gebhart/patrepeval huggingface dataset:
Immunomodulation by thalidomide: systematic review of the literature and of unpublished observations. (1997)

Three decades of immunological investigations using thalidomide are reviewed. Both in vitro and in vivo investigations are in accordance with the clinical finding that thalidomide does not impede T-cell competence in the control of infection by mycobacteriae. The term immunosuppressant does not apply. The immunomodulatory effects of thalidomide are evident in a myriad of phenomenological changes, and a molecularly defined common denominator of these activities is not known at present. Critical assessment with the objective to account for the clinical activity of thalidomide in specific human diseases leads to a focus on effects of thalidomide on phagocytic leukocytes and endothelia. The former are responsive to thalidomide by modulation of cytokine synthesis in vitro and in vivo; this activity can be shown using monocyte-specific stimuli in peripheral blood mononuclear cells but also in other phagocytic cells like microglia. For technical reasons, endothelial cells have until now been tested primarily in vitro. However, there is solid evidence now from intravital microscopy that the induction of adhesivity in postcapillary venules by LPS is modulated by thalidomide. Altered surface antigen expression has been described on leukocytes obtained from humans and experimental animals treated with thalidomide, but convincing evidence is lacking for in vitro modulation of surface antigen expression on leukocytes (as opposed to the modulation of adhesion antigens on endothelial cells stimulated by LPS or exogenous TNF alpha in the presence of thalidomide). Therefore, in vivo redistribution is likely to account for some, if not all, changes in circulating leukocyte phenotypes. The immunopathological conditions most clearly responsive to thalidomide are vasculitic alterations of post-capillary venules either in the context of mycobacterial infection (in the case of erythema nodosum leprosum) or mucocutaneous aphths. In both instances (as in the majority of focal inflammatory lesions), leukocyte infiltration and cytokine responses, in particular TNF alpha, are present. Thalidomide acts clinically not only by palliation of existing lesions but also by prevention of recurrence. The mechanism operates in skin, mucosa and parts of the nervous system and is most readily explained by synergism of TNF alpha modulation and a separate point of action on leukocyte migration patterns.
An Efficient Framework for Searching Text in Noisy Document Images (2012)

An efficient word spotting framework is proposed to search text in scanned books. The proposed method allows one to search for words when optical character recognition (OCR) fails due to noise or for languages where there is no OCR. Given a query word image, the aim is to retrieve matching words in the book sorted by the similarity. In the offline stage, SIFT descriptors are extracted over the corner points of each word image. Those features are quantized into visual terms (visterms) using hierarchical K-Means algorithm and indexed using an inverted file. In the query resolution stage, the candidate matches are efficiently identified using the inverted index. These word images are then forwarded to the next stage where the configuration of visterms on the image plane are tested. Configuration matching is efficiently performed by projecting the visterms on the horizontal axis and searching for the Longest Common Subsequence (LCS) between the sequences of visterms. The proposed framework is tested on one English and two Telugu books. It is shown that the proposed method resolves a typical user query under 10 milliseconds providing very high retrieval accuracy (Mean Average Precision 0.93). The search accuracy for the English book is comparable to searching text in the high accuracy output of a commercial OCR engine.
Assessment of Spectral Attenuated Inversion Recovery (SPAIR) MR Imaging: Normal and Osteomyelitis in the Mandible (2008)

