gebhart/patrepeval huggingface dataset:
The immunological activity of a deletion mutant of influenza virus haemagglutinin lacking the globular region (1996)

A deletion mutant of influenza virus haemagglutinin (HA; headless HA) lacking the globular region was expressed in CV-1 cells and detected with a monoclonal antibody, C179, which recognizes a conformational epitope in the middle of the stem region of HA and neutralizes all H1 and H2 subtypes. The cDNA coding for the headless HA was constructed from influenza virus A/Okuda/57 (H2N2), which was also used to select C179. The conformational epitope recognized by C179 was highly stable even after removal of the globular region. The survival rate of mice immunized with the headless HA and challenged with lethal influenza virus A/FM/l/47 (H1N1) was significantly higher than that of the control mice. The headless HA has the potential to induce cross-protection against influenza virus infection.
Evidence of fibrinogen as a target of citrullination in IgM rheumatoid factor-positive polyarticular juvenile idiopathic arthritis (2011)

Abstract Background Several studies have noted the significance of measuring anti-cyclic citrullinated peptide (CCP) antibodies in juvenile idiopathic arthritis (JIA) as an important indicator for destructive disease, as is the case in rheumatoid arthritis (RA). While the role of anti-CCP antibodies in RA and JIA has become better understood, the identity of the target proteins of this modification has remained elusive. In this study, we evaluated serum from patients with various subtypes of JIA to investigate the presence of anti-deiminated (citrullinated) fibrinogen and anti-citrullinated α-enolase antibodies, and their association with RF and anti-CCP antibody isotypes. Methods Sera were obtained from 96 JIA patients, 19 systemic lupus erythematosus (SLE) patients, and 10 healthy children. All sera were measured for antibodies against citrullinated and native fibrinogen and α-enolase by an enzyme linked immunosorbent assay (ELISA). In addition, all sera were assayed for anti-CCP antibody isotypes and rheumatoid factor (RF) isotypes by ELISA. The relationship between anti-citrullinated fibrinogen and anti-α-enolase antibodies and disease activity and joint damage were also investigated. All results were correlated with clinical and laboratory parameters using Spearman's rho correlation coefficient. Multiple logistic regression analysis was utilized to identify which variables were associated with joint erosions and diagnosis of JIA. Results Thirty-one JIA patients (32%) demonstrated reactivity to citrullinated fibrinogen and 9 (9%) to citrullinated α-enolase. Reactivity to citrullinated fibrinogen and α-enolase was predominantly found in IgM RF-positive polyarthritis patients. Fourteen JIA patients reacted with native α-enolase and a higher percentage of SLE patients reacted with citrullinated α-enolase when compared to JIA patients. Anti-citrullinated fibrinogen antibodies correlated with the presence of IgG anti-CCP antibodies and IgA and IgM RF. The presence of anti-citrullinated α-enolase antibodies correlated with IgA anti-CCP antibodies. IgG anti-CCP antibodies were significantly associated with joint damage and anti-citrullinated fibrinogen antibodies were strongly associated with JIA when compared to control groups. Anti-citrullinated fibrinogen antibodies demonstrated high sensitivity (81%) for IgM RF-positive polyarticular JIA. IgG anti-CCP antibodies had the highest specificity (95%) for JIA, with anti-citrullinated fibrinogen antibodies, IgA anti-CCP antibodies and IgA RF all following at 84%. Conclusions JIA patient sera exhibited strong reactivity to anti-citrullinated fibrinogen antibodies and demonstrated high sensitivity and specificity for JIA, primarily in IgM RF-positive polyarthritis patients. Fibrinogen is one of several protein targets for citrullination in JIA.
A unique natural human IgG antibody with anti-alpha-galactosyl specificity. (1984)

