gebhart/patrepeval huggingface dataset:
B Cell Development Arrest Upon Insertion of a neo Gene Between JH and Eμ: Promoter Competition Results in Transcriptional Silencing of Germline JH and Complete V(D)J Rearrangements (2002)

Previous targeting experiments within the IgH locus have shown that V(D)J recombination was affected by an insertion of a neo gene within E(mu) upstream of the core enhancer, but not by insertions downstream of the enhancer. Similarly, class switch recombination to a given (C) gene was affected only by interposition of neo in between that gene and the 3' IgH enhancers. Here we show that insertion of neo upstream E(mu) only marginally impairs V(D)J recombination, but results in an altered D and J(H) gene usage and completely blocks transcription of the germline J(H) region and the rearranged VDJ segments. Although transcriptional silencing of J(H) occurs upstream of the insertion and results in the lack of mature B cells in homozygous mutant animals, IgH transcription is maintained downstream of the insertion together with neo transcription and can be up-regulated by LPS stimulation or upon fusion with plasmacytoma cells. Altogether these data argue for a polarized "neo effect" involving promoter competition and further show that V(D)J rearrangement can be uncoupled from transcription.
Glucose and Lactate Metabolism By Actinomyces Naeslundii (1999)

Actinomyces are among the predominant bacteria in the oral microflora. This review discusses the glucose and lactate metabolism of Actinomyces naeslundii and its ecological significance in dental plaque. This bacterium has the Embden-Meyerhof-Parnas (EMP) pathway as the main route to degrade glucose. The EMP pathway-derived metabolic intermediates, phosphoenolpyruvate (PEP) and pyruvate, are further converted into different end-products, depending on the environment. Under anaerobic conditions in the absence of bicarbonate, the pyruvate is converted into lactate by a lactate dehydrogenase. In the presence of bicarbonate, the PEP is combined with bicarbonate and then converted into succinate through the succinate pathway, while the pyruvate is converted into formate and acetate through the pyruvate formate-lyase pathway. Under aerobic conditions, the pyruvate liberates acetate and CO2 through a pathway initiated by a pyruvate dehydrogenase. A. naeslundii strains also degrade lactate, aerobically, to acetate and CO2 through the conversion of lactate into pyruvate by a NAD-independent lactate dehydrogenase. These strains also synthesize glycogen from a glycolytic intermediate, glucose 6-phosphate. Besides atmospheric conditions and bicarbonate, the intracellular reduction-oxidation potential, carbohydrate concentration, and environmental pH also modulate the metabolism of A. naeslundii. Some of the phosphorylating enzymes involved in A. naeslundii metabolism--e.g., GTP/polyphosphate (PPn)-dependent glucokinase, pyrophosphate (PPi)-dependent phosphofructokinase, UDP-glucose pyrophosphorylase, and GDP/IDP-dependent PEP carboxykinase--are unique to A. naeslundii and have not been found in other oral bacteria. The utilization of PPn and PPi as phosphoryl donors, together with glycogen synthesis and lactate utilization, could contribute to the efficient energy metabolism found in A. naeslundii. Through this flexible and efficient metabolic capacity, A. naeslundii can adapt to fluctuating environments and compete with other bacteria in dental plaque. Further, this bacterium may modify the dental plaque environment and promote the microbial population shifts in dental plaque.
A model for heat flow in deep borehole disposals of high‐level nuclear waste (2008)

Deep borehole disposal (DBD) is emerging as a viable alternative to mined repositories for many forms of highly radioactive waste. It is geologically safer, more secure, less environmentally disruptive and potentially more cost‐effective. All high‐level wastes generate heat leading to elevated temperatures in and around the disposal. In some versions of DBD this heat is an essential part of the disposal while in others it affects the performances of materials and waste forms and can threaten the success of the disposal. Different versions of DBD are outlined, for all of which it is essential to predict the distribution of temperature with time. A generic physical model is established and a mathematical model set up involving the transient conductive heat flow differential equation for a cylindrical source term with realistic decay. This equation is solved using the method of Finite Differences. A Fortran computer code (GRANITE) has been developed for the model in the context of DBD and validated against theoretical and other benchmarks. The limitations of the model, code, input parameters and data used are discussed and it is concluded that the model provides a satisfactory basis for predicting temperatures in DBD. Examples of applications to some DBD scenarios are given and it is shown that the results are essential to the design strategy of the DBD versions, geometric details and choice of materials used. Without such modeling it would be impossible to progress DBD of nuclear wastes; something that is now being given serious consideration in several countries.
High level of mitogen‐activated protein kinase phosphatase‐1 expression is associated with cisplatin resistance in osteosarcoma (2008)

