gebhart/patrepeval huggingface dataset:
The sheep Ig variable region repertoire consists of a single VH family (1996)

Nine germ-line Ig heavy chain variable (VH) segments (including three pseudogenes) were isolated from a genomic DNA library, and the other six were obtained by PCR, using 5'and 3' primers deduced from the first three. They appear to belong to a homogeneous VH gene family, with >80% sequence identity. This sheep VH gene family is related to the human VH4 family and to the murine VH1 subgroup (clan II). Southern blot analysis shows a maximum of 10 positive restriction fragments; therefore, the nine VH genes isolated probably constitute the major part of the repertoire. Thirty-one expressed mu variable regions (and one gamma 1 variable region) were obtained from adult spleen by either cDNA cloning or anchored reverse transcriptase-PCR; they are >80% similar to each other (in their leader to framework 3 regions) and to the germ-line sequences as well. The sheep VH repertoire thus seems to derive from a small (approximately 10 members) germ-line gene family, and its diversification must rely chiefly on junctional (D and/or N regions) diversity and somatic hypermutations.
Apoptosis and Caspases in Neurodegenerative Diseases (2003)

A form of cell death called apoptosis is a prominent feature in a broad spectrum of neurodegenerative diseases, ranging from stroke to Huntington's disease. Hypoxia, toxic cytokines, damage to mitochondria, and noxious peptides are capable of inducing apoptosis; each of these mechanisms can account for the death of specific types of neurons in neurodegenerative diseases. Pharmacologic interference with the induction or completion of apoptosis holds promise for the treatment of these disorders, and clinical trials with one such agent are already under way.
Impaired glucose tolerance and impaired fasting glucose. (2004)

Impaired glucose tolerance and impaired fasting glucose form an intermediate stage in the natural history of diabetes mellitus. From 10 to 15 percent of adults in the United States have one of these conditions. Impaired glucose tolerance is defined as two-hour glucose levels of 140 to 199 mg per dL (7.8 to 11.0 mmol) on the 75-g oral glucose tolerance test, and impaired fasting glucose is defined as glucose levels of 100 to 125 mg per dL (5.6 to 6.9 mmol per L) in fasting patients. These glucose levels are above normal but below the level that is diagnostic for diabetes. Patients with impaired glucose tolerance or impaired fasting glucose have a significant risk of developing diabetes and thus are an important target group for primary prevention. Risk factors for diabetes include family history of diabetes, body mass index greater than 25 kg per m2, sedentary lifestyle, hypertension, dyslipidemia, history of gestational diabetes or large-for-gestational-age infant, and polycystic ovary syndrome. Blacks, Latin Americans, Native Americans, and Asian-Pacific Islanders also are at increased risk for diabetes. Patients at higher risk should be screened with a fasting plasma glucose level. When the diagnosis of impaired glucose tolerance or impaired fasting glucose is made, physicians should counsel patients to lose 5 to 7 percent of their body weight and engage in moderate physical activity for at least 150 minutes per week. Drug therapy with metformin or acarbose has been shown to delay or prevent the onset of diabetes. However, medications are not as effective as lifestyle changes, and it is not known if treatment with these drugs is cost effective in the management of impaired glucose tolerance.
Gaussian-Apodized Apertures And Small-Angle Scatter Measurement (1989)

Gaussian-apodized apertures are investigated for the purpose of reducing the diffraction background of a small-angle scatterometer. The farfield irradiance distributions of weakly truncated and untruncated Gaussian beams are compared. The envelope of diffraction ringing is shown to decrease proportionately with the level of truncation in the pupil. Spherical aberration and defocus are shown to have little effect on the higher-order diffraction rings of Gaussian-apodized apertures. A method is presented for determining the scattered irradiance level for a given bidirectional reflectance distribution function in relation to the peak irradiance of the point spread function. An example is provided that demonstrates that the small-angle diffraction background can be reduced by orders of magnitude as compared with a scatterometer with an unapodized pupil. Analysis of the point spread function is provided from 0 to 16 arcmin for an exit pupil diameter of 25.4 mm and A = 0.6328 Am. The numerical methods utilized to obtain these results are discussed.
Functional and pathological effects of prolonged hyperoxia in neonatal mice (1998)

