gebhart/patrepeval huggingface dataset:
Cytoplasmic microvesicular form of Fas ligand in human early placenta: switching the tissue immune privilege hypothesis from cellular to vesicular level (2004)

The local immune privilege of the fetus is created by the placenta. Fas ligand (FasL) expression in trophoblast has been implied as one of the mechanisms of fetal tolerance. However, the expression of membranal FasL by trophoblast has failed to explain this role of FasL. Two objections can be raised: (1) there have been contradictions considering which trophoblast cells, syncytiotrophoblast (ST) or cytotrophoblast, express FasL; (2) in vivo and in vitro studies have shown that the membranal form of FasL evokes inflammatory response and thus may promote fetal rejection. Using different assays and the FasL-specific antibody G247-4 we demonstrate beyond doubt that in vivo, (1) FasL is produced by and stored in the first trimester human ST only and (2) the human ST lacks surface membranal FasL. Instead, FasL, loaded in microvesicles, is stored in cytoplasmic granules. These results complement the recent in vitro studies of the microvesicular form of FasL secretion by cultured trophoblast cells, and suggest that placental FasL is synthesized by villous ST, stored in microvesicular form and secreted as exosomes. Secretion of the exosome-associated form of FasL may be one mechanism by which the placenta promotes a state of immune privilege. Additionally, FasL expression in Hofbauer cells is also demonstrated.
Low Cost Wafer Level Packaging of MEMS Devices (2003)

This paper presents a packaging solution at wafer level for MEMS devices using silicon as packaging material and glass frit wafer-to-wafer bonding techniques for sealing. The MEMS devices wafer is bonded between two other silicon wafers. These cover wafers must assure the protection of the sensitive parts of MEMS devices and also the electrical and mechanical connection with PCB. For characterizing our wafer level packaging (WLP) solution we chose, as test chip, a sensitive piezoresistive pressure sensor (operating range 0 to 0.4 bars). The main advantage of using this sensor is that the offset variation of the tensometric bridge, measured before and after the packaging, gives us the information on the residual stress induced by packaging technique. Very good results were obtain, the variation of the tensometric bridge offset was less than 5 mV at a supply voltage of 5 V.
Multipotential stem cells from the adult mouse brain proliferate and self-renew in response to basic fibroblast growth factor (1996)

It has been established that the adult mouse forebrain contains multipotential (neuronal/glial) progenitor cells that can be induced to proliferate in vitro when epidermal growth factor is provided. These cells are found within the subventricular zone of the lateral ventricles, together with other progenitor cell populations, whose requirements for proliferation remain undefined. Using basic fibroblast growth factor (bFGF), we have isolated multipotential progenitors from adult mouse striatum. These progenitors proliferate and can differentiate into cells displaying the antigenic properties of astrocytes, oligodendrocytes, and neurons. The neuron-like cells possess neuronal features, exhibit neuronal electrophysiological properties, and are immunoreactive for GABA, substance P, choline acetyl-transferase, and glutamate. Clonal analysis confirmed the multipotency of these bFGF-dependent cells. Most significantly, subcloning experiments demonstrated that they were capable of self-renewal, which led to a progressive increase in population size over serial passaging. These results demonstrate that bFGF is mitogenic for multipotential cells from adult mammalian forebrain that possess stem cell properties.
Antibodies against conserved antigens provide opportunities for reform in influenza vaccine design (2011)

High-performance neutralizing antibody against influenza virus typically recognizes the globular head region of its hemagglutinin (HA) envelope glycoprotein. To-date, approved human vaccination strategies have been designed to induce such antibodies as a sole means of preventing the consequences of this infection. However, frequent amino-acid changes in the HA globular head allow for efficient immune evasion. Consequently, vaccines inducing such neutralizing antibodies need to be annually re-designed and re-administered at a great expense. These vaccines furthermore provide little-to-no immunity against antigenic-shift strains, which arise from complete replacement of HA or of neuraminidase genes, and pose pandemic risks. To address these issues, laboratory research has focused on inducing immunity effective against all strains, regardless of changes in the HA globular head. Despite prior dogma that such cross-protection needs to be induced by cellular immunity alone, several advances in recent years demonstrate that antibodies of other specificities are capable of cross-strain protection in mice. This review discusses the reactivity, induction, efficacy, and mechanisms of antibodies that react with poorly accessible epitopes in the HA stalk, with the matrix 2 membrane ion channel, and even with the internal nucleoprotein. These advances warrant further investigation of the inducibility and efficacy of such revolutionary antibody strategies in humans.
Isolation from Phage Display Libraries of Single Chain Variable Fragment Antibodies That Recognize Conformational Epitopes in the Malaria Vaccine Candidate, Apical Membrane Antigen-1 (1997)

