gebhart/patrepeval huggingface dataset:
Identification of in vivo expressed vaccine candidate antigens from Staphylococcus aureus (2002)

For the design of potent subunit vaccines, it is of paramount importance to identify all antigens immunologically recognized by a patient population infected with a pathogen. We have developed a rapid and efficient procedure to identify such commonly recognized antigens, and here we provide a comprehensive in vivo antigenic profile of Staphylococcus aureus, an important human pathogen. S. aureus peptides were displayed on the surface of Escherichia coli via fusion to one of two outer membrane proteins (LamB and FhuA) and probed with sera selected for high Ab titer and opsonic activity. A total of 60 antigenic proteins were identified, most of which are located or predicted to be located on the surface of the bacterium or secreted. The identification of these antigens and their reactivity with individual sera from patients and healthy individuals greatly facilitate the selection of promising vaccine candidates for further evaluation. This approach, which makes use of whole genome sequence information, has the potential to greatly accelerate and facilitate the formulation of novel vaccines and is applicable to any pathogen that induces Abs in humans and/or experimental animals.
Compounded oral ketamine. (2012)

The nonnarcotic nonaddictive neuropathic pain reliever ketamine, which was synthesized in the early 1960s by Parke-Davis, was first administered to human patients in 1965. Used by the U. S. military as a field anesthetic during the Vietnam War, it slowly became popular as both an induction and maintenance agent for the general anesthesia required during brief surgical procedures. The use of ketamine in the past has been limited primarily to intravenous administration in hospitalized patients. Very recently, several published reports have described the use of low-dose ketamine for the relief of pain, refractory depression, and anxiety in patients with or without cancer. Because chronic pain, depression, and anxiety often occur in hospice patients with or without cancer and in palliative care patients who are not eligible for hospice, the discovery of new and effective uses for an established drug to treat those conditions has excited interest in the palliative care community. We support that interest with this case report, which describes our experience in treating a 44-year-old male hospice patient with severe constant anxiety, fear, and depression in addition to multiple near-terminal comorbid physical conditions that produce chronic pain. Prior treatments prescribed to resolve this patient's pain, anxiety, and depression had proven ineffective. However, a single low-dose (0.5 mg/kg) subcutaneous test injection of ketamine provided dramatic relief from those symptoms for 80 hours, although the anesthetic effects of that drug are not of long duration. This good outcome has been sustained to date by daily treatment with a compounded flavored oral ketamine solution (40 mg/5 mL) that is not commercially available. Flavoring the solution masks the bitter taste of ketamine and renders the treatment palatable. We found ketamine to be a well-tolerated and effective treatment for the triad of severe anxiety, chronic pain, and severe depression in a hospice patient with multiple comorbid conditions. To our knowledge, this report chronicles the first use of compounded oral ketamine for home-based palliative or hospice care in Louisiana. A formulation for a flavored oral ketamine solution is provided for easy reference.
Calmodulin-Binding Function of LLP Segments from the HIV Type 1 Transmembrane Protein Is Conserved among Natural Sequence Variants (1997)

LLP1 is a peptide, derived from the cytoplasmic tail of HIV-1 TM glycoprotein, that binds and inhibits calmodulin; this region is generally conserved among isolates, but amino acid variation does exist both within clade B and among different clades, as well as SIV. In light of previous studies showing that selected single amino acid changes can have a qualitatively significant effect on the calmodulin-binding properties of this peptide, we sought to examine the properties of naturally occurring variant LLP1 sequences. Using a quantitative fluorescence-based method to measure dissociation constants of calmodulin-LLP1 complexes, a remarkable conservation of calmodulin-binding function among natural variants was revealed. In contrast, engineered nonconservative single amino acid changes altered the affinity of the peptide for calmodulin. The results show that the calmodulin-binding function is well preserved despite the sequence variation observed in nature, suggesting that this region of the TM protein is important to viral replication.
Blocks-based methods for detecting protein homology (2000)

