gebhart/patrepeval huggingface dataset:
The Epidemiology of Invasive Group A Streptococcal Infection and Potential Vaccine Implications: United States, 2000-2004 (2007)

GAS remains an important cause of severe disease in the United States. The introduction of a vaccine could significantly reduce morbidity and mortality due to these infections.
B7-CD28 interaction is a late acting co-stimulatory signal for human T cell responses (1997)

The interaction of CD28 with one of the B7 molecules (CD80 and CD86) on professional antigen-presenting cells (APC) is generally considered as the most important co-stimulatory signal for T cell activation. APC in a resting condition express either no or only low levels of B7 molecules. These are up-regulated as a result of interactions with activated T cells, thus suggesting that B7-CD28 interaction is not required at initiation of T cell activation. To study this issue, we blocked B7-CD28 interaction at various time points after in vitro stimulation of peripheral blood T cells with allogeneic monocytes. Epstein-Barr virus-transformed B cells or soluble antigens. We observed that T cell proliferation and IL-2 production were inhibited by B7-blocking agents (CTLA-4-Ig or anti-B7 mAb) almost to the same degree when added either at initiation of culture or 24 h later. B7-blocking agents still resulted in significant inhibition of allogeneic T cell activation when added after 48 h. Furthermore, when CTLA-4-Ig was added at the start of an allogeneic T cell stimulation, addition of anti-CD28 mAb after 24 h of culture nearly fully restored T cell proliferation to control levels. Finally, we demonstrate that delayed addition of B7-blocking agents together with cyclosporin A 1 day after the onset of culture of T cells with allogeneic B cells is highly efficient to induce energy as evaluated by lack of proliferation, cytotoxic T lymphocyte reactivity and IFN-gamma or IL-5 production upon alloantigen rechallenge. Taken together, our data can explain why B7 expression on APC is not required at the time of initial APC-T cell contact, and suggest that the effect of the CD28 signal indeed consists in prolonging IL-2 production and amplifying T cell responses, rather than in providing a critical co-stimulatory signal at the time of initial TCR triggering.
The lipid composition of drusen, Bruch's membrane, and sclera by hot stage polarizing light microscopy. (2001)

HSPM is a valuable technique for evaluating the nature of lipid deposits in aging eyes. Further studies are warranted to determine whether similar changes are also present in eyes with age-related macular degeneration.
T helper type-1 (Th1)/Th2 profiles of peripheral blood mononuclear cells (PBMC); responses to antigens of Chlamydia trachomatis in subjects with severe trachomatous scarring (1996)

Increased stimulation of Th2 cytokines may contribute to the development of persistent ocular chlamydial infection, resulting in the blinding pathological changes of trachoma. Proliferation and cytokine production profiles of PBMC in response to stimulation with antigens of Chlamydia trachomatis were compared in 30 patients with severe conjunctival scarring due to trachoma and in 30 age-, sex- and location-matched controls. Interferon-gamma (IFN-gamma) and IL-4 were detected at the single-cell level by ELISPOT assay. Transcription of the genes encoding IFN-gamma, IL-4 and IL-10 was detected in mRNA isolated from parallel cultures of PBMC using reverse transcriptase-polymerase chain reaction (RT-PCR). Incubation with the chlamydial heat shock protein (hsp)60 resulted in increased numbers of IL-4-producing cells in PBMC isolated from patients with scarring disease and increased secretion of IFN-gamma from PBMC of control subjects. Incubation with the chlamydial major outer membrane protein (MOMP) increased the number of IFN-gamma-producing cells in the control group only. Messenger RNA encoding IL-4 was only detected in PBMC of patients with scarring disease after in vitro stimulation with chlamydial antigens, but IFN-gamma mRNA and IL-10 mRNA were also more frequently detected in this group. Thirty-eight subjects were HLA-DRB1 and -DQB1 typed. Associations were observed between certain HLA class II alleles and cellular immune responses to chlamydial antigens. No HLA associations were found with clinical status, and overall we found no evidence of strong associations and the type of immune response. These data are consistent with a role for Th2 cells and cytokines in the pathogenesis of trachomatous scarring.
HOXB13-to-IL17BR Expression Ratio Is Related With Tumor Aggressiveness and Response to Tamoxifen of Recurrent Breast Cancer: A Retrospective Study (2007)