Phage display of single chain variable fragment (scFv) antibodies is a powerful tool for the selection of important and useful antibody specificities. We have constructed such a library from mice protected from malaria challenge by immunization with recombinant Plasmodium chabaudi DS apical membrane antigen (AMA-1). Panning on refolded AMA-1 enriched a population of scFvs which specifically bound the antigen. The single chain antibodies recognize conformational epitopes on AMA-1 from the P. chabaudi DS strain but not on AMA-1 of the 556KA strain of P. chabaudi. A subset of the antibody fragments recognized AMA-1 from the human malaria parasite Plasmodium falciparum. Nucleotide sequencing revealed that at least four unique scFv genes were selected by the panning procedure. These scFv antibodies are valuable reagents for probing the structure and function of AMA-1 and will be used to test the feasibility of using recombinant antibodies in a passive immunization therapy against malaria.
Bispecific antibodies overcome the opsonin-receptor mismatch of cystic fibrosis in vitro: restoration of neutrophil-mediated phagocytosis and killing of Pseudomonas aeruginosa (1997)

Inflammation and infection associated with bacterial pathogens, primarily Pseudomonas aeruginosa (Pa), are the primary causes of morbidity and mortality for cystic fibrosis (CF) patients. CF patients may be predisposed to these bacterial infections by a defect in phagocytosis due to "opsonin-receptor mismatch," in which a complement receptor (CR1) and an important opsonin (iC3b) are destroyed by proteolytic enzymes. We show that opsonin-receptor mismatch can be mitigated in vitro using a bispecific Ab (bsAb) to cross-link neutrophils via the beta-chain of leukocyte integrins (CD18) to bacterial epitopes or C3d on opsonized Pa. Two chemically cross-linked bsAb were constructed with mAb specific for C3d (or the O-specific side chain of Fisher Devlin Immunotype 1 Pa) and CD18. Using an in vitro model of elastase-mediated opsonin-receptor mismatch, these bsAb specifically enhanced Pa phagocytosis and killing, with the anti-C3d-containing bsAb restoring the levels of phagocytosis to approximately those for the non-elastase-treated opsonic control. These results encourage the further investigation of bsAb as therapeutic agents for bacterial infection in the lungs of CF patients.
MACULAR HEMORRHAGE IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION AFTER STABILIZATION WITH ANTIANGIOGENIC THERAPY (2009)

Sight-threatening macular hemorrhages from AMD can occur within days to weeks after a stable examination and absence of fluid on OCT. Regimens that treat "as needed" based on clinical findings and OCT may not be appropriate for certain patients.
Viral aetiology of enzootic pneumonia in Danish dairy herds: diagnostic tools and epidemiology (1996)

Ten outbreaks of calf respiratory disease in Danish dairy herds were investigated by lung lavage, and in eight of the herds paired blood samples were tested serologically. In six of the 10 herds bovine respiratory syncytial virus (BRSV) antigen was detected in the lung lavage fluids. In only one calf was coronavirus and BRSV detected simultaneously. The paired blood samples confirmed that four of the herds were BRSV-infected, and in one herd the BRSV infection was diagnosed by the paired blood samples alone. Significant increases in antibody titres against coronavirus were observed in two herds, both in combination with other virological agents. No adenovirus antigen was detected in any of the lavage samples, but in two herds a significant increase in antibody titres against adenovirus was observed. Parainfluenza-3 (PI-3) virus was not detected in the lung lavage fluids, and in four of the herds, no antibodies to PI-3 were detected. In three herds no viral involvement could be found. The findings suggest that BRSV may be an important causative agent in calf respiratory disease in Denmark, even in very young calves.
Multivariate and Propensity Score Matching Software with Automated Balance Optimization: TheMatchingPackage forR (2011)

