gebhart/patrepeval huggingface dataset:
Molecular signatures of apomictic and sexual ovules in the Boechera holboellii complex (2009)

Apomixis, a natural form of asexual seed production in plants, has evolved independently in various taxa, and represents an important potential technology for agriculture. The switch to apomixis is based on de-regulation of developmental pathways originally leading to sexual seed formation. Hybridization and polyploidy, both typical characteristics of asexual plants and animals, are mechanisms that could trigger de-regulation. Here we show that up-regulation of alleles in apomeiotic ovules is mediated by genomic duplication, heterochrony and the residual effects of ancient hybridization in diploid apomicts of the Boechera holboellii complex. Using SuperSAGE, we have identified over 4000 differentially expressed mRNA tags between micro-dissected ovules from two diploid sexual (Boechera stricta and B. holboellii) and two diploid apomictic (Boechera divaricarpa) accessions. Pairwise sequence comparisons between tags enabled identification of allelic variants of the same loci. Up-regulated candidate apomeiosis alleles consistently have more than three related alleles, thus demonstrating transcription from duplicated loci. A further 543 alleles were heterochronically expressed between sexual and apomeiotic ovules at developmental stages 2-II to 2-IV. Intriguingly, 69 B. holboellii specific alleles were preferentially up-regulated in apomeiotic ovules, thus showing a remnant'parent of origin' effect stemming from the Pleistocene origin of the hybrid B. divaricarpa from taxa related to B. holboellii and B. stricta. These data implicate polyploid gene dosage in the expression of asexual seed formation, and support hypotheses of de-regulation of the sexual pathway. The observed 'parent of origin' effect suggests that the genomic memory of hybridization has somehow been maintained after hundreds, if not thousands, of asexual generations.
Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics (2001)

Acute myeloid leukemia (AML) is a heterogeneous group of diseases. Normal cytogenetics (CN) constitutes the single largest group, while trisomy 8 (+8) as a sole abnormality is the most frequent trisomy. How trisomy contributes to tumorigenesis is unknown. We used oligonucleotide-based DNA microarrays to study global gene expression in AML+8 patients with +8 as the sole chromosomal abnormality and AML-CN patients. CD34(+) cells purified from normal bone marrow (BM) were also analyzed as a representative heterogeneous population of stem and progenitor cells. Expression patterns of AML patients were clearly distinct from those of CD34(+) cells of normal individuals. We show that AML+8 blasts overexpress genes on chromosome 8, estimated at 32% on average, suggesting gene-dosage effects underlying AML+8. Systematic analysis by cellular function indicated up-regulation of genes involved in cell adhesion in both groups of AML compared with CD34(+) blasts from normal individuals. Perhaps most interestingly, apoptosis-regulating genes were significantly down-regulated in AML+8 compared with AML-CN. We conclude that the clinical and cytogenetic heterogeneity of AML is due to fundamental biological differences.
In Pursuit of the Optimal Fed‐Batch Process for Monoclonal Antibody Production (1995)

Fed-batch culture currently represents the most attractive choice for large scale production for monoclonal antibodies (MAbs), due to its operational simplicity, reliability, and flexibility for implementation in multipurpose facilities. Development of highly productive cell lines, maximization of cell culture longevity, and maintenance of high specific antibody secretion rates through genetic engineering techniques, nutrition supplementation, waste product minimization, and control of environmental conditions are important for the design of high-yield fed-batch processes. Initially simple supplementation protocols have evolved into sophisticated serum-free multi-nutrient feeds that result in MAb titers on the order of 1-2 g/L. Limited research has been published to date on the effect of various culture parameters on potentially important quality issues, such as MAb glycosylation and stability. Although most fed-batch protocols to date have relied on relatively simple control schemes, increasingly sophisticated algorithms must be applied in order to take full advantage of the potentially additive effects of manipulating nutrient and environmental parameters to maximize fed-batch process productivity.
OSI IS-IS Intra-domain Routing Protocol (1990)

This RFC is a republication of ISO DP 10589 as a service to the
Internet community. This is not an Internet standard.
A Protein Encoded within the Down Syndrome Critical Region Is Enriched in Striated Muscles and Inhibits Calcineurin Signaling (2000)

Here we describe a small family of proteins, termed MCIP1 and MCIP2 (for myocyte-enriched calcineurin interacting protein), that are expressed most abundantly in striated muscles and that form a physical complex with calcineurin A. MCIP1 is encoded by DSCR1, a gene located in the Down syndrome critical region. Expression of the MCIP family of proteins is up-regulated during muscle differentiation, and their forced overexpression inhibits calcineurin signaling to a muscle-specific target gene in a myocyte cell background. Binding of MCIP1 to calcineurin A requires sequence motifs that resemble calcineurin interacting domains found in NFAT proteins. The inhibitory action of MCIP1 involves a direct association with the catalytic domain of calcineurin, rather than interference with the function of downstream components of the calcineurin signaling pathway. The interaction between MCIP proteins and calcineurin may modulate calcineurin-dependent pathways that control hypertrophic growth and selective programs of gene expression in striated muscles.
Dietary fiber: classification, chemical analyses, and food sources. (1987)

