gebhart/patrepeval huggingface dataset:
The Relative Importance of T Cell Subsets in Immunity and Immunopathology of Airborne Mycobacterium tuberculosis Infection in Mice (2001)

Wild-type (WT) and targeted-mutant mice incapable of making alphabeta T cells, gammadelta T cells, class I major histocompatibility complex (MHC), class II MHC, interferon (IFN)-gamma, or inducible nitric oxide synthase (NOS2), were infected with Mycobacterium tuberculosis (Mtb) by aerosol, and monitored over time for their ability to (a) control infection, (b) develop histopathology at sites of infection, and (c) survive. WT mice acquired the ability to control and to hold infection at a stationary level from day 20 on. This was associated with the development of a macrophage-dominated alveolitis at sites of infection, with increased synthesis of IFN-gamma and NOS2 mRNA, and with an median survival time (MST) of 258.5 d. In the absence of alphabeta T cells, Mtb grew progressively and rapidly to induce a necrotic, neutrophil-dominated lung pathology that killed mice with an MST of 48 d. In the absence of CD4-mediated immunity (class II(-/-) mice), progressive bacterial growth continued in the lungs and in other organs beyond day 20, resulting in an MST of 77 d. By contrast, in the absence of CD8 T cell-mediated immunity, lung infection was controlled at a 1 log higher stationary level that induced a similar histopathologic response to that of WT mice, and resulted in an MST of 232 d.
Targeting the β-catenin/TCF transcriptional complex in the treatment of multiple myeloma (2007)

Multiple myeloma (MM) is an invariably fatal form of cancer characterized by clonal proliferation of malignant plasma cells in the bone marrow. The canonical Wnt signaling pathway is activated in MM cells through constitutively active beta-catenin, a messenger molecule relevant to growth, survival, and migration of MM cells. The identification of a number of small molecular compounds, such as PKF115-584, which disrupt the interaction of the transcriptionally active beta-catenin/TCF protein complex, provides valuable new therapeutic tools to target an alternative pathway in MM independent of the proteasome. Here we evaluated the transcriptional, proteomic, signaling changes, and biological sequelae associated with the inhibition of Wnt signaling in MM by PKF115-584. The compound blocks expression of Wnt target genes and induces cytotoxicity in both patient MM cells and MM cell lines without a significant effect in normal plasma cells. In xenograft models of human MM, PKF115-584 inhibits tumor growth and prolongs survival. Taken together, these data demonstrate the efficacy of disrupting the beta-catenin/TCF transcriptional complex to exploit tumor dependence on Wnt signaling as a therapeutic approach in the treatment of MM.
In Vitro Fertilisation (IVF) (1995)

In vitro fertilisation (IVF) is the process used to conceive a child outside the body. A woman's eggs and man's sperm are placed together in a plastic dish for fertilisation. Once the eggs are fertilised, the resulting embryos are placed in the woman's uterus in the hope that a successful pregnancy will follow.
Toll-Like Receptor-7 Modulates Immune Complex Glomerulonephritis (2005)

Viral infections may trigger immune complex glomerulonephritis via Toll-like receptors (TLR), as certain TLR trigger immunity upon recognition of viral nucleic acids. On the basis of previous findings regarding viral double-stranded RNA and TLR3 in experimental lupus erythematosus, a similar role for TLR7 that recognizes viral single-stranded RNA was hypothesized. Immunostaining of kidney sections of nephritic MRLlpr/lpr mice revealed TLR7 expression in infiltrating ER-HR3-positive macrophages and few CD11c-positive dendritic cells but not in glomerular mesangial cells as observed for TLR3. This finding was consistent with the distribution pattern of intravenously injected single-stranded RNA in nephritic MRLlpr/lpr mice. TLR7 ligation activated monocytes and dendritic cells, both isolated from MRLlpr/lpr mice, to secrete IFN-alpha, IL-12p70, IL-6, and CCL2. In vivo, a single injection of the TLR7 ligand imiquimod increased serum levels of IL-12p70, IFN-alpha, and IL-6. A course of 25 microg of imiquimod given every other day from week 16 to 18 of age aggravated lupus nephritis in MRLlpr/lpr mice. This was associated with increased glomerular immune complex deposits as well as interstitial expression of CCL2 in imiquimod-treated MRLlpr/lpr mice. Different types of viral nucleic acids seem to modulate systemic autoimmunity through specific interactions with their respective TLR. Different TLR expression profiles on immune cell subsets and nonimmune parenchymal cell types determine the molecular mechanisms involved in viral infection-associated exacerbation of lupus nephritis and possibly other types of immune complex glomerulonephritis.
On-line Synthesis of the Human Ascending Aortic Pressure Pulse From the Finger Pulse (1997)