A new natural anti-alpha-galactosyl IgG antibody (anti-Gal) was found to be present in high titer in the serum of every normal individual studied. The antibody was isolated by affinity chromatography on a melibiose-Sepharose column. The reactivity of the antibody was assessed by its interaction with alpha-galactosyl residues on rabbit erythrocytes (RabRBC). The specificity was determined by inhibition experiments with various carbohydrates. The anti-Gal interacts with alpha-galactosyl residues, possibly on glycolipids of human RBC (HuRBC), after removal of membrane proteins by treatment with pronase. In addition, the anti-Gal bind specifically to normal and pathologically senescent HuRBC, suggesting a physiological role for this natural antibody in the aging of RBC. The ubiquitous presence of anti-Gal in high titers throughout life implies a constant antigenic stimulation. In addition to the theoretical interest in the antibody, the study of the anti-Gal reactivity seems to bear immunodiagnostic significance. Decrease in the antibody titer was found to reflect humoral immunodeficiency disorders.
A radiographic analysis of tooth morphology following the use of a novel cyclical force device in orthodontics (2011)

No statistically significant findings were noted for root length change at the end of treatment compared to the start of treatment when using this novel robotic device. No significant differences were noted between roots of anterior and posterior teeth. No clinically significant changes between root lengths were noted above 0.5 mm.
Host-derived adiponectin is tumor-suppressive and a novel therapeutic target for multiple myeloma and the associated bone disease (2011)

The contributions of the host microenvironment to the pathogenesis of multiple myeloma, including progression from the non-malignant disorder monoclonal gammopathy of undetermined significance, are poorly understood. In the present study, microarray analysis of a murine model requiring a unique host microenvironment for myeloma development identified decreased host-derived adiponectin compared with normal mice. In support, clinical analysis revealed decreased serum adiponectin concentrations in monoclonal gammopathy of undetermined significance patients who subsequently progressed to myeloma. We investigated the role of adiponectin in myeloma pathogenesis and as a treatment approach, using both mice deficient in adiponectin and pharmacologic enhancement of circulating adiponectin. Increased tumor burden and bone disease were observed in myeloma-bearing adiponectin-deficient mice, and adiponectin was found to induce myeloma cell apoptosis. The apolipoprotein peptide mimetic L-4F was used for pharmacologic enhancement of adiponectin. L-4F reduced tumor burden, increased survival of myeloma-bearing mice, and prevented myeloma bone disease. Collectively, our studies have identified a novel mechanism whereby decreased host-derived adiponectin promotes myeloma tumor growth and osteolysis. Furthermore, we have established the potential therapeutic benefit of increasing adiponectin for the treatment of myeloma and the associated bone disease.
ChemInform Abstract: Synthesis of (1R,4R,7S)‐ and (1S,4S,7S)‐2‐(4‐Tolylsulfonyl)‐5‐ phenylmethyl‐7‐methyl‐2,5‐diazabicyclo(2.2.1)heptanes via Regioselective Opening of 3,4‐Epoxy‐D‐proline with Lithium Dimethyl Cuprate. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
First Borehole to Surface Electromagnetic Survey in KSA: Reservoir Mapping and Monitoring at a New Scale (2011)

Abstract The first Borehole to Surface Electromagnetic (BSEM) pilot field survey in the Kingdom of Saudi Arabia (KSA) was successfully executed to identify oil and water bearing reservoir layers in a carbonate oilfield water injection zone. Maximizing recovery factor by means of detailed mapping of hydrocarbon accumulations in the reservoirs is a key requirement for oil producing companies. This mapping is done routinely by accurate measurements of fluid distribution at the wells’ locations, but a knowledge gap exists in the inter-well volumes, where typically only density-based measurements are available (seismic and gravity). Such technologies are not always effective to discriminate and quantify the fluids in the porous space (especially when difference in fluid densities is small, such as oil and water). On the contrary, when high electrical resistivity contrasts exist between hydrocarbons and water, electromagnetic (EM) based technologies have the potential to map the distribution of the fluids and monitor their movement during the life of the field, hundreds of meters or kilometers away from the wellbores. The objective of a BSEM survey is to obtain fluid sensitive resistivity and induced polarization maps. These are based on an acquisition grid at the surface, a few kilometers around the EM transmitting well, which reveal oil and water bearing zones in the investigated reservoir layers. In this pilot field test, BSEM showed the potential to map water-front movements in an area of about 4km from the single well surveyed, evaluate the sweep efficiency, identify bypassed/ lagged oil zones, and eventually monitor the fluid displacements, if surveys are repeated over time. The data quality of the recorded signals is highly satisfactory. Fluid distribution maps obtained with BSEM are coherent with production data measured at the wells’ locations, filling the knowledge gap of the interwells area. Three key R&amp;D objectives for this BSEM pilot are achieved. Firstly, the capability to record at the surface EM signals generated in the reservoir, secondly, the capability of BSEM to discriminate between oil and water saturated reservoir zones, and finally obtain resistivity maps and a fluid distribution estimate plausible and coherent with the information obtained from well logs, crosswell EM, production data and reservoir models. In addition to reservoir monitoring, BSEM can be very useful in non-diagnosed areas like exploration fields for hydrocarbon exploitations.
The ALK-2 and ALK-4 activin receptors transduce distinct mesoderm-inducing signals during early Xenopus development but do not co-operate to establish thresholds (1997)

