gebhart/patrepeval huggingface dataset:
Cloning and sequence analysis of an EnvCD homologue in Pseudomonas aeruginosa: regulation by iron and possible involvement in the secretion of the siderophore pyoverdine (1993)

Pseudomonas aeruginosa strain K437 is defective in the production of a 90kDa ferripyoverdine receptor and is unable to grow in an iron-deficient medium in the presence of the non-metabolizable iron chelator 2,2'-dipyridyl (0.25 mM). An attempt to clone the ferripyoverdine receptor gene was made by complementing this growth defect. A number of clones restoring growth of K437 on dipyridyl-containing medium were obtained and several of these restored moderate expression of the 90 kDa receptor. A 5.5 kb xhoI-HindIII fragment derived from one of these clones was similarly capable of complementing the dipyridyl growth defect although it failed to restore expression of the 90 kDa ferripyoverdine receptor. Nucleotide sequencing of the 5.5 kb fragment revealed two large open reading frames (ORFs), designated ORFA and ORFB, which appeared to form an operon and were capable of encoding products of 41 kDa and 112 kDa, respectively. Using a phage T7-based expression system, products of 42 kDa and c. 108 kDa were produced from the cloned DNA, confirming that the ORFs were, indeed, expressed. The cloned ORFAB operon was inducible under conditions of iron limitation in both P. aeruginosa and Escherichia coli. In addition, mutants expressing ORFAB constitutively were constitutive for pyoverdine and ferripyoverdine receptor production suggesting that components of the pyoverdine-mediated iron-transport system are co-regulated with ORFAB. The predicted products of ORFA and ORFB showed significant homology to the Escherichia coli EnvC and EnvD polypeptides which are reportedly involved in septum formation. In addition, the ORFB product showed moderate homology to the CzcA polypeptide identified as a component of a membrane-associated plasmid-encoded cation efflux system in Alcaligenes eutrophus. Using in vitro mutagenesis and gene replacement, ORFA- and ORFB-deficient mutants of K372, the parent strain of K437, were constructed. These mutants were unable to grow on iron-deficient minimal medium containing 0.25 mM dipyridyl although they expressed the ferripyoverdine receptor and were proficient in pyoverdine-mediated iron uptake. Despite the homology of the ORFA and ORFB products to EnvC and EnvD, respectively, the ORFA-ORFB-deficient mutants were not defective in septum formation.(ABSTRACT TRUNCATED AT 400 WORDS)
Lentiviral vectors: excellent tools for experimental gene transfer and promising candidates for gene therapy (2000)

Lentiviral vectors are tools for gene transfer derived from lentiviruses. From their first application to now they have been strongly developed in design, in biosafety and in their ability of transgene expression into target cells. Primate and non-primate derived lentiviral vectors are now available and with both types of systems a lot of studies tuned to improve their performances in a large number of tissues are ongoing. Here we review the state of the art of lentiviral vector systems discussing their potential for gene therapy.
Endogenous gamma interferon mediates resistance to Brucella abortus infection (1993)

Depletion of endogenous gamma interferon (IFN-gamma) with anti-IFN-gamma monoclonal antibody resulted in increased numbers of Brucella abortus in the spleen and liver of infected CBA mice. This increase was accompanied by a decrease in splenomegaly and a lower proportion of macrophages in the spleen. Furthermore, treatment of recipient mice with anti-IFN-gamma antibody blocked the adoptive transfer of resistance with immune T cells. Together, the results indicated that endogenous IFN-gamma plays an important role in mediating resistance to primary and secondary Brucella infection.
SpoIIE Regulates Sporulation but Does Not Directly Affect Solventogenesis in Clostridium acetobutylicum ATCC 824 (2005)

