gebhart/patrepeval huggingface dataset:
Establishment of Early Lymphoid Organ Infrastructure in Transplanted Tumors Mediated by Local Production of Lymphotoxin α and in the Combined Absence of Functional B and T Cells (2004)

Lymphoid organogenesis is a highly coordinated process involving orchestrated expression of a number of genes. Although the essential role of lymphotoxin alpha (LTalpha) for the normal development of secondary lymphoid organs is well established, it is not clear to which extent it depends upon cooperation with T and B lymphocytes for lymphoid neo-organogenesis. To determine whether LTalpha is sufficient to mediate recruitment of basic elements needed for lymphoid organogenesis, we made use of a LTalpha-transfected cell line as an experimental tool and established tumors in nude and SCID mice. Our data showed that high endothelial venules formed and follicular dendritic cells accumulated and differentiated in response to LTalpha in the absence of lymphocytes. A CD4(+)CD3(-)CD11c(+) cell population that is found in the secondary lymphoid organ was also recruited into tumors expressing LTalpha. Furthermore, in nude mice, B cells migrated in response to LTalpha and formed intratumoral follicles. These B cell follicles were structurally well equipped with follicular dendritic cell networks and high endothelial venules; however, they were not functionally active; e.g., those B cells specific for a surrogate Ag expressed by the tumor were found in the spleen, but not in the tumor. We show that, even in the absence of functional T and B lymphocytes, local expression of LTalpha in transplanted tumors induced typical stromal characteristics of lymphoid tissue, emphasizing that LTalpha is a critically important cytokine for formation of lymphoid organ infrastructure.
Effects of Herpes Simplex Virus Amplicon Transduction on Murine Dendritic Cells (2009)

The herpes simplex virus (HSV)-based amplicon is a versatile vaccine platform that has been preclinically vetted as a gene-based immunotherapeutic for cancer, HIV, and neurodegenerative disorders. Although it is well known that injection of dendritic cells (DCs) transduced ex vivo with helper virus-free HSV amplicon vectors expressing disease-relevant antigens induces antigen-specific immune responses, the cellular receptor(s) by which the amplicon virion gains entry into DCs, as well as the effects that viral vector transduction impinges on the physiological status of these cells, is less understood. Herein, we examine the effects of amplicon transduction on mouse bone marrow-derived DCs. We demonstrate that HSV-1 cellular receptors HveC and HveA are expressed on the cell surface of murine DCs, and that HSV amplicons transduce DCs at high efficiency (>90%) with minimal effects on cell viability. Transduction of dendritic cells with amplicons induces a transient DC maturation phenotype as represented by self-limited upregulation of MHCII and CD11c markers. Mature DCs are less sensitive to HSV amplicon transduction than immature DCs regarding DC-related surface marker maintenance. From this and our previous work, we conclude that HSV amplicons transduce DCs efficiently, but impart differential and transient physiological effects on mature and immature DC pools, which will facilitate fine-tuning of this vaccination platform and further exploit its potential in immunotherapy.
Characterization of receptors for thyrotropin-releasing hormone-potentiating peptide on rat anterior pituitary membranes. (1992)