High MKP-1 expression is associated with decreased sensitivity or increased resistance to cisplatin-induced cell death in OS cell lines, and MKP-1 could potentially be used as a marker of cisplatin resistance and a therapeutic target for molecular therapies.
Structure‐activity studies on endothelin (16–21), the C‐terminal hexapeptide of the endothelins, in the guinea‐pig bronchus (1990)

1. We describe the results of a structure-activity study in which the C-terminal hexapeptide of the endothelins, endothelin (16-21), is compared with shorter fragments; hexapeptides bearing amino-acid substitutions and the corresponding C-terminal fragments of sarafotoxins. The guinea-pig bronchus was used in this study since it is the most sensitive preparation for endothelin (16-21) thus far developed. 2. The biological results obtained with endothelin (16-21) and analogues demonstrate that the contractile activity of the C-terminal hexapeptide of endothelin on the guinea-pig bronchus depends on quite close structural requirements, strongly suggestive of a receptor interaction. The following features appear to be essential for the biological activity: (a) the C-terminal free carboxylic function; (b) the L-configuration of Trp-21; (c) the beta-carboxylic function of Asp-18; (d) the presence of Leu-17 and (e) the imidazole moiety of His-16. 3. The hexapeptide corresponding to the C-terminal portion of sarafotoxin, sarafotoxin (16-21), was devoid of biological activity. This behaviour might be related to the proposed existence of more than one receptor for the endothelin/sarafotoxin family in the guinea-pig bronchus.
Synthesis and Characterization of Chitosan/ Dextran‐Based Hydrogels for Surgical Use (2009)

Abstract A series of hydrogels were formed from the reaction between an amine functionalized succinyl chitosan and an oxidized dextran. The properties and rate of formation of the gel were related to both the amine and aldehyde levels of the precursors. These levels could be readily changed by altering the reaction conditions, and allowed good control of the gel properties. Oxidation of the dextran with periodate was accompanied by chain scission and a large reduction in molecular weight. The gel showed excellent haemostatic properties and reduction of adhesions in animal models.
Properties of glucocorticoid receptors in Epstein-Barr virus-transformed lymphocytes from patients with familial cortisol resistance. (1989)

In a previous report of two patients with familial glucocorticoid resistance due to reduced numbers of glucocorticoid receptors (GR), we have shown decreased numbers of GR in peripheral mononuclear cells and cultured fibroblasts but normal affinity of GR in both patients. In this study, peripheral lymphocytes from these patients, one patient's son and daughter, and normal subjects were transformed with Epstein-Barr virus. Reduced numbers and normal affinity of GR were found in the Epstein-Barr virus-transformed lymphocytes from both patients while the son and daughter had normal numbers and affinity of GR. The thermal stability of GR and thermal activation of cytosolic receptors in both patients were found to be normal. Although the percentages of nuclear bound GR were similar in both patients and normal controls, the absolute amounts of nuclear bound GR of the patients were about one-half that of normal controls. These abnormal properties of GR (reduced numbers of GR) were preserved in the transformed cells from the patients.
Tyrosine kinase oncogenes abrogate interleukin-3 dependence of murine myeloid cells through signaling pathways involving c-myc: conditional regulation of c-myc transcription by temperature-sensitive v-abl. (1989)