Although systolic pressure in the ascending aorta (AA) can be determined accurately from the radial arterial waveform using a single generalized transfer function (TF) of the upper limb, a better on-line methods is needed for accurate noninvasive synthesis of the AA pressure contour to characterize left ventricular contractile function and ventricular-vascular coupling. AA, tonometric carotid (CA), and photoplethysmographic finger (FA) arterial pressure waveforms were recorded in 12 subjects (10 male, aged 59.1+/-10.3 years, mean+/-SD) during cardiac catheterization. The AA-FA TF was estimated using (1) a single generalized TF (GAA), (2) individualized TFs directly determined from CA-FA recordings in each patient (DAA), and (3) individualized TFs computed from CA-FA recordings in each patient with a mathematical model of the human upper limb (MAA). AA pressure waveforms were synthesized from FA recordings in real time using convolution windows derived from these TFs. Under steady state conditions, the root mean square error (RMSE) between measured and synthesized AA was lower by DAA (3.3+/-1.3 mm Hg) and MAA (3.9+/-1.2 mmHg) than by GAA (4.8+/-2.0 mm Hg, P<.05). During dynamic load alteration induced by the Valsalva maneuver, however, the MAA method performed better (5.4+/-2.8 mm Hg) than both the GAA (5.8+/-3.3 mm Hg, P<.05) and DAA (6.5+/-2.7 mm Hg, P<.01) methods. The beat-to-beat AA contour can be accurately and noninvasively synthesized on-line using individualized TFs. During dynamic load alteration, individualized TFs derived with an upper limb arterial model provide greater accuracy.
Lichtinduzierte Reaktionen der Sydnone in Gegenwart von Mehrfachbindungssystemen (1979)

Abstract Der lichtinduzierte Zerfall der Sydnone 1 a – g liefert – vermutlich über eine bicyclische Form 2 –unter Kohlendioxid‐Freisetzung eine reaktive Nitrilimin‐Zwischenstufe vom Typ 5 , die mit Dreifachbindungs‐Dipolarophilen nach dem Schema der [3 + 2]‐Cycloaddition unter Bildung der Pyrazol‐Abkömmlinge 6a –o (84–13%) der Tab. 1 abfangbar ist. Mit Doppelbindungs‐Dipolarophilen vereinigen sich die Nitrilimine 5 zu den 2‐Pyrazolinen 9a –f,‐10. Gleichfalls zu 2‐Pyrazolinen 9 e oder 15 , 16 reagiert das aus l a photochemisch gebildete Diphenylnitrilimin mit 2,3‐Dimethyl‐1,3‐butadien bzw. Cyclopentadien bei 17° und –40°C. Bei der Behandlung mit Kieselgel in Gegenwart von Luftsauerstoff erleidet 9 e Oxidation zum Pyrazolinol 17 , das teilweise unter Dehydratisierung in das Propenylpyrazol 18 umlagert. Photochemisch wird 18 in das Dihydropyrazolochinolin 24 (83%) übergeführt. Weiterhin reagiert l a bei Bestrahlung in Gegenwart von Kohlenstoffdisulfid zu den Nitrilimin‐Addukten 25 und 26 . Die bei Einsatz unsymmetrisch substituierter Alkene und Alkine beobachtete Regioselektivität wird qualitativ auf der Basis der MO‐Störungstheorie diskutiert.
Characterization of Novel Antimicrobial Peptoids (1999)

Peptoids differ from peptides in that peptoids are composed of N-substituted rather than alpha-carbon-substituted glycine units. In this paper we report the in vitro and in vivo antibacterial activities of several antibacterial peptoids discovered by screening combinatorial chemistry libraries for bacterial growth inhibition. In vitro, the peptoid CHIR29498 and some of its analogues were active in the range of 3 to 12 microg/ml against a panel of gram-positive and gram-negative bacteria which included isolates which were resistant to known antibiotics. Peptoid antimicrobial activity against Staphylococcus aureus was rapid, bactericidal, and independent of protein synthesis. beta-Galactosidase and propidium iodide leakage assays indicated that the membrane is the most likely target of activity. Positional isomers of an active peptoid were also active, consistent with a mode of action, such as membrane disruption, that does not require a specific fit between the molecule and its target. In vivo, CHIR29498 protected S. aureus-infected mice in a simple infection model.
Alterations in Gene Expression in the Caput Epididymides of Nonobstructive Azoospermic Men1 (2007)