Previous studies (Bulant, M., Delfour, A., Vaudry, H., and Nicolas, P. (1988) J. Biol. Chem. 263, 17189-17196; Bulant, M., Roussel, J. P., Astier, H., Nicolas, P., and Vaudry, H. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4439-4443) have shown that post-translational processing of rat thyrotropin-releasing hormone prohormone (pro-TRH) generates, besides thyrotropin-releasing hormone (TRH), a connecting decapeptide corresponding to prepro-TRH-(160-169), i.e. Ser-Phe-Pro-Trp-Met-Glu-Ser-Asp-Val-Thr. This peptide, which is named TRH-potentiating peptide (Ps4), is co-localized with TRH in the median eminence nerve endings and is involved in potentiation of the action of TRH on thyrotropin hormone release by pituitary in vitro and in vivo. To characterize the receptor(s) for TRH-potentiating peptide in the pituitary, a highly potent and metabolically stable derivative of Ps4, [I-Tyr0]Ps4, was radioiodinated. Binding of [125I-Tyr-0]Ps4 to rat pituitary membrane homogenates was specific, saturable, reversible, and linear with membrane protein concentration. Equilibrium measurements performed over a large range of concentrations revealed a single homogeneous population of high affinity binding sites (Kd = 0.22 nM; Bmax = 517 fmol/mg of membrane proteins). Several naturally occurring neuropeptides and hormones, including TRH, did not compete with [125I-Tyr0]Ps4 in the binding, which suggests the binding sites are specific to Ps4. Using C-terminal deletion analogs of [Tyr0]Ps4, we further showed the critical role the C-terminal residues Thr10, Val9, and Asp8 play in conferring high binding affinity and selectivity. Binding site tissue distribution and cross-reactivity binding studies suggest that the action of TRH-potentiating peptide is mediated through interaction with a specific pituitary cell-surface receptor which differ from those for TRH. [I-Tyr0]Ps4 reported in this paper, through its high binding affinity and specificity, its very low nonspecific binding, its high resistance to enzymatic degradation, and its high potentiating action in vitro should allow further progress in understanding the in vivo physiological function of Ps4.
B cells lacking RP105, a novel B cell antigen, in systemic lupus erythematosus (1999)

These findings suggest that loss of RP105 is associated with B cell activation and increased disease activity in SLE patients.
Transition between virtual environment and workstation environment with projective head mounted display (2002)

The construction of virtual worlds often requires the user to use various tools in different environments to create several types of elements which have geometrical properties and behavioral characteristics. Due to the inconveniences associated with this task, a compound environment for the task of constructing virtual worlds was proposed. This environment contains both the popular workstation as well as a surrounding virtual world. To realize this compound environment, a Projective Head Mounted Display (PHMD) prototype was developed, which effectively minimized the difficulty of going and coming between workstation and virtual environments. The PHMD was also able to address the problem that is common to traditional HMDs which involve false images. The concept and development behind the PHMD and the compound environment are discussed, and the prototype PHMD and the prototype application examples are constructed.
Constrained self-calibration (2003)

This paper focuses on the estimation of the intrinsic camera parameters and the trajectory of the camera from an image sequence. Intrinsic camera calibration and pose estimation are the prerequisites for many applications involving navigation tasks, scene reconstruction, and merging of virtual and real environments. Proposed and evaluated is a technical solution to decrease the sensitivity of self-calibration by placing easily identifiable targets of known shape in the environment. The relative position of the targets need not be known a priori. Assuming an appropriate ratio of size to distance these targets resolve known ambiguities. Constraints on the target placement and the cameras' motions are explored. The algorithm is extensively tested in a variety of real-world scenarios.
Global epidemiology of tuberculosis. Morbidity and mortality of a worldwide epidemic (1995)

This article describes the global epidemiology of tuberculosis and reviews recent estimates of tuberculosis incidence and mortality in the world. The highest prevalence of tuberculosis infection and estimated annual risk of tuberculosis infection are in sub-Saharan Africa and Southeast Asia. Overall, almost 3.8 million cases of tuberculosis were reported in the world in 1990, of which 49% were in Southeast Asia. From the period 1984 through 1986 to the period 1989 through 1991, notification rates increased in all World Health Organization regions, except the American and the European regions. In 1990, there were an estimated 7.5 million cases of tuberculosis and 2.5 million deaths worldwide. The human immunodeficiency virus epidemic is causing increases in the number of tuberculosis cases, particularly in Africa, although increases are also expected in Southeast Asia. In many industrialized countries, tuberculosis has recently failed to decline, and in eastern Europe and the former Soviet Union, cases and deaths are increasing. Drug resistance is a serious problem, especially in the United States. If worldwide control of tuberculosis does not improve, 90 million new cases and 30 million deaths are expected in the decade 1990 through 1999. (<i>JAMA</i>. 1995;273:220-226)
Modification of Different IgG1 Antibodies via Glutamine and Lysine using Bacterial and Human Tissue Transglutaminase (2007)