The TGFbeta family member activin induces different mesodermal cell types in a dose-dependent fashion in the Xenopus animal cap assay. High concentrations of activin induce dorsal and anterior cell types such as notochord and muscle, while low concentrations induce ventral and posterior tissues such as mesenchyme and mesothelium. In this paper we investigate whether this threshold phenomenon involves the differential effects of the two type I activin receptors ALK-2 and ALK-4. Injection of RNA encoding constitutively active forms of the receptors (here designated ALK-2* and ALK-4*) reveals that ALK-4* strongly induces the more posterior mesodermal marker Xbra and the dorsoanterior marker goosecoid in animal cap explants. Maximal levels of Xbra expression are attained using lower concentrations of RNA than are required for the strongest activation of goosecoid, and at the highest doses of ALK-4*, levels of Xbra transcription decrease, as is seen with high concentrations of activin. By contrast, the ALK-2* receptor activates Xbra but fails to induce goosecoid to significant levels. Analysis at later stages reveals that ALK-4* signalling induces the formation of a variety of mesodermal derivatives, including dorsal cell types, in a dose-dependent fashion, and that high levels also induce endoderm. By contrast, the ALK-2* receptor induces only ventral mesodermal markers. Consistent with these observations, ALK-4* is capable of inducing a secondary axis when injected into the ventral side of 32-cell stage embryos whilst ALK-2* cannot. Co-injection of RNAs encoding constitutively active forms of both receptors reveals that ventralising signals from ALK-2* antagonise the dorsal mesoderm-inducing signal derived from ALK-4*, suggesting that the two receptors use distinct and interfering signalling pathways. Together, these results show that although ALK-2* and ALK-4* transduce distinct signals, the threshold responses characteristic of activin cannot be due to interactions between these two pathways; rather, thresholds can be established by ALK-4* alone. Furthermore, the effects of ALK-2* signalling are at odds with it behaving as an activin receptor in the early Xenopus embryo.
A Watermarking-Based Method for Informed Source Separation of Audio Signals With a Single Sensor (2009)

In this paper, the issue of audio source separation from a single channel is addressed, i.e., the estimation of several source signals from a single observation of their mixture. This challenging problem is tackled with a specific two levels coder-decoder configuration. At the coder, source signals are assumed to be available before the mix is processed. Each source signal is characterized by a set of parameters that provide additional information useful for separation. We propose an original method using a watermarking technique to imperceptibly embed this information about the source signals into the mix signal. At the decoder, the watermark is extracted from the mix signal to enable an end-user who has no access to the original sources to separate these signals from their mixture. Hence, we call this separation process informed source separation (ISS). Thereby, several instruments or voice signals can be segregated from a single piece of music to enable post-mixing processing such as volume control, echo addition, spatialization, or timbre transformation. Good performances are obtained for the separation of up to four source signals, from mixtures of speech or music signals. Promising results open up new perspectives in both under-determined source separation and audio watermarking domains.
Endotoxic properties of chemically synthesized lipid A part structures. Comparison of synthetic lipid A precursor and synthetic analogues with biosynthetic lipid A precursor and free lipid A (1984)