High HOXB13-to-IL17BR ratio expression levels associate with both tumor aggressiveness and tamoxifen therapy failure.
Estimating Drivable Collision-Free Space from Monocular Video (2015)

In this paper we propose a novel algorithm for estimating the drivable collision-free space for autonomous navigation of on-road and on-water vehicles. In contrast to previous approaches that use stereo cameras or LIDAR, we show a method to solve this problem using a single camera. Inspired by the success of many vision algorithms that employ dynamic programming for efficient inference, we reduce the free space estimation task to an inference problem on a 1D graph, where each node represents a column in the image and its label denotes a position that separates the free space from the obstacles. Our algorithm exploits several image and geometric features based on edges, color, and homography to define potential functions on the 1D graph, whose parameters are learned through structured SVM. We show promising results on the challenging KITTI dataset as well as video collected from boats.
Active Radar Cross Section Reduction (2015)

This book discusses the active and passive radar cross section (RCS) estimation and techniques to examine the low observable aerospace platforms. It begins with the fundamentals of RCS, followed by the dielectric, magnetic and metamaterials parameters of the constituent materials and then explains various methods and the emerging trends followed in this area of study. The RCS estimation of phased array including the mutual coupling effect is also presented in detail in the book. The active RCS reduction is carefully touched upon through the performance of phased arrays, sidelobe cancellers and mitigation of multipath effect. Providing information on various adaptive algorithms like least mean square (LMS), recursive least square (RLS) and weighted least square algorithms, the authors also mention the recent developments in the area of embedded antennas, conformal load bearing antenna, metamaterials and frequency selective surface (FSS) based RCS reduction.
Boron Dipyrromethene Chromophores: Next Generation Triplet Acceptors/Annihilators for Low Power Upconversion Schemes (2008)

In the present study, the red-light absorbing platinum(II) tetraphenyltetrabenzoporphyrin (PtTPBP) was used as a triplet sensitizer in conjunction with two distinct iodophenyl-bearing BODIPY derivatives independently serving as triplet acceptors/annihilators poised for photon upconversion based on triplet-triplet annihilation. In deaerated benzene solutions, extremely stable and high quantum efficiency green (Phi(UC) = 0.0313 +/- 0.0005) and yellow (Phi(UC) = 0.0753 +/- 0.0036) upconverted emissions were observed from selective red excitation of the PtTPBP sensitizer at 635 +/- 5 nm. The current systems represent the first examples of photon upconversion where aromatic hydrocarbons do not serve the role of triplet acceptor/annihilator. Notably, the nature of the current chromophore compositions permitted highly reproducible upconversion quantum efficiency determinations while permitting the evaluation of the triplet-triplet annihilation quantum yields in both instances.
Ultralow Surface Energy Plasma Polymer Films (2000)

Room-temperature pulsed plasma polymerization of long-chain perfluoroacrylates produces well-adhered liquid-repellent (hydrophobic and oleophobic) films. Critical surface tension values as low as γc = 4.3 mN m-1 have been measured on coated flat glass substrates. X-ray photoelectron spectroscopy, Fourier transform infrared, and atomic force microscopy characterization of these surfaces indicates that the low surface energy perfluoroalkyl chains remain intact, while polymerization occurs predominantly via the acrylate carbon−carbon double bond during the plasma duty cycle off-period.
Production ofNeisseria meningitidisTransferrin-Binding Protein B by RecombinantBordetella pertussis (2001)

