gebhart/patrepeval huggingface dataset:
Introduction (2002)

On 1 January 1875, William M. Cash, an Alexandria, Louisiana news carrier, had a special New Year's Day gift for the customers on his paper route: he presented each with The Bells, a handsome, eight-page pamphlet reprinting the well-known poem by Edgar Allan Poe. Louisiana newspaper subscribers were not the only people to receive copies of The Bells as presents during the 1870s. In Philadelphia, a china and glassware retailer issued a complimentary edition of the poem for its customers during Christmas time, 1872, and the week after Christmas, grocery boys in the employ of Philadelphia grocer, Mitchell and Fletcher, gave copies of The Bells to their customers as New Year's Day presents. Since bells had been a commonplace holiday motif for centuries, perhaps it should come as no surprise that copies of The Bells were being distributed to Philadelphia grocery shoppers or Louisiana newspaper subscribers. Anyone who believed what they read in the literary periodicals of the day, however, would hardly find Poe's writings suitable material to pass through the hands of impressionable young news carriers and grocery boys.
Crystal Structure of the V α Domain of a T Cell Antigen Receptor (1995)

The crystal structure of the V alpha domain of a T cell antigen receptor (TCR) was determined at a resolution of 2.2 angstroms. This structure represents an immunoglobulin topology set different from those previously described. A switch in a polypeptide strand from one beta sheet to the other enables a pair of V alpha homodimers to pack together to form a tetramer, such that the homodimers are parallel to each other and all hypervariable loops face in one direction. On the basis of the observed mode of V alpha association, a model of an (alpha beta)2 TCR tetramer can be positioned relative to the major histocompatibility complex class II (alpha beta)2 tetramer with the third hypervariable loop of V alpha over the amino-terminal portion of the antigenic peptide and the corresponding loop of V beta over its carboxyl-terminal residues. TCR dimerization that is mediated by the alpha chain may contribute to the coupling of antigen recognition to signal transduction during T cell activation.
Post Prandial Changes in Colonic Motility Related to Serum Gastrin Levels (1976)

Colonic motor activity and serum gastrin levels were correlated during a basal period and after a meal in 16 subjects. Motor activity preceded the gastrin response. The motility index and the serum gastrin levels rose in parallel, but the motility fell before later showing a second rise. The frequency response showed the earliest change and since it preceded the gastrin rise may be neurogenic. This response was later "extinguished" and replaced by one of waves of increasing amplitude; the sustained nature of this response fitted more closely the gastrin response.
Macrophages that have ingested apoptotic cells in vitro inhibit proinflammatory cytokine production through autocrine/paracrine mechanisms involving TGF-beta, PGE2, and PAF. (1998)

Apoptosis in vivo is followed almost inevitably by rapid uptake into adjacent phagocytic cells, a critical process in tissue remodeling, regulation of the immune response, or resolution of inflammation. Phagocytosis of apoptotic cells by macrophages has been suggested to be a quiet process that does not lead to production of inflammatory mediators. Here we show that phagocytosis of apoptotic neutrophils (in contrast to immunoglobulin G-opsonized apoptotic cells) actively inhibited the production of interleukin (IL)-1beta, IL-8, IL-10, granulocyte macrophage colony-stimulating factor, and tumor necrosis factor-alpha, as well as leukotriene C4 and thromboxane B2, by human monocyte-derived macrophages. In contrast, production of transforming growth factor (TGF)-beta1, prostaglandin E2, and platelet-activating factor (PAF) was increased. The latter appeared to be involved in the inhibition of proinflammatory cytokine production because addition of exogenous TGF-beta1, prostaglandin E2, or PAF resulted in inhibition of lipopolysaccharide-stimulated cytokine production. Furthermore, anti-TGF-beta antibody, indomethacin, or PAF receptor antagonists restored cytokine production in lipopolysaccharide-stimulated macrophages that had phagocytosed apoptotic cells. These results suggest that binding and/or phagocytosis of apoptotic cells induces active antiinflammatory or suppressive properties in human macrophages. Therefore, it is likely that resolution of inflammation depends not only on the removal of apoptotic cells but on active suppression of inflammatory mediator production. Disorders in either could result in chronic inflammatory diseases.
Photoacoustic Tomography (2009)