<b>Matching</b> is an R package which provides functions for multivariate and propensity score matching and for finding optimal covariate balance based on a genetic search algorithm. A variety of univariate and multivariate metrics to determine if balance actually has been obtained are provided. The underlying matching algorithm is written in C++, makes extensive use of system BLAS and scales efficiently with dataset size. The genetic algorithm which finds optimal balance is parallelized and can make use of multiple CPUs or a cluster of computers. A large number of options are provided which control exactly how the matching is conducted and how balance is evaluated.
Interval estimation of the density of organisms using a serial-dilution experiment. (1984)

The serial-dilution assay is a standard microbiological method for estimating the density of organisms in a solution. The commonly used interval-estimation procedures of Woodward and deMan are described and compared. A new method for the calculation of two-sided confidence intervals, which is superior to the standard procedures, is presented. The computations are illustrated for a decimal dilution assay with three samples at each of three dilutions.
The cytokine response element of the rat alpha 1-acid glycoprotein gene is a complex of several interacting regulatory sequences. (1990)

Expression of the rat alpha 1-acid glycoprotein gene is stimulated by interleukin-1 (IL-1) and interleukin-6 (IL-6) and is synergistically enhanced by the combination of the two. The distal regulatory element (DRE), a 142-base-pair (bp) sequence located 5 kilobase pairs upstream of the transcriptional start site, appears to be crucial for this cytokine response. The cytokine-specific regulatory sequences within the DRE have been identified by inserting individual DRE subregions, selected combinations of these, or a few linker mutated fragments into a plasmid containing an enhancerless simian virus 40 promoter linked to the chloramphenicol acetyltransferase gene. The regulatory activity was determined in transiently transfected human and rat hepatoma cells. The IL-1 response region was confined to the 5'-most 62 bp of the DRE, and its function seemed to depend on at least two separate components. The same region was also responsive to phorbol ester treatment. The IL-6 regulatory function was dependent on a 54-bp sequence located within the 3' half of the DRE. When the IL-1 response region was recombined with the IL-6 regulatory region of the DRE or with IL-6 response elements of other plasma protein genes, a strong cooperative action by IL-1 and IL-6 was achieved. The functional DRE sequences were recognized by nuclear proteins extracted from rat liver and hepatoma cells. However, no cytokine-inducible binding activity was detectable, which suggests that transcriptional regulation through the DRE might be controlled by posttranslational modification of constitutively bound trans-acting factors.
Formation of indoles, isoquinolines, and other fused pyridines from azidoacrylates (1984)

Mild thermal decomposition in boiling toluene or xylene of the azidocinnamates (1)–(6), readily prepared from the corresponding aldehyde and ethyl azidoacetate, gives indoles in good yield when there is an unsubstituted ortho position, and dihydroisoquinolines, and hence isoquinolines, when there is an o-methyl or methylene group. In the presence of iodine, which seems to favour a radical type process, the yield of isoquinoline is increased, and isoquinoline formation can compete with the indole-forming cyclisation to a free ortho-position. Iodine also catalyses primary enamine formation by a hydrogen abstraction process. The thiophene (7) and pyrazole (8) are formed and decomposed similarly to give the corresponding c-fused pyridines (28) and (29). The 2,6-dichloro compound (9) thermolyses to the stable 2H-azirine (32) which isomerises to the nitrile (33) on stronger heating. Yields in these azide decompositions are sometimes high, though they can be variable and the reactions, though easily carried out, can be complex.
Diamond-like carbon films prepared with a laser ion source (1988)

Diamond-like carbon films have been deposited onto clean, unseeded substrates using a hybrid ion beam technique. In this method the ion fluences available for acceleration were particularly enhanced by the use of laser ablation plumes ejected from highly purified graphite targets. The combination of levels of purity characteristic of ultrahigh vacuum environments, large ratios of ion to neutral concentrations, and high fluences showed considerable merit for the growth of large-area (10 cm2 ) films of optical quality and uniformity at deposition rates approaching 20 μm/h.
TCP-friendly congestion control schemes in the Internet (2002)