Using gene expression reporter vectors, we examined the activity of the spoIIE promoter in wild-type and spo0A-deleted strains of Clostridium acetobutylicum ATCC 824. In wild-type cells, the spoIIE promoter is active in a transient manner during late solventogenesis, but in strain SKO1, where the sporulation initiator spo0A is disrupted, no spoIIE promoter activity is detectable at any stage of growth. Strains 824(pMSpo) and 824(pASspo) were created to overexpress spoIIE and to decrease spoIIE expression via antisense RNA targeted against spoIIE, respectively. Some cultures of strains 824(pMSpo) degenerated during fermentations by losing the pSOL1 megaplasmid and hence did not produce the solvents ethanol, acetone, and butanol. The frequent degeneration event was shown to require an intact copy of spoIIE. Nondegenerate cultures of 824(pMSpo) exhibited normal growth and solvent production. Strain 824(pASspo) exhibited prolonged solventogenesis characterized by increased production of ethanol (225%), acetone (43%), and butanol (110%). Sporulation in strains harboring pASspo was significantly delayed, with sporulating cells exhibiting altered morphology. These results suggest that SpoIIE has no direct effect on the control of solventogenesis and that the changes in solvent production in spoIIE-downregulated cells are mediated by effects on the cell during sporulation.
Synthesis and characterization of gold nanorods and their application for photothermal cell damage (2011)

Gold nanorods injected subcutaneously and irradiated with 980 nm laser caused injury to rat tissue, demonstrating that gold nanorods may be used to kill cancerous cells in tumor tissue.
Characterization of Three Plasmid Deoxyribonucleic Acid Molecules in a Strain of Streptococcus faecalis : Identification of a Plasmid Determining Erythromycin Resistance (1974)

Three plasmids designated alpha, beta, and gamma, distinguishable by their molecular weights (6, 17, and 34 million, respectively) were isolated from Streptococcus faecalis strain DS-5 (ATCC 14508). Derivatives of this strain "cured" for erythromycin resistance lacked the beta-plasmid. In the parent strain the beta-plasmid was estimated to be present to the extent of one to two copies per chromosomal genome equivalent whereas the alpha- and gamma-plasmids were about nine and five copies, respectively.
Basic physics of MR contrast agents and maximization of image contrast (1993)

This review summarizes the physical basis of magnetic resonance (MR) imaging contrast agents, including both T1 agents, such as gadolinium-DTPA (diethylenetriaminepentaacetic acid), and T2 or T2* agents, such as superparamagnetic iron oxides. The maximization of image contrast and lesion visibility with contrast agents is described, and the use of contrast agents in MR angiography and perfusion imaging is discussed.
[1H, 13C NMR and stereochemistry studies of 3S-substituted alkoxylquinuclidine by two-dimensional and NOE difference NMR techniques]. (1989)

By using optically pure 3S-quinuclidinol, two diastereoisomers (3S-1) and (3S-2) of 3-(substituted) alkoxy-quinuclidine were synthesized. 1H and 13C NMR spectra of (3S-1) and (3S-2) have been completely analyzed utilizing double-quantum filtered COSY, 13C-1H COSY and NOE difference experiment. The NOE difference experiment was used to determine the absolute configuration at C-11 of the diastereomers. According to the results of NOE difference and variable concentration NMR experiments, the configuration about C-11 of (3S-1) is designated as R (1A), whereas the configuration about C-11 of (3S-2) is designated as S (1B). The result was confirmed by X-ray diffraction analysis.
Radiolabeled COX-2 Inhibitors for Non-Invasive Visualization of COX-2 Expression and Activity — A Critical Update (2013)

Cyclooxygenase-2 (COX-2) is a key player in inflammation. Its overexpression is directly associated with various inflammatory diseases and, additionally, with several processes of carcinogenesis. The development of new selective COX-2 inhibitors (COXIBs) for use in cancer treatment is in the focus of the medicinal chemistry research field. For this purpose, a set of methods is available to determine COX-2 expression and activity in vitro and ex vivo but it is still a problem to functionally characterize COX-2 in vivo. This review focusses on imaging agents targeting COX-2 which have been developed for positron emission tomography (PET) and single photon emission computed tomography (SPECT) since 2005. The literature reveals that different radiochemical methods are available to synthesize COXIBs radiolabeled with fluorine-18, carbon-11, and isotopes of radioiodine. Unfortunately, most of the compounds tested did not show sufficient stability in vivo due to de[¹⁸F]fluorination or de[¹¹C]methylation or they failed to bind specifically in the target region. So, suitable stability in vivo, matching lipophilicity for the target compartment and both high affinity and selectivity for COX-2 were identified as prominent criteria for radiotracer development. Up to now, it is not clear what approach and which model is the most suited to evaluate COX-2 targeting imaging agents in vivo. However, for proof of principle it has been shown that some radiolabeled compounds can bind specifically in COX-2 overexpressing tissue which gives hope for future work in this field.
Role of accessory proteins of HTLV-1 in viral replication, T cell activation, and cellular gene expression (2004)