Retroviral expression vectors carrying the tyrosine kinase oncogenes abl, fms, src, and trk abrogate the requirements of murine myeloid FDC-P1 cells for interleukin-3 (IL-3). Factor-independent clones constitutively express c-myc in the absence of IL-3, whereas in parental cultures c-myc transcription requires the presence of the ligand. To directly test the effect of a tyrosine kinase oncogene on c-myc expression, retroviral constructs containing three different temperature-sensitive mutants of v-abl were introduced into myeloid IL-3-dependent FDC-P1 and 32D cells. At the permissive temperature, clones expressing temperature-sensitive abl behaved like wild-type abl-containing cells in their growth properties and expressed c-myc constitutively. Temperature shift experiments demonstrated that both IL-3 abrogation and the regulation of c-myc expression correlated with the presence of functional v-abl. Induction of c-myc expression by reactivation of temperature-sensitive v-abl mimicked c-myc induction by IL-3 in that it did not require protein synthesis and occurred at the level of transcription, with effects on both initiation and a transcription elongation block. However, v-abl-regulated FDC-P1 cell growth differed from IL-3-regulated growth in that c-fos and junB, which are normally induced by IL-3, were not induced by activation of v-abl.
Development of an electromagnetic micro-generator (1997)

An electromagnetic micro-generator is described, based on a planar pick-up coil and flexible polyimide membrane of diameter 2 mm with attached magnet. During large amplitudes of vibration of the device, the membrane displacement characteristics become nonlinear due to the spring stiffening effect, limiting the maximum generated power to 0.3 µW.
Immunotherapy Following Hematopoietic Stem Cell Transplantation: Potential for Synergistic Effects (2010)

Hematopoietic stem cell transplantation (HSCT) is a particularly important treatment for hematologic malignancies. Unfortunately, following allogeneic HSCT, graft-versus-host disease, immunosuppression and susceptibility to opportunistic infections remain among the most substantial problems restricting the efficacy and use of this procedure, particularly for cancer. Adoptive immunotherapy and/or manipulation of the graft offer ways to attack residual cancer as well as other transplant-related complications. Recent exciting discoveries have demonstrated that HSCT could be expanded to solid tissue cancers with profound effects on the effectiveness of adoptive immunotherapy. This review will provide a background regarding HSCT, discuss the complications that make it such a complex treatment procedure following up with current immunotherapeutic strategies and discuss emerging approaches in applying immunotherapy in HSCT for cancer.
Memory deficits correlate with tau and spine pathology in P301S MAPT transgenic mice (2014)

In P301S mice, memory deficits precede the onset of locomotor dysfunction and coincide with the appearance of conformationally changed, S202-phosphorylated tau and reduced spine density in the absence of neuronal cell loss in the hippocampus. Our finding provides insights into the toxic effects of different tau species in vivo and may facilitate the development of new therapies against neurodegenerative tauopathies.
CC Chemokine Receptor-1 Activates Intimal Smooth Muscle–Like Cells in Graft Arterial Disease (2009)

These studies provide a novel mechanistic insight into the formation of vascular intimal hyperplasia and suggest a novel therapeutic strategy for preventing allograft arteriopathy.
The Role of the Small Intestine in Ammonia Production after Gastric Blood Administration (1987)

It is commonly believed that the digestion of intraluminal blood by colonic bacteria is the primary cause of increased ammonia production after upper gastrointestinal hemorrhage. To evaluate the role of the small intestine in ammonia production, blood, amino acids, or water (5 mL/kg) was administered as a meal or enema to awake dogs with chronic indwelling catheters. After blood meals, intestinal ammonia production increased rapidly to peak at 60 minutes and returned to basal levels. This response was mimicked by the gastric administration of ammoniagenic amino acids. No change in ammonia production occurred with water administration. In contrast, colonic blood administration resulted in a gradual rise in ammonia production, and peaked at 150 minutes. Amino acid enemas resulted in a similar but somewhat more rapid response. No change occurred with water enemas. After gut decontamination, ammonia production did not increase after blood enemas. However, the rapid increase in ammonia production persisted after blood meals. It is concluded that both the small bowel and colon participate in the augmented ammonia production that occurs after upper gastrointestinal hemorrhage. Gut decontamination reduces ammonia production by altering the colonic microflora, but is not specific therapy directed towards amino acid metabolism by the enterocytes of the small bowel and thus, does not alter the ammonia produced by the small intestine.
Physical map of the genome of Treponema pallidum subsp. pallidum (Nichols) (1995)