A pulsed laser produces a rapid small temperature rise in biological tissue, which leads to emission of ultrasonic waves due to thermoelastic expansion. The short-wavelength ultrasonic waves are then detected to form high-resolution tomographic images.
Human amnion in the treatment of vaginal malformations (1986)

Vaginoplasty using human amnion has been performed in 27 patients aged from 13 to 28 years. Excellent epithelialization occurred with good functional results; the technique appears to be preferable to other surgical methods.
Hydrogels as extracellular matrix mimics for 3D cell culture (2009)

Methods for culturing mammalian cells ex vivo are increasingly needed to study cell and tissue physiology and to grow replacement tissue for regenerative medicine. Two-dimensional culture has been the paradigm for typical in vitro cell culture; however, it has been demonstrated that cells behave more natively when cultured in three-dimensional environments. Permissive, synthetic hydrogels and promoting, natural hydrogels have become popular as three-dimensional cell culture platforms; yet, both of these systems possess limitations. In this perspective, we discuss the use of both synthetic and natural hydrogels as scaffolds for three-dimensional cell culture as well as synthetic hydrogels that incorporate sophisticated biochemical and mechanical cues as mimics of the native extracellular matrix. Ultimately, advances in synthetic-biologic hydrogel hybrids are needed to provide robust platforms for investigating cell physiology and fabricating tissue outside of the organism.
A rapid and sensitive method to measure the enzymatic activity of ribosome-inactivating proteins (1998)

A method is described in which the adenosine- N -glycosidase activity of ribosome-inactivating proteins (RIPs) is measured using as substrate a 2251 bp [3H]DNA obtained by PCR amplification of the 731-2981 region of the pBR322 plasmid. The DNA, labelled in the purine ring of adenine, proved a good substrate for all three RIPs tested (PAP-S, ricin and shiga-like toxin I). The method, which measures directly the [3H]adenine released, is highly specific, extremely rapid and quantitative in a wide range of RIP concentrations.
Spread spectrum techniques for the Space Shuttle (1979)

The Space Shuttle will employ spread spectrum techniques for both communication and navigation. During on-orbit phases of flight, two-way S-band and Ku-band communication links between the Shuttle and the ground will be available via the tracking and data relay satellite system (TDRSS). A pseudonoise (PN) code will spread the forward-link data spectrum from 32 kbps to 216 kbps to reduce the signal spectral density impinging on the earth's surface, with the S-band code search and acquisition being performed at C/NO-values of around 5 dB-Hz, and with a code length of 2047 chips at a rate of 11.232 Mchips/sec. C/NO-values in the region of 60 dB-Hz to 63 dB-Hz will characterize PN code acquisition in the Ku-band, whose forward-link PN clock is 3.03 Mchips/sec on a 1023-chip length sequence. Primary operational navigation will be provided by the Global Positioning System (GPS), which, after measuring transit time of the PN spread spectrum signal between a number of GPS satellites and itself, scales it by the velocity of light. GPS will enable position estimation accuracy to 30 feet and velocity estimation accuracy to 0.02 ft/sec.
Vinorelbine and Prednisone in older Cancer Patients with Hormone-Refractory Metastatic Prostate Cancer a Phase II Study (2003)

The schedule is able to control the evolution of hormone-refractory prostate cancer and to give a clinical benefit. These results provide information for further clinical trials in a large series of elderly cancer patients.
Patterns of light interference produced by damaged cuticle cells in human hair. (2007)

Colorful patterns of light interference have been observed to occur in human hair cuticle cells. The light interference phenomenon has been analyzed by optical microscopy. The strong patterns of light interference appeared only in cuticle cells that had been damaged either mechanically or by thermal stresses. Cuticle cells that were not damaged did not produce this phenomenon. The zones of light interference on the hair surface were seen to extend to cuticle sheath areas whose damage was not apparent when analyzed under the Scanning Electron Microscope. The presence of oils and other hydrophobic materials in the hair had a strong effect in the appearance or disappearance of the interference patterns.
On the design of low-density parity-check codes within 0.0045 dB of the Shannon limit (2001)

