gebhart/patrepeval huggingface dataset:
CD4+T Cell Responses in HIV‐Exposed Seronegative Women Are Qualitatively Distinct from Those in HIV‐Infected Women (2004)

The immune response of human immunodeficiency virus (HIV)-exposed seronegative (ESN) women may be qualitatively different from that in those infected with HIV (HIV(+)). In a cohort of female commercial sex workers in Nairobi, Kenya, we found significantly lower (P< or =.01) levels of CD4(+)-specific immune activation and apoptosis in the ESN women compared with those in the HIV(+) women. Compared with the HIV(+) women, a lower proportion of the ESN women showed p24 peptide pool responses by the short-term, CD4(+)-specific, interferon (IFN)- gamma intracellular cytokine staining assay, whereas the proportion showing responses by the long-term, CD8(+)-depleted T cell proliferation assay was similar. Interestingly, the ESN responders had a 4.5-fold stronger proliferation response (P=.002) than the HIV(+) group. These data suggest that, compared with those in HIV(+) women, CD4(+) T cells in ESN women have a much greater ability to proliferate in response to p24 peptides.
The Effect of Interferon‐γ Intramammary Administration on Mammary Phagocyte Function (1990)

The effect of recombinant bovine interferon-gamma on intramammary phagocyte function of mammary gland was studied in 4 Holstein cows (Study 1) and 7 Holstein cows (Study 2). Recombinant bovine interferon-gamma was intramammarily infused on day 6 of the dry period and phagocytes were collected from lacteal secretions and tested in vitro 24 hours later. Results from Study 1 indicate that phagocytosis of Escherichia coli and Staphylococcus aureus was significantly increased after than before interferon treatment. Similarly, the number of bacteria killed/active phagocyte was enhanced by treatment. Results from Study 2 suggested a trend towards increased production of oxygen dependent bactericidal components and increased killing ability by phagocytes exposed to interferon as compared to control phagocytes. These results from both studies suggest that intramammary infusions of bovine interferon-gamma can stimulate phagocyte function during the early phase of the dry period.
Multiple joined genes prevent product degradation in Escherichia coli. (1984)

A method is described that allows the expression of a stable human proinsulin product in Escherichia coli as encoded by either a fused or an unfused gene construction. In the fused system, the human proinsulin coding sequence is joined to the 3' side of a fragment containing the lac promoter and the coding sequence for a small part of the NH2 terminus of beta-galactosidase. In the unfused system, the proinsulin coding sequence is linked directly to a fragment containing the Tac promoter followed by a bacterial Shine-Dalgarno sequence. In both systems, the human proinsulin product is too unstable to be detected by NaDodSO4/polyacrylamide gel electrophoresis or even pulse-chase analysis. However, when multiple copies of the proinsulin coding sequence are tandemly linked such that the resultant protein product contains multiple copies of the proinsulin domain, the stability of the product is markedly increased in both the fused and the unfused expression systems. In the unfused system, three tandemly linked proinsulin polypeptide domains are required for stabilization, whereas two proinsulin domains plus the bacterial leader protein enhance stability in the fused system. The polypeptide product of a multiple copy proinsulin gene can be cleaved into single proinsulin units by cyanogen bromide treatment.
Progress in assessing the role of serotonin in the control of food intake. (1988)

There is evidence that serotonin inhibits food intake, particularly intake of carbohydrate and that induced by activation of catecholamine-containing neurons in different brain circuits. An agent that has contributed considerably to the hypothesis of a role of serotonin in feeding is fenfluramine, used as an anorexigenic drug in obese people. Experiments using synaptosomal preparations for studying monoamine uptake and release have shown that d-norfenfluramine preferentially releases serotonin from a reserpine-insensitive compartment. Studies on brain monoamine release and metabolism in intact animals have shown that d and l isomers of fenfluramine at relatively low doses have a specific action on brain serotonin and catecholamines, respectively. Several findings suggest that d-fenfluramine and d-norfenfluramine cause anorexia by increasing the availability of serotonin at postsynaptic receptors. Evidence has recently been provided that d-fenfluramine uses preferentially serotonin1 sites, particularly of the serotonin1B type, in the rat brain to cause anorexia in this animal species. Activation of serotonin1A sites by agents such as 8-OH-DPAT and buspirone instead has been shown to cause overeating. It is suggested that serotonin1B sites in the hypothalamus and serotonin1A sites in the serotonin neurons of the midbrain raphe nuclei mediate these effects. Evidence is provided that [3H]d-fenfluramine binding to rat brain membranes is different from serotonin uptake sites ([3H]imipramine binding) and serotonin receptors. It is, however, displaced by some drugs using serotonin to cause anorexia, raising the possibility that it is somewhat related to serotonin mechanisms involved in feeding control. These studies provide evidence that the serotoninergic system in the brain is a likely target for drugs affecting food intake and suggest new ways to develop novel and potent strategies for the treatment of clinical hyperphagia and anorexia.
In vivo High Angular Resolution Diffusion-Weighted Imaging of Mouse Brain at 16.4 Tesla (2015)