A physical map of the chromosome of Treponema pallidum subsp. pallidum (Nichols), the causative agent of syphilis, was constructed from restriction fragments produced by NotI, SfiI, and SrfI. These rare-cutting restriction endonucleases cleaved the T. pallidum genome into 16, 8, and 15 fragments, respectively. Summation of the physical lengths of the fragments indicates that the chromosome of T. pallidum subsp. pallidum is approximately 1,030 to 1,080 kbp in size. The physical map was constructed by hybridizing a variety of probes to Southern blots of single and double digests of T. pallidum genomic DNA separated by contour-clamped homogeneous electric field electrophoresis. Probes included cosmid clones constructed from T. pallidum subsp. pallidum genomic DNA, restriction fragments excised from gels, and selected genes. Physical mapping confirmed that the chromosome of T. pallidum subsp. pallidum is circular, as the SfiI and SrfI maps formed complete circles. A total of 13 genes, including those encoding five membrane lipoproteins (tpn47, tpn41, tpn29-35, tpn17, and tpn15), a putative outer membrane porin (tpn50), the flagellar sheath and hook proteins (flaA and flgE), the cytoplasmic filament protein (cfpA), 16S rRNA (rrnA), a major sigma factor (rpoD), and a homolog of cysteinyl-tRNA synthetase (cysS), have been localized in the physical map as a first step toward studying the genetic organization of this noncultivable pathogen.
Synthesis of New Photoresponsive Stilbene Dendrons and Dendrimers (2006)

A new convergent synthetic route for the synthesis of functionalized photoactive dendrimers having bis-stilbenoid skeletons on planar and tetrahedral cores, endowed with methoxy/methyl group has been developed. Optical spectroscopic techniques have been used to study absorption and emission properties and isomerization behavior of the stilbene dendrimers.
Sugar chains of serum transferrin from patients with carbohydrate deficient glycoprotein syndrome. Evidence of asparagine-N-linked oligosaccharide transfer deficiency. (1993)

The structure of over 93% of the sugar chains of serum transferrin purified from three patients with carbohydrate-deficient glycoprotein (CDG) syndrome was Neu5Ac alpha 2-->6Gal beta 1-->4GlcNAc beta 1-->2Man alpha 1-->6 (Neu5Ac alpha 2-->6Gal beta 1-->4GlcNAc beta 1-->2Man alpha 1-->3)Man beta 1-->4GlcNac beta 1-->4GlcNAc, similar to that in a healthy control. On chromatofocusing, CDG syndrome transferrin was separated into three major isoforms, S4, S2, and S0, containing 4, 2, and 0 sialic acids/molecule at pH 5.12 (5.16), 5.42, and 5.80, respectively. On 7.5% SDS-polyacrylamide gel electrophoresis, the molecular masses of transferrin isoforms S4, S2, and S0 were 80, 77, and 74 kDa, respectively. Transferrin isoforms S4 and S2 were linked to 2 and 1 mol of sialylated biantennary sugar chain/transferrin molecule, on the other hand, isoform S0 was not linked to any asparagine-N-linked oligosaccharide. Accordingly, CDG syndrome can be concluded to be an asparagine-N-linked oligosaccharide transfer deficiency, although the primary deficient enzyme has not yet been determined.
Limiting dilution analysis of the frequency of antigen-reactive lymphocytes isolated from the central nervous system of Lewis rats with experimental allergic encephalomyelitis (1987)

