gebhart/patrepeval huggingface dataset:
Detection ofEhrlichia canisin Canine Carrier Blood and in Individual Experimentally Infected Ticks with ap30-Based PCR Assay (2002)

Detection of vector-borne pathogens is necessary for investigation of their association with vertebrate and invertebrate hosts. The ability to detect Ehrlichia spp. within individual experimentally infected ticks would be valuable for studies to evaluate the relative competence of different vector species and transmission scenarios. The purpose of this study was to develop a sensitive PCR assay based on oligonucleotide sequences from the unique Ehrlichia canis gene, p30, to facilitate studies that require monitoring this pathogen in canine and tick hosts during experimental transmission. Homologous sequences for Ehrlichia chaffeensis p28 were compared to sequences of primers derived from a sequence conserved among E. canis isolates. Criteria for primer selection included annealing scores, identity of the primers to homologous E. chaffeensis sequences, and the availability of similarly optimal primers that were nested within the target template sequence. The p30-based assay was at least 100-fold more sensitive than a previously reported nested 16S ribosomal DNA (rDNA)-based assay and did not amplify the 200-bp target amplicon from E. chaffeensis, the human granulocytic ehrlichiosis agent, or Ehrlichia muris DNA. The assay was used to detect E. canis in canine carrier blood and in experimentally infected Rhipicephalus sanguineus ticks. Optimized procedures for preparing tissues from these hosts for PCR assay are described. Our results indicated that this p30-based PCR assay will be useful for experimental investigations, that it has potential as a routine test, and that this approach to PCR assay design may be applicable to other pathogens that occur at low levels in affected hosts.
Detection of BCR-ABL in Hematological Malignancies by RT-PCR (2003)

The presence of a novel, minute chromosome m the cells of patients with chrome myeloid leukemia (CML) was first described m 1960 by Nowell and Hungerford (1). The Philadelphia (Ph) chromosome, as it became known, was shown subsequently by banding techniques to result from a recrprocal translocanon between the long arms of chromosomes 9 and 22 t(9;22) (q34;qll) (2). Molecular studies demonstrated that the translocatton disrupted the normal ABL and BCR genes on chromosomes 9 and 22, respectively, grvmg rise to a chimeric BCR-ABL gene encoding a fusion protein with transforming ability (3). The reciprocal ABL-BCR product is also transcriptionally active in the majority of cases (4, 5).
Selection of the initiator tRNA by Escherichia coli initiation factors. (1989)

We have developed a new technique, called 'toeprinting,' which has allowed a study of the tRNA-binding properties of Escherichia coli translation initiation complexes. In response to natural mRNAs, the initiator tRNA and a variety of elongator tRNAs bind to the same tRNA-binding site on the 30S ribosomal subunit as long as a cognate codon is present near the Shine and Dalgarno sequence. The selection of the initiator tRNA in 30S initiation complexes is accomplished by initiation factors IF2 and IF3. 70S ribosomes accept both initiator tRNA and elongator tRNAs on natural mRNAs, much like 30S ribosomal subunits; IF3 and IF2 do not, however, select the initiator tRNA on 70S initiation complexes unless the initiation factor IF1 is present.
Molecular Cloning, Sequencing, and Expression of a cDNA Encoding -Glucosidase from Mucor javanicus (1996)

A cDNA encoding Mucor javanicus alpha-glucosidase was cloned and sequenced by the reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends methods. The cDNA comprised 2,751 bp, and included an open reading frame which encodes a polypeptide of 864 amino acid residues with a molecular mass of 98,759 Da. The deduced amino acid sequence showed homology of fungal and mammalian alpha-glucosidases and related enzymes, and the sequence around the putative active site was well conserved among these enzymes. The cloned gene was expressed in Escherichia coli cells to produce the alpha-glucosidase, which hydrolyzes not only maltose, but also soluble starch.
Variation and evolution in plants and microorganisms: Toward a new synthesis 50 years after Stebbins (2000)