Bronchopulmonary dysplasia (BPD) commonly develops in premature infants. An improved understanding of the pathophysiology of BPD requires better models. In this study, neonatal FVB/N mice were exposed to room air or 85% oxygen for 28 days. Neonatal hyperoxia resulted in decreased alveolar septation, increased terminal air space size, and increased lung fibrosis. These changes were evident after 7 days and more pronounced by 28 days. Decreased alveolarization was preceded by decreased proliferation of lung cells. After 3 days of hyperoxia, cell proliferation was decreased compared with room air littermates. Cell proliferation continued to be decreased in the first 2 wk but normalized by 4 wk. Hyperoxia caused an increased number of inflammatory cells in lung tissue and in lung lavage fluid. Analysis of lung tissue RNA by RT-PCR showed that hyperoxia increased expression of the proinflammatory cytokines interleukin-1alpha and macrophage inflammatory protein-1alpha. Prolonged neonatal hyperoxia caused functional changes, decreasing lung volume and pulmonary compliance. We conclude that prolonged exposure of neonatal mice to hyperoxia creates a lesion that is very similar to human BPD and suggests that altered cell proliferation may be important in the pathogenesis of chronic neonatal lung disease.
Modulation of Inducible Nitric Oxide Synthase Expression by the Attaching and Effacing Bacterial Pathogen Citrobacter rodentium in Infected Mice (2002)

Citrobacter rodentium belongs to the attaching and effacing family of enteric bacterial pathogens that includes both enteropathogenic and enterohemorrhagic Escherichia coli. These bacteria infect their hosts by colonizing the intestinal mucosal surface and intimately attaching to underlying epithelial cells. The abilities of these pathogens to exploit the cytoskeleton and signaling pathways of host cells are well documented, but their interactions with the host's antimicrobial defenses, such as inducible nitric oxide synthase (iNOS), are poorly understood. To address this issue, we infected mice with C. rodentium and found that iNOS mRNA expression in the colon significantly increased during infection. Immunostaining identified epithelial cells as the major source for immunoreactive iNOS. Finding that nitric oxide (NO) donors were bacteriostatic for C. rodentium in vitro, we examined whether iNOS expression contributed to host defense by infecting iNOS-deficient mice. Loss of iNOS expression caused a small but significant delay in bacterial clearance without affecting tissue pathology. Finally, immunofluorescence staining was used to determine if iNOS expression was localized to infected cells by staining for the C. rodentium virulence factor, translocated intimin receptor (Tir), as well as iNOS. Interestingly, while more than 85% of uninfected epithelial cells expressed iNOS, fewer than 15% of infected (Tir-positive) cells expressed detectable iNOS. These results demonstrate that both iNOS and intestinal epithelial cells play an active role in host defense during C. rodentium infection. However, the selective expression of iNOS by uninfected but not infected cells suggests that this pathogen has developed mechanisms to locally limit its exposure to host-derived NO.
Endothelial Endocytic Pathways: Gates for Vascular Drug Delivery (2004)

Vascular endothelium plays strategic roles in many drug delivery paradigms, both as an important therapeutic target itself and as a barrier for reaching tissues beyond the vascular wall. Diverse means are being developed to improve vascular drug delivery including stealth liposomes and polymer carriers. Affinity carriers including antibodies or peptides that specifically bind to endothelial surface determinants, either constitutive or pathological, enhance targeting of drugs to endothelial cells (EC) in diverse vascular areas. In many cases, binding to endothelial surface determinants facilitates internalization of the drug/carrier complex. There are several main endocytic pathways in EC, including clathrin- and caveoli-mediated endocytosis, phagocytosis and macropinocytosis (these two are less characteristic of generic EC) and the recently described Cell Adhesion Molecule (CAM)-mediated endocytosis. The latter may be of interest for intracellular drug delivery to EC involved in inflammation or thrombosis. The metabolism and effects of internalized drugs largely depend on the routes of intracellular trafficking, which may lead to degrading lysosomal compartments or other organelles, recycling to the plasma membrane or transcytosis to the basal surface of endothelium. The latter route, characteristic of caveoli-mediated endocytosis, may serve for trans-endothelial drug delivery. Paracellular trafficking, which can be enhanced under pathological conditions or by auxiliary agents, represents an alternative for transcytosis. Endothelial surface determinants involved in endocytosis, mechanisms of the latter and trafficking pathways, as well as specific characteristics of EC in different vascular areas, are discussed in detail in the context of modern paradigms of vascular drug delivery.
Site-specific mutagenesis of Agrobacterium Ti plasmids and transfer of genes to plant cells. (1981)