Human T-cell lymphotropic virus type 1 (HTLV-1), causes adult T cell leukemia/lymphoma (ATLL), and initiates a variety of immune mediated disorders. The viral genome encodes common structural and enzymatic proteins characteristic of all retroviruses and utilizes alternative splicing and alternate codon usage to make several regulatory and accessory proteins encoded in the pX region (pX ORF I to IV). Recent studies indicate that the accessory proteins p12I, p27I, p13II, and p30II, encoded by pX ORF I and II, contribute to viral replication and the ability of the virus to maintain typical in vivo expression levels. Proviral clones that are mutated in either pX ORF I or II, while fully competent in cell culture, are severely limited in their replicative capacity in a rabbit model. These HTLV-1 accessory proteins are critical for establishment of viral infectivity, enhance T-lymphocyte activation and potentially alter gene transcription and mitochondrial function. HTLV-1 pX ORF I expression is critical to the viral infectivity in resting primary lymphocytes suggesting a role for the calcineurin-binding protein p12I in lymphocyte activation. The endoplasmic reticulum and cis-Golgi localizing p12I activates NFAT, a key T cell transcription factor, through calcium-mediated signaling pathways and may lower the threshold of lymphocyte activation via the JAK/STAT pathway. In contrast p30II localizes to the nucleus and represses viral promoter activity, but may regulate cellular gene expression through p300/CBP or related co-activators of transcription. The mitochondrial localizing p13II induces morphologic changes in the organelle and may influence energy metabolism infected cells. Future studies of the molecular details HTLV-1 "accessory" proteins interactions will provide important new directions for investigations of HTLV-1 and related viruses associated with lymphoproliferative diseases. Thus, the accessory proteins of HTLV-1, once thought to be dispensable for viral replication, have proven to be directly involved in viral spread in vivo and represent potential targets for therapeutic intervention against HTLV-1 infection and disease.
Interleukin 7 is a T-cell growth factor. (1989)

Interleukin 7 (IL-7) is a 25-kDa cytokine which was purified and its corresponding cDNA was cloned based upon its ability to stimulate the proliferation of pre-B cells. It has been shown that IL-7 can also function as a costimulator with Con A for the proliferation of T lymphocytes by inducing the production of interleukin 2 (IL-2). We demonstrate here that IL-7 in combination with phorbol 12-myristate 13-acetate can directly drive the proliferation of purified T cells and that this response is not inhibited by cyclosporine A or by antibodies to IL-2 and IL-4. Stimulation of T cells with phorbol myristate acetate and IL-2, IL-4, or IL-7 prepared T cells to respond to any of the three lymphokines. Although T cells activated in vitro by anti-CD3 or allogeneic cells failed to proliferate when challenged with IL-7, T cells primed in vivo to the same stimuli demonstrated a significant proliferative response when restimulated in vitro with IL-7. IL-7 can, therefore, function both as a growth factor for T cells in an IL-2-independent manner and as a competence factor for the induction of lymphokine responsiveness. The ability to induce IL-7 responsiveness via stimulation of the T-cell receptor complex in vivo, but not in vitro, raises the possibility that IL-7 may play a role in T-cell growth and differentiation in vivo.
Pomegranate seed oil consumption during a period of high-fat feeding reduces weight gain and reduces type 2 diabetes risk in CD-1 mice (2008)