To describe signal characteristics of normal structures in the mandibular region using spectral attenuated inversion recovery (SPAIR) magnetic resonance (MR) imaging and evaluate the usefulness of SPAIR MR images in mandibular osteomyelitis compared with T1- and T2-weighted spin echo (SE) images. SPAIR MR images of 212 normal subjects and T1- and T2-weighted SE images of 21 subjects of mandibular osteomyelitis were evaluated. T1- and T2-weighted images were obtained in all patients. MR images were evaluated in terms of signal characteristics of normal and abnormal mandibular bone marrow, and surrounding soft tissue. In normal subjects, the mandibular bone marrow demonstrated low signal intensities (100%) and cortical bone showed no signal intensities (100%) on SPAIR images. In surrounding soft tissue of normal subjects, the submandibular glands demonstrated high signal intensities (100%), the parotid glands showed intermediate to high signal intensities (100%), the sublingual glands showed high (92%) and intermediate to high (8%) signal intensities, the lymph nodes showed high signal intensities (100%), and the masseter muscles showed intermediate signal intensities (100%) on SPAIR images. The lesions in mandibular bone marrow were low (86%) and low to intermediate (14%) signal intensities on T1-weighted images and high (52%), intermediate to high (33%), and intermediate (15%) signal intensities on T2-weighted images. On SPAIR images, the signal intensities resulted in high (86%), and intermediate to high (14%). The use of SPAIR imaging is useful for evaluating normal mandibular bone marrow and detecting osteomyelitis in the mandible and identifying the spread of inflammation to soft tissue.
Adaptive Bitrate Selection: A Survey (2017)

HTTP adaptive streaming (HAS) is the most recent attempt regarding video quality adaptation. It enables cheap and easy to implement streaming technology without the need for a dedicated infrastructure. By using a combination of TCP and HTTP it has the advantage of reusing all the existing technologies designed for ordinary web. Equally important is that HAS traffic passes through firewalls and works well when NAT is deployed. The rate adaptation controller of HAS, commonly called adaptive bitrate selection (ABR), is currently receiving a lot of attention from both industry and academia. However, most of the research efforts concentrate on a specific aspect or a particular methodology without considering the overall context. This paper presents a comprehensive survey of the most significant research activities in the area of client-side HTTP-based adaptive video streaming. It starts by decomposing the ABR module into three subcomponents, namely: resource estimation function, chunk request scheduling, and adaptation module. Each subcomponent encapsulates a particular function that is vital to the operation of an ABR scheme. A review of each of the subcomponents and how they interact with each other is presented. Furthermore, those external factors that are known to have a direct impact on the performance of an ABR module, such as content nature, CDN, and context, are discussed. In conclusion, this paper provides an extensive reference for further research in the field.
Femtosecond transient-grating techniques: Population and coherence dynamics involving ground and excited states (1999)

Time-resolved transient grating techniques (TG) arising from four-wave mixing (FWM) processes are explored for the study of molecular dynamics in gas-phase systems ranging from single atoms to large polyatomic molecules. For atomic species such as Ar and Xe, each TG signal shows only a peak at zero time delay when all three incident pulses are overlapped temporally. For diatomic O2 and N2 and linear triatomic CS2 molecules, the TG signals exhibit ground state rotational wave packet recurrences that can be analyzed to obtain accurate rotational constants for these molecules. With heavier systems such as HgI2, ground state vibrational and rotational wave packet dynamics are observed. Resonant excitation allows us to select between measurements that monitor wave packet dynamics, i.e., populations in the ground or excited states or coherences between the two electronic states. To illustrate these two cases we chose the X→B transition in I2. TG measurements yield dynamic information characteristic of vibrational and rotational wave packets from the ground and excited states. Reverse transient grating (RTG) experiments monitor the time evolution of an electronic coherence between the ground and excited states which includes vibrational and rotational information as well. Early time TG signal for the polyatomic samples CH2Cl2, CH2Br2, benzene, and toluene exhibit a coherence coupling feature at time zero followed by rotational dephasing. Differences in the amplitude of these two components are related to the contributions from the isotropic and anisotropic components of the molecular polarizability. A theoretical formalism is developed and used successfully to interpret and simulate the experimental transients. The measurements in this study provide gas-phase rotational and vibrational dephasing information that is contrasted, in the case of CS2, with liquid-phase measurements. This comparison provides a time scale for intramolecular dynamics, intermolecular collisions, and solvation dynamics.
Enantioselective Hydrogenation of Imines in Ionic Liquid/Carbon Dioxide Media (2004)

