gebhart/patrepeval huggingface dataset:
Differential gene expression in mononuclear phagocytes infected with pathogenic and non-pathogenic mycobacteria (2004)

The pathogenic mycobacteria are an insidious group of bacterial pathogens that cause the deaths of millions of people every year. One of the reasons these pathogens are so successful is that they are able to invade and replicate within host macrophages, one of the first lines of defence against intruding pathogens. In contrast, non-pathogenic mycobacteria, such as Mycobacterium smegmatis are killed rapidly by macrophages. In order to understand better the series of events that allow pathogenic mycobacteria to survive and replicate within macrophages, while the non-pathogenic mycobacteria are killed rapidly, we inoculated the human monocytic cell line U937 with pathogenic (M. tuberculosis and M. avium) and non-pathogenic (M. smegmatis) mycobacteria and monitored the expression of over 3500 genes at 4, 12 and 24 h post-inoculation using a commercially available gene array system. We observed multiple differences in the gene expression patterns of monocytes infected with pathogenic and non-pathogenic mycobacteria including genes involved in cytokine, lymphokine and chemokine production, adhesion, apoptosis, signal transduction, transcription, protein cleavage, actin polymerization and growth. We also observed differences in gene expression profiles in monocytes infected with M. tuberculosis or M. avium, indicating that there are differences in the host pathogen interactions of mononuclear phagocytes infected with different pathogenic mycobacterial species. These results increase the understanding of the mechanisms used by pathogenic mycobacteria to cause disease, the host response to these organisms, and provide new insights for antimycobacterial intervention strategies.
Crystal Orientation Fluctuation of Epitaxial-Lateral-Overgrown GaN with W Mask and SiO<sub>2</sub> Mask Observed by Transmission Electron Diffraction and X-Ray Rocking Curves (1999)

Fluctuation of the crystal orientation of epitaxial-lateral-overgrown (ELO) GaN with a tungsten (W) mask is compared to that with a SiO 2 mask by means of selected-area transmission electron diffraction (TED) and X-ray rocking curves (XRCs). XRCs of (0004) reflection exhibited three peaks for ELO-GaN on a SiO 2 mask, and were confirmed to originate from domains of different c -axis orientation by TED. On the other hand, fluctuation of the c -axis was not observed for ELO-GaN with a W mask. These results indicate that the crystalline quality of ELO-GaN with a W mask is better than that with a SiO 2 mask.
Systemic Carnitine Deficiency Presenting as Familial Endocardial Fibroelastosis (1981)

ENDOCARDIAL fibroelastosis is a cardiomyopathy of unknown origin that affects infants and young children. It is characterized by poor myocardial contractility with hypertrophy and dilatation of the heart, especially of the left ventricle. At autopsy, a milky-white thickening of the endocardium is found.1 Because similar endocardial thickening is seen in congenital cardiac anomalies complicated by subendocardial ischemia (e.g., aortic atresia), it has been suggested that endocardial fibroelastosis may be related to myocardial hypoxia.2 Familial cases suggest that the disease may result from a genetically transmitted abnormality affecting cardiac metabolism.3 The cardiac tissue in congestive cardiomyopathy contains increased numbers of mitochondria, . . .
EFFECT OF DYDROGESTERONE ON HUMAN ENDOMETRIUM AND OVARIAN ACTIVITY (1962)

ABSTRACT Some of the pharmacological properties of dydrogesterone (9β,10α-pregna-4,6-diene-3,20-dione) were studied in the human female. When dydrogesterone was administered by mouth in daily doses of 10 mg for 10 to 14 days to amenorrhoeic women primed with ethinyloestradiol progestational transformation of the endometrium was found in 30 out of 32 artificial cycles. When administration of ethinyloestradiol was not continued until the end of the artificial cycle, break-through bleeding occurred in 30 out of 35 occasions, whereas it took place in only 9 out of 30 cycles, when ethinyloestradiol was given throughout the cycle. Dydrogesterone was administered in 77 cycles to women with incapacitating dysmenorrhoea from the 5th to the 25th day. When the daily dose was 10 mg, the subsequent period was not incapacitating on 20 out of 31 occasions whereas with daily doses of 15 or 20 mg the corresponding results were 40 out of 46. Forty-eight out of 60 cycles labelled »not incapacitating« were completely painless. No side-effects whatsover were observed. Studies of basal temperature records in amenorrhoeic and dysmenorrhoeic women indicate that dydrogesterone has no thermogenic activity. When the compound was given to normally menstruating women in daily doses of 10 to 40 mg from the beginning of the cycle, it did not interfere with the characteristic biphasic temperature pattern, with the urinary excretion of oestrogen and pregnanediol or with the formation of a corpus luteum as proved at laparotomy. Even following the administration of as much as 400 mg per day a corpus luteum was found. It is concluded therefore, that dydrogesterone does not inhibit ovulation. In a previous paper the effect of alterations in the stereochemical configuration of steroid hormones at C-9 and C-10 on their pharmacological properties was reported ( Reerink et al. 1960). Among various derivatives of 9β,10α-progesterone ( retro -progesterone) tested, one, 9β,10α-pregna-4,6-diene-3,20-dione (hereafter referred to as »dydrogesterone«), see Fig. 1, was found to be a potent progestational agent when administered orally to rabbits ( Schöler 1960) and to amenorrhoeic women ( Tillinger & Diczfalusy 1960). The purpose of the present communication is to report on some of the pharmacological properties of this compound in the human female.
Assessing Response to Treatment and Recognizing Residual Depressive Symptoms (2014)