Dietary fiber's role in the prevention and treatment of constipation has long been known, but now fiber is touted as a cure for many of the ills in Western countries. Although some data exist to relate dietary fiber intake to certain diseases, lack of agreement on what dietary fiber is and how it should be measured make interpreting the data difficult. Further, not all dietary fiber is created equal. Water-soluble fibers, such as pectin and gums, have little effect on stool weight and hence are not appropriate treatment for patients with constipation. Water-insoluble fibers, such as cellulose and hemicellulose, are most effective in aiding laxation but may also limit absorption of minerals and possibly vitamins. Wheat bran is a good source of hemicellulose; vegetables supply cellulose to the diet. Most agencies are recommending a doubling or tripling of dietary fiber intake. Typical recommendations are set at 25 to 50 grams of dietary fiber daily. Different analytical methods for dietary fiber yield conflicting fiber values, and dietary fiber values do not exist for many foods, making fiber recommendations controversial and difficult to achieve. Fiber in the diet should ideally be increased by the consumption of unrefined breads and cereals and more fruits and vegetables. Vegetarians routinely consume 40 to 50 gm dietary fiber daily without ill effect. Fiber supplements may be appropriate for some patients, but the composition of the fiber should be known and be appropriate for the disease being treated. Before fiber supplements are marketed, clinical trials should be conducted to support the use of the supplements in the prevention and treatment of disease.(ABSTRACT TRUNCATED AT 250 WORDS)
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes (1998)

The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.
An algebraic approach to network coding (2003)

We take a new look at the issue of network capacity. It is shown that network coding is an essential ingredient in achieving the capacity of a network. Building on recent work by Li et al.(see Proc. 2001 IEEE Int. Symp. Information Theory, p.102), who examined the network capacity of multicast networks, we extend the network coding framework to arbitrary networks and robust networking. For networks which are restricted to using linear network codes, we find necessary and sufficient conditions for the feasibility of any given set of connections over a given network. We also consider the problem of network recovery for nonergodic link failures. For the multicast setup we prove that there exist coding strategies that provide maximally robust networks and that do not require adaptation of the network interior to the failure pattern in question. The results are derived for both delay-free networks and networks with delays.
Effects of human DNA reair gene hR24L on MCF7 cell apoptosis (2001)

hR24L was over-expressed in MCF7 cells transfected with sense recombinant vectors, while the expression was down-regulated in cells transfected with anti-sense recombinant vectors. Moreover, both sense and anti-sense recombinants of hR24L gene inhbiited the apoptosis caused by H_(2)O_(2) and serum starvation, but not the apoptosis caused by sodium butyrate. It is concluded that the human repair gene hR24L is involved in the regulation of apoptosis.
Orthogonal Assembly of Nanoparticle Building Blocks on Dip-Pen Nanolithographically Generated Templates of DNA (2001)

Nanoscale construction work with DNA: Dip-pen nanolithography (DPN) is used to generate nanostructures which can be subsequently functionalized with oligonucleotides a' and b' and used to assemble, in an orthogonal manner, gold nanoparticles (a, b in scheme) functionalized with sequences complementary to the DPN-generated structures.
Monoclonal antibodies which prevent experimental lung metastases (1984)

Cellular adhesion is important during metastasis, as metastatic cells must escape from the primary site into lymph and blood systems, there to adhere specifically to sites in distant organs. We have recently selected monoclonal antibodies which prevent adherence of B16 mouse melanoma cells to tissue culture dishes, and also markedly reduce experimental lung metastasis in mice when injected before or with the tumor cells. Here, we investigated which step in the metastatic process may be affected by the antibodies. The possible inhibitory effect of antibody on tumour cell adherence to vascular endothelial monolayers and to purified components of the underlying extracellular matrix - fibronectin, laminin and collagen type IV - was studied using in vitro assays. We found that the antibodies significantly blocked attachment to laminin, suggesting that specific basement membrane components play an important role in attracting or otherwise modifying the behaviour of metastatic tumour cells.
Stearoyl-CoA Desaturase 1 Is a Novel Molecular Therapeutic Target for Clear Cell Renal Cell Carcinoma (2013)

Increased SCD1 expression supports ccRCC viability and therefore we propose it as a novel molecular target for therapy either independently or in combination with an mTOR inhibitor for patients whose disease cannot be remedied with surgical intervention, such as in cases of advanced or metastatic disease.
CTLA-4–B7 Interaction Is Sufficient to Costimulate T Cell Clonal Expansion (1997)