The health benefits of pomegranate consumption have recently received considerable scientific focus, with most studies examining fruit and/or juice consumption. Pomegranate seed oil (POMo) is a rich source of 9-cis, 11-trans conjugate linolenic acid (CLA), which may offset the side-effects associated with weight gain. Male, wild-type CD-1 mice were divided into one of three groups (twenty per group): high-fat (HF), HF+seed oil (HF + POMo) or lean control (LN). In HF and HF + POMo, mice were provided access ad libitum to a high-fat chow (60 % of energy from fat). HF + POMo was supplemented with 61.79 mg POMo/d. LN consumed a restricted low-fat (10 % of energy from fat) chow to maintain body weight within 5 % of initial weight. Plasma was analysed for biomarkers associated with cholesterol profile (total cholesterol, HDL and TAG), glucose sensitivity (glucose and insulin), adipose tissue accumulation (leptin and adiponectin) and systemic low-grade inflammation (C-reactive protein and haptoglobin). The key findings of this study were that weight gain was associated with an increase in biomarkers of cholesterol profile, glucose sensitivity, adipose tissue accumulation and systemic low-grade inflammation (P < 0.05). POMo only altered body weight accumulation, final body weight, leptin, adiponectin and insulin (P < 0.05). We found that despite a similar level of energy intake, HF mice had a greater concentration of leptin and a lower concentration of adiponectin compared to HF + POMo mice. POMo intake was associated with an improvement in insulin sensitivity, suggesting that risk of developing type 2 diabetes may have been reduced; however, CVD risk did not change.
Genetic Subtypes, Humoral Immunity, and Human Immunodeficiency Virus Type 1 Vaccine Development (2001)

Successful vaccination programs, particularly against influenza virus infection, have provided us with an awareness of the need to immunize against the predominant circulating viral strains or genetic subtypes.The lessons and language derived from experience with influenza (and a few other) viruses have often been directly translated to human immunodeficiency virus type 1 (HIV-1) vaccine development.But how appropriate is this?Should an HIV-1 vaccine antigen always be based on the dominant genetic subtype that circulates in the geographical area where a vaccine candidate is to be tested?The answers lie, at least in part, in a consideration of the humoral response to HIV-1 and, in particular, in the relationships between the HIV-1 genetic subtypes and antigenic and neutralization serotypes.Here, we will review what is known about these relationships and seek to clarify confusion that has been created by the use of serological assays that generate misleading, or sometimes artifactual, results.Broadly similar issues are raised when considering the relationship between cellular immune responses and the HIV-1 genetic subtypes, but we will not discuss these here.Instead, we refer the reader to recent articles written by leading cellular immunologists (9,30,39,79).Significantly, a recent study on the cross-clade activity of cytotoxic T-lymphocyte responses in HIV-1-infected Ugandans argued that the use of nonendemic vaccine strains may be initially justified from the perspective of inducing cellular immunity to HIV-1 (15).
Microscopy cell counting and detection with fully convolutional regression networks (2016)

This paper concerns automated cell counting and detection in microscopy images. The approach we take is to use convolutional neural networks (CNNs) to regress a cell spatial density map across the image. This is applicable to situations where traditional single-cell segmentation-based methods do not work well due to cell clumping or overlaps. We make the following contributions: (i) we develop and compare architectures for two fully convolutional regression networks (FCRNs) for this task; (ii) since the networks are fully convolutional, they can predict a density map for an input image of arbitrary size, and we exploit this to improve efficiency by end-to-end training on image patches; (iii) we show that FCRNs trained entirely on synthetic data are able to give excellent predictions on microscopy images from real biological experiments without fine-tuning, and that the performance can be further improved by fine-tuning on these real images. Finally, (iv) by inverting feature representations, we show to what extent the information from an input image has been encoded by feature responses in different layers. We set a new state-of-the-art performance for cell counting on standard synthetic image benchmarks and show that the FCRNs trained entirely with synthetic data can generalise well to real microscopy images both for cell counting and detections for the case of overlapping cells.
The anti-idiotypic response by cynomolgus monkeys to humanized anti-Tac is primarily directed to complementarity-determining regions H1, H2, and L3 (1993)

The anti-ld response developed by cynomolgus monkeys to the humanized anti-Tac antibody was analyzed by using 12 humanized anti-Tac variants differing in V region structure. The majority of the monkey response was directed against idiotopes composed wholly or in part of complementarity-determining regions H1, H2, and L3. There was no detectable response directed solely to five single complementarity-determining regions examined or solely to the modified human V region framework.
A new three-step search algorithm for block motion estimation (1994)

