplification demonstrated an increased frequency of chromosomal aberrations previously associated with tumor progression, suggesting an oncogenic effect of amplified REL in B-lymphoid cells that already contained a transforming genetic lesion. Thus, REL amplification is a frequent event in DLLC, and probably constitutes a progression-associated marker of primary extranodal lymphomas. This study shows the usefulness of the CGH technique in identifying chromosomal regions overrepresented in tumors that can point to amplified genes and may be correlated with clinical features of the disease.
IMPACT OF PERMETHRIN-TREATED BED NETS ON ENTOMOLOGIC INDICES IN AN AREA OF INTENSE YEAR-ROUND MALARIA TRANSMISSION (2003)

The effect of permethrin-treated bed nets (ITNs) on malaria vectors was studied as part of a large-scale, randomized, controlled trial in western Kenya. Indoor resting densities of fed Anopheles gambiae s.l. and An. funestus in intervention houses were 58.5% (P = 0.010) and 94.5% (P = 0.001) lower, respectively, compared with control houses. The sporozoite infection rate in An. gambiae s.l. was 0.8% in intervention areas compared with 3.4% (P = 0.026) in control areas, while the sporozoite infection rates in An. funestus were not significantly different between the two areas. We estimated the overall transmission of Plasmodium falciparum in intervention areas to be 90% lower than in control areas. Permethrin resistance was not detected during the study period. As measured by densities of An. gambiae s.l., the efficacy of bed nets decreased if one or more residents did not sleep under a net or if bed nets had not been re-treated within six months. These results indicate that ITNs are optimally effective if used every night and if permethrin is reapplied at least biannually.
Antimicrobial Peptides, Isolated from Horseshoe Crab Hemocytes, Tachyplesin II, and Polyphemusins I and II: Chemical Structures and Biological Activity1 (1989)

Tachyplesin is an antimicrobial peptide recently found in the acid extract of hemocytes from the Japanese horseshoe crab (Tachypleus tridentatus) [Nakamura, T. et al. (1988) J. Biol. Chem. 263, 16709-16713]. In our continuing studies on the peptide, we have found an isopeptide, tachyplesin II, and also polyphemusins I and II in hemocytes of the American horseshoe crab (Limulus polyphemus). The complete primary structures of these peptides, which are very similar to that of the previously isolated peptide, now named tachyplesin I, were determined to be as follows: (Table: see text). The isopeptide, tachyplesin II, consists of 17 residues with a COOH-terminal arginine alpha-amide. On the other hand, both polyphemusins I and II were found to contain 18 residues due to an additional Arg residue at the NH2-terminal end as well as a COOH-terminal arginine alpha-amide. The disulfide linkages for polyphemusin I consisted of two bridges between Cys-4 and Cys-17 and between Cys-8 and Cys-13, which was identical to in the case of tachyplesin I. Moreover, all of these peptides inhibited the growth of not only Gram-negative and -positive bacteria but also fungi, such as Candida albicans M9. Furthermore, complex formation between these peptides and bacterial lipopolysaccharides was also observed in a double diffusion test. These results suggest that tachyplesins and polyphemusins are probably located in the hemocyte membrane, where they act on antimicrobial peptides as a self-defense mechanism in the horseshoe crab against invading microorganisms.
In Vitro Fermentability of Differently Substituted Xylo-oligosaccharides (2002)

Xylo-oligosaccharides (XOS) with various substituents were fermented in vitro by fecal inocula (FI) from four human volunteers to study the influence of substitution on the ability and rate of fermentation and on the production of short-chain fatty acids (SCFA) and lactate. By all FI used nonsubstituted XOS (nXOS) and arabino-XOS (AXOS) were fermented more quickly than the more complex structures of acetylated XOS (AcXOS) and XOS containing a 4-O-methylglucuronic acid group (GlcA(me)XOS). In the first stage (0-40 h) of the fermentations of nXOS and AXOS mainly acetate and lactate were formed. The fermentations of AcXOS and GlcA(me)XOS resulted in a lower lactate production, whereas the concentration of propionate and butyrate increased. These results put emphasis on the detailed elucidation of the structural features of nondigestible oligosaccharides in general to understand their fermentation mechanisms more precisely.
Differential dynamic baroreflex regulation of cardiac and renal sympathetic nerve activities (2001)