T cell costimulation, particularly by the B7 family members B7-1 and B7-2, plays a critical role in regulating T cell-mediated immunity. Two molecules on T cells, CD28 and CTLA-4, are known to bind to B7. It has been suggested that CD28-B7 interaction promotes T cell response, whereas B7-CTLA-4 interaction downregulates T cell clonal expansion. However, the proposed responses of individual receptors to B7 have not been verified directly. Here, we report that B7-1 promotes clonal expansion of CD28-deficient T cells, and that the CD28-independent costimulatory activity is mediated by CTLA-4, as it is completely blocked by intact and Fab of anti-CTLA-4 mAb. In addition, a mutant B7-1 molecule, B7W88 >A, which has lost binding to CD28 but retained significant CTLA-4 binding activity, promotes T cell clonal expansion. Furthermore, while presence of CD28 enhances T cell response to B7-1, such response is also completely blocked by anti-CTLA-4 mAb. Taken together, our results demonstrate that B7-CTLA-4 interaction promotes T cell clonal expansion, and that optimal T cell response to B7 is achieved when both CD28 and CTLA-4 interact with B7. These results establish an important function of CTLA-4 in promoting T cell activation, and suggest an alternative interpretation of the function of CTLA-4 in T cell activation.
Purification of a protein doublet that binds to six TGG-containing sequences in the promoter for hamster 3-hydroxy-3-methylglutaryl-coenzyme A reductase. (1988)

The gene for 3-hydroxy-3-methylglutaryl-coenzyme A reductase, the rate-controlling enzyme of cholesterol biosynthesis, is transcribed at a relatively high level when cellular sterols are depleted and is repressed when sterols accumulate. We have previously reported that the regulatory region of the hamster reductase gene contains eight different sequences that bind nuclear proteins as determined by DNase I footprinting assays. We here report the purification of a single activity that accounts for six of these footprints. This activity was found in a doublet of proteins (designated reductase promoter factor 1, RPF-1) that have apparent molecular weights of 33,000 and 35,000. They were isolated by DNA affinity chromatography using oligonucleotides corresponding to either of two footprinted sequences. The 33- and 35-kDa species were present as monomers, as indicated by gel filtration and gradient ultracentrifugation. Oligonucleotides corresponding to any one of the six footprinted sequences prevented the binding of RPF-1 to all of the other sequences, indicating that all six bind to a single site in RPF-1. The only sequence shared by all six footprinted sequences is the trinucleotide, TGG, both of whose guanosines made contact with RPF-1, as determined by methylation interference assays. The footprinted sequence that binds RPF-1 with highest affinity contains the palindrome, TGG(N7)CCA, which conforms to the consensus sequence for binding NF-1, a nuclear protein that stimulates replication of adeno-virus-2. Purified RPF-1 was shown to bind to the adenovirus NF-1 binding site with high affinity. Although the apparent molecular weight of the RPF-1 doublet was lower than the molecular weight range for NF-1 proteins (52,000-66,000), it is likely that the 33-35-kDa doublet is derived from a larger NF-1-like protein as a result of proteolysis. We conclude that RPF-1 belongs to a group of TGG-binding proteins that includes NF-1 and other proteins previously described as CCAAT binding proteins. This protein binds to six sites in the promoter region for hamster 3-hydroxy-3-methylglutaryl CoA reductase, where its function remains to be determined.
Addition of Biphasic, Prandial, or Basal Insulin to Oral Therapy in Type 2 Diabetes (2007)

A single analogue-insulin formulation added to metformin and sulfonylurea resulted in a glycated hemoglobin level of 6.5% or less in a minority of patients at 1 year. The addition of biphasic or prandial insulin aspart reduced levels more than the addition of basal insulin detemir but was associated with greater risks of hypoglycemia and weight gain. (Current Controlled Trials number, ISRCTN51125379 [controlled-trials.com].).
The Pfam Protein Families Database (2002)

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
The ErbB signaling network in embryogenesis and oncogenesis: signal diversification through combinatorial ligand‐receptor interactions (1997)

Ligand-induced activation of receptor tyrosine kinases (RTK) results in the initiation of diverse cellular pathways, including proliferation, differentiation and cell migration. The ErbB family of RTKs represents a model for signal diversification through the formation of homo- and heterodimeric receptor complexes. Each dimeric receptor complex will initiate a distinct signaling pathway by recruiting a different set of Src homology 2- (SH2-) containing effector proteins. Further complexity is added due to the existence of an oncogenic receptor that enhances and stabilizes dimerization but has no ligand (ErbB-2), and a receptor that can recruit novel SH-2-containing proteins, but is itself devoid of kinase activity (ErbB-3). The resulting signaling network has important implications for embryonic development and malignant transformation.
Tissue‐specific expression pattern of estrogen receptors (ER): Quantification of ERα and ERβ mRNA with real‐time RT‐PCRNote (2001)