Synthetic lipid A part structures corresponding structurally to a biosynthetic lipid A disaccharide precursor have been analyzed for endotoxic activity in several systems in vivo and in vitro. It was found that a synthetic beta-1,6-linked D-glucosamine disaccharide, which carries four molar equivalents of (R)-3-hydroxytetradecanoyl residues in positions 2, 3, 2' and 3' and phosphoryl groups in positions 1 and 4' (preparation 406), exhibited lethal toxicity, B lymphocyte mitogenicity, the capacity to engender prostaglandin formation in macrophages and to induce endotoxic tolerance, as well as serological lipid A antigenicity. On a weight basis, preparation 406 was of comparable activity to lipid A precursor and bacterial free lipid A. Preparation 406, like lipid A precursor, lacked, however, the ability to induce the local Shwartzman phenomenon and both preparations were of moderate pyrogenicity. Two further synthetic analogues which contained only one phosphoryl group (preparation 404 at C-4', preparation 405 at C-1) showed comparable or diminished activity depending on the test system employed, except in the capacity to inactivate complement where they exhibited, in contrast to preparation 406, significant activity. The results show that the endotoxic principle of lipopolysaccharides, as postulated previously is embedded in the lipid A component. Our results also suggest initial conclusions on the structural requirements for the expression of endotoxin activities.
[Drug-eluting stents do they make the difference? ]. (2002)

The main limitation to further expansion of PTCI (percutaneous transluminal coronary intervention) is restenosis that occurs in 30% of the patients within 6-months after the procedure. Coronary stenting decreases the percent of restenosis due to arterial remodeling after PTCI but proliferation of smooth muscle cells due to vascular injury still remains. A mechanical approach the only treatment up to now (further balloon expansion, plaque removal with rotablator or directional atherectomy) failed. Because the restenotic process is due to a complex series of biological events which start with platelet aggregation, grow-factors and cytochine release, the use of antiflammatory, antithrombotic and antiproliferative drugs were attempted. Cortisone and heparin showed low benefits in clinical trial. New drugs (rapamycin, taxol, actinomycin D, tacrolimus, estradiol, dexamethazone) with antiproliferative and antiflammatory activities are under evaluation. They act as inhibitors of the cell migration and of the cell cicle progression with different specific molecular mechanisms. The first pilot study performed in 45 patients with sirolimus-eluting stents has shown a sustained suppression (25% in the fast release group and 23% in the slow release group) of neointimal formation at 12 months after procedure with absence of restenosis. The Ravel study, a randomized trial, has enrolled 238 patients treated with sirolimus coated stent vs a control group: the results confirm the previous data with a complete suppression of intimal hyperproliferation and restenosis at six months follow-up. The first 400 patients treated in the Sirius trial a similar study which will randomize 1100 pts show a low, but not a complete inhibition of the restenotic process probably due to a more complexity of the lesions treated in comparison to Ravel trial (9.2% of restenosis). Another very promising drug is taxol (paclitaxel). It is an antiproliferative and antinflammatory molecule tested in a series of clinical trials called Taxus. The still unpublished data of TAXUS I and TAXUS II randomized trial show extremely low restenosis rate. Other drugs (actinomycin D, estradiol, tacrolimus, dexamethazone) show to have a potential effect on restenosis and neointimal proliferation and are under investigation. Is very important to maintain lessons learned from the past. The design, the type, the smooth surface of the stent still remains very important as it is a good expansion and a full coverage of the lesions with a "good stent" in the attempt to reduce restenosis. Drug-eluting stents will add further improvement.
Human apolipoprotein B-100 heparin-binding sites. (1987)