The most highly conserved regions of proteins can be represented as blocks of aligned sequence segments, typically with multiple blocks for a given protein family. The Blocks Database World Wide Web (http://blocks.fhcrc.org) and e-mail (blocks@blocks. fhcrc.org) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments. We describe features for detection of distant relationships using blocks. Blocks+ includes protein families from the PROSITE, Prints, Pfam-A, ProDom and Domo databases. Other features include searching Blocks+ with the BLIMPS and NCBI's IMPALA programs, sequence logos, phylogenetic trees, three-dimensional display of blocks on PDB structures, and a polymerase chain reaction (PCR) primer design strategy based on blocks.
Targeted inhibition of interleukin‐6 with CNTO 328 sensitizes pre‐clinical models of multiple myeloma to dexamethasone‐mediated cell death (2009)

Interleukin (IL)-6-mediated signalling attenuates the anti-myeloma activity of glucocorticoids (GCs). We therefore sought to evaluate whether CNTO 328, an anti-IL-6 monoclonal antibody in clinical development, could enhance the apoptotic activity of dexamethasone (dex) in pre-clinical models of myeloma. CNTO 328 potently increased the cytotoxicity of dex in IL-6-dependent and -independent human myeloma cell lines (HMCLs), including a bortezomib-resistant HMCL. Isobologram analysis revealed that the CNTO 328/dex combination was highly synergistic. Addition of bortezomib to CNTO 328/dex further enhanced the cytotoxicity of the combination. Experiments with pharmacologic inhibitors revealed a role for the p44/42 mitogen-activated protein kinase pathway in IL-6-mediated GC resistance. Although CNTO 328 alone induced minimal cell death, it potentiated dex-mediated apoptosis, as evidenced by increased activation of caspases-8, -9 and -3, Annexin-V staining and DNA fragmentation. The ability of CNTO 328 to sensitize HMCLs to dex-mediated apoptosis was preserved in the presence of human bone marrow stromal cells. Importantly, the increased activity of the combination was also seen in plasma cells from patients with GC-resistant myeloma. Taken together, our data provide a strong rationale for the clinical development of the CNTO 328/dex regimen for patients with myeloma.
Well-Defined Nanoparticles Formed by Hydrophobic Assembly of a Short and Polydisperse Random Terpolymer, Amphipol A8-35 (2006)

Amphipols are short amphilic polymers designed for applications in membrane biochemistry and biophysics and used, in particular, to stabilize membrane proteins in aqueous solutions. Amphipol A8-35 was obtained by modification of a short-chain parent polymer (poly(acrylic acid); PAA) with octyl- and isopropylamine, to yield an amphiphilic product with an average molar mass of 9-10 kg x mol(-1) (sodium salt form) and a polydispersity index of 2.0 to 3.1, depending on the source of PAA. The behavior of A8-35 in aqueous buffers was studied by size exclusion chromatography, static and dynamic light scattering, equilibrium and sedimentation velocity analytical ultracentrifugation, and small angle neutron scattering. Despite the variable length of the chains and the random distribution of hydrophobic groups along them, A8-35 self-organizes into well-defined assemblies. The data are best compatible with most of the polymer forming compact assemblies (particles) with a molar mass of approximately 40 kg x mol(-1), a radius of gyration of approximately 2.4 nm, and a Stokes radius of approximately 3.15 nm. Each particle contains, on average, four A8-35 macromolecules and 75-80 octyl chains. Neutron scattering reveals a sharp interface between the particles and water. A minor (approximately 0.1%) mass fraction of the material forms much larger aggregates, whose proportion may increase under certain conditions of preparation or handling, such as low pH. They can be removed by gel filtration.
Modulation of ASIC channels in rat cerebellar purkinje neurons by ischaemia‐related signals (2002)