We have examined the tissue-specific mRNA expression of ER alpha and ER beta in various bovine tissues using real-time RT-PCR. The goal of this study was to evaluate the deviating tissue sensitivities and the influence of the estrogenic active preparation RALGRO on the tissue-specific expression and regulation of both ER subtypes. RALGRO contains Zeranol (alpha-Zearalanol), a derivative of the mycotoxin Zearalenon, shows strong estrogenic and anabolic effects, and exhibits all symptoms of hyperestrogenism, in particular reproductive and developmental disorders. Eight heifers were treated over 8 weeks with multiple-dose implantations (0x, 1x, 3x, 10x) of Zeranol. Plasma Zeranol concentration, measured by enzyme immunoassay, of multiple treated heifers was elevated. To quantify ER alpha and ER beta transcripts also in low-abundant tissues, sensitive and reliable real-time RT-PCR quantification methods were developed and validated on the LightCycler. Expression results indicate the existence of both ER subtypes in all 15 investigated tissues. All tissues exhibited a specific ER alpha and ER beta expression pattern and regulation. With increasing Zeranol concentrations, a significant downregulation of ER alpha mRNA expression could be observed in jejunum (p<0.001) and kidney medulla (p<0.05). These data support the hypothesis that ER beta may have different biological functions than ER alpha, especially in kidney and jejunum.
Molecular Imaging, Pharmacokinetics, and Dosimetry of 111In‐AMBA in Human Prostate Tumor‐Bearing Mice (2011)

Molecular imaging with promise of personalized medicine can provide patient-specific information noninvasively, thus enabling treatment to be tailored to the specific biological attributes of both the disease and the patient. This study was to investigate the characterization of DO3A-CH(2)CO-G-4-aminobenzoyl-Q-W-A-V-G-H-L-M-NH(2) (AMBA) in vitro, MicroSPECT/CT imaging, and biological activities of (111)In-AMBA in PC-3 prostate tumor-bearing SCID mice. The uptake of (111)In-AMBA reached highest with 3.87 ± 0.65% ID/g at 8 h. MicroSPECT/CT imaging studies suggested that the uptake of (111)In-AMBA was clearly visualized between 8 and 48 h postinjection. The distribution half-life (t(1/2α)) and the elimination half-life (t(1/2β)) of (111)In-AMBA in mice were 1.53 h and 30.7 h, respectively. The C(max) and AUC of (111)In-AMBA were 7.57% ID/g and 66.39 h % ID/g, respectively. The effective dose appeared to be 0.11 mSv/MBq(-1). We demonstrated a good uptake of (111)In-AMBA in the GRPR-overexpressed PC-3 tumor-bearing SCID mice. (111)In-AMBA is a safe, potential molecular image-guided diagnostic agent for human GRPR-positive tumors, ranging from simple and straightforward biodistribution studies to improve the efficacy of combined modality anticancer therapy.
Strategy for Analysis of Cardiac Troponins in Biological Samples with a Combination of Affinity Chromatography and Mass Spectrometry (2003)

Affinity chromatography-mass spectrometry allows the extraction and analysis of cardiac troponins from biological samples in their natural forms. We were, for the first time, able to directly confirm the presence of cardiac troponin complexes in human serum after AMI. This approach could assist in more personalized risk stratification as well as the search for reference materials for cardiac troponin diagnostics.
CIPER, a Novel NF κB-activating Protein Containing a Caspase Recruitment Domain with Homology to Herpesvirus-2 Protein E10 (1999)

We have identified and characterized CIPER, a novel protein containing a caspase recruitment domain (CARD) in its N terminus and a C-terminal region rich in serine and threonine residues. The CARD of CIPER showed striking similarity to E10, a product of the equine herpesvirus-2. CIPER formed homodimers via its CARD and interacted with viral E10 but not with several apoptosis regulators containing CARDs including ARC, RAIDD, RICK, caspase-2, caspase-9, or Apaf-1. Expression of CIPER induced NF-kappaB activation, which was inhibited by dominant-negative NIK and a nonphosphorylable IkappaB-alpha mutant but not by dominant-negative RIP. Mutational analysis revealed that the N-terminal region of CIPER containing the CARD was sufficient and necessary for NF-kappaB-inducing activity. Point mutations in highly conserved residues in the CARD of CIPER disrupted the ability of CIPER to activate NF-kappaB and to form homodimers, indicating that the CARD is essential for NF-kappaB activation and dimerization. We propose that CIPER acts in a NIK-dependent pathway of NF-kappaB activation.