The three-step search (TSS) algorithm has been widely used as the motion estimation technique in some low bit-rate video compression applications, owing to its simplicity and effectiveness. However, TSS uses a uniformly allocated checking point pattern in its first step, which becomes inefficient for the estimation of small motions. A new three-step search (NTSS) algorithm is proposed in the paper. The features of NTSS are that it employs a center-biased checking point pattern in the first step, which is derived by making the search adaptive to the motion vector distribution, and a halfway-stop technique to reduce the computation cost. Simulation results show that, as compared to TSS, NTSS is much more robust, produces smaller motion compensation errors, and has a very compatible computational complexity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Simple Preparation of Chloromethyl Esters of the Blocked Amino Acids (1994)

Abstract An efficient synthesis of various chloromethyl esters of the blocked amino acids, very useful reagents for prodrug, are described.
Heparin‐binding epidermal growth factor‐like growth factor as a novel targeting molecule for cancer therapy (2006)

HB-EGF, a member of the EGF family of growth factors, exerts its biological activity through activation of the EGFR and other ErbB receptors. HB-EGF participates in diverse biological processes, including heart development and maintenance, skin wound healing, eyelid formation, blastocyst implantation, progression of atherosclerosis and tumor formation, through the activation of signaling molecules downstream of ErbB receptors and interactions with molecules associated with HB-EGF. Recent studies have indicated that HB-EGF gene expression is significantly elevated in many human cancers and its expression level in a number of cancer-derived cell lines is much higher than those of other EGFR ligands. Several lines of evidence have indicated that HB-EGF plays a key role in the acquisition of malignant phenotypes, such as tumorigenicity, invasion, metastasis and resistance to chemotherapy. Studies in vitro and in vivo have indicated that HB-EGF expression is essential for tumor formation of cancer-derived cell lines. CRM197, a specific inhibitor of HB-EGF, and an antibody against HB-EGF are both able to inhibit tumor growth in nude mice. These results indicate that HB-EGF is a promising target for cancer therapy, and that the development of targeting tools against HB-EGF could represent a novel type of therapeutic strategy, as an alternative to targeting ErbB receptors.
Preventing Spams and Relays (1998)

The smtpd package is a useful mail demon for stopping spam, thereby saving money and resources
The Accreditation Process as a Quality Assurance Method for Individual Monitoring (1992)

Occupational monitoring for radiation protection purposes has been performed for many years. However, technological difficulties still exist in the measurement of the small dose equivalent values encountered in radiation protection. In addition, the measurement of neutron and beta particle sources can present special difficulties if small uncertainties are required. International intercomparisons conducted by the International Atomic Energy Agency (IAEA) have demonstrated that some dosimetry systems exhibited significant differences between the dose delivered by the irradiation laboratory and the dose assessed by the dosimetry service. Accreditation of dosimetry services may be one way to ensure a certain level of performance for these services. This paper will discuss the role of the accreditation process in the quality assurance of individual dose monitoring.
The Japanese Experience with Vaccinating Schoolchildren against Influenza (2001)

The effect of influenza on mortality is much greater in Japan than in the United States and can be measured about equally well in terms of deaths from all causes and deaths attributed to pneumonia or influenza. Vaccinating schoolchildren against influenza provides protection and reduces mortality from influenza among older persons.
Capsaicin: actions on nociceptive C-fibres and therapeutic potential (1990)

Recent work on the excitatory action of capsaicin on somatic and visceral afferent neurones shows that depolarization is selective for C-fibre polymodal nociceptor afferents and involves opening a non-selective cation channel. Exposure to significantly suprathreshold amounts of capsaicin causes permanent degeneration of C-fibre afferents in adult rats. Functional changes in rats (hypalgesia, diminished neurogenic inflammation) are likely to be a direct consequence of the loss of C-fibre nociceptors, and so are the reductions in neuropeptide levels that follow adult capsaicin treatment. Clinical trials of topical capsaicin treatment for post-herpetic neuralgia have yielded promising results. The selective nature of the action of capsaicin in reducing just C-nociceptor activity may make it particularly useful for treating pain states triggered by C-fibre input.