A general method is described for the use of tumor-inducing (Ti) plasmids as experimental gene-vectors for plant cells. Intermediate vectors, containing specific Ti plasmid sequences and capable of replication in both E. coli and Agrobacterium strains, were constructed and used for the in vitro introduction of isolated DNA fragments into predetermined sites of the T-region derived fragments. Site-specific inserts and/or deletions-substitutions in Ti plasmids were produced by exchange of the modified T-region sequences for the wild-type sequence by in vivo recombination between intermediate vectors and resident Ti plasmids. This method was applied for the isolation of mutant Ti plasmids affecting either morphogenetic properties or opine synthesis in crown gall tumors. Foreign DNA, inserted at different sites in the T-region of both octopine and nopaline Ti plasmids, was shown to be cotransferred with the T-DNA and to be stably maintained in the transformed plant cells.
Dual Blockade of PD-1 and CTLA-4 Combined with Tumor Vaccine Effectively Restores T-Cell Rejection Function in Tumors (2013)

Tumor progression is facilitated by regulatory T cells (Treg) and restricted by effector T cells. In this study, we document parallel regulation of CD8(+) T cells and Foxp3(+) Tregs by programmed death-1 (PD-1, PDCD1). In addition, we identify an additional role of CTL antigen-4 (CTLA-4) inhibitory receptor in further promoting dysfunction of CD8(+) T effector cells in tumor models (CT26 colon carcinoma and ID8-VEGF ovarian carcinoma). Two thirds of CD8(+) tumor-infiltrating lymphocytes (TIL) expressed PD-1, whereas one third to half of CD8(+) TIL coexpressed PD-1 and CTLA-4. Double-positive (PD-1(+)CTLA-4(+)) CD8(+) TIL had characteristics of more severe dysfunction than single-positive (PD-1(+) or CTLA-4(+)) TIL, including an inability to proliferate and secrete effector cytokines. Blockade of both PD-1 and CTLA-4 resulted in reversal of CD8(+) TIL dysfunction and led to tumor rejection in two thirds of mice. Double blockade was associated with increased proliferation of antigen-specific effector CD8(+) and CD4(+) T cells, antigen-specific cytokine release, inhibition of suppressive functions of Tregs, and upregulation of key signaling molecules critical for T-cell function. When used in combination with GVAX vaccination (consisting of granulocyte macrophage colony-stimulating factor-expressing irradiated tumor cells), inhibitory pathway blockade induced rejection of CT26 tumors in 100% of mice and ID8-VEGF tumors in 75% of mice. Our study indicates that PD-1 signaling in tumors is required for both suppressing effector T cells and maintaining tumor Tregs, and that PD-1/PD-L1 pathway (CD274) blockade augments tumor inhibition by increasing effector T-cell activity, thereby attenuating Treg suppression.
Influenza Hemagglutination-Inhibition Antibody Titer as a Correlate of Vaccine-Induced Protection (2011)

Background. Antibody to influenza virus hemagglutinin has been traditionally associated with protection. Questions have been raised about its use as a surrogate for vaccine efficacy, particularly with regard to an absolute titer indicating seroprotection.
Deletion ofAdam6inMus musculusleads to male subfertility and deficits in sperm ascent into the oviduct (2018)