The modification of proteins by chemical methods is well-established, however usually difficult to control. In this paper, we describe the posttranslational modification of different IgGs via the Lys or Gln side chains catalyzed by bacterial and human tissue transglutaminase (BTGase and TG2). For proof of concept, different IgG1s (commercial bovine IgG1, and L1CAM targeting chCE7 and chCE7 aglycosylated) were enzymatically functionalization with different fluorescent TGase substrates based on the CY3 analogue Dy547. The optimal reaction conditions were determined in order to assess the two enzymes. The efficiency of the enzymatic method was also compared with a standard chemical method employing a reactive NHS ester of Dy547. Three new TGase substrates were synthesized for this study including Lys-substrate 1 useful for BTGase and TG2 and two Gln-substrates tailor-made for BTGase (substrate 2) and TG2 (substrate 3). Of the two TGases tested, BTGase incorporated Lys-substrate 1 more efficiently than TG2. On the other hand, both enzymes reacted equally efficiently with the corresponding Gln-substrates 2 and 3. Reproducible labeling could be achieved in a broad concentration "window" of the substrates (up to 400 microM) without the risk of overlabeling of chCE7 or chCE7 aglycosylated. The biological activities of the functionalized antibodies were unaltered as shown by in vitro antigen affinity measurements and cell internalization experiments using confocal laser scanning microscopy. A maximum label-to-protein ratio of approximately 1 was achieved with chCE7 aglycosylated and substrate 1 using BTGase. It is important to recognize that the enzymatic activity of TGases enables the stable functionalization of proteins via the side chains of Gln, which is not possible by any chemical method available today. In addition, we could prove that the enzymatic modification of all antibodies occurred selectively at the heavy chain whereas the chemical method led to labeling of both the heavy and the light chains.
Brimonidine (1997)

Brimonidine tartrate is a highly selective alpha2-adrenergic receptor agonist indicated for the chronic treatment of glaucoma and ocular hypertension. Glaucoma, a serious worldwide public health problem causing blindness in 5.2 million people, is treated by drugs that lower the intraocular pressure (IOP), a primary risk factor in glaucomatous optic neuropathy. Currently, beta-blockers are the most common therapy. In two 12-month clinical comparison trials with timolol 0.5% (n = 926), twice-daily brimonidine produced IOP lowering comparable to twice-daily timolol. In a 3-month trial with betaxolol 0.25% suspension (n = 206), twice-daily brimonidine was more effective in lowering IOP than twice-daily betaxolol. Brimonidine was well-tolerated ocularly and systemically in these trials. It caused no clinically significant mean changes in heart rate or blood pressure. Brimonidine produced no significant effect on FEV1 in clinical trials, and it is not contraindicated in patients with cardiopulmonary disease. Brimonidine 0.2% dosed twice daily has clinical utility as a first-line drug therapy. It is an effective and safe alternative to beta-blockers, particularly in patients at risk for pulmonary or cardiovascular disease. It decreases aqueous humour production and increases uveoscleral outflow, and has an additive ocular hypotensive effect used concomitantly with other agents. Brimonidine has demonstrated neuroprotective properties in laboratory animal studies. Additional studies are warranted to determine whether brimonidine has clinical benefit in protecting the optic nerve head from glaucomatous damage. Brimonidine is an important contribution to glaucoma management.
Varicella-Zoster Virus Infection of Human Fibroblast Cells Activates the c-Jun N-Terminal Kinase Pathway (2006)

The transcription factors ATF-2 and c-Jun are important for transactivation of varicella-zoster virus (VZV) genes. c-Jun is activated by the c-Jun N-terminal kinase (JNK), a member of the mitogen-activated protein kinase pathway that responds to stress and cytokines. To study the effects of VZV on this pathway, confluent human foreskin fibroblasts were infected with cell-associated VZV for 1 to 4 days. Immunoblots showed that phosphorylated JNK and c-Jun levels increased in VZV-infected cells, and kinase assays determined that phospho-JNK was active. Phospho-JNK was detected after 24 h, and levels rose steadily over 4 days in parallel with accumulation of VZV antigen. The two main activators of JNK are MKK4 and MKK7, and levels of their active, phosphorylated forms also increased. The competitive inhibitor of JNK, SP600125, caused a dose-dependent reduction in VZV yield (50% effective concentration, congruent with 8 microM). Specificity was verified by immunoblotting; phospho-c-Jun was eliminated by 18 microM SP600125 in VZV-infected cells. Immunofluorescent confocal microscopy showed that phospho-c-Jun and most of phospho-JNK were in the nuclei of VZV-infected cells; some phospho-JNK was in the cytoplasm. MKK4, MKK7, JNK, and phospho-JNK were detected by immunoblotting in purified preparations of VZV virions, but c-Jun was absent. JNK was located in the virion tegument, as determined by biochemical fractionation and immunogold transmission electron microscopy. Overall, these results demonstrate the importance of the JNK pathway for VZV replication and advance the idea that JNK is a useful drug target against VZV.
Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin (2014)