Magnetic Resonance Imaging (MRI) of the rodent brain at ultra-high magnetic fields (> 9.4 Tesla) offers a higher signal-to-noise ratio that can be exploited to reduce image acquisition time or provide higher spatial resolution. However, significant challenges are presented due to a combination of longer T1 and shorter T2/T2* relaxation times and increased sensitivity to magnetic susceptibility resulting in severe local-field inhomogeneity artefacts from air pockets and bone/brain interfaces. The Stejskal-Tanner spin echo diffusion-weighted imaging (DWI) sequence is often used in high-field rodent brain MRI due to its immunity to these artefacts. To accurately determine diffusion-tensor or fibre-orientation distribution, high angular resolution diffusion imaging (HARDI) with strong diffusion weighting (b >3000 s/mm2) and at least 30 diffusion-encoding directions are required. However, this results in long image acquisition times unsuitable for live animal imaging. In this study, we describe the optimization of HARDI acquisition parameters at 16.4T using a Stejskal-Tanner sequence with echo-planar imaging (EPI) readout. EPI segmentation and partial Fourier encoding acceleration were applied to reduce the echo time (TE), thereby minimizing signal decay and distortion artefacts while maintaining a reasonably short acquisition time. The final HARDI acquisition protocol was achieved with the following parameters: 4 shot EPI, b = 3000 s/mm2, 64 diffusion-encoding directions, 125×150 μm2 in-plane resolution, 0.6 mm slice thickness, and 2h acquisition time. This protocol was used to image a cohort of adult C57BL/6 male mice, whereby the quality of the acquired data was assessed and diffusion tensor imaging (DTI) derived parameters were measured. High-quality images with high spatial and angular resolution, low distortion and low variability in DTI-derived parameters were obtained, indicating that EPI-DWI is feasible at 16.4T to study animal models of white matter (WM) diseases.
A high proportion of T lymphocytes that infiltrate H-2-incompatible heart allografts in vivo express genes encoding cytotoxic cell-specific serine proteases, but do not express the MEL-14-defined lymph node homing receptor. (1988)

The role of cytotoxic cells in in vivo immune functions such as allograft rejection is unknown. To begin to assess the function of cytolytic cells in vivo we have begun with cytolytic cell-specific functional molecules: we have isolated and characterized cytolytic cell-specific cDNA clones from cytolytic T cell clones, both encoding distinct serine esterases. The HF gene encodes a trypsin-like enzyme while the C11 gene encodes an enzyme with likely specificity for acidic residues. Here we demonstrate, using in situ hybridization with RNA probe, that both genes are expressed selectively in a subset of T lymphocytes that have infiltrated cardiac allografts. The phenotype of these cells is consistent with the most frequent phenotype of active CTL raised in vitro: they are predominantly CD4-, CD8+, MEL-14- T cell blasts. Thus the expression of these genes, each of which encodes serine esterase found in killer cell granules in vitro, is a valid marker for these cells in vivo as well. The kinetics of their accumulation is consistent with, but not proof of, a putative role in allograft rejection. It is likely that HF and C11 gene expression will be of diagnostic value.
Design and Construction of Synthetic Phage-Displayed Fab Libraries (2009)

Diversity-the variability carried by the amino acid sequences of a synthetic antibody library-can be generated by synthetic degenerate oligonucleotides. One can experiment with different diversity designs in the variable domains of light and heavy chains (V(H) and V(L)) to generate antibody libraries with different properties. The ability to precisely define the final diversity of a library facilitates the process of isolating, characterizing, and optimizing an antibody lead. Here we describe detailed protocols for the design and construction of phage-displayed synthetic antibody libraries in which diversity is generated in the complementarity determining regions (CDRs) of the V(H) of a single humanized bivalent Fab scaffold. The example used in the protocol provides a general methodology for generation of libraries with engineered CDR diversity that can be applied to a template antibody sequence of choice.
Phosphoinositol phosphatase SHIP2 promotes cancer development and metastasis coupled with alterations in EGF receptor turnover (2007)