We develop improved algorithms to construct good low-density parity-check codes that approach the Shannon limit very closely. For rate 1/2, the best code found has a threshold within 0.0045 dB of the Shannon limit of the binary-input additive white Gaussian noise channel. Simulation results with a somewhat simpler code show that we can achieve within 0.04 dB of the Shannon limit at a bit error rate of 10/sup -6/ using a block length of 10/sup 7/.
Gene transfer in bovine blastocysts using replication‐defective retroviral vectors packaged with gibbon ape leukemia virus envelopes (1993)

With this work we demonstrate that murine leukemia virus (MLV)-based replication-defective retroviral vectors encapsidated with Gibbon ape leukemia virus (GaLV) envelopes are significantly more infectious to bovine embryonic trachea (EBTr) cells than vectors encapsidated with murine xenotropic envelope proteins. In a test of internal promoter activity in an MLV retroviral vector, the rat beta-actin promoter was shown to be better than the herpes simplex virus type 1 thymidine kinase (TK) and human cytomegalovirus (CMV) immediate early promoters for the expression of an E. coli beta-galactosidase marker gene in bovine target cells. By co-culture of bovine blastocysts and virus-producing cells, or by culture of embryos in the medium harvested from virus-producing cells, we transferred the E. coli beta-galactosidase gene into trophoblasts and also into inner cell mass (ICM) cells of a bovine embryo through the infection of the MLV-based replication-defective retroviruses encapsidated with GaLV envelope proteins. The infection was confirmed by the expression of the E. coli beta-galactosidase gene under a beta-actin internal promoter. In addition, co-culture of ICM cells with virus-producing cells resulted in differentiation of ICM cells into embryoid bodies expressing the marker genes.
Pacing and Lapping Movements Among Institutionalized Patients With Dementia (2010)

Wandering is a complex behavior, and defining wandering has been challenging. The current study used the integrated circuit (IC) tag monitoring system to describe the distance moved per day and the spatial movements of patients with dementia. The study was conducted in a 60-bed semiacute dementia care unit in a general hospital in Japan over a 3-month period in 2006. The distance moved per day, the numbers of pacing and lapping movements, and the proportions of the distance moved that was paced or lapped were tabulated in 23 patients diagnosed with dementia. The distance moved per day and the numbers of pacing and lapping movements varied greatly within and among study participants. The median distance moved per day was inversely correlated with participants' age and Mini-Mental State Examination (MMSE) scores (adjusted r(2) = .34, P = .01). Consecutive lapping and pacing movements were rare patients with in Alzheimer's disease (AD), while 2 patients with frontotemporal dementia paced or lapped repeatedly.
Low anticoagulant heparin targets multiple sites of inflammation, suppresses heparin-induced thrombocytopenia, and inhibits interaction of RAGE with its ligands (2010)

While heparin has been used almost exclusively as a blood anticoagulant, important literature demonstrates that it also has broad anti-inflammatory activity. Herein, using low anti-coagulant 2-O,3-O-desulfated heparin (ODSH), we demonstrate that most of the anti-inflammatory pharmacology of heparin is unrelated to anticoagulant activity. ODSH has low affinity for anti-thrombin III, low anti-Xa, and anti-IIa anticoagulant activities and does not activate Hageman factor (factor XII). Unlike heparin, ODSH does not interact with heparin-platelet factor-4 antibodies present in patients with heparin-induced thrombocytopenia and even suppresses platelet activation in the presence of activating concentrations of heparin. Like heparin, ODSH inhibits complement activation, binding to the leukocyte adhesion molecule P-selectin, and the leukocyte cationic granular proteins azurocidin, human leukocyte elastase, and cathepsin G. In addition, ODSH and heparin disrupt Mac-1 (CD11b/CD18)-mediated leukocyte adhesion to the receptor for advanced glycation end products (RAGE) and inhibit ligation of RAGE by its many proinflammatory ligands, including the advanced glycation end-product carboxymethyl lysine-bovine serum albumin, the nuclear protein high mobility group box protein-1 (HMGB-1), and S100 calgranulins. In mice, ODSH is more effective than heparin in reducing selectin-mediated lung metastasis from melanoma and inhibits RAGE-mediated airway inflammation from intratracheal HMGB-1. In humans, 50% inhibitory concentrations of ODSH for these anti-inflammatory activities can be achieved in the blood without anticoagulation. These results demonstrate that the anticoagulant activity of heparin is distinct from its anti-inflammatory actions and indicate that 2-O and 3-O sulfate groups can be removed to reduce anticoagulant activity of heparin without impairing its anti-inflammatory pharmacology.
Eotaxin-3/CCL26 Is a Natural Antagonist for CC Chemokine Receptors 1 and 5 (2004)