“The present book is intended as a progress report on [the] synthetic approach to evolution as it applies to the plant kingdom” (ref. 1, p. ix). With this simple statement, G. Ledyard Stebbins formulated the objectives of Variation and Evolution in Plants (1), published in 1950, the last of a quartet of classics that, in the second quarter of the 20th century, set forth what became known as the “synthetic theory of evolution” or “the modern synthesis.” The other books are Theodosius Dobzhansky's Genetics and the Origin of Species (2), Ernst Mayr's Systematics and the Origin of Species (3), and George Gaylord Simpson's Tempo and Mode in Evolution (4). The pervading theory of these books is the molding of Darwin's evolution by natural selection within the framework of rapidly advancing genetic knowledge. Stebbins said it simply: “In brief, evolution is here visualized as primarily the resultant of the interaction of environmental variation and the genetic variability recurring in the evolving population” (ref. 1, p. xi).
Dihomo‐γ‐linolenic acid inhibits tumour necrosis factor‐α production by human leucocytes independently of cyclooxygenase activity (2003)

Dietary oils (such as borage oil), which are rich in gamma-linolenic acid (GLA), have been shown to be beneficial under inflammatory conditions. Dihomo-GLA (DGLA) is synthesized directly from GLA and forms a substrate for cyclooxygenase (COX) enzymes, resulting in the synthesis of lipid mediators (eicosanoids). In the present study, the immunomodulatory effects of DGLA were investigated and compared with those of other relevant fatty acids. Freshly isolated human peripheral blood mononuclear cells (PBMC) were cultured in fatty acid (100 microm)-enriched medium for 48 hr. Subsequently, cells were stimulated with lipopolysaccharide (LPS) for 20 hr and the cytokine levels were measured, in supernatants, by enzyme-linked immunosorbent assay (ELISA). Phospholipids were analysed by gas chromatography. Fatty acids were readily taken up, metabolized and incorporated into cellular phospholipids. Compared with the other fatty acids tested, DGLA exerted pronounced modulatory effects on cytokine production. Tumour necrosis factor-alpha (TNF-alpha) and interleukin (IL)-10 levels were reduced to 60% of control levels, whereas IL-6 levels were not affected by DGLA. Kinetic studies showed that peak levels of TNF-alpha, occurring early after LPS addition, were inhibited strongly, whereas IL-10 levels were not affected until 15 hr after stimulation. Both the reduction of cytokine levels and the decrease in arachidonic acid levels in these cells, induced by DGLA, were dose dependent, suggesting a shift in eicosanoid-subtype synthesis. However, although some DGLA-derived eicosanoids similarly reduced TNF-alpha levels, the effects of DGLA were probably not mediated by COX products, as the addition of indomethacin did not alter the effects of DGLA. In conclusion, these results suggest that DGLA affects cytokine production by human PBMC independently of COX activation.
Application of Screen Printing in the Fabrication of Organic Light-Emitting Devices (2000)

Screen printing as a new approach to fabricating and patterning OLEDs is reported here. The method allows the deposition of organic layers with less than 100 nm film thickness, and is reported to be versatile, simple, fast, and cost-effective, making it valuable for producing low information content displays. The Figure shows a photoluminescent image of a conducting-polymer logo printed using this technique.
Dual regulation by phospho‐OmpR of ssrA/B gene expression in Salmonella pathogenicity island 2 (2003)

Expression of genes located on Salmonella pathogenicity island 2 (SPI-2) is required for systemic infection in mice. This region encodes a type III secretion system, secreted effectors and the two-component regulatory system SsrA/B (also referred to as SpiR), as well as additional uncharacterized genes. In the present work, we demonstrate that phospho-OmpR (OmpR-P) functions as an activator at the spiC-ssrA/B locus. There are two promoters at spiR; one is upstream of ssrA and the other upstream of ssrB. Our results indicate that, in contrast to many two-component regulatory systems, regulation of the sensor kinase SsrA appears to be uncoupled and distinct from regulation of the response regulator SsrB. OmpR regulation of ssrA/B is one of only a few examples known in which a two-component response regulator directly regulates the expression of another two-component regulatory system.
A Mild Chemically Cleavable Linker System for Functional Proteomic Applications (2007)

Im Guten getrennt: Mit niedermolekularen Sonden gelingt die Anreicherung bestimmter Zielproteine aus einem komplexen Proteom. Ein Linkersystem für die milde und hoch selektive Spaltung sondenmarkierter Proteine verhindert die Freisetzung unerwünschter, nichtspezifisch gebundener Proteine. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z603811_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Noninvasive imaging of protein‐protein interactions from live cells and living subjects using bioluminescence resonance energy transfer (2005)