The Adisintegrin and metalloprotease domain-containing (ADAM) family of proteins is involved in cell adhesion, migration, proteolysis, and signaling. Many ADAMs are required for reproduction; however, the role of Adam6 has remained largely unknown. In the course of humanizing the mouse immunoglobulin heavy chain (IgH) locus, we generated Adam6-deficient mice that demonstrate severe subfertility. We decided to elucidate the role of ADAM6 in fertility and explore the underlying mechanisms. Despite normal sperm development and motility, Adam6-deficient mice display diminished male fertility, have abnormal sperm adhesion, and most importantly cannot transition from uterus to oviduct. To test whether ADAM6 is required for sperm's binding to extracellular matrix (ECM) components, we used a panel of ECM components and showed that unlike normal sperm, Adam6-deficient sperm cannot bind fibronectin, laminin, and tenascin. Reintroduction of Adam6 into these deficient mice repaired sperm interaction with ECM, restored male fertility, and corrected the sperm transport deficit. Together, our data suggest that ADAM6, either alone or in complex with other proteins, aids sperm transport through the female reproductive tract by providing a temporary site of attachment of sperm to ECM components prior to ascent into the oviduct.
Suppression of nitric oxide generated by inflammatory macrophages by calcitonin gene-related peptide in aqueous humor. (1998)

Calcitonin gene-related peptide is a constitutive neuropeptide in aqueous humor. Through CGRP, aqueous humor suppresses nitric oxide production by activated macrophages. This suppression appears to result from inhibiting NOS2 enzymatic activity, rather than from suppressing NOS2 synthesis. The results imply that the ocular microenvironment has diverse immunoregulatory mechanisms that suppress induction, activation, and mediation of immunogenic inflammation.
Ockham: Avignon, Before and After (1987)

In this paper I shall ask and try to respond to two questions. The first question is: why did William of Ockham go to Avignon?; the second is: what effect did his visit there have on him?
3D articulated models and multi-view tracking with silhouettes (1999)

We propose a method to estimate the motion of a person filmed by two or more fixed cameras. The novelty of our technique is its ability to cope with fast movements, self-occlusions and noisy images. Our algorithms are based on the latest works on calibration and image segmentation developed in our lab. We compare the projections of a 3D model of a person on the images to the detected silhouettes of the person, and by creating forces that will move the 3D model towards the final estimation of the real pose. We developed a fast algorithm that computes the motion of the articulated 3D model. We show that our results are good, even if the cameras are not synchronized.
Fast Forward — Neoadjuvant Cancer Immunotherapy (2018)

Immunotherapies that are based on blocking the axis of the programmed death 1 (PD-1) pathway are having a transformational effect in cancer medicine. To date, the Food and Drug Administration has approved PD-1 pathway inhibitors for 10 types of cancer, with continued clinical study under way. The therapeutic efficacy of these drugs relies on endogenous tumor-antigen–specific T cells that are functionally held in check by negative signaling through PD-1. Preclinical models and human correlative biomarker data indicate that efficacy depends on antitumor CD8+ T cells that are recruited into the tumor microenvironment and that are functionally restrained. Treatment with PD-1 . . .
The epidermal growth factor receptor and the product of the neu protooncogene are members of a receptor tyrosine phosphorylation cascade. (1990)

The protein product of the neu protooncogene, p185, is a tyrosine kinase with a high degree of sequence homology to the epidermal growth factor (EGF) receptor. Although p185 does not bind EGF, EGF stimulates tyrosine phosphorylation of p185. To determine the mechanism of this interaction we have used a vaccinia virus/bacteriophage T7-based transient gene expression system to induce production of normal and kinase-deficient forms of p185 in the absence and presence of EGF receptors. Tyrosine phosphorylation of kinase-deficient p185 was observed, but only in the presence of the EGF receptor. These findings strongly support the hypothesis that p185 is a substrate for the EGF receptor tyrosine kinase in a tyrosine kinase cascade.
Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years (1997)