Although regional difference in sympathetic efferent nerve activity has been well investigated, whether this regional difference exists in the dynamic baroreflex regulation of sympathetic nerve activity remains uncertain. In anesthetized, vagotomized, and aortic-denervated rabbits, we isolated carotid sinuses and randomly perturbed intracarotid sinus pressure (CSP) while simultaneously recording cardiac (CSNA) and renal sympathetic nerve activities (RSNA). The neural arc transfer function from CSP to CSNA and that from CSP to RSNA revealed high-pass characteristics. The increasing slope of the transfer gain in the frequencies between 0.03 and 0.3 Hz was significantly greater for CSNA than for RSNA (2.96 ± 0.72 vs. 1.64 ± 0.73 dB/octave, P &lt; 0.01, n = 9). The difference was hardly explained by the difference in static nonlinear characteristics of CSP-CSNA and CSP-RSNA relationships or by the difference in conduction velocities in the multifiber recording. These results indicate that the central processing in the brain stem differs between CSNA and RSNA. The neural arc of the baroreflex may exert differential effects on the heart and kidney in response to dynamic baroreflex activation.
The release of Alzheimer's disease beta amyloid peptide is reduced by phorbol treatment. (1994)

Amyloid precursor protein (APP) is cleaved predominantly within the beta amyloid peptide (BAP) domain to release a non-amyloidogenic amino-terminal PN2 fragment. Treatment of cells with phorbol dibutyrate, an agent which activates protein kinase C, has been shown to increase the release of an amino-terminal fragment. A panel of mutant APP reporter constructs was expressed in which each of the potential phosphorylation sites located within the cytoplasmic domain of APP was replaced with alanine residues. Phorbol response patterns were unchanged for each of these mutants, suggesting that induced cleavage occurs independently of APP substrate phosphorylation. We find that phorbol (a) increases the release of a PN2 fragment that is consistent with the normal secretase activity, (b) decreases the release of a shorter amino-terminal APP fragment that is cleaved near the amino terminus of BAP, and (c) decreases the release of BAP which was identified based on electrophoretic mobility, epitope mapping, and radio-sequencing. These data demonstrate that pharmacological treatment can reduce the formation of BAP and suggests that protein kinase C activators could be developed as therapeutic agents to block BAP formation.
Physical and Functional Interactions between Pim-1 Kinase and Cdc25A Phosphatase (1999)

The pim-1 oncogene encodes a serine/threonine kinase (Pim-1) involved in the transduction of cytokine-triggered mitogenic signals. Pim-1 is unique in that it closely cooperates with c-Myc not only in oncogenesis, but also in apoptosis induction. However, the molecular basis of Pim-1 function remains poorly understood, largely because the downstream effector molecule(s) for Pim-1 kinase has not been identified. Here we provide several lines of evidence that Cdc25A cell cycle phosphatase, a direct transcriptional target for c-Myc, is a substrate for Pim-1 kinase and functions as an effector for Pim-1. We found that Pim-1 physically interacts with Cdc25A both in vitro and in vivo and phosphorylates Cdc25A. We also observed that Pim-1-mediated phosphorylation of Cdc25A increases its phosphatase activity. In addition, wild-type Pim-1, but not kinase-inactive Pim-1, enhanced Cdc25A-mediated cellular transformation and apoptosis. Our results indicate that Cdc25A might be a key molecule that links Pim-1 and c-Myc and that also ties Pim-1-mediated mitogenic signals to cell cycle machinery.
Metabolic Engineering of Corynebacterium glutamicum for l -Serine Production (2005)