The enantioselective hydrogenation of N-(1-phenylethylidene)aniline using cationic iridium complexes with chiral phosphinooxazoline ligands was studied as a chemical probe to assess the potential of ionic liquid/carbon dioxide (IL/CO2) media for, multiphase catalysis. The biphasic system leads to activation, tuning, and immobilization of the catalyst that would be impossible in classical organic solvent systems or in either of the two unconventional media separately. In particular it is demonstrated that (i) the presence of CO2 can be beneficial or even mandatory for efficient hydrogenation in the IL; (ii) the precursor is activated in the IL by anion exchange allowing one to use in situ catalysts; (iii) the anion of the IL greatly influences the selectivity of the catalyst; (iv) the products are readily isolated from the catalyst solution by CO2 extraction without cross contamination of IL or catalyst; and (v) the IL leads to enhanced stability of the catalyst. These results are corroborated and rationalized on the basis of the physicochemical properties of the biphasic medium and the chemical characteristics of the catalytic systems.
Nanophotonic integration in state-of-the-art CMOS foundries (2011)

We demonstrate a monolithic photonic integration platform that leverages the existing state-of-the-art CMOS foundry infrastructure. In our approach, proven XeF2 post-processing technology and compliance with electronic foundry process flows eliminate the need for specialized substrates or wafer bonding. This approach enables intimate integration of large numbers of nanophotonic devices alongside high-density, high-performance transistors at low initial and incremental cost. We demonstrate this platform by presenting grating-coupled, microring-resonator filter banks fabricated in an unmodified 28 nm bulk-CMOS process by sharing a mask set with standard electronic projects. The lithographic fidelity of this process enables the high-throughput fabrication of second-order, wavelength-division-multiplexing (WDM) filter banks that achieve low insertion loss without post-fabrication trimming.
Advances in ultrarapid freezing for the preservation of cellular ultrastructure (1986)

Abstract Most of our current knowledge of cellular ultrastructure is derived from studies of chemically fixed and chemically cryoprotected preparations. In the first part of this review, we document the many artifacts associated with chemical techniques that render them unsuitable for further refinement of our understanding of cellular ultrastructure. The best method currently available for the preservation of cellular ultrastructure is ultrarapid freezing. The second part of this review is a consideration of the physics of ice crystal formation in biological systems, which suggests that ice crystals will be present in any frozen, uncryoprotected specimen. We define an ultrarapidly frozen preparation as one in which the ice crystals are so small as to be invisible at the electron microscopic level. Improvements in the ease of application and reliability of ultrarapid freezing techniques have reached the point that these techniques can be used by anyone requiring the best achievable preservation of cellular ultrastructure. In the third part of this review, we describe and critique the five methods of ultrarapid freezing in current use.
Duo Brings Hope of Immune Restoration (1998)

Paris—When Brigitte Autran and Christine Katlama attended medical school in Paris together in the 1970s, they had much in common: Both were specializing in infectious diseases, a field long dominated by men; both were avid and competitive skiers; and a few years later, as newly graduated doctors, they were among the first French physicians to take care of AIDS patients. Yet their paths diverged soon afterward. While Katlama continued caring for patients, Autran left clinical medicine for a career in basic immunological research.
Antimicrobial activity of gallium against virulentRhodococcus equiin vitroandin vivo (2006)

Rhodococcus equi, a facultative intracellular bacterium, causes severe pneumonia in foals. Evidence suggests that most foals become infected very early in life, when they have immature or ineffective innate immune responses. This study evaluated the antimicrobial activity of gallium against R. equi, as a potential chemoprophylactic and therapeutic agent. Rhodococcus equi was grown in media with various concentrations of gallium nitrate (GN), with and without excess iron. GN significantly inhibited growth and killed R. equi, and these effects were abolished with excess iron. Antimicrobial effects of Ga appear to be related to its interference with iron metabolism. Mice were treated orally with gallium maltolate (GaM), 10 or 50 mg/kg BW, or distilled H2O prior to and after experimental infection with R. equi. Six days post-infection, organs were harvested and R. equi concentrations assessed, and serum gallium concentrations determined. GaM was absorbed in a dose-dependent manner, and R. equi tissue burdens were greater in control mice than in all GaM-treated mice. GaM may aid in the control of disease by preventing development of overwhelming R. equi tissue burdens prior to the establishment of requisite innate and adaptive immune responses.
RET oligonucleotide microarray for the detection of RET mutations in multiple endocrine neoplasia type 2 syndromes. (2002)