The genetic mechanisms of human immunodeficiency virus type 1 (HIV-1) resistance to dideoxyinosine (ddI) in vivo have been described based on data from primary HIV-1 isolates. To better define the spectrum of HIV-1 reverse transcriptase (RT) changes occurring during ddI therapy, we determined the genotype and ddI susceptibility of the RT gene of HIV RNA isolated from the plasma of 23 patients who had received 1 to 2 years (mean, 87 +/- 16 weeks) of ddI monotherapy. Population-based sequencing of plasma virus showed that 12 of 23 (52%) patients developed known ddI resistance mutations: L74V (7 patients), K65R (2 patients), L74V with M184V (3 patients), and L74V with K65R (1 patient). Five patients developed one or more known zidovudine resistance mutations (at codons 41, 67, 70, 215, and/or 219) during the study. Other amino acid substitutions were found, but only S68G and L210W occurred in more than one patient. Studies of sensitivity to ddI were performed on population-based recombinant-virus stocks generated by homologous recombination between a plasmid containing an HXB2 clone with the RT gene deleted and RT-PCR products of the RT genes from patients' plasma RNA. The sequences of the virus stocks produced by this procedure were typically identical to the sequence of the input PCR product from plasma RNA. Both an MT-2 cell-based culture assay and a cell-free virion-associated RT inhibition assay showed that viruses possessing an L74V and/or M184V mutation or a K65R mutation had reduced sensitivity to ddI. Viruses without these specific mutations had no change in sensitivity to ddI. The results presented here show that the spectrum of RT mutations in a population of patients on ddI monotherapy is more complex than previously described. The development of multiple mutational patterns, including those that confer resistance to other nucleoside analogs, highlights the complexity of using the currently available nucleoside analogs for antiretroviral therapy.
Lipopolysaccharide from Escherichia coli. Heterogeneity and mechanism of reversible inactivation by sodium deoxycholate (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLipopolysaccharide from Escherichia coli. Heterogeneity and mechanism of reversible inactivation by sodium deoxycholateFloyd C. McIntire, Grant H. Barlow, H. William Sievert, Richard A. Finley, and Agnes L. YooCite this: Biochemistry 1969, 8, 10, 4063–4067Publication Date (Print):October 1, 1969Publication History Published online1 May 2002Published inissue 1 October 1969https://pubs.acs.org/doi/10.1021/bi00838a024https://doi.org/10.1021/bi00838a024research-articleACS PublicationsRequest reuse permissionsArticle Views198Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Targeting of HPV-16+ Epithelial Cancer Cells by TCR Gene Engineered T Cells Directed against E6 (2015)

These findings demonstrate that HPV-16(+) tumors can be targeted by E6-specific TCR gene engineered T cells, and they provide the foundation for a novel cellular therapy directed against HPV-16(+) malignancies, including cervical, oropharyngeal, anal, vulvar, vaginal, and penile cancers.
Methylcobalamin:Coenzyme M Methyltransferase Isoenzymes MtaA and MtbA from Methanosarcina barkeri (1996)

Methanosarcina barkeri is known to contain two methyltransferase isoenzymes, here designated MtaA and MtbA, which catalyze the formation of methyl-coenzyme M from methylcobalamin and coenzyme M. The genes encoding the two soluble 34-kDa proteins have been cloned and sequenced. mtaA and mtbA wee found to be located in different parts of the genome, each forming a monocystronic transcription unit. Northern blot analysis revealed that mtaA is preferentially transcribed when M. barkeri is grown on methanol and the mtbA gene when the organism is grown on H2/CO2 or trimethylamine. Comparison of the deduced amino acid sequences revealed the sequences of the two isoenzymes to be 37% identical. Both isoenzymes showed sequence similarity to uroporphyrinogen III decarboxylase from Escherichia coli. The mtaA gene was tagged with a sequence encoding six His placed bp before the mtaA start codon, and was functionally overexpressed in E. coli. 25% of the E. coli protein was found to be active methyltransferase which could be purified in two steps to apparent homogeneity with a 70% yield.
Expression of the envelope antigen F1 of Yersinia pestis is mediated by the product of caf1M gene having homology with the chaperone protein PapD of Escherichia coli (1991)

The effective synthesis of the envelope antigen F1 of Y. pestis in E. coli HB101 is mediated by the expression of the caf1M gene. This gene was sequenced, and the protein encoded was found to have a significant homology with the chaperone protein PapD of uropathogenic E. coli. The data presented allow one to suppose Caf1M and PapD proteins perform similar functions in the biogenesis of the Y. pestis capsule and E. coli P-pili, respectively.