Acid-sensing ion channels (ASICs), activated by a decrease of extracellular pH, are found in neurons throughout the nervous system. They have an amino acid sequence similar to that of ion channels activated by membrane stretch, and have been implicated in touch sensation. Here we characterize the pH-dependent activation of ASICs in cerebellar Purkinje cells and investigate how they are modulated by factors released in ischaemia. Lowering the external pH from 7.4 activated an inward current at -66 mV, carried largely by Na+ ions, which was half-maximal for a step to pH 6.4 and was blocked by amiloride and gadolinium. The H+-gated current desensitized within a few seconds, but approximately 30 % of cells showed a sustained inward current (11 % of the peak current) in response to the maintained presence of pH 6 solution. The peak H+-evoked current was potentiated by membrane stretch (which occurs in ischaemia when [K+]o rises) and by arachidonic acid (which is released when [Ca2+]i rises in ischaemia). Arachidonic acid increased to 77 % the fraction of cells showing a sustained current evoked by acid pH. The ASIC currents were also potentiated by lactate (which is released when metabolism becomes anaerobic in ischaemia) and by FMRFamide (which may mimic the action of related mammalian RFamide transmitters). These data reinforce suggestions of a mechanosensory aspect to ASIC channel function, and show that the activation of ASICs reflects the integration of multiple signals which are present during ischaemia.
Microscopic Dynamics of Recovery in Sheared Depletion Gels (2006)

We report x-ray photon correlation spectroscopy and diffusing wave spectroscopy studies of depletion gels formed from nanoscale silica colloids in solutions of nonabsorbing polymer following the cessation of shear. The two techniques provide a quantitatively coherent picture of the dynamics as ballistic or convective motion of colloidal clusters whose internal motion is arrested. While the dynamics possesses features characteristic of nonergodic soft solids, including a relaxation time that grows linearly with the time since shear, comparison with behavior of quenched supercooled liquids indicates that this evolution is not directly related to traditional aging phenomena in glasses.
Prolactin and interleukin-2 receptors in T lymphocytes signal through a MGF-STAT5-like transcription factor. (1995)

The cell surface receptors for PRL and interleukin-2 (IL-2) are structurally distinct, but share regulatory tasks in T lymphocytes. They can stimulate proliferation and activate transcription of over-lapping sets of genes of T cells. PRL and IL-2 receptor activation are both linked to the Jak/Stat (signal transducer and activator of transcription) pathway. We investigated the ability of PRL and IL-2 to activate Stat proteins in different T cell lines. The DNA binding specificities, the reactivities toward Stat-specific antisera, and the mol wt of IL-2- and PRL-induced DNA-binding proteins in Nb2 and C196 T cell lines were investigated. A comparison with the Stat proteins induced by interferon-gamma, PRL, and IL-6 in T47D mammary tumor cells was made. We found that these parameters were indistinguishable for one of the PRL- and IL-2-induced factors. A transcription factor closely related to mammary gland factor-Stat5 is rapidly activated upon interaction of IL-2 and PRL with their respective receptors. Activation of a second protein related to Stat1 was also observed. Our results emphasize the role of PRL as a regulator of the immune response and indicate that the Stat factors mammary gland factor-Stat5 and Stat1 play a role in the regulation of gene expression during T cell development.
C4 Cycles: Past, Present, and Future Research on C4 Photosynthesis (2011)

In the late 1960s, a vibrant new research field was ignited by the discovery that instead of fixing CO(2) into a C(3) compound, some plants initially fix CO(2) into a four-carbon (C(4)) compound. The term C(4) photosynthesis was born. In the 20 years that followed, physiologists, biochemists, and molecular and developmental biologists grappled to understand how the C(4) photosynthetic pathway was partitioned between two morphologically distinct cell types in the leaf. By the early 1990s, much was known about C(4) biochemistry, the types of leaf anatomy that facilitated the pathway, and the patterns of gene expression that underpinned the biochemistry. However, virtually nothing was known about how the pathway was regulated. It should have been an exciting time, but many of the original researchers were approaching retirement, C(4) plants were proving recalcitrant to genetic manipulation, and whole-genome sequences were not even a dream. In combination, these factors led to reduced funding and the failure to attract young people into the field; the endgame seemed to be underway. But over the last 5 years, there has been a resurgence of interest and funding, not least because of ambitious multinational projects that aim to increase crop yields by introducing C(4) traits into C(3) plants. Combined with new technologies, this renewed interest has resulted in the development of more sophisticated approaches toward understanding how the C(4) pathway evolved, how it is regulated, and how it might be manipulated. The extent of this resurgence is manifest by the publication in 2011 of more than 650 pages of reviews on different aspects of C(4). Here, I provide an overview of our current understanding, the questions that are being addressed, and the issues that lie ahead.
New DNA-analysis techniques (minireview). (1991)