Effective assessment of antidepressant response is necessary in order to detect and resolve residual symptoms. Most patients will experience residual symptoms, but no single rating scale or assessment method is able to effectively detect all of the symptoms that patients may experience. Residual symptoms comprise symptoms as described in the Diagnostic and Statistical Manual of Mental Disorders (DSM) as well as non-DSM symptoms. Therefore, clinicians need to use a variety of assessment methods and consider several factors that may be contributing to residual symptoms. When residual symptoms are detected, clinicians must decide on the next-step treatment strategy, which can include continuing the current treatment, switching to within-class agents, switching to agents with a different mechanism of action, or augmenting medications.
Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking (2015)

Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.
ChemInform Abstract: A Catalytic Reactor for the Organocatalyzed Enantioselective Continuous Flow Alkylation of Aldehydes. (2015)

Abstract A series of chiral alcohols (III), (V), and (VII) is prepared by a reaction of cationic electrophiles with aldehydes in a packed‐bed reactor filled with a polymer‐supported enantiopure imidazolidinone catalyst.
Transmural Mapping of Myocardial Refractoriness and Endocardial Dispersion of Repolarization in an Ovine Model of Chronic Myocardial Infarction (2009)

We confirmed histologically that scarring contributes to prolongation of repolarization, increased refractoriness, and reductions in conduction and voltage post-MI. Prolongation of repolarization may be further augmented when local activation is earliest or electrogram voltage is decreased within scar.
Natural Convection for Air and Molten Gallium in Square- and Elbow-Shaped Enclosures (2015)

Natural convection flow of air and molten gallium in square and elbow-shaped enclosures is studied by a two-dimensional numerical scheme developed by the lead author. The dependence of the flow field and Nusselt number (Nu) on the Rayleigh (Ra) and Prandtl (Pr) numbers is examined in both enclosures. Results are obtained with sufficiently large Rayleigh numbers to observe transition from steady to damped or undamped oscillatory, and chaotic flow. Constant and oscillatory heat transfer rates are compared in both enclosures for air (Pr=0.71) and molten gallium (Pr=0.024).
Experimental production of hypomagnesaemia in ewes and its control by small magnesium supplements (1962)

1. A low magnesium diet is described, consisting of barley straw, sucrose and casein, which induced hypomagnesaemia and one case of clinical tetany in non-pregnant, non-lactating ewes. 2. On the above diet a daily drench of 0·25 g. MgO maintained plasma magnesium levels at 1·60–1·80 mg./100 ml. which was significantly higher than the plasma magnesium level of 1·09–1·20 mg./100 ml. for the unsupplemented group. 3. An experimental formulation of a magnesium heavy pellet is described and its use as a method of supplementation was investigated. On the above diet it was found that two or four heavy pellets also maintained plasma magnesium values at 1·601–80 mg./100 ml. which was significantly higher ( P = 0·01) than the level of the unsupplemented group. 4. Five sheep out of the forty ewes used in this experiment were found to have consistently lower plasma magnesium values than the remaining thirty-five. 5. A preliminary trial of the use of heavy pellets as a magnesium supplement in non-pregnant, non-lactating ewes on winter grazing is described. The results of the trial under these conditions were encouraging.
The density matrix formalism of nuclear relaxation: A review (1988)

This is a review of the density matrix formalism of quantum statistical mechanics as it relates to nuclear relaxation. The single spin and coupled exchanging two spin systems are treated explicitly. We show the circumstances under which these models reduce to the more familiar expressions used to describe proton relaxation in tissue. The effect of radiofrequency (rf) pulses on the density matrix is presented as well as the density matrix description of the Carr-Purcell pulse technique and conditions under which even and odd echo trains will superpose or are independent of rf pulse rate.
Strengthening of enterococcal biofilms by Esp (2022)