Although L-serine proceeds in just three steps from the glycolytic intermediate 3-phosphoglycerate, and as much as 8% of the carbon assimilated from glucose is directed via L-serine formation, previous attempts to obtain a strain producing L-serine from glucose have not been successful. We functionally identified the genes serC and serB from Corynebacterium glutamicum, coding for phosphoserine aminotransferase and phosphoserine phosphatase, respectively. The overexpression of these genes, together with the third biosynthetic serA gene, serA(delta197), encoding an L-serine-insensitive 3-phosphoglycerate dehydrogenase, yielded only traces of L-serine, as did the overexpression of these genes in a strain with the L-serine dehydratase gene sdaA deleted. However, reduced expression of the serine hydroxymethyltransferase gene glyA, in combination with the overexpression of serA(delta197), serC, and serB, resulted in a transient accumulation of up to 16 mM L-serine in the culture medium. When sdaA was also deleted, the resulting strain, C. glutamicum delta sdaA::pK18mobglyA'(pEC-T18mob2serA(delta197)CB), accumulated up to 86 mM L-serine with a maximal specific productivity of 1.2 mmol h(-1) g (dry weight)(-1). This illustrates a high rate of L-serine formation and also utilization in the C. glutamicum wild type. Therefore, metabolic engineering of L-serine production from glucose can be achieved only by addressing the apparent key position of this amino acid in the central metabolism.
The B-Cell Transcription Factors BSAP, Oct-2, and BOB.1 and the Pan-B-Cell Markers CD20, CD22, and CD79a Are Useful in the Differential Diagnosis of Classic Hodgkin Lymphoma (2003)

Even with routine immunohistochemical evaluation, distinguishing classic Hodgkin lymphoma (CHL) from diffuse large B-cell lymphoma (DLBCL) or anaplastic large cell lymphoma (ALCL) can be difficult. In these cases, the transcription factors (B cell-specific activator protein [BSAP], octamer-binding transcription factor 2 [Oct-2], and B-cell Oct-binding protein 1 [BOB.1]) and the pan-B-cell markers (CD20, CD22, and CD79a) may aid in clarifying the diagnosis. In 57 cases of CHL, 5 cases of nodular lymphocyte predominant Hodgkin lymphoma (NLPHL), and 33 cases of non-Hodgkin lymphoma (25 DLBCL and 8 ALCL) we found the transcription factor phenotype BSAP+ and either Oct-2- or BOB.1- to be predictive of CHL; BSAP+/Oct-2+/BOB.1+ was predictive of NLPHL or DLBCL, while BSAP- was predictive of ALCL. Expression of all 3 pan-B-cell markers was seen only in NLPHL and DLBCL; positivity for a single B-cell marker was present only in CHL. Thus, together, the transcription factors and pan-B-cell markers might be useful in the differential diagnosis of CHL.
Speaker- and language-independent speech recognition in mobile communication systems (2002)

We investigate the technical challenges that are faced when making a transition from the speaker-dependent to speaker-independent speech recognition technology in mobile communication devices. Due to globalization as well as the international nature of the markets and the future applications, speaker independence implies the development and use of language-independent automatic speech recognition (ASR) to avoid logistic difficulties. We propose an architecture for embedded multilingual speech recognition systems. Multilingual acoustic modeling, automatic language identification, and on-line pronunciation modeling are the key features which enable the creation of truly language- and speaker-independent ASR applications with dynamic vocabularies and sparse implementation resources. Our experimental results confirm the viability of the proposed architecture. While the use of multilingual acoustic models degrades the recognition rates only marginally, a recognition accuracy decrease of approximately 4% is observed due to sub-optimal on-line text-to-phoneme mapping and automatic language identification. This performance loss can nevertheless be compensated by applying acoustic model adaptation techniques.
Detection and processing of peripheral myelin protein PMP22 in cultured Schwann cells (1993)