This study demonstrates a significant advancement of imaging of a distance-dependent physical process, known as the bioluminescent resonance energy transfer (BRET2) signal in living subjects, by using a cooled charge-coupled device (CCD) camera. A CCD camera-based spectral imaging strategy enables simultaneous visualization and quantitation of BRET signal from live cells and cells implanted in living mice. We used the BRET2 system, which utilizes Renilla luciferase (hRluc) protein and its substrate DeepBlueC (DBC) as an energy donor and a mutant green fluorescent protein (GFP2) as the acceptor. To accomplish this objective in this proof-of-principle study, the donor and acceptor proteins were fused to FKBP12 and FRB, respectively, which are known to interact only in the presence of the small molecule mediator rapamycin. Mammalian cells expressing these fusion constructs were imaged using a cooled-CCD camera either directly from culture dishes or by implanting them into mice. By comparing the emission photon yields in the presence and absence of rapamycin, the specific BRET signal was determined. The CCD imaging approach of BRET signal is particularly appealing due to its capacity to seamlessly bridge the gap between in vitro and in vivo studies. This work validates BRET as a powerful tool for interrogating and observing protein-protein interactions directly at limited depths in living mice.
Epithelioid and fibroblastic rat kidney cell clones: Epidermal growth factor (EGF) receptors and the effect of mouse sarcoma virus transformation (1978)

Fibroblastic and epithelioid clones have been isolated from the normal rat kidney line, NRK. These clones were studied for their ability to bind epidermal growth factor (EGF), susceptibility to transformation by mouse sarcoma virus (MSV), and alteration in EGF binding upon sarcoma virus transformation. The epithelioid clones bound much more EGF than the fibroblastic clones; Scatchard plots on two of these clones, one epithelioid and one fibroblastic, showed that the higher EGF binding (1.3 x 10(5) molecules per cell for the epithelioid clone and 1.3 x 10(4) molecules per cell for the fibroblastic clone) was due to a greater number or receptors on the epithelioid cells rather than to a difference in the apparent affinity constant. When the clones were transformed by Moloney murine sarcoma virus the EGF binding decreased, the effect being greater with the fibroblastic clones. In 20 out of 20 independently isolated sarcoma virus transformed fibroblastic clones, the level of EGF binding was either greatly reduced or completely eliminated. In contrast to EGF, another growth factor, multiplication stimulating activity (MSA), bound to a greater extent to the fibroblastic clones than the epithelioid clones, and its binding was not decreased by sarcoma virus transformation. The results show that loss of EGF binding ability correlates with expression of the murine sarcoma virus transformation.
Bone marrow-derived mesenchymal stem cells (2005)

Human mesenchymal stem cells (MSCs) contribute to the regeneration of mesenchymal tissues, and are essential in providing support for the growth and differentiation of primitive hemopoietic cells within the bone marrow microenvironment. Techniques are now available to isolate human MSCs and manipulate their expansion in vitro under defined culture conditions without change of phenotype or loss of function. Mesenchymal stem cells have generated a great deal of interest in many clinical settings, including that of regenerative medicine, immune modulation and tissue engineering. Studies have already demonstrated the feasibility of transplanted MSCs providing crucial new cellular therapy. In this review, many aspects of the MSC will be discussed, with the main focus being on clinical studies that describe the potential of MSCs to treat patients with hematological malignancies who are undergoing chemotherapy and/or radiotherapy.
Update on Pharmacology for Restenosis. (2001)

Coronary restenosis remains a major limitation of percutaneous coronary intervention and has become epidemic in the developed countries. Because almost 80% of the contemporary interventional procedures are performed with the use of coronary stents, strategies aimed at eradicating neointimal hyperplasia are the current research focus. Antiproliferative agents, such as rapamycin, tranilast, and trapidil, are undergoing phase III clinical trials to determine the efficacy of these drugs in preventing restenosis. Stent-based pharmacologic therapy to enhance local delivery of the drug has emerged as a promising anti-restenosis strategy. This article provides an update on the development of the pharmacologic therapy for coronary restenosis.
Enhanced cell-mediated tumor killing in patients immunized with human monoclonal antiidiotypic antibody 105AD7. (1994)