Multiple endocrine neoplasia type 2 (MEN2) syndromes are inherited in an autosomal dominant fashion with high penetrance. There are three subtypes, namely, MEN2A (multiple endocrine neoplasia type 2A), MEN2B (multiple endocrine neoplasia type 2B), and familial medullary thyroid carcinoma. The variations in the RET gene play an important role in the MEN2 syndromes. In this work, we have developed a RET oligonucleotide microarray of 67 oligonucleotides to quickly detect RET mutations in MEN2 syndromes. The predominant RET mutations are missense mutations and are restricted to nine codons (codons 609, 611, 618, 620, 630, 634, 768, 804, and 918) in MEN2 syndromes. Missense mutations at codons 609, 611, 618, 620, and 634 have been identified in 98% of MEN2A families and in 85% of familial medullary thyroid carcinoma families. More than 95% of MEN2B patients also had a predominant mutation type at codon 918 (Met-->Thr). RET oligonucleotide microarray can detect RET missense mutations at these nine codons. Theoretically, a total of 55 missense mutation types can occur at eight codons (codons 609, 611, 618, 620, 630, 634, 768, and 804). RET oligonucleotide microarray is designed to detect all of these 55 missense mutation types at these eight codons and one predominant type at codon 918. Fifty-six oligonucleotides were designed for the 56 mutation types at nine codons, and 11 oligonucleotides were designed for the wild types and positive controls. We found RET mutations in all eight of the Korean MEN2A families (a total of 75 members; 27 affected members, 19 gene carriers, and 29 unaffected members) using the developed RET oligonucleotide microarray and an automatic sequencing. Because we found only five mutation types from eight MEN2A families, the international collaborations are required to see whether the RET oligonucleotide microarray may be used as a genetic diagnostic tool. Taken together, the RET oligonucleotide microarray can function as a fast and reliable genetic diagnostic device, which simplifies the process of detecting RET mutations.
Endothelium and control of vascular function. State of the Art lecture. (1989)

The response of isolated blood vessels to a variety of vasoactive agonists is modulated by the presence of endothelial cells. Indeed, these cells can release both dilator and constrictor substances. The major endothelium-derived relaxing factor may be nitric oxide, which activates soluble guanylate cyclase in the smooth muscle, although the endothelial cells also secrete an unidentified hyperpolarizing factor. Among the natural stimuli for the release of endothelium-derived relaxing factors are circulating hormones, platelet products, thrombin, shear stress, and certain autacoids. Endothelium-derived relaxing factors may contribute to the regulation of the release of atrial natriuretic factor and renin. The endothelial cells can also release constricting factors; among the likely candidates are superoxide anions or the peptide endothelin. In hypertensive blood vessels, the ability to release endothelium-derived relaxing factors but not endothelium-derived contracting factors is blunted.
Gli1can rescue the in vivo function ofGli2 (2001)

In mice, three Gli genes are thought to mediate sonic hedgehog (Shh) signaling collectively. Mis-expression studies and analysis of null mutants for each gene have indicated that the Gli proteins have different functions. In particular, Gli1 appears to be a constitutive activator, and Gli2 and Gli3 have repressor functions. To determine the precise functional differences between Gli1 and Gli2, we have expressed Gli1 in place of Gli2 from the endogenous Gli2 locus in mice. Strikingly, a low level of Gli1 can rescue all the Shh signaling defects in Gli2 mutants; however, only in the presence of a wild-type Shh gene. These studies demonstrate that only the activator function of Gli2 is actually required, and indicates that in specific situations, Shh can modulate the ability of Gli1 to activate target genes. Furthermore, expression of both copies of Gli1 in place of Gli2 does not disrupt spinal cord patterning, but does result in new gain-of-function defects that lead to lethality. We show that the defects are enhanced when Gli3 function is reduced, demonstrating that an important difference between Gli1 and Gli2 is the ability of Gli1 to antagonize Gli3 function.
Terrestrial Mammal Families and Creationist Perspectives on Speciation (2011)