Peripheral myelin protein, 22 kDa (PMP22), is a myelin molecule associated with Schwann cells in peripheral nerves (Snipes, G. J., Suter, U., Welcher, A. A., and Shooter, E. M. (1992) J. Cell Biol. 117, 225-238). Mutations affecting the PMP22 gene have been implicated in the trembler mutation in mice (Suter, U., Welcher, A. A., Ozcelik, T., Snipes, G. J., Kosaras, B., Francke, U., Billings-Gagliardi, S., Sidman, R. L., and Shooter, E. M. (1992) Nature 356, 241-244; Suter, U., Moskow, J. J., Welcher, A. A., Snipes, G. J., Kosaras, B., Sidman, R. L., Buchberg, A. M., and Shooter, E. M. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 4382-4386) and Charcot-Marie-Tooth Disease in humans (Patel, P. I., Roa, B. B., Welcher, A. A., Schoener-Scott, R., Trask, B. J., Pentao, L., Snipes, G. J., Garcia, C. A., Francke, U., Shooter, E. M., Lupski, J. R., and Suter, U. (1992) Nature genet. 1, 159-165). In this report, we have studied PMP22 production in cultured rat Schwann cells. Schwann cells contain a 1.8-kilobase mRNA transcript coding for PMP22, and its production is up-regulated in vitro by forskolin. Metabolic labeling combined with immunoprecipitation methods using antibodies raised against synthetic peptides of PMP22 reveal that Schwann cells generate the protein from an 18-kDa precursor form which is post-translationally modified by N-linked glycosylation. A second molecule (molecular mass, 48 kDa) that reacted with PMP22 antibodies was also detected in Schwann cells but is not related chemically to PMP22 as determined by pulse-chase labeling. Metabolic labeling of rat sciatic nerve and Western blot analyses of purified rat sciatic nerve myelin reveal that deglycosylation of PMP22 gives rise to an 18-kDa protein similar in size to that in Schwann cells. These results indicate that cultured Schwann cells may provide a good model in which to investigate the production and function of PMP22 and to establish the cellular basis for the protein's involvement in inherited peripheral neuropathies.
SERUM CYTOKINES IN HUMAN HEART TRANSPLANT RECIPIENTS (1996)

Cytokines are important in the pathogenesis of allograft rejection. Some studies have suggested a positive relationship between serum levels of cytokines and rejection, so this study was designed to investigate the presence of a range of cytokines in a large cohort of cardiac transplant recipients. We used enzyme linked immunosorbent assays (ELISA) to examine sequential serum samples from 28 consecutive heart transplant recipients; length of follow up varied between 2 and 566 days (median 357 days). Serum levels of IL-2, 4, 6, 10, TNF-alpha, and IFN-gamma were measured. We compared these results with detailed data on patients' clinical courses, including histological rejection, infection, and therapeutic use of antithymocyte globulin (ATG). No significant relationship was found between rejection and serum cytokine levels for samples taken more than 30 days after transplantation. Prior to this cytokine levels were significantly disturbed by the use of cytolytic therapy for induction immunosuppression. Serum cytokine levels sometimes showed peaks that appeared to be related to rejection, or occasionally to infection, but these relationships were not consistent. Serum TNF-alpha and IL-6 were consistently elevated within a few days of administration of ATG. We conclude that there is no systematic relationship between serum cytokine levels and histological rejection or infection in cardiac transplant recipients.
Multi-sensor distributed estimation fusion using minimum distance sum (2014)

In multi-sensor distributed estimation fusion, local estimation errors are correlated in general.Two extreme ways to handle this correlation is either to ignore them completely or to have them fully considered.There is another case in the middle: it admits the existence of the correlation, but does not know how large it is.A sensible way is to set up an optimality criterion and optimize it over all possible such correlations.This work is a new development in the third class.First, a new general objective function is introduced, which is the minimum sum of statistical distances between the fused density and the local posterior densities.Then it is shown that the new criterion leads to a convex optimization problem if the Kullback-Leibler (KL) divergence is used as the statistical distance between assumed Gaussian densities.It is found that although the analytically obtained fused estimate using the new criterion differs from the simple convex combination rule only in mean squared error (MSE) by a scaling factor N (the number of sensors used), it is pessimistic semi-definite in MSE.Numerical examples illustrate the effectiveness of the proposed distributed fuser by comparing with several widely used distributed fusers.