A human antiidiotypic monoclonal antibody (105AD7) has been shown to induce antitumor cellular responses in animals and appears to prolong survival in patients with metastatic colorectal cancer without associated toxicity. Proliferative leukocyte responses to the targeted tumor antigen gp72 were observed in these patients and plasma interleukin 2 levels were increased following immunization. Autologous tumor tissue was not available in these patients, so antitumor cytotoxicity could not be measured. This issue has now been addressed in an adjuvant clinical study in primary rectal cancer patients. Six patients with rectal cancer were immunized preoperatively with 105AD7. Peripheral blood lymphocytes taken prior to immunization were tested against tumor cells extracted from biopsies also obtained prior to immunization or from natural killer (NK)-sensitive target cells. Cryopreserved lymphocytes taken before and after tumor immunization, fresh peripheral blood lymphocytes taken immediately prior to surgery, and lymphocytes from tumor-draining lymph nodes were tested against autologous cells from the resected specimen or NK-sensitive target cells. Significant killing of autologous tumor cells, which was not due to NK activity, was seen with cryopreserved lymphocytes or lymph node cells of three patients at 1-2 weeks postimmunization with 105AD7 but not on pretreatment biopsies. Enhanced NK activity was seen 2-3 weeks postimmunization in 3 of 6 patients. These results indicate that 105AD7 human monoclonal antibody immunization enhances cytotoxicity in rectal cancer patients by specific and nonspecific effector mechanisms.
Haploidentical Stem Cell Transplantation: The Always Present but Overlooked Donor (2005)

Haploidentical stem cell transplantation is a treatment option for the approximately 70% of patients who do not have an HLA-identical sibling donor. The availability of a haploidentical donor in most families is a potential advantage, both for avoiding the need to find an alternative unrelated donor, and for the potentially more potent graft-versus-tumor effect that can be induced. The early complications of severe graft-versus-host disease (GVHD) following T-cell replete stem cell transplantation (SCT), and graft failure and recurrent malignancy (after T-cell depleted SCT) have limited the applications of this approach. Newer strategies employing T-cell depletion of the graft, using either very high-dose peripheral blood stem cells and/or more intensive conditioning therapy have overcome some of the problems of conventional transplantation. Nonmyeloablative SCT approaches have overcome some of the morbidity and mortality associated with the early complications of SCT and have been associated with favorable engraftment and GVHD profiles. Induction of mixed lymphohematopoietic chimerism as a platform for adoptive cellular immunotherapy (via delayed donor lymphocyte infusions) may have important application in avoiding early GVHD, while ultimately capturing a very potent graft-versus-tumor effect. Current strategies are focusing on improvement of immune reconstitution and prevention of recurrence of the underlying malignancy.
Evolutionary conserved modules associated with zinc fingers in Xenopus laevis. (1989)

Many DNA-binding proteins that are involved in the differential regulation of gene expression are composed of multiple discrete modules. Association of the homeobox-encoded helix-turn-helix DNA-binding motif with conserved modules, such as the paired box or the POU domain, has led to the definition of structurally and functionally related subfamilies of regulatory proteins. The zinc finger, which is the second major nucleic acid-binding motif characterized to date, defines large multigene families in higher eukaryotes; we have isolated more than 100 Xenopus finger protein-encoding cDNAs and in this study we show that at least 10 of these clones share extensive sequence homologies in a region of more than 200 amino acids in the N-terminal nonfinger portion of the predicted proteins, which is connected to variable finger clusters. We refer to this element as a finger-associated boxes (FAX) domain. Cross-hybridization with human genomic DNA indicates that the finger-associated boxes domain is evolutionary conserved. Northern blot analysis shows that the corresponding genes are differentially expressed in the course of early Xenopus embryogenesis.
Use‐dependent changes in synaptic efficacy in rat prefrontal neurons in vitro. (1990)