Spermatozoal maturation in the epididymis is dependent on proteins secreted by the epithelium and those that create the proper ionic composition and pH of the lumen as well as the blood-epididymal barrier. For the human epididymis, little information exists about the regulation of these proteins in male infertility. Our objectives were to assess gene expression profiles in the caput epididymidis from men with normal spermatogenesis and men with nonobstructive azoospermia. With microarrays, we identified 414 genes in the caput epididymidis that were differentially regulated in infertile men by at least 2-fold compared with the fertile men. They were mostly involved in transcription, intracellular signaling, immunity, and fertility. Although the expression of genes encoding tight junctional proteins was not affected, the localization of CLDN10 and TJP1, but not CLDNs 1, 3, and 8, was altered in infertile patients, suggesting that there are changes in the paracellular functions of the blood-epididymal barrier. Differentially regulated genes included several encoding proteins involved in spermatozoal maturation, water and ion channels, and beta-defensins: CRISP1, SPINLW1, FAM12B, and DEFB129 were upregulated, whereas CFTR, AQP5, KCNK4, KCNK17, SLC6A20, SLC13A3, DEFB126, and DEFB106A were downregulated. Furthermore, the immunolocalization of AQP5, but not of CFTR or CRISP1, varied in infertile and fertile patients. The observation that the expression of genes involved in water and ion transport were repressed in infertile patients suggests that these genes are regulated by the presence of testicular products or spermatozoa in the epididymal lumen or are part of a broader syndrome associated with nonobstructive azoospermia.
Molecular biology of Hel308 helicase in archaea (2009)

Hel308 is an SF2 (superfamily 2) helicase with clear homologues in metazoans and archaea, but not in fungi or bacteria. Evidence from biochemistry and genetics implicates Hel308 in remodelling compromised replication forks. In the last 4 years, significant advances have been made in understanding the biochemistry of archaeal Hel308, most recently through atomic structures from cren- and eury-archaea. These are good templates for SF2 helicase function more generally, highlighting co-ordinated actions of accessory domains around RecA folds. We review the emerging molecular biology of Hel308, drawing together ideas of how it may contribute to genome stability through the control of recombination, with reference to paradigms developed in bacteria.
An evaluation of MOS interface-trap charge pump as an ultralow constant-current generator (2003)

Explores the MOS interface-trap charge-pump as an ultralow constant-current generator for analog CMOS applications. Charge pumping techniques in general are more suitable than conventional continuous-time techniques for ultralow current generation because the linear controllability of current by frequency is maintained regardless of the level of current. An interface-trap pump has the same property but the minimum charge it puts out per cycle is at least two orders of magnitude smaller than that of a switched-capacitor charge pump. This helps generate the same current more accurately at a much higher frequency with a much smaller filter capacitance. The paper presents a simplified model of the terminal characteristics of the interface-trap pump and an evaluation of its performance as a stand-alone current generator. Cascoding and complementary pumping are introduced as measures of performance improvement. Temperature sensitivity, pulse feedthrough, controllability, matching, reliability, and trimming issues are addressed. Transconductor circuits built with the charge pump are presented and experimentally evaluated.
Synthesis and complexation behaviour of an effective octadentate complexone 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis[methylene(methylphosphinic acid)] (1990)

C. J. Broan, K. J. Jankowski, R. Kataky, D. Parker, A. M. Randall and A. Harrison, J. Chem. Soc., Chem. Commun., 1990, 1739 DOI: 10.1039/C39900001739
Parametrization and Range of Motion of the Ball-and-Socket Joint (2001)