Neisseria meningitidis serogroup B infections are among the major causes of fulminant septicemia and meningitis, especially severe in young children, and no broad vaccine is available yet. Because of poor immunogenicity of the serogroup B capsule, many efforts are now devoted to the identification of protective protein antigens. Among those are PorA and, more recently, transferrin-binding protein B (TbpB). In this study, TbpB of N. meningitidis was genetically fused to the N-terminal domain of the Bordetella pertussis filamentous hemagglutinin (FHA), and the fha-tbpB hybrid gene was expressed in B. pertussis either as a plasmid-borne gene or as a single copy inserted into the chromosome. The hybrid protein was efficiently secreted by the recombinant strains, despite its large size, and was recognized by both anti-FHA and anti-TbpB antibodies. A single intranasal administration of recombinant virulent or pertussis-toxin-deficient, attenuated B. pertussis to mice resulted in the production of antigen-specific systemic immunoglobulin G (IgG), as well as local IgG and IgA. The anti-TbpB serum antibodies were of the IgG1, IgG2a, and IgG2b isotypes and were found to express complement-mediated bactericidal activity against N. meningitidis. These observations indicate that recombinant B. pertussis may be a promising vector for the development of a mucosal vaccine against serogroup B meningococci.
Defect modes in photonic band structures: a Green’s function approach using vector Wannier functions (1993)

I present a treatment of highly localized defect states in photonic band-gap crystals. Vector Wannier functions, which are expected to be highly localized about the atomic sites, are introduced as an orthonormal basis to expand the fields within the crystal. A Green’s function formalism is employed to take advantage of the fact that the defect occupies only a small fraction of the volume within a primitive cell and the localized nature of the vector Wannier functions. This suggests that the size of the matrices involved in determining the defect mode frequencies may be relatively modest.
BRAF Mutations in Thyroid Tumors Are Restricted to Papillary Carcinomas and Anaplastic or Poorly Differentiated Carcinomas Arising from Papillary Carcinomas (2003)

Activating point mutations of the BRAF gene have been recently reported in papillary thyroid carcinomas. In this study, we analyzed 320 thyroid tumors and six anaplastic carcinoma cell lines and detected BRAF mutations in 45 (38%) papillary carcinomas, two (13%) poorly-differentiated carcinomas, three (10%) anaplastic carcinomas, and five (83%) thyroid anaplastic carcinoma cell lines but not in follicular, Hürthle cell, and medullary carcinomas, follicular and Hürthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-->A transversion at nucleotide 1796. In papillary carcinomas, BRAF mutations were associated with older age, classic papillary carcinoma or tall cell variant histology, extrathyroidal extension, and more frequent presentation at stages III and IV. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well-differentiated and dedifferentiated components. These data indicate that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas. They are associated with distinct phenotypical and biological properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.
Organogenesis in a dish: Modeling development and disease using organoid technologies (2014)

Classical experiments performed half a century ago demonstrated the immense self-organizing capacity of vertebrate cells. Even after complete dissociation, cells can reaggregate and reconstruct the original architecture of an organ. More recently, this outstanding feature was used to rebuild organ parts or even complete organs from tissue or embryonic stem cells. Such stem cell-derived three-dimensional cultures are called organoids. Because organoids can be grown from human stem cells and from patient-derived induced pluripotent stem cells, they have the potential to model human development and disease. Furthermore, they have potential for drug testing and even future organ replacement strategies. Here, we summarize this rapidly evolving field and outline the potential of organoid technology for future biomedical research.
Physical mapping of human loci homologous to the chicken nov proto-oncogene. (1992)

The human locus (novH) corresponding to the nov protooncogene overexpressed in avian nephroblastoma has been identified and mapped on chromosome 8q24.1. Another locus sharing homology with novH and corresponding to the connective tissue growth factor (CTGF) gene has also been mapped on chromosome 6q23.1. The chromosomal assignment of nov and CTGF proximal to c-myc and c-myb respectively is of interest because chromosomal abnormalities involving these regions have been associated with different human tumors including Wilms'.
Outpatient closure of the patent ductus arteriosus. (1988)

We have modified and applied to selected outpatients the transvenous approach to correction of patent ductus arteriosus (PDA) with the Rashkind PDA Occluder. Modifications included establishing the diagnosis and PDA anatomy before catheterization with echocardiography. The sedation/anesthetic regimen was altered to meet the needs with respect to transcatheter PDA closure rather than diagnostic cardiac catheterization. Anticoagulation was avoided. A strategy for management of pin entrapment in the foam was devised. Residual trans-PDA flow after umbrella placement was temporarily occluded with balloon-tipped catheters. These modifications were used in 23 consecutive patients with uncomplicated PDA. Closure was successful in each child. Nineteen of 23 patients were discharged on the day of the procedure. No serious complications were encountered.
Combined Yeast β-Glucan and Antitumor Monoclonal Antibody Therapy Requires C5a-Mediated Neutrophil Chemotaxis via Regulation of Decay-Accelerating Factor CD55 (2007)