Lymphocytes were isolated from the spinal cord and draining lymph nodes of Lewis rats with acute experimental allergic encephalomyelitis (EAE) 12 days after immunization with myelin basic protein (MBP) and tetanus toxoid (TT). An average of 8.0 +/- 2.0 X 10(6) cells was obtained from the spinal cord. Of these 71.1 +/- 8.6% expressed the helper-T-cell marker W3/25 and 14.8 +/- 6.2% expressed the killer/suppressor-T-cell marker OX8. By limiting dilution analysis of cells exhibiting an antigen-specific proliferative response, the average frequencies of cells reactive to MBP and TT were 3.36 +/- 2.4 and 7.60 +/- 4.1 per 10(4), respectively. In the draining lymph nodes, the frequencies of cells reactive to MBP and TT were 2.24 +/- 1.7 and 2.69 +/- 2.5 per 10(4). At a relatively early stage of clinical EAE, MBP-reactive T cells comprise only a small minority of the cells which can be isolated from the spinal cord; lymphocytes reactive to a protein antigen irrelevant to EAE pathogenesis are present in comparable numbers. This finding suggests that most of these cells accumulate as a result of mechanisms not specific for MBP-reactive lymphocytes.
Delay of Disease Development in Transgenic Plants That Express the Tobacco Mosaic Virus Coat Protein Gene (1986)

A chimeric gene containing a cloned cDNA of the coat protein (CP) gene of tobacco mosaic virus (TMV) was introduced into tobacco cells on a Ti plasmid of Agrobacterium tumefaciens from which tumor inducing genes had been removed. Plants regenerated from transformed cells expressed TMV mRNA and CP as a nuclear trait. Seedlings from self-fertilized transgenic plants were inoculated with TMV and observed for development of disease symptoms. The seedlings that expressed the CP gene were delayed in symptom development and 10 to 60 percent of the transgenic plants failed to develop symptoms for the duration of the experiments. Increasing the concentration of TMV in the inoculum shortened the delay in appearance of symptoms. The results of these experiments indicate that plants can be genetically transformed for resistance to virus disease development.
Defective CD8 T Cell Memory Following Acute Infection Without CD4 T Cell Help (2003)

The CD8+ cytotoxic T cell response to pathogens is thought to be CD4+ helper T cell independent because infectious agents provide their own inflammatory signals. Mice that lack CD4+ T cells mount a primary CD8 response to Listeria monocytogenes equal to that of wild-type mice and rapidly clear the infection. However, protective memory to a challenge is gradually lost in the former animals. Memory CD8+ T cells from normal mice can respond rapidly, but memory CD8+ T cells that are generated without CD4 help are defective in their ability to respond to secondary encounters with antigen. The results highlight a previously undescribed role for CD4 help in promoting protective CD8 memory development.
Solvated Electrons in the Synthesis of Ionic Clusters in Zeolites (1991)

Larger metal aggregates do not form when the alkali‐metal ions in zeolites are reduced to low‐valent ion clusters by solvated electrons. Besides the ion cluster Na (n = 4–6) and K (n = 3,4) previously reported, the new cluster Na was obtained selectively and reproducibly. The solvated electron were prepared in situ from highly purified Li granules and propyl‐ or butylamine. One intriguing feature of these ion clusters is the unusual nature of the valence electrons‐not bound to one atom but also not completely delocalized as in a metal.
Astrocytic Dysfunction and Addiction (2014)

Addiction is characterized as a chronic relapsing disorder whereby addicted individuals persistently engage in drug seeking and use despite profound negative consequences. The results of studies using animal models of addiction and relapse indicate that drug seeking is mediated by alterations in cortico-accumbal plasticity induced by chronic drug exposure. Among the maladaptive responses to drug exposure are long-lasting alterations in the expression of proteins localized to accumbal astrocytes, which are responsible for maintaining glutamate homeostasis. These alterations engender an aberrant potentiation of glutamate transmission in the cortico-accumbens circuit that is linked to the reinstatement of drug seeking. Accordingly, pharmacological restoration of glutamate homeostasis functions as an efficient method of reversing drug-induced plasticity and inhibiting drug seeking in both rodents and humans.
Volumetric motility-contrast imaging of tissue response to cytoskeletal anti-cancer drugs (2007)

Microscopic imaging of cellular motility has recently advanced from two dimensions to three dimensions for applications in drug development. However, significant degradation in resolution occurs with increasing imaging depth, limiting access to motility information from deep inside the sample. Here, digital holographic optical coherence imaging is adapted to allow visualization of motility in tissue at depths inaccessible to conventional motility assay approaches. This method tracks the effect of cytoskeletal anti-cancer drugs on tissue inside its natural three-dimensional environment using time-course measurement of motility within tumor tissue.