Phosphoinositol phosphatases are important regulators of signaling pathways relevant to both diabetes and cancer. A 3'-phosphoinositol phosphatase, phosphatase homologous to tensin (PTEN), is both a tumor suppressor and a negative regulator of insulin action. A 5'-phosphoinositol phosphatase, SH2-containing 5'-inositol phosphatase (SHIP2), regulates insulin signaling and its genetic knockout prevents high-fat diet-induced obesity in mice. SHIP2 also regulates cytoskeleton remodeling and receptor endocytosis. This and the fact that both PTEN and SHIP2 act on the same substrate suggest a potential role for SHIP2 in cancer. Here we report that, in direct contrast to PTEN, SHIP2 protein expression is elevated in a number of breast cancer cell lines. RNA interference-mediated silencing of SHIP2 in MDA-231 cells suppresses epidermal growth factor receptor (EGFR) levels by means of enhanced receptor degradation. Furthermore, endogenous SHIP2 in MDA-231 breast cancer cells supports in vitro cell proliferation, increases cellular sensitivity to drugs targeting the EGFR and supports cancer development and metastasis in nude mice. In addition, significantly high proportions (44%; P = 0.0001) of clinical specimens of breast cancer tissues in comparison with non-cancerous breast tissues contain elevated expression of SHIP2 protein. Taken together, our results demonstrate that SHIP2 is a clinically relevant novel anticancer target that links perturbed metabolism to cancer development.
Progression model for pancreatic cancer. (2000)

It has been >10 years since Vogelstein and colleagues [(1][1] [, 2)][2] proposed a progression model for colorectal neoplasia in which they hypothesized that the progression from normal colonic epithelium, to small adenomatous polyps, to infiltrating adenocarcinoma is associated with the activation
Neutralization Profiles of Primary Human Immunodeficiency Virus Type 1 Isolates in the Context of Coreceptor Usage (1998)

Most strains of human immunodeficiency virus type 1 (HIV-1) which have only been carried in vitro in peripheral blood mononuclear cells (primary isolates) can be neutralized by antibodies, but their sensitivity to neutralization varies considerably. To study the parameters that contribute to the differential neutralization sensitivity of primary HIV-1 isolates, we developed a neutralization assay with a panel of genetically engineered cell lines (GHOST cells) that express CD4, one of eight chemokine receptors which function as HIV-1 coreceptors, and a Tat-dependent green fluorescent protein reporter cassette which permits the evaluation and quantitation of HIV-1 infection by flow cytometry. All 21 primary isolates from several clades could grow in the various GHOST cell lines, and their use of one or more coreceptors could easily be defined by flow cytometric analysis. Ten of these primary isolates, three that were CXCR4 (X4)-tropic, three that were CCR5 (R5)-tropic, and four that were dual- or polytropic were chosen for study of their sensitivity to neutralization by human monoclonal and polyclonal antibodies. Viruses from the X4-tropic category of viruses were first tested since they have generally been considered to be particularly neutralization sensitive. It was found that the X4-tropic virus group contained both neutralization-sensitive and neutralization-resistant viruses. Similar results were obtained with R5-tropic viruses and with dual- or polytropic viruses. Within each category of viruses, neutralization sensitivity and resistance could be observed. Therefore, sensitivity to neutralization appears to be the consequence of factors that influence the antibody-virus interaction and its sequelae rather than coreceptor usage. Neutralization of various viruses by the V3-specific monoclonal antibody, 447-52D, was shown to be dependent not only on the presence of the relevant epitope but also on its presentation. An epitope within the envelope of a particular virus is not sufficient to render a virus sensitive to neutralization by an antibody that recognizes that epitope. Moreover, conformation-dependent factors may overcome the need for absolute fidelity in the match between an antibody and its core epitope, permitting sufficient affinity between the viral envelope protein and the antibody to neutralize the virus. The studies indicate that the neutralization sensitivity of HIV-1 primary isolates is a consequence of the complex interaction between virus, antibody, and target cell.
Child maltreatment moderates the association of MAOA with symptoms of depression and antisocial personality disorder. (2010)

There is a growing body of data indicating that Gene x Child Maltreatment interactions at monoamine oxidase A (MAOA) play a role in vulnerability to symptoms of antisocial personality disorder (ASPD) but not major depression (MD). Using a sample of 538 participants from the Iowa Adoption Studies, we introduce a conceptual model that highlights two distinct pathways from child maltreatment to symptoms of MD, suggesting that maltreatment has different effects depending on genotype and highlighting the importance of including the indirect pathway through ASPD. As predicted by the model, high activity alleles predispose to symptoms of MD in the context of child maltreatment whereas low activity alleles predispose to symptoms of ASPD. We conclude that the Gene x Environment interplay at this locus (MAOA) contributes to both symptoms of ASPD and MD and that careful specification of child maltreatment may be essential if genetic association research is to produce replicable results.
Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer (2013)

Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P < 5 × 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P < 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P < 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 × 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 × 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 × 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.
Iron isomaltoside 1000: a new high dose option for parenteral iron therapy (2012)