Intrabaraminic speciation is a topic of concern to creationists, although creationists do not have a general idea of the magnitude of the speciation problem.  To rectify that, three mammal classifications were surveyed in order to identify the number of species or genera in a typical terrestrial mammal family, assuming that the rank of family approximates the baramin.  The results of this survey indicate that most mammal families contain relatively few species, but a few families are extremely speciose.  Any creationist mechanism of speciation must therefore account for both trends: widespread lack of speciation but occasional extravagant speciation.  Likewise, baraminology methods might need to be modified to accommodate the prevalence of small or monospecific baramins.
Death by a B Cell Superantigen (2003)

Amongst the many ploys used by microbial pathogens to interfere with host immune responses is the production of proteins with the properties of superantigens. These properties enable superantigens to interact with conserved variable region framework subdomains of the antigen receptors of lymphocytes rather than the complementarity determining region involved in the binding of conventional antigens. To understand how a B cell superantigen affects the host immune system, we infused protein A of Staphylococcus aureus (SpA) and followed the fate of peripheral B cells expressing B cell receptors (BCRs) with VH regions capable of binding SpA. Within hours, a sequence of events was initiated in SpA-binding splenic B cells, with rapid down-regulation of BCRs and coreceptors, CD19 and CD21, the induction of an activation phenotype, and limited rounds of proliferation. Apoptosis followed through a process heralded by the dissipation of mitochondrial membrane potential, the induction of the caspase pathway, and DNA fragmentation. After exposure, B cell apoptotic bodies were deposited in the spleen, lymph nodes, and Peyer's patches. Although in vivo apoptosis did not require the Fas death receptor, B cells were protected by interleukin (IL)-4 or CD40L, or overexpression of Bcl-2. These studies define a pathway for BCR-mediated programmed cell death that is VH region targeted by a superantigen.
The highly selective 5‐hydroxytryptamine (5‐HT)2A receptor antagonist, EMD 281014, significantly increases swimming and decreases immobility in male congenital learned helpless rats in the forced swim test (2004)

We examined the effect of the highly selective 5-hydroxytryptamine (5-HT)(2A) receptor antagonist 7-[4-[2-(4-fluoro-phenyl)-ethyl]-piperazine-1-carbonyl]-1H-indole-3-carbonitrile HCl (EMD 281014) in congenital learned helpless male rats in the forced swim test. The administration of EMD-281014 (0.3-30 mg/kg i.p.) to congenital learned helpless rats dose-dependently and significantly (at 10 and 30 mg/kg) decreased immobility and increased swimming compared to vehicle-treated animals. Thus, EMD 281014 produces effects in the forced swim test resembling those of antidepressants.
Identification of a Receptor-Binding Region within Domain 4 of the Protective Antigen Component of Anthrax Toxin (1999)

Anthrax toxin from Bacillus anthracis is a three-component toxin consisting of lethal factor (LF), edema factor (EF), and protective antigen (PA). LF and EF are the catalytic components of the toxin, whereas PA is the receptor-binding component. To identify residues of PA that are involved in interaction with the cellular receptor, two solvent-exposed loops of domain 4 of PA (amino acids [aa] 679 to 693 and 704 to 723) were mutagenized, and the altered proteins purified and tested for toxicity in the presence of LF. In addition to the intended substitutions, novel mutations were introduced by errors that occurred during PCR. Substitutions within the large loop (aa 704 to 723) had no effect on PA activity. A mutated protein, LST-35, with three substitutions in the small loop (aa 679 to 693), bound weakly to the receptor and was nontoxic. A mutated protein, LST-8, with changes in three separate regions did not bind to receptor and was nontoxic. Toxicity was greatly decreased by truncation of the C-terminal 3 to 5 aa, but not by their substitution with nonnative residues or the extension of the terminus with nonnative sequences. Comparison of the 28 mutant proteins described here showed that the large loop (aa 704 to 722) is not involved in receptor binding, whereas residues in and near the small loop (aa 679 to 693) play an important role in receptor interaction. Other regions of domain 4, in particular residues at the extreme C terminus, appear to play a role in stabilizing a conformation needed for receptor-binding activity.