Eotaxin-3 (CCL26), like eotaxin (CCL11) and eotaxin-2 (CCL24), has long been considered a specific agonist for CC chemokine receptor 3 (CCR3), attracting and activating eosinophils, basophils, and Th2 type T lymphocytes. Although not characterized extensively yet, its expression profile coincides with a potential role in allergic inflammation. We recently reported that eotaxin-3 is an antagonist for CCR2 (Ogilvie, P., Paoletti, S., Clark-Lewis, I., and Uguccioni, M. (2003) Blood 102, 789-784). In the present report, we provide evidence that eotaxin-3 acts as a natural antagonist on CCR1 and -5 as well. Eotaxin-3 bound to cells transfected with either CCR1 or -5 as well as to monocytes expressing both receptors. Further, it inhibited chemotaxis, the release of free intracellular calcium, and actin polymerization when cells were stimulated with known agonists of CCR1 and -5. An analysis of its three-dimensional structure indicated the presence of two distinct epitopes that may be involved in specific binding to CCR1, -2, -3, and -5. Taken together, our data thus indicate eotaxin-3 to be the first human chemokine that features broadband antagonistic activities, suggesting that it may have a modulatory rather than an inflammatory function. Further, eotaxin-3 may play an unrecognized role in the polarization of cellular recruitment by attracting Th2 lymphocytes as well as eosinophils and basophils via CCR3, while concomitantly blocking the recruitment of Th1 lymphocytes and monocytes via CCR1, -2, and -5.
Evaluating intelligent measurement systems: a study in ventilator management (1989)

Two types of intelligent measurement systems are considered: commercially produced instrumentation systems with intelligence incorporated as a part of the product and instrumentation systems developed in-house in which the intelligence resides in stand-alone microcomputers linked by an appropriate machine level interface. The system evaluated is an example of the latter type, but the comments are equally relevant to the former. Evaluation is considered as a mainstream activity and illustrated by reference to an intelligent management system for patients who require ventilatory therapy. It is carried out for small functional units individually becoming a more transparent activity. Its more explicit nature has aided system designers and system users to view potential problems from the same perspective.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prodrugs of Nitroxyl and Nitrosobenzene as Cascade Latentiated Inhibitors of Aldehyde Dehydrogenase (1998)

The prototypic aromatic C-nitroso compound, nitrosobenzene (NB), was shown previously to mimic the effect of nitroxyl (HN=O), the putative active metabolite of cyanamide, in inhibiting aldehyde dehydrogenase (AlDH). To minimize the toxicity of NB in vivo, pro-prodrug forms of NB, which were designed to be bioactivated either by an esterase intrinsic to AlDH or the mixed function oxidase enzymes of liver microsomes, were prepared. Accordingly, the prodrug N-benzenesulfonyl-N-phenylhydroxylamine (3) was further latentiated by conversion to its O-acetyl (1a), O-methoxycarbonyl (1b), O-ethoxycarbonyl (1c), and O-methyl (2) derivatives. Similarly, pro-prodrug forms of nitroxyl were prepared by derivatization of the hydroxylamino moiety of methanesulfohydroxamic acid with N, O-bis-acetyl (7a), N,O-bis-methoxycarbonyl (7b), N, O-bis-ethoxycarbonyl (7c), and N-methoxycarbonyl-O-methyl (7d) groups. It was expected that the bioactivation of these prodrugs would initiate a cascade of nonenzymatic reactions leading to the ultimate liberation of NB or nitroxyl, thereby inhibiting AlDH. Indeed, the ester pro-prodrugs of both series were highly active in inhibiting yeast AlDH in vitro with IC50 values ranging from 21 to 64 microM. However, only 7d significantly raised ethanol-derived blood acetaldehyde levels when administered to rats, a reflection of the inhibition of hepatic mitochondrial AlDH-2.
Phylogenetic Diversity of the Deinococci as Determined by 16S Ribosomal DNA Sequence Comparison (1997)