Administration of a combination of yeast-derived beta-glucan with antitumor monoclonal antibodies (mAb) has significant therapeutic efficacy in a variety of syngeneic murine tumor models. We have now tested this strategy using human carcinomas implanted in immunocompromised severe combined immunodeficient mice. Combined immunotherapy was therapeutically effective in vivo against NCI-H23 human non-small-cell lung carcinomas, but this modality was surprisingly ineffective against SKOV-3 human ovarian carcinomas. Whereas NCI-H23 tumors responded to this combination therapy with increased intratumoral neutrophil infiltration and C5a production, these responses were lacking in treated SKOV-3 tumors. Further results suggested that SKOV-3 tumors were protected by up-regulation of the membrane complement regulatory protein CD55 (decay-accelerating factor). Blockade of CD55 in vitro led to enhanced deposition of C activation product C3b and increased cytotoxicity mediated by beta-glucan-primed neutrophils. In vivo, administration of anti-CD55 mAb along with beta-glucan and anti-Her-2/neu mAb caused tumor regression and greatly improved long-term survival in animals bearing the previously resistant SKOV-3 tumors. This was accompanied by increased intratumoral neutrophil accumulation and C5a production. We conclude that CD55 suppresses tumor killing by antitumor mAb plus beta-glucan therapy (and, perhaps, in other circumstances). These results suggest a critical role for CD55 to regulate iC3b and C5a release and in turn to influence the recruitment of beta-glucan-primed neutrophils eliciting killing activity.
The Murine Double-Stranded RNA-Dependent Protein Kinase PKR Is Required for Resistance to Vesicular Stomatitis Virus (2000)

Interferon (IFN)-induced antiviral responses are mediated through a variety of proteins, including the double-stranded RNA-dependent protein kinase PKR. Here we show that fibroblasts derived from PKR(-/-) mice are more permissive for vesicular stomatitis virus (VSV) infection than are wild-type fibroblasts and demonstrate a deficiency in alpha/beta-IFN-mediated protection. We further show that mice lacking PKR are extremely susceptible to intranasal VSV infection, succumbing within days after instillation with as few as 50 infectious viral particles. Again, alpha/beta-IFN was unable to rescue PKR(-/-) mice from VSV infection. Surprisingly, intranasally infected PKR(-/-) mice died not from pathology of the central nervous system but rather from acute infection of the respiratory tract, demonstrating high virus titers in the lungs compared to similarly infected wild-type animals. These results confirm the role of PKR as the major component of IFN-mediated resistance to VSV infection. Since previous reports have shown PKR to be nonessential for survival in animals challenged with encephalomyocarditis virus, influenza virus, and vaccinia virus (N. Abraham et al., J. Biol. Chem. 274:5953-5962, 1999; Y. Yang et al., EMBO J. 14:6095-6106, 1995), our findings serve to highlight the premise that host dependence on the various mediators of IFN-induced antiviral defenses is pathogen specific.
Polymeric synthetic nanoparticles for the induction of antigen-specific immunological tolerance (2014)

Current treatments to control pathological or unwanted immune responses often use broadly immunosuppressive drugs. New approaches to induce antigen-specific immunological tolerance that control both cellular and humoral immune responses are desirable. Here we describe the use of synthetic, biodegradable nanoparticles carrying either protein or peptide antigens and a tolerogenic immunomodulator, rapamycin, to induce durable and antigen-specific immune tolerance, even in the presence of potent Toll-like receptor agonists. Treatment with tolerogenic nanoparticles results in the inhibition of CD4+ and CD8+ T-cell activation, an increase in regulatory cells, durable B-cell tolerance resistant to multiple immunogenic challenges, and the inhibition of antigen-specific hypersensitivity reactions, relapsing experimental autoimmune encephalomyelitis, and antibody responses against coagulation factor VIII in hemophilia A mice, even in animals previously sensitized to antigen. Only encapsulated rapamycin, not the free form, could induce immunological tolerance. Tolerogenic nanoparticle therapy represents a potential novel approach for the treatment of allergies, autoimmune diseases, and prevention of antidrug antibodies against biologic therapies.
Dominant negative mutant Cyclin T1 proteins inhibit HIV transcription by specifically degrading Tat (2008)