The increasing knowledge about specific human genes and their alterations causing genetic diseases, requires new strategies and methods for mutation-detection. However, the large molecular heterogeneity of such mutations in each gene sets serious limitations to this approach. The polymerase chain reaction has become the basis of several new developments aiming to overcome this problem. Recently developed methods to search for unknown mutations are the denaturing gradient electrophoresis, chemical mismatch cleavage, single stranded conformation polymorphisms and direct genomic sequencing. Known mutations in a particular gene can be detected by the allele specific hybridization, the amplification refractory mutation system, the competitive oligonucleotide priming reaction or the oligonucleotide ligation assay. As spin-off of the human genome sequencing projects, automated DNA-sequencing may in the future become the easiest, fastest, most reliable and most informative technique and a powerful day-to-day method in every genetics and clinical chemistry laboratory.
Heterogeneity of Breast Cancer Metastases: Comparison of Therapeutic Target Expression and Promoter Methylation Between Primary Tumors and Their Multifocal Metastases (2008)

Therapeutic targets identified in the PBC or even some MBC may not reflect targets present in all metastatic sites.
Use of HSV vectors to modify the nervous system. (2002)

Herpes simplex virus (HSV) is a natural human pathogen that efficiently infects sensory neurons to establish a life-long latent state. Recombinant replication-defective vectors, created by disruption of critical viral gene functions, nonetheless target neurons and can be used to express transgenes to alter the structure and/or function of the nervous system. Specific applications of these vectors to models of neurodegeneration (Parkinson's disease), trauma (spinal root avulsion), peripheral neuropathy and neuronal function (pain) have been published within the last year. With these applications and the clinical experience in human tumor trials with HSV vectors, the stage is set for the use of HSV-based vectors to treat neurologic disease in humans in the near future.
Effect on cortical blood flow of electrical stimulation of trigeminal cerebrovascular nerve fibres in the rat (1990)

It has recently been demonstrated in the rat that the majority of cerebrovascular pain fibres containing immunoreactive substance P and calcitonin gene-related peptide reach the vessels via the nasociliary nerve, a branch of the ophthalmic trigeminal division. In order to elucidate the effect of these nerves on blood flow in vivo, the relative changes in cortical microvascular flow were continuously monitored by a laser-Doppler flowmeter system during electrical nerve stimulation, with the central nerve connection cut and after removal of neighbouring dilatory parasympathetic nerves. The nasociliary nerve on one side was stimulated proximal to the ethmoidal foramen by a bipolar platinum electrode. Activation at different frequencies, continuously or as bursts with a constant voltage, impulse duration and total stimulus length, revealed that a maximum increase in blood flow amounting to 16.7% after 36 s was obtained with continuous stimulation at 10 Hz. Flow markedly declined during the following 1-min stimulation period. No changes in contralateral cortical blood flow, mean arterial blood pressure or blood gases were observed during or after stimulation. The present study demonstrates for the first time that direct and selective electrical activation of trigeminal cerebrovascular nerves induces an increase, albeit small and transient, in blood flow within the brain.
Metabolite Cross-Feeding Enhances Virulence in a Model Polymicrobial Infection (2011)

Microbes within polymicrobial infections often display synergistic interactions resulting in enhanced pathogenesis; however, the molecular mechanisms governing these interactions are not well understood. Development of model systems that allow detailed mechanistic studies of polymicrobial synergy is a critical step towards a comprehensive understanding of these infections in vivo. In this study, we used a model polymicrobial infection including the opportunistic pathogen Aggregatibacter actinomycetemcomitans and the commensal Streptococcus gordonii to examine the importance of metabolite cross-feeding for establishing co-culture infections. Our results reveal that co-culture with S. gordonii enhances the pathogenesis of A. actinomycetemcomitans in a murine abscess model of infection. Interestingly, the ability of A. actinomycetemcomitans to utilize L-lactate as an energy source is essential for these co-culture benefits. Surprisingly, inactivation of L-lactate catabolism had no impact on mono-culture growth in vitro and in vivo suggesting that A. actinomycetemcomitans L-lactate catabolism is only critical for establishing co-culture infections. These results demonstrate that metabolite cross-feeding is critical for A. actinomycetemcomitans to persist in a polymicrobial infection with S. gordonii supporting the idea that the metabolic properties of commensal bacteria alter the course of pathogenesis in polymicrobial communities.
De novo assembly of highly diverse viral populations (2012)