Abstract Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.
Analysis of the ability of recombinant yeast (Saccharomyces cerevisiae)vector encoding carcinoembrionic antigen (CEA) to infect dendritic cells and activate antigen-specific T-cell responses (2007)

A103 Tumor-associated antigens are poorly immunogenic in the host. Dendritic cells (DCs) are the most potent antigen presenting cells (APCs). Various strategies have been used to enhance the ability of DCs to activate T-cell responses to multiple antigens. We report here the analysis of the ability of a Saccharomyces cerevisiae vector containing a transgene encoding CEA (Yeast-CEA) to activate human DC and to stimulate specific T-cell immune responses. Activation of DCs exposed to Yeast-CEA was studied by phenotypic analysis and cytokine and chemokine production profiles. The functional activity of DCs exposed to Yeast-CEA was analyzed by their ability to activate CEA-specific T cells as measured by IFN-γ production and their ability to function as APC for the generation of CEA-specific T cell lines. In addition, the gene expression profiles of 260 APC related genes of the DCs exposed to Yeast-CEA were also investigated. Our results have demonstrated that Yeast-CEA can be used to activate human DCs as a consequence the level the expression of CD80 and CD83 increases substantially. The increase in the expression of CD54, CD58, MHC class II on Yeast-CEA treated DCs is moderate. There was no increase in the expression of MHC class I since nearly 100% of the human DCs were MHC class I positive. Increases in the production of IL-12p70, TNF-α, and IFN-γ were also observed in the Yeast-CEA treated DCs. Human DCs exposed to Yeast-CEA were shown to be able to activate CEA-specific T cell lines. In addition, human DCs exposed to Yeast-CEA can be used as APC to generate CEA-specific T-cell line which in turn was shown to be capable of lysing human tumor cells expressing CEA. Analysis of the gene expression profiles of human DCs exposed to Yeast-CEA have shown the increases in the expression of chemokines, cytokines and their receptors genes and genes related to antigen uptake, antigen presentation as well as signal transduction. These studies provide the rationale for the clinical evaluation of the S. cerevisiae vector containing a transgene encoding CEA in patients with a range of carcinomas expressing CEA.
Two Cobaltacyclopentadiene Complexes and One Cyclobutadiene Complex (1995)

The structures of three cobalt complexes, [1,4-bis(1-propynyl)-2,3-dimethyl-1,3-butadiene-1,4-diyl](η 5 -cyclopentadienyl)(triphenylphosphine)cobalt, [Co(C 5 H 5 )-(C 12 H 12 )(C 18 H 15 P)], (η 5 -cyclopentadienyl)[2,4-diphenyl-1,3-bis(phenylethynyl)-1,3-butadiene-1,4-diyl](triphenyl phosphine)cobalt, [Co(C 5 H 5 )(C 32 H 20 )(C 18 H 15 P)], and {η 4 -1,3-bis(trimethylsilyl)-2,4-bis[4'-(trimethylsilylethynyl)biphenyl-4-yl]cyclobutadiene} (η 5 -cyclopentadienyl)cobalt, [Co(C 5 H 5 )(C 44 H 52 Si 4 )], have been determined by single-crystal X-ray diffraction.
Design of novel RNA ligands that bind stem–bulge HIV-1 TAR RNA (2010)

We report here the rational design and the synthesis of a new series of RNA ligands. These molecules are constituted of various binding motifs that interact cooperatively with HIV-1 TAR RNA, used as a model.
Capsaicin and carbon dioxide act by distinct mechanisms on sensory nerve terminals in the cat cornea (1997)

The discharge of single afferent units recorded from filaments of the mixed ciliary nerve of anaesthetised cats was used to study the effects of CO2, capsaicin and the capsaicin antagonist, capsazepine, on sensory nerve terminals in the cornea. Units were selected on the basis of their sensitivity to CO2 (98.5% applied to the cornea for 30 s in a moist gas stream). Of these units, about 50% (18/38) also responded to capsaicin (0.1 microM applied as droplet and washed off after 20 s), with a discharge of similar magnitude to that produced by CO2. The other CO2-sensitive units (20/38) did not respond to capsaicin. Capsaicin-sensitive units responded more rapidly to CO2 (mean latency to first spike 0.7 +/- 0.2 s) than capsaicin-insensitive units (mean latency to first spike 5.1 +/- 1.2 s). On the basis of their conduction velocity, both the capsaicin-sensitive and the capsaicin-insensitive groups included both A- and C-fibres. Application of capsazepine (10 microM for 5-20 min) to the cornea reversibly blocked the response of the units to capsaicin without affecting responses to CO2. Units that were acutely desensitised by exposure to capsaicin (0.1 microM) for 30 s, during which time the discharge evoked by capsaicin declined to zero, still responded to CO2, though the response was reduced by 44% compared with controls. It is concluded that activation of sensory afferents in the cat cornea by capsaicin and by CO2 appear to involve distinct mechanisms, since: (a) many CO2- sensitive units are not excited by capsaicin; (b) capsazepine selectively blocks excitation by capsaicin without affecting responses to CO2; and (c) desensitisation to capsaicin impairs only partially the responsiveness to CO2.
Impact of polarisation mode dispersion on 10 Gbit/sterrestrial systems over non-dispersion-shifted fibre (1995)