1. An in vitro slice preparation of rat prefrontal cortex was used to analyse the responses of layer V pyramidal cells to electrical stimulation of layer II. We also studied the long-lasting modifications of synaptic efficacy following high-frequency stimulation of the same region. 2. Stable intracellular recordings were obtained from forty-three regular spiking pyramidal cells. The input resistance was 56 +/- 18 M omega (mean +/- S.D.) at a resting membrane potential of -71 +/- 4 mV. 3. At rest, a single stimulus of increasing strength evoked a monophasic, purely depolarizing postsynaptic potential (PSP) of increasing amplitude. In neurons recorded with potassium acetate-filled micropipettes, membrane depolarization disclosed an excitatory-inhibitory (EPSP-IPSP) sequence (onset latency of the EPSP, 3.6 +/- 0.6 ms). 4. Superfusion with the non-N-methyl-D-aspartate (NMDA) receptor antagonist, 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) reduced the EPSP and suppressed the IPSP. The small EPSP which remained was blocked by the NMDA receptor antagonist, D,L-2-amino-5-phosphonovalerate (APV). 5. In five cells, administration of 0.5 mumol l-1 bicuculline revealed a postsynaptic NMDA component in the evoked response as evidenced by its anomalous voltage dependence in the presence of Mg2+ and its sensitivity to APV. In these cells the latency of the APV-sensitive EPSP was the same as that of the APV-insensitive EPSP. 6. In six cells superfused with a high-Mg2+, low-Ca2+ artificial cerebrospinal fluid (ACSF) a small monosynaptic EPSP remained which had the same latency as the PSP recorded in control ACSF. 7. Patterned high-frequency stimulation (50-100 Hz) was applied to the afferents of twenty-eight neurons (twenty-three of them were recorded in the presence of bicuculline). During the train the membrane potential depolarized some 20 mV and each stimulus evoked a small PSP. The tetanic stimulation was followed by a short-term enhancement of the PSP amplitude and a slight increase in membrane input resistance. 8. Out of the twenty-eight cells, twenty-four showed long-lasting (over 30 min) modifications of the PSP. Long-term depression (LTD) of the evoked PSP was observed in fourteen cells and long-term potentiation (LTP) in ten cells. There was no significant change in the steady-state membrane properties and in the latency of the response. 9. In 64% of the cells that showed LTD and 70% of those that showed LTP of synaptic efficacy, the latency of the enhanced or depressed component of the PSP was the same as the control.(ABSTRACT TRUNCATED AT 400 WORDS)
Determination of Transport Properties in Chromium Disilicide Nanowires via Combined Thermoelectric and Structural Characterizations (2007)

The Seebeck coefficient, electrical conductivity, and thermal conductivity of individual chromium disilicide nanowires were characterized using a suspended microdevice and correlated with the crystal structure and growth direction obtained by transmission electron microscopy on the same nanowires. The obtained thermoelectric figure of merit of the nanowires was comparable to the bulk values. We show that combined Seebeck coefficient and electrical conductivity measurements provide an effective approach to probing the Fermi Level, carrier concentration and mobility in nanowires.
Of sound mind and body: depression, disease, and accelerated aging (2011)

Major depressive disorder (MDD) is associated with a high rate of developing serious medical comorbidities such as cardiovascular disease, stroke, dementia, osteoporosis, diabetes, and the metabolic syndrome. These are conditions that typically occur late in life, and it has been suggested that MDD may be associated with "accelerated aging." We review several moderators and mediators that may accompany MDD and that may give rise to these comorbid medical conditions. We first review the moderating effects of psychological styles of coping, genetic predisposition, and epigenetic modifications (eg, secondary to childhood adversity). We then focus on several interlinked mediators occurring in MDD (or at least in subtypes of MDD) that may contribute to the medical comorbidity burden and to accelerated aging: limbic-hypothalamic-pituitary-adrenal axis alterations, diminution in glucocorticoid receptor function, altered glucose tolerance and insulin sensitivity, excitotoxicity, increases in intracellular calcium, oxidative stress, a proinflammatory milieu, lowered levels of "counter-regulatory" neurosteroids (such as allopregnanolone and dehydroepiandrosterone), diminished neurotrophic activity, and accelerated cell aging, manifest as alterations in telomerase activity and as shortening of telomeres, which can lead to apoptosis and cell death. In this model, MDD is characterized by a surfeit of potentially destructive mediators and an insufficiency of protective or restorative ones. These factors interact in increasing the likelihood of physical disease and of accelerated aging at the cellular level. We conclude with suggestions for novel mechanism-based therapeutics based on these mediators.