The ball-and-socket joint model is used to represent articulations with three rotational degrees of freedom (DOF), such as the human shoulder and the hip. The goal of this paper is to discuss two related problems: the parametrization and the definition of realistic joint boundaries for ball-and-socket joints. Doing this accurately is difficult, yet important for motion generators (such as inverse kinematics and dynamics engines) and for motion manipulators (such as motion retargeting), since the resulting motions should satisfy the anatomic constraints. The difficulty mainly comes from the complex nature of 3D orientations and of human articulations. The underlying question of parametrization must be addressed before realistic and meaningful boundaries can be defined over the set of 3D orientations. In this paper, we review and compare several known methods, and advocate the use of the swing-and-twist parametrization, that partitions an arbitrary orientation into two meaningful components. Finally, we review two joint boundaries representations based on this decomposition, and show an example.
A comparative study of the quantitative accuracy of three‐dimensional reconstructions of spinal cord from serial histological sections (2003)

We evaluated the accuracy of estimating the volume of biological soft tissues from their three-dimensional (3D) computer wireframe models, reconstructed from histological data sets obtained from guinea-pig spinal cords. We compared quantification from two methods of three-dimensional surface reconstruction to standard quantitative techniques, Cavalieri method employing planimetry and point counting and Geometric Best-Fitting. This involved measuring a group of spinal cord segments and test objects to evaluate the accuracy of our novel quantification approaches. Once a quantitative methodology was standardized there was no statistical difference in volume measurement of spinal segments between quantification methods. We found that our 3D surface reconstructions' ability to model precisely actual soft tissues provided an accurate volume quantification of complex anatomical structures as standard approaches of Cavalieri estimation and Geometric Best-Fitting. Additionally, 3D reconstruction quantitatively interrogates and three-dimensionally images spinal cord segments and obscured internal pathological features with approximately the same effort required for standard quantification alone.
Phase I Dose-Finding Study of a New Taxane, RPR 109881A, Administered as a One-Hour Intravenous Infusion Days 1 and 8 to Patients With Advanced Solid Tumors (2000)

The RD of RPR 109881A given as a 1-hour infusion on days 1 and 8 of a 21-day cycle is 45 mg/m(2). At this dose the drug is well tolerated and should be further studied.
High-Quality GaN on Si Substrate Using AlGaN/AlN Intermediate Layer (1999)

A single crystal GaN thin film was successfully grown on a Si(111) substrate by means of atmospheric-pressure metalorganic chemical vapor deposition. An intermediate layer consisting of AlN and AlGaN improved the quality of GaN on Si with a mirror-like surface and reduced the pits and cracks over the surface. The full width at half maximum (FWHM) of the double-crystal X-ray rocking curve for GaN(0004) was 600 arcsec. Photoluminescence measurement at 4.2 K for a nondoped film revealed a sharp band-edge emission with a FWHM of 8.8 meV, which is the narrowest value reported to date. GaInN multi-quantum-well structure was grown on this structure and showed a strong blue emission peaking at 470 nm. The results suggest GaN on Si with an AlGaN/AlN intermediate layer provides reliable light emitting devices on Si substrate.
Cerebrospinal-fluid-derived Immunoglobulin G of Different Multiple Sclerosis Patients Shares Mutated Sequences in Complementarity Determining Regions (2013)

B lymphocytes play a pivotal role in multiple sclerosis pathology, possibly via both antibody-dependent and -independent pathways. Intrathecal immunoglobulin G in multiple sclerosis is produced by clonally expanded B-cell populations. Recent studies indicate that the complementarity determining regions of immunoglobulins specific for certain antigens are frequently shared between different individuals. In this study, our main objective was to identify specific proteomic profiles of mutated complementarity determining regions of immunoglobulin G present in multiple sclerosis patients but absent in healthy controls. To achieve this objective, we purified immunoglobulin G from the cerebrospinal fluid of 29 multiple sclerosis patients and 30 healthy controls and separated the corresponding heavy and light chains via SDS-PAGE. Subsequently, bands were excised, trypsinized, and measured with high-resolution mass spectrometry. We sequenced 841 heavy and 771 light chain variable region peptides. We observed 24 heavy and 26 light chain complementarity determining regions that were solely present in a number of multiple sclerosis patients. Using stringent criteria for the identification of common peptides, we found five complementarity determining regions shared in three or more patients and not in controls. Interestingly, one complementarity determining region with a single mutation was found in six patients. Additionally, one other patient carrying a similar complementarity determining region with another mutation was observed. In addition, we found a skew in the κ-to-λ ratio and in the usage of certain variable heavy regions that was previously observed at the transcriptome level. At the protein level, cerebrospinal fluid immunoglobulin G shares common characteristics in the antigen binding region among different multiple sclerosis patients. The indication of a shared fingerprint may indicate common antigens for B-cell activation.
Measuring Protein–Ligand Interactions Using Liquid Sample Desorption Electrospray Ionization Mass Spectrometry (2013)