Depending on the launched state of polarisation, 10 Gbit/s system impairments are investigated experimentally in the presence of chromatic dispersion and variable differential group delay caused by polarisation mode dispersion. In addition, an actual fibre cable, not an optical simulator, was used to bring polarisation mode dispersion.
The Development of a New Class of Holographic Materials. (1984)

Abstract : The research described in this final report involves the development of a new class of holographic materials. These materials exhibit two-photon photochemistry and thus are quadratic in their photochemical response to the intensity of the two recording laser beams. Unlike other previously suggested two-photon systems, the systems we have been developing can be used with milliwatts as opposed to megawatts of laser power. The holographic material consists of a photoactive organic molecule embedded in a polymer host. Grain free holograms can thus be recorded and no development or fixing step is necessary. Work has focused on four different areas: (1) Investigation of new two-photon holographic materials, particularly ones with higher maximum holographic efficiency; (2) Demonstration of gating of the holographic recording process using an auxiliary light source; (3) Development of two-photon holographic materials which respond to infrared laser wavelengths and their application in gated holography; and (4) Production of simple holographic optical elements using these materials.
Demonstration, localization, and development of galanin receptors in the quail oviduct (1997)

We recently isolated an oviposition-inducing peptide that was identified as avian galanin from the oviducts of the Japanese quail. Avian galanin was localized in neural fibers distributed in muscle layers in the uterine and vaginal oviduct regions, and potentiated spontaneous contractions of the uterus and vagina. To elucidate whether an oviposition-inducing effect of avian galanin is due to the direct action on the oviduct, therefore, a specific binding site for avian galanin was determined in the functional quail oviduct in this study. The binding of [125I]iodoavian galanin was primarily located in the oviduct as well as the brain. The galanin binding was specifically inhibited as a function of the concentrations of both avian and rat galanins. The specific binding of avian galanin to the quail oviduct was temperature dependent and reached the maximum level for 1 h at 20 degrees C. In several regions of the oviduct, a higher level of specific galanin binding was observed only in the uterus and vagina. In contrast, the specific binding was low in the isthmus and negligible in the magnum. A similar localization was evident in the functional chicken oviduct. The Scatchard plot analysis of the binding of avian galanin to the uterine preparation revealed that the dissociation constant (Kd) was 0.249 (95% confidence interval, 0.192-0.356) nM, and the number of binding sites was 1.13 (0.99-1.36) fmol per mg tissue, respectively. During development, the galanin-binding sites were apparent in the quail oviduct at 3 weeks of age and the number of binding sites markedly increased between 3 weeks and 3 months of age. However, there was no significant change in the Kd value in the developing quail oviduct. This is the first demonstration of the presence of galanin receptors in the reproductive tract, such as the uterine and vaginal oviduct. The present results suggest that the number of galanin receptors in the oviduct increases during development and that galanin acts directly on the mature uterus and vagina to induce their contractions. This mechanism may be essential to the avian oviposition.
167. p-Aminodimethylaniline. Part II. The o-chloro- and -nitro-derivatives (1942)

E. E. Ayling, J. H. Gorvin and L. E. Hinkel, J. Chem. Soc., 1942, 755 DOI: 10.1039/JR9420000755
Biomarkers for Alzheimer's disease – Clinical needs and application (2006)

Biomarkers for Alzheimer's disease have many diagnostic and therapeutic uses. They can be used to facilitate diagnosis, particularly early diagnosis and possibly presymptomatic diagnosis. In evaluating treatment aimed at modifying the course of AD, biomarkers can help to assess whether the drug is hitting a target or influencing disease mechanisms in the brain, and can help with dose-finding. In definitive clinical trails, biomarkers can be used as surrogate outcome measures. Progress has been made in investigating candidate biomarkers in cerebrospinal fluid and plasma. At present, cerebrospinal fluid levels of amyloid-beta, tau and phospho-tau come closest to meeting criteria proposed for useful biomarkers for diagnosis. Other biomarkers can provide insight into processes such as inflammation and oxidative damage. Unbiased and broad-based searches for novel biomarkers using proteomics have much potential. As efforts to diagnose and treat AD move towards earlier intervention and even towards prevention, biomarkers will gain significance as tools to aid research and ultimately clinical practice.