This paper investigates several TCP-friendly congestion control mechanisms and sorts them according to their implementation methods. The advantages and disadvantages of every kind of these TCP-friendly schemes are listed after their principles are outlined. This paper also suggests that a combination of end-to-end mechanisms and hop-by-hop mechanisms is the future of TCP-friendly congestion control as well as a combination of the additive-increase multiplicative-decrease (AIMD)-based scheme and the model-based scheme.
Senescent human fibroblasts resist programmed cell death, and failure to suppress bcl2 is involved. (1995)

Programmed cell death (apoptosis) is an active process by which cells initiate their own self-destruction. Growing evidence shows that this event is controlled by the activation of unique gene expression; some function as survival genes, such as bcl2, and others as killer genes, such as ced3 or interleukin converting enzyme. Likewise, external factors, such as the presence or absence of stimuli in the microenvironment of a cell, play a key role in ushering it towards survival or suicidal fate. Previously, I and others have reported that withdrawal of serum from culture medium can induce contact-inhibited quiescent mouse 3T3 fibroblasts to undergo rapid programmed cell death, as evidenced by the presence of massive DNA fragmentation within 24 h. I now report that, although the same process of serum withdrawal is capable of inducing apoptotic death in quiescent young human fibroblasts, the process takes as long as 2 weeks. Repeated attempts at the same serum withdrawal with cultures of senescent human fibroblasts show that phenotypic signs of apoptosis, such as DNA fragmentation and loss of cell viability, are not observed for up to 4 weeks; I suggest that in vitro aged human fibroblasts are resistant to undergoing programmed cell death. I have investigated the level of bcl2 presence as a possible protector of senescent human fibroblasts from apoptotic death; biochemical characterization shows that in mouse as well as human fibroblasts, bcl2 is present as an easily extractable (0.1% Triton) cytoplasmic protein. bcl2 level is in inverse relationship with the ease of induction of apoptotic death between young and senescent human fibroblasts. Immunofluorescence staining shows that, in senescent human fibroblasts, bcl2 is present not only in the cytoplasmic punctate spots seen in both mouse and young human fibroblasts but also in the nuclei as well as large granules surrounding the nuclei. Upon serum deprivation, the bcl2 level is reduced to undetectable in mouse 3T3 fibroblasts within 24 h and in young and intermediate aged human fibroblasts within 2 weeks; however, it remains unchanged in senescent human fibroblasts after the deprivation of serum for 2 weeks. These findings lead me to conclude that senescent fibroblasts are resistant to the induction of apoptotic death by serum deprivation. Furthermore, I suggest that repeated serial passaging during the in vitro aging process has inadvertently instituted a molecular mechanism whereby the bcl2 level cannot be repressed upon serum deprivation, which may subsequently allow senescent fibroblasts to be long-lived and protected from self-destruction.
Inflammasomes are activated in response to SARS-CoV-2 infection and are associated with COVID-19 severity in patients (2020)

Severe cases of COVID-19 are characterized by a strong inflammatory process that may ultimately lead to organ failure and patient death. The NLRP3 inflammasome is a molecular platform that promotes inflammation via cleavage and activation of key inflammatory molecules including active caspase-1 (Casp1p20), IL-1β, and IL-18. Although participation of the inflammasome in COVID-19 has been highly speculated, the inflammasome activation and participation in the outcome of the disease are unknown. Here we demonstrate that the NLRP3 inflammasome is activated in response to SARS-CoV-2 infection and is active in COVID-19 patients. Studying moderate and severe COVID-19 patients, we found active NLRP3 inflammasome in PBMCs and tissues of postmortem patients upon autopsy. Inflammasome-derived products such as Casp1p20 and IL-18 in the sera correlated with the markers of COVID-19 severity, including IL-6 and LDH. Moreover, higher levels of IL-18 and Casp1p20 are associated with disease severity and poor clinical outcome. Our results suggest that inflammasomes participate in the pathophysiology of the disease, indicating that these platforms might be a marker of disease severity and a potential therapeutic target for COVID-19.
Lymphatic or Hematogenous Dissemination: How Does a Metastatic Tumor Cell Decide? (2006)

The formation of distant metastases is the deadliest phase of cancer progression. Although numerous studies have identified genes and mechanisms that affect metastasis after tumors have reached secondary sites, our knowledge about how cancer cells initially gain access to systemic circulation is limited. Since tumors can enter the blood directly by intravasating into venous capillaries or indirectly via lymphatics, it is important to evaluate the relative contributions of both pathways as routes of egress from the primary site. Insights into tumor and stromal factors governing the intravasation process may help explain why certain tumors exhibit "preferred" pathways for metastatic dissemination, both clinically and in experimental animal models.
Implanted upper airway stimulation device for obstructive sleep apnea (2012)