We have previously shown that liquid sample desorption electrospray ionization-mass spectrometry (DESI-MS) is able to measure large proteins and noncovalently bound protein complexes (to 150 kDa) (Ferguson et al., Anal. Chem. 2011, 83, 6468-6473). In this study, we further investigate the application of liquid sample DESI-MS to probe protein-ligand interactions. Liquid sample DESI allows the direct formation of intact protein-ligand complex ions by spraying ligands toward separate protein sample solutions. This type of "reactive" DESI methodology can provide rapid information on binding stiochiometry, selectivity, and kinetics, as demonstrated by the binding of ribonuclease A (RNaseA, 13.7 kDa) with cytidine nucleotide ligands and the binding of lysozyme (14.3 kDa) with acetyl chitose ligands. A higher throughput method for ligand screening by liquid sample DESI was demonstrated, in which different ligands were sequentially injected as a segmented flow for DESI ionization. Furthermore, supercharging to enhance analyte charge can be integrated with liquid sample DESI-MS, without interfering with the formation of protein-ligand complexes.
Epoxy-free high-temperature fiber optic pressure sensors for gas turbine engine applications (2004)

Pressure measurements at various locations of a gas turbine engine are highly desirable to improve the operational performance and reliability. However, measurement of dynamic pressure (1psi (6.9kPa) variation superimposed on the static bias) in the operating environment of the engine, where temperatures might exceed 600°C and pressures might exceed 100psi (690kPa), is a great challenge to currently available sensors. To meet these requirements, a novel type of fiber optic engine pressure sensor has been developed. This pressure sensor functions as a diaphragm-based extrinsic Fabry-Perot interferometric (EFPI) sensor. The structure of the sensor head, composed entirely of fused silica, allows a much higher operating temperature to be achieved in conjunction with a low temperature dependence. The sensor head and the fiber tail have been packaged in a metal fitting connected to a piece of metal extension tubing, which improves the mechanical strength of the sensor and facilitates easy sensor installation. The sensor exhibited very good performance in an engine field test, demonstrating not only that the sensors' package is robust enough for engine operation, but also that its performance is consistent with that of a commercial Kulite sensor.
Herpes Simplex Virus Type 1 and Bovine Herpesvirus 1 Latency (2003)

Primary infection by herpes simplex virus type 1 (HSV-1) can cause clinical symptoms in the peripheral and central nervous system, upper respiratory tract, and gastrointestinal tract. Recurrent ocular shedding leads to corneal scarring that can progress to vision loss. Consequently, HSV-1 is the leading cause of corneal blindness due to an infectious agent. Bovine herpesvirus 1 (BHV-1) has similar biological properties to HSV-1 and is a significant health concern to the cattle industry. Latency of BHV-1 and HSV-1 is established in sensory neurons of trigeminal ganglia, but latency can be interrupted periodically, leading to reactivation from latency and spread of infectious virus. The ability of HSV-1 and BHV-1 to reactivate from latency leads to virus transmission and can lead to recurrent disease in individuals latently infected with HSV-1. During latency, the only abundant HSV-1 RNA expressed is the latency-associated transcript (LAT). In latently infected cattle, the latency-related (LR) RNA is the only abundant transcript that is expressed. LAT and LR RNA are antisense to ICP0 or bICP0, viral genes that are crucial for productive infection, suggesting that LAT and LR RNA interfere with productive infection by inhibiting ICP0 or bICP0 expression. Numerous studies have concluded that LAT expression is important for the latency-reactivation cycle in animal models. The LR gene has recently been demonstrated to be required for the latency-reactivation cycle in cattle. Several recent studies have demonstrated that LAT and the LR gene inhibit apoptosis (programmed cell death) in trigeminal ganglia of infected animals and transiently transfected cells. The antiapoptotic properties of LAT map to the same sequences that are necessary for promoting reactivation from latency. This review summarizes our current knowledge of factors regulating the latency-reactivation cycle of HSV-1 and BHV-1.
HIV antibodies and vaccine design (1989)

From the Departments of Surgery and Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710, USA.