We present an innovative centrifugal microfluidic immunoassay platform (SpinDx) to address the urgent biodefense and public health need for ultrasensitive point-of-care/incident detection of botulinum toxin. The simple, sample-to-answer centrifugal microfluidic immunoassay approach is based on binding of toxins to antibody-laden capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk and quantification by laser-induced fluorescence. A blind, head-to-head comparison study of SpinDx versus the gold-standard mouse bioassay demonstrates 100-fold improvement in sensitivity (limit of detection = 0.09 pg/mL), while achieving total sample-to-answer time of <30 min with 2-μL required volume of the unprocessed sample. We further demonstrate quantification of botulinum toxin in both exogeneous (human blood and serum spiked with toxins) and endogeneous (serum from mice intoxicated via oral, intranasal, and intravenous routes) samples. SpinDx can analyze, without any sample preparation, multiple sample types including whole blood, serum, and food. It is readily expandable to additional analytes as the assay reagents (i.e., the capture beads and detection antibodies) are disconnected from the disk architecture and the reader, facilitating rapid development of new assays. SpinDx can also serve as a general-purpose immunoassay platform applicable to diagnosis of other conditions and diseases.
Neutralization of HIV-1 by anti-idiotypes to monoclonal anti-CD4. Potential for idiotype immunization against HIV (1992)

Anti-idiotypic antibodies were raised in rabbits against a panel of 11 murine mAb directed to the human CD4 receptor. Selection of mAb for vaccination was based on inhibition studies demonstrating that these mAb recognized CD4/V1 epitopes implicated in HIV-1-gp120 binding. Purified antisera showed high titer anti-Id activity and reacted specifically with Ag-combining site-related Id of the mAb used for their generation. Anti-Id either detected a private Id of the immunizing mAb or displayed a partial cross-reactivity with Id of other mAb to CD4. Eight anti-Id to six different mAb were shown to recognize determinants of recombinant HIV-1-gp120 or of HIV-1-gp160 as shown by ELISA and radioimmunoprecipitation assay. These anti-Id were capable of inhibiting HIV infection up to 100% in a MT-4 cell assay in vitro. In addition to neutralizing infectivity of cell-free virus, anti-Id to two mAb--the mAb IOT4a and 7.3F11--were also shown to inhibit HIV-induced syncytia formation up to 100%. Anti-Id to the mAb IOT4a, 7.3F11, and to the mAb anti-Leu3a interfered with rgp120 binding to cellular CD4 as assessed by flow cytometry. These results demonstrated that mAb specific for both CDR2- and CDR3-like regions of CD4 were capable of inducing HIV-1-gp120 cross-reacting anti-Id neutralizing HIV-1 in vitro. These studies may have implications for the development of a gp120 internal image based vaccine against HIV.
Dye-coupling in the root epidermis of Arabidopsis is progressively reduced during development (1994)