Seven distinct heparin-binding sites have been demonstrated on human apolipoprotein (apo) B-100 by using a combination of digestion with cyanogen bromide or Staphylococcus aureus V-8 protease and heparin-Sepharose affinity chromatography. Based on fragment analysis, the approximate boundaries of the seven binding sites are as follows: site A, residues 5-99; site B, residues 205-279; site C, residues 875-932; site D, residues 2016-2151; site E, residues 3134-3209; site F, 3356-3489; and site G, residues 3659-3719. In sites E and F, two short regions enriched in basic amino acids have been identified, and it is likely that they are responsible for a major portion of the heparin-binding properties of these sites. The relative binding affinity of each of the seven sites was estimated in two ways. First, the affinity was assessed in a ligand blot assay using a 125I-labeled high-reactive heparin subfraction. Second, apoB-100 fragments generated by cyanogen bromide or S. aureus V-8 protease were separated into low- and high-affinity fractions by gradient salt elution of a heparin-Sepharose column. The distribution of the seven binding sites in the two fractions was determined in an immunoblotting assay using antibodies specific to each site, i.e. antibodies raised against synthetic peptide sequences found within each of the seven sites. The results of these two approaches demonstrate that site E and, to a somewhat lesser extent, site F bind to heparin with the highest affinity. Based on the analogy with apoE, in which the high-affinity heparin-binding site coincides with the domain of the protein that interacts with apoB,E (low density lipoprotein) receptors, the results of this study indicate that site E and site F, either singly or in combination, might constitute the receptor binding domain of apoB-100.
Immunization with viable Brucella organisms. Results of a safety test in humans. (1962)

In many parts of the world contact with infected livestock may involve a serious risk of the spread of human brucellosis. Partial control of bovine brucellosis has been achieved by slaughter of infected herds and immunization of cattle with Brucella abortus strain 19 living vaccine. However, in areas where such measures are unpractical there remains a need for protection of humans. This study compares the safety of two living Brucella vaccine preparations in human volunteers.Some 32 healthy male volunteers with no evidence of past exposure to brucellosis were divided into two comparable groups; one group received 19-BA vaccine derived from Br. abortus and the other received Rev 1 vaccine derived from Br. melitensis. Detailed studies over a six-month period of the clinical effects, bacteraemia, Brucella agglutinin response and dermal hypersensitivity revealed striking differences between the two groups. Two of the 16 men in the 19-BA group developed acute brucellosis, and another had a positive blood culture. In the Rev 1 group, 11 of 16 developed acute brucellosis, and brucellae were recovered from 12.All 32 men developed Brucella agglutinins, the Rev 1 group having higher titres. Dermal hypersensitivity occurred in all of the Rev. 1 group but in only nine of the 19-BA group.Tetracycline treatment in all the Rev 1 group and in the two brucellosis cases in the 19-BA group resulted in complete recovery.The authors conclude from this study that neither the Rev 1 vaccine nor the 19-BA vaccine inoculated subcutaneously is sufficiently safe in the dosage used to warrant being used for vaccination of humans for prophylactic purposes.
Substructure search procedures for macromolecular structures (2003)

This paper accompanies a lecture given at the 2003 CCP4 Study Weekend on experimental phasing. The first part is an overview of the fundamentals of Patterson methods and direct methods with the audience of the CCP4 Study Weekend in mind. In the second part, a new hybrid substructure search is outlined.
Specific decrease of Th1-like activity in mice with plasma cell tumors (1995)

Previously we examined the ability of the host's immune responses to regulate Ig production in an IgE-secreting murine plasma cell tumor (B53). In the present study we have examined the reverse phenomenon, in that we have investigated the effects of this and other plasma cell tumors on the immune responses of their hosts. We found that splenocytes from plasma cell tumor-bearing mice demonstrate decreased proliferation in response to polyclonal stimulation by either Con A or a combination of PMA and calcium ionophore (A23187). Fractionation of the splenocytes demonstrated that this reduction in proliferation was confined to CD4+ T cells and that the proliferation of CD8+ T cells was unaffected. In order to determine whether the down-modulatory effects of the tumor were confined to a particular CD4+ helper T cell subset, we examined the production of cytokines representing the Th1 subset (IL-2 and IFN-gamma) and the Th2 subset (IL-4 and IL-10) from stimulated splenocytes and from stimulated enriched splenic T cells. We found that both stimulated splenocytes and T cells from plasma cell tumor-bearing mice produced lower levels of the Th1 cytokines IL-2 and IFN-gamma compared with normal cultures, demonstrating that Th1-like responses are inhibited in the hosts of these tumors. However, no alterations in the production of the Th2 cytokines IL-4 and IL-10 were observed in these stimulated splenocyte or T cell cultures from the tumor-bearing mice.(ABSTRACT TRUNCATED AT 250 WORDS)