These results suggest that CycT1-U7 inhibits HIV transcription by promoting a rapid degradation of Tat. These mutant CycT1 proteins represent a novel class of specific inhibitors for HIV transcription that could potentially be used in the design of anti-viral therapy.
Monitoring of heart and respiratory rates by photoplethysmography using a digital filtering technique (1996)

An apparatus for simultaneously monitoring heart and respiratory rates was developed using photoplethysmography (PPG) and digital filters, and compared with conventional methods. The PPG signal, which includes both heart and respiratory components, was measured at the earlobe with an original transmission mode photoplethysmographic device. A digital filtering technique was used to distinguish heart and respiratory signals from the PPG signal. The cut-off frequency of the respiratory signal filter was selected automatically depending on the heart rate. Using digital filtering techniques, heart and respiratory signals were separated at rest and during exercise. The digital signal processor was employed to realize an adaptive and real-time filtering. The heart rate was calculated by the zero-crossing method and the respiratory rate from the peak interval of the filtered signal. To evaluate the newly developed monitor, an ECG for heart rate and a transthoracic impedance plethysmogram for respiratory rate were monitored simultaneously. To obtain higher heart and respiratory rates, exercise was performed on an electrical bicycle ergometer. Heart and respiratory rates calculated by the new method compare to those obtained from ECG and the transthoracic impedance plethysmogram. The maximum error of heart and respiratory rates was 10 beats/min and 7 breaths/min, respectively.
The first bromodomain of Brdt, a testis-specific member of the BET sub-family of double-bromodomain-containing proteins, is essential for male germ cell differentiation (2007)

Brdt is a testis-specific member of the distinctive BET sub-family of bromodomain motif-containing proteins, a motif that binds acetylated lysines and is implicated in chromatin remodeling. Its expression is restricted to the germ line, specifically to pachytene and diplotene spermatocytes and early spermatids. Targeted mutagenesis was used to generate mice carrying a mutant allele of Brdt, Brdt(Delta)(BD1), which lacks only the first of the two bromodomains that uniquely characterize BET proteins. Homozygous Brdt(Delta)(BD1/)(Delta)(BD1) mice were viable but males were sterile, producing fewer and morphologically abnormal sperm. Aberrant morphogenesis was first detected in step 9 elongating spermatids, and those elongated spermatids that were formed lacked the distinctive foci of heterochromatin at the peri-nuclear envelope. Quantitative reverse transcription (RT)-PCR showed threefold increased levels of histone H1t (Hist1h1t) in Brdt(Delta)(BD1/)(Delta)(BD1) testes and chromatin immunoprecipitation revealed that Brdt protein, but not Brdt(DeltaBD1) protein, was associated with the promoter of H1t. Intracytoplasmic sperm injection suggested that the DNA in the Brdt(Delta)(BD1) mutant sperm could support early embryonic development and yield functional embryonic stem cells. This is the first demonstration that deletion of just one of the two bromodomains in members of the BET sub-family of bromodomain-containing proteins has profound effects on in vivo differentiation.
Using a sentence compression pipeline for the summarization of email threads in an archive (2015)

Automatic text summarization is an important subfield in Natural Language Processing (NLP). In this paper, we examine how to summarize the contents of an email thread into a single short summary. We implement a multi stage NLP pipeline that includes key sentence extraction, sentence compression, machine learning and language models to summarize email threads in the SIGCSE email list archives. We then analyze our results using the automated summary evaluation technique known as ROUGE-2, with our ROUGE-2 scores averaging 8.01. These results compare favorably to other summarization approaches.