Iron isomaltoside 1000 (Monofer®) is a new dextran-free parenteral iron product, currently approved in 22 EU countries. Iron isomaltoside 1000 consists of iron and a carbohydrate moiety where the iron is tightly bound in a matrix structure, which enables a controlled and slow release of iron to iron-binding proteins, avoiding toxicity. The carbohydrate,isomaltoside 1000, is a purely linear chemical structure with low immunological activity. Due to the structure of iron isomaltoside 1000 and the low anaphylactic potential, there is no requirement for a test dose, and it can be administered in high doses with a maximum dosage of 20 mg/kg within 30-60 minutes in one visit. Thus, iron isomaltoside 1000 offers the broadest dosage range compared to other parenteral iron products on the market. Due to the dose flexibility, the possibility of providing full iron correction in one single visit makes iron isomaltoside 1000 highly convenient for both the health care professional and the patient. Clinical studies of iron isomaltoside 1000 show that it is an effective and well-tolerated treatment of iron deficiency anaemia with a favourable safety profile. Furthermore, iron isomaltoside 1000 does not seem to induce hypophosphataemia.
Etude de la Réaction d'Hydrolyse de l'Anion PO3F2− en Solution Aqueuse (1990)

Abstract L'hydrolyse de solutions de monofluorophosphates a été étudiée par chromatographie ionique. Nous avons montré que le facteur prédominant est le pH. En effet la constante de vitesse est quarante fois plus élevée à pH = 2 qu'à pH = 4, quelle que soit la température. L'hydrolyse est peu sensible à la nature du cation présent dans la solution et à celle de l'acide rajouté pour obtenir le pH désiré. Cette réaction d'hydrolyse du premier ordre s'effectue avec une énergie d'activation de 24 kcal/mole.
Synthesis of 2-Fluoro-11-hydroxy-N-propylnoraporphine:  A Potential Dopamine D2 Agonist (2005)

2-Fluoro-11-hydroxy-N-propylnoraporphine 4 (2-F-11-OH-NPa) was synthesized from thebaine in 13 steps with an overall yield of 1.35%. The key steps included the Pd-catalyzed 3-dehydroxylation of 14-hydroxymorphine, SN2 substitution of Ts- by F-, and CH3SO2OH-promoted rearrangement of the substituted morphinandiene. The dopamine binding affinity of this compound was also investigated on rat brain membranes, and as expected, this compound displayed high affinity and selectivity at the D2 receptor.
Site Specific 1:1 Opioid:Albumin Conjugate with in Vitro Activity and Long in Vivo Duration (2000)

A site-specific 1:1 dynorphin A-(1-13)-NH(2) derivative conjugated specifically to Cys 34 on human serum albumin (CCI-1035) was shown to be an opioid receptor agonist in vitro and to be a long lasting antinociceptive agent when administered intravenously to mice as assessed by an acetic acid writhing assay. When 10 micromol/kg of CCI-1035 was administered to mice, rapid antinociception was observed within 5 min following intravenous bolus injection and was sustained beyond 8 h. Antinociceptive activity was absent in a heat induced pain model using a mouse tail-flick assay. This finding represents the first report of a 1:1 albumin opioid conjugate retaining potent in vivo activity equal to or greater than dynorphin A, accompanied by a dramatic extension in duration of action. This novel site-specific bioconjugation technology produces an agent that may be useful for peripheral pain therapy.
Cytoarchitecture of the human cerebral cortex: MR microscopy of excised specimens at 9.4 Tesla. (2002)

MRM at 9.4 T depicts important aspects of the cytoarchitecture of normal formalin-fixed human cortex.
Self-Supervised Deep Reinforcement Learning with Generalized Computation Graphs for Robot Navigation (2018)

Enabling robots to autonomously navigate complex environments is essential for real-world deployment. Prior methods approach this problem by having the robot maintain an internal map of the world, and then use a localization and planning method to navigate through the internal map. However, these approaches often include a variety of assumptions, are computationally intensive, and do not learn from failures. In contrast, learning-based methods improve as the robot acts in the environment, but are difficult to deploy in the real-world due to their high sample complexity. To address the need to learn complex policies with few samples, we propose a generalized computation graph that subsumes value-based model-free methods and model-based methods, with specific instantiations interpolating between model-free and model-based. We then instantiate this graph to form a navigation model that learns from raw images and is sample efficient. Our simulated car experiments explore the design decisions of our navigation model, and show our approach outperforms single-step and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> -step double Q-learning. We also evaluate our approach on a real-world RC car and show it can learn to navigate through a complex indoor environment with a few hours of fully autonomous, self-supervised training. Videos of the experiments and code can be found at github.com/gkahn13/gcg.