16S ribosomal DNA (rDNA) sequences were determined for the five species of the genus Deinococcus (Deinococcus erythromyxa, Deinococcus proteolyticus, Deinococcus radiodurans, Deinococcus radiophilus, and Deinococcus radiopugnans) and the single species of the genus. Deinobacter (Deinobacter grandis). With the exception of Deinococcus erythromyxa, the deinococci form a coherent phylogenetic cluster which is related to the Thermus-Meiothermus lineage. An analysis of the 16S rDNA sequence of Deinococcus erythromyxa revealed that this organism is an actinomycete and a member of the genus Kocuria. Deinobacter grandis falls within the radiation of the genus Deinococcus and phylogenetically can be considered a member of this genus. The results of the phylogenetic analyses are consistent with chemotaxonomic data. On the basis of our data, Deinobacter grandis is transferred to the genus Deinococcus as Deinococcus grandis comb. nov., the description of the genus Deinococcus is emended accordingly, and Deinococcus erythromyxa is transferred to the genus Kocuria as Kocuria erythromyxa comb. nov. The description of the family Deinococcaceae is emended to include organisms with rod-shaped cells, and a set of 16S rDNA signature nucleotides is designated for this group. On the basis of the distinct phylogenetic position of the Deinococcus lineage and a set of 16S rDNA signature nucleotides, the order Deinococcales ord. nov. is described.
Rapid Near-Infrared Raman Spectroscopy of Human Tissue with a Spectrograph and CCD Detector (1992)

We demonstrate the use of a single-stage spectrograph and charge-coupled-device (CCD) detector to collect near-infrared (NIR) Raman spectra from intact human arterial tissue. With 810-nm excitation, the fluorescence emission from human artery is sufficiently weak to allow observation of Raman bands more rapidly with the spectrograph/CCD system than with 1064-nm excited FT-Raman systems. We also present a method for removing the broad-band emission from the spectra by computing the difference of two emission spectra collected at slightly different excitation frequencies. Our results indicate that NIR Raman spectra can be collected in under one second with the spectrograph/CCD system and an optical fiber probe, opening the possibility of in vivo clinical applications.
Synthesis, SAR and Unanticipated Pharmacological Profiles of Analogues of the mGluR5 Ago‐potentiator ADX‐47273 (2009)

An iterative analogue library synthesis strategy rapidly developed comprehensive SAR for the mGluR5 ago-potentiator ADX-47273. This effort identified key substituents in the 3-position of oxadiazole that engendered either mGluR5 ago-potentiation or pure mGluR5 positive allosteric modulation. The mGluR5 positive allosteric modulators identified possessed the largest fold shifts (up to 27.9-fold) of the glutamate CRC reported to date as well as providing improved physiochemical properties.
Indoleamine 2,3-dioxygenase is a critical resistance mechanism in antitumor T cell immunotherapy targeting CTLA-4 (2013)

The cytotoxic T lymphocyte antigen-4 (CTLA-4)-blocking antibody ipilimumab results in durable responses in metastatic melanoma, though therapeutic benefit has been limited to a fraction of patients. This calls for identification of resistance mechanisms and development of combinatorial strategies. Here, we examine the inhibitory role of indoleamine 2,3-dioxygenase (IDO) on the antitumor efficacy of CTLA-4 blockade. In IDO knockout mice treated with anti-CTLA-4 antibody, we demonstrate a striking delay in B16 melanoma tumor growth and increased overall survival when compared with wild-type mice. This was also observed with antibodies targeting PD-1-PD-L1 and GITR. To highlight the therapeutic relevance of these findings, we show that CTLA-4 blockade strongly synergizes with IDO inhibitors to mediate rejection of both IDO-expressing and nonexpressing poorly immunogenic tumors, emphasizing the importance of the inhibitory role of both tumor- and host-derived IDO. This effect was T cell dependent, leading to enhanced infiltration of tumor-specific effector T cells and a marked increase in the effector-to-regulatory T cell ratios in the tumors. Overall, these data demonstrate the immunosuppressive role of IDO in the context of immunotherapies targeting immune checkpoints and provide a strong incentive to clinically explore combination therapies using IDO inhibitors irrespective of IDO expression by the tumor cells.