The current study has demonstrated that therapy with upper airway stimulation is safe and efficacious in a select group of patients with moderate to severe OSA who cannot or will not use CPAP as primary treatment.
Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma (2011)

Central nervous system primitive neuroectodermal tumor (CNS PNET) and pineoblastoma are highly malignant embryonal brain tumors with poor prognoses. Current therapies are based on the treatment of pediatric medulloblastoma, even though these tumors are distinct at both the anatomical and molecular level. CNS PNET and pineoblastoma have a worse clinical outcome than medulloblastoma; thus, improved therapies based on an understanding of the underlying biology of CNS PNET and pineoblastoma are needed. To this end, we characterized the genomic alterations of 36 pediatric CNS PNETs and 8 pineoblastomas using Affymetrix single nucleotide polymorphism arrays. Overall, the majority of CNS PNETs contained a greater degree of genomic imbalance than pineoblastomas, with gain of 19p (8 [27.6%] of 29), 2p (7 [24.1%] of 29), and 1q (6 [20.7%] of 29) common events in primary CNS PNETs. Novel gene copy number alterations were identified and corroborated by Genomic Identification of Significant Targets In Cancer (GISTIC) analysis: gain of PCDHGA3, 5q31.3 in 62.1% of primary CNS PNETs and all primary pineoblastomas and FAM129A, 1q25 in 55.2% of primary CNS PNETs and 50% of primary pineoblastomas. Comparison of our GISTIC data with publically available data for medulloblastoma confirmed these CNS PNET-specific copy number alterations. With use of the collection of 5 primary and recurrent CNS PNET pairs, we found that gain of 2p21 was maintained at relapse in 80% of cases. Novel gene copy number losses included OR4C12, 11p11.12 in 48.2% of primary CNS PNETs and 50% of primary pineoblastomas. Loss of CDKN2A/B (9p21.3) was identified in 14% of primary CNS PNETs and was significantly associated with older age among children (P = .05). CADPS, 3p14.2 was lost in 27.6% of primary CNS PNETs and was associated with poor prognosis (P = .043). This genome-wide analysis revealed the marked molecular heterogeneity of CNS PNETs and enabled the identification of novel genes and clinical associations potentially involved in the pathogenesis of these tumors.
Effects of administration of an anti‐cd5 plus immunoconjugate in rheumatoid arthritis. results of two phase ii studies (1993)

These findings suggest activity of anti-CD5 IC in active RA and warrant confirmation in a multicenter randomized study (currently underway).
Follicular Dendritic Cells Catalyze Hepatocyte Growth Factor (HGF) Activation in the Germinal Center Microenvironment by Secreting the Serine Protease HGF Activator (2005)

Ag-specific B cell differentiation, the process that gives rise to plasma cells and memory B cells, involves the formation of germinal centers (GC). Within the GC microenvironment, multiple steps of B cell proliferation, selection, and maturation take place, which are controlled by the BCR in concert with cytokines and contact-dependent signals from follicular dendritic cells (FDCs) and T cells. Signaling by the multifunctional cytokine hepatocyte growth factor (HGF) and its receptor MET has been shown to induce integrin-mediated adhesion of B cells to VCAM-1, which is expressed by FDCs. In the present study we have examined the expression of regulatory components of the HGF/MET pathway, including HGF activator (HGFA), within the secondary lymphoid organ microenvironment. We show that MET is expressed by both centroblasts and plasma cells, and that HGFA is expressed by plasma cells. Because we have shown that HGF is a potent growth and survival factor for malignant plasma cells, HGF may also serve as a survival factor for normal plasma cells. Furthermore, we demonstrate that FDCs are the major source for HGF and its activator within the GC microenvironment. Both HGF and HGFA are expressed by FDCs in the GC dark zone (CD21high/CD23low), but not in the light zone (CD21high/CD23high). These findings suggest that HGF and HGFA provided by dark zone FDCs help to regulate the proliferation, survival, and/or adhesion of MET-positive centroblasts.