We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.
Fem Simulations To Study The Effects Of Laser Power And Scan Speed On Molten Pool Size In Additive Manufacturing (2017)

Additive manufacturing (AM) is increasingly crucial in biomedical and aerospace industries. As a recently developed AM technique, selective laser melting (SLM) has become a commercial method for various manufacturing processes. However, the molten pool configuration during SLM of metal powders is a decisive issue for the product quality. It is very important to investigate the heat transfer characteristics during the laser heating process. In this work, the finite element method (FEM) software ANSYS<sup>®</sup> (work bench module 16.0) was used to predict the unsteady temperature distribution for resolving molten pool dimensions with consideration of temperature-dependent thermal physical properties of TiAl6V4 at different laser powers and scanning speeds. The simulated results of the temperature distributions illustrated that the ratio of laser power to scanning speed can greatly influence the size of molten pool of titanium alloy powder for SLM development.
Tumor location impacts immune response in mouse models of colon cancer (2017)

Existing preclinical models of human colorectal cancer (CRC) that rely on syngeneic subcutaneous grafts are problematic, because of increasing evidence that the immune microenvironment in subcutaneous tissue is significantly different from the gastrointestinal tract. Similarly, existing orthotopic models that use a laparotomy for establishing grafts are also problematic, because the surgical procedure results in extensive inflammation, thereby creating a nonphysiologic tumor microenvironment. To facilitate the bench-to-bedside translation of CRC immunotherapy strategies, we developed a novel orthotopic model in mice that uses endoscopy-guided microinjection of syngeneic cancer cells. When we compared immune system infiltration, we found that tumors in the subcutaneous model had fewer T cells, B cells, and natural killer (NK) cells, but more immunosuppressive myeloid cells; in contrast, tumors in our orthotopic model had a higher number of tumor-infiltrating T cells, B cells, and NK cells, with fewer immunosuppressive myeloid cells. The number of immune-stimulating cytokines, such as interleukin (IL)-2, IL-6, interferon (IFN)-gamma, and granzyme B, was also higher in tumors in our model, as compared with the subcutaneous model. Those differences resulted in heightened sensitivity to immune checkpoint blockade therapy in our endoscopy-guided orthotopic CRC model. Our study indicates that tumor location affects immune response in CRC mouse models; choosing the appropriate preclinical model is important when testing immunotherapy in CRC.
Mitochondrial DNA mutations are established in human colonic stem cells, and mutated clones expand by crypt fission (2006)

The understanding of the fixation of mutations within human tissues and their subsequent clonal expansion is a considerable problem, of which little is known. We have previously shown that nononcogenic mutations in the mitochondrial genome occur in one of a number of morphologically normal colonic crypt stem cells, the progeny of which later occupy the whole crypt. We propose that these wholly mutated crypts then clonally expand by crypt fission, where each crypt divides into two mutated daughter crypts. Here we show that (i) mutated crypts in the process of fission share the same mutated mitochondrial genotype not present in neighboring cytochrome c oxidase-positive crypts (the odds of this being a random event are >or=2.48 x 10(9):1); (ii) neighboring mutated crypts have the same genotype, which is different from adjacent cytochrome c oxidase-positive crypts; (iii) mutated crypts are clustered together throughout the colon; and (iv) patches of cytochrome c oxidase-deficient crypts increase in size with age. We thus demonstrate definitively that crypt fission is the mechanism by which mutations spread in the normal human colon. This has important implications for the biology of the normal adult human colon and possibly for the growth and spread of colorectal neoplasms.