ABSTRACT Epidermal cells of the Arabidopsis thaliana root are derived from a ring of 16 or so initials (stem cells) that are located just below the quiescent centre of four central cells. Derivatives of these initials divide transversely in the meristem-atic region of the root to produce files of cells that subsequently elongate and differentiate. There are two kinds of cell file in the epidermis, hair cells and non-hair cells, that are organised in an ordered pattern and become distinguishable within a few divisions of the initials. It is likely that local intercellular communication plays an important role in the early establishment of this pattern, enabling cells to register their position and fate. We have therefore examined the extent to which cells in the root apex are sym-plastically coupled through plasmodesmata. Using a variety of dye loading methods we show that the undifferentiated cells are dye-coupled i.e. cells in the meristem and the elongation zone are symplastically connected, but that cells gradually become symplastically isolated as the cells differentiate. By the time that visible hair outgrowth is observed the cells of the epidermis are symplastically isolated. This resembles the pattern of gap-junction connectivity observed in many animal systems where cells are coupled at the stage that cell patterns become established, but become progressively more isolated as they differentiate.
Expression ofAnaplasma marginaleMajor Surface Protein 2 Variants during Persistent Cyclic Rickettsemia (1998)

Anaplasma marginale is an intraerythrocytic rickettsial pathogen of cattle in which infection persists for the life of the animal. Persistent A. marginale infection is characterized by repetitive rickettsemic cycles which we hypothesize reflect emergence of A. marginale antigenic variants. In this study, we determined whether variants of major surface protein 2 (MSP-2), a target of protective immunity encoded by a polymorphic multigene family, arise during persistent rickettsemia. By using a quantitative competitive PCR to identify rickettsemic cycles, msp-2 transcripts expressed in vivo were isolated from peak rickettsemia of sequential cycles. Cloning and sequencing of msp-2 cDNA revealed that genetic variants of MSP-2 emerge representing a minimum of four genetic variant types in each cycle during persistent infection. Two-color immunofluorescence using variant-specific antibody showed that emergence of MSP-2 variants resulted in expression of a minimum of three antigenic types of MSP-2 within one rickettsemic cycle. Therefore immune control of each cycle would require responses to an antigenically diverse A. marginale population. These findings demonstrate that polymorphic MSP-2 variants emerge during cyclic rickettsemia in persistent A. marginale infection and suggest that emergent variants play an important role in persistence.
Lipoplex-Mediated Gene Delivery to the Lung Occurs within 60 Minutes of Intravenous Administration (1999)

We have defined the critical time period for gene delivery in the lung after intravenous administration of cationic lipoplex. We accomplished this through the displacement of intravenously injected cationic lipoplexes from the lungs by the subsequent administration of anionic liposomes. When reporter gene-bearing lipoplexes were injected intravenously and followed by anionic liposomes 5 min later, reporter gene expression was reduced up to 400-fold compared with animals into which lipoplex alone was administered. Administration of anionic liposomes 60-90 min after lipoplex injection yielded no significant reduction in lung transfection. When lipoplexes were disrupted 5 min after administration, the pulmonary distribution of the cationic lipid and DNA components was reduced by 80%. Lipids subsequently accumulated primarily in the liver, while the plasmid DNA constituent distributed into the blood and liver. As the interval between lipoplex and anionic liposome injection increased, the degree of lipoplex displacement from the lung decreased to such a point that, 60 min after lipoplex injection, the anionic liposome injection did not displace significant quantities of the lipoplex. We conclude that cationic lipid-DNA complexes can be disrupted in vivo via the administration of anionic liposomes; moreover, we have employed this phenomenon to demonstrate that transfectionally active DNA is taken up within 60 min of systemic lipoplex administration.
A computational approach to chemistry (1991)

Molecular electronic structure Molecular mechanics Molecular spectroscopy Reaction kinetics Dynamics of chemical reactions The liquid state The simulation of proteins and macromolecules.
Circadian rhythms of arterial blood pressure. (1987)

We measured variations of blood pressure during the day in 46 untreated outpatients (25 hypertensives and 21 normotensives) to assess their circadian patterns. The self-measured blood pressures (autorhythmometry), determined at 08:00, 12:00, 16:00, 20:00 and 23:00 for 40 consecutive days were evaluated chronobiologically from single and population mean cosinors. On the basis of the results, we conclude that it is impossible to propose a common schedule of temporal therapy that will be effective for all hypertensive patients because of the unpredictable circadian behavior of blood pressure in this kind of subjects. Therefore, we suggest that individual circadian patterns of arterial pressure be studied when therapy is being established, so that the best therapeutic results can be achieved.