gebhart/patrepeval huggingface dataset:
Involvement of a Plasmid in Production of Ropiness (Mucoidness) in Milk Cultures by Streptococcus cremoris MS (1986)

Curing and genetic transfer experiments showed that lactose-fermenting ability (Lac) and the ability to produce mucoidness in milk cultures (Muc) in Streptococcus cremoris MS were coded on plasmids. The Lac phenotype was associated with a 75.8-megadalton plasmid, pSRQ2201. The Muc phenotype was associated with a 18.5-megadalton plasmid, pSRQ2202. The Lac plasmid, pSRQ2201, was first conjugatively transferred from S. cremoris MS to LacS. lactis ML-3/2.2. Later, the Muc plasmid, pSRQ2202, was conjugatively transferred from Lac MucS. cremoris MS04 to Lac nonmucoid S. lactis transconjugant ML-3/2.201. Subsequently, pSRQ2201 and pSRQ2202 were cotransferred from Lac MucS. lactis transconjugant ML-3/2.202 to Lac, nonmucoid, malty S. lactis 4/4.2 and S. lactis subsp. diacetylactis SLA3.25. Transconjugants showing pSRQ2201 were Lac; those containing pSRQ2202 were Muc. With the transfer of pSRQ2202, the transconjugants S. lactis ML-3/2.202 and S. lactis subsp. diacetylactis SLA3.2501 not only acquired the Muc phenotype but also resistance to bacteriophages, which were lytic to the respective parent strains S. lactis ML-3/2.201 and S. lactis subsp. diacetylactis SLA3.25.
Rapid Pharmacokinetic and Biodistribution Studies Using Cholorotoxin-Conjugated Iron Oxide Nanoparticles: A Novel Non-Radioactive Method (2010)

We report here a simple near-infrared fluorescence based methodology to assess PK properties of nanoparticles in order to integrate pharmacokinetic data into early nanoparticle design and synthesis. The nanoparticles tested demonstrate properties that are excellent for future clinical imaging strategies and potentially suitable for targeted therapy.
Eculizumab treatment and impaired opsonophagocytic killing of meningococci by whole blood from immunized adults (2017)

Eculizumab, a humanized anti-complement C5 monoclonal antibody (mAb) for treatment of paroxysmal nocturnal hemoglobinuria (PNH) and atypical hemolytic uremic syndrome, blocks the terminal complement pathway required for serum bactericidal activity (SBA). Because treated patients are at >1000-fold increased risk of meningococcal disease, vaccination is recommended; whether vaccination can protect by opsonophagocytic activity in the absence of SBA is not known. Meningococci were added to anticoagulated blood from 12 healthy adults vaccinated with meningococcal serogroup B and serogroup A, C, W, Y vaccines. Bacterial survival was measured after 3-hour incubation in the presence of eculizumab or control complement factor D inhibitor ACH-4471, which blocks the complement alternative pathway (AP) and is in phase 2 development for treatment of PNH. In the absence of inhibitors, colony formation units (CFUs) per milliliter in blood from all 12 immunized subjects decreased from ∼4000 at time 0 to sterile cultures at 3 hours. In the presence of eculizumab, there was a >22-fold increase in geometric mean CFUs per milliliter (90 596 and 114 683 CFU/mL for serogroup B and C strains, respectively; <i>P</i> < .0001 compared with time 0). In the presence of ACH-4471, there was a >12-fold decrease (23 and 331 CFU/mL, respectively; <i>P</i> < .0001). The lack of meningococci killing by blood containing eculizumab resulted from inhibition of release of C5a, a C5 split product needed for upregulation of phagocytosis. The results provide an explanation for the large number of cases of meningococcal disease in immunized patients being treated with eculizumab and suggest that vaccination may provide better protection against meningococcal disease in patients treated with an AP-specific inhibitor.
Molecular cloning and expression of pectin methylesterase genes in Lycopersicon esculentum (tomato) (1990)

Pectin methylesterase (PME) is a ubiquitous plant enzyme which demethoxylates pectin resulting in the formation of free carboxyl groups which may form Ca$\sp{++}$ cross-bridges. While PME has been found in every plant examined, it is a particularly abundant protein in developing tomato fruit. Deesterification of pectin by PME and depolymerization by polygalacturonase are proposed to be involved in fruit softening during tomato fruit ripening. To study the expression of PME in developing tomato fruit, PME was purified from the pericarp of mature green (MG) tomato fruit, anti-PME antibodies were raised in chickens and a cDNA clone was isolated from a $\lambda$gt11 expression library constructed with pericarp MG poly A$\sp{+}$ RNA. Anti-PME antibodies and a PME cDNA clone were used to study PME's expression at the protein, specific activity, and mRNA levels. A gradual increase in PME activity begins at day 20 and continues until the MG stage when a 2-fold increase occurs between the MG and breaker (Br) stages. Only low levels of PME activity are detected in 10 and 15 day old fruit. The increase in activity parallels an increase in PME protein, however the level of PME protein increases beyond the Br stage while PME activity begins to decline. Even though PME activity levels comparable to 25 day old fruit were found in root tissue, no detectable PME protein was observed using Western blot analysis. PME mRNA was first detected in 15 day old fruit and reached a steady-state maximum by 30 DAF. Elevated levels of PME mRNA were maintained through the MG stage and began decreasing as the fruit ripened. No detectable PME mRNA was observed in root, stem, leaf and 10 day old fruit. Localization of PME and PG mRNA in developing tomato fruit using tissue-printing demonstrated PME and PG mRNA are expressed in the same tissue, however PME mRNA was detectable in 15 day old fruit, while PG mRNA first appeared in Br fruit. Genomic analysis of PME gene structure was aided by the isolation of two genomic DNA clones ('VFNT Cherry'). Partial sequencing demonstrated the existence of three tandemly repeated PME genes. Southern blotting for PME genes of genomic DNA isolated from the cultivars 'VFNT Cherry' and 'Rutgers' showed considerable restriction fragment length polymorphism. Two introns have been located within the coding region of the PME genes studied.
Blind identification of MIMO-OSTBC channels combining second and higher order statistics (2006)

It has been recently shown that some multiple-input multipleoutput (MIMO) channels under orthogonal space-time block coding (OSTBC) transmissions can not be unambiguously identified by only exploiting the second order statistics (SOS) of the received signal. This ambiguity, which is due to properties of the OSTBC, is traduced in the fact that the largest eigenvalue of the associated eigenvalue problem has multiplicity larger than one. Fortunately, for most OSTBCs that produce ambiguity, the multiplicity is two. This means that the channel estimate lies in a rank-2 subspace, which can be easily determined applying a first principal component analysis (PCA) step. To eliminate the remaining ambiguity, we propose to apply a constant modulus algorithm (CMA). This combined PCA+CMA approach provides an effective solution for the blind identification of those OSTBCs that can not be identified using only SOS. Some simulation results are presented to show the performance of the proposed method. 1.
Growth Management and the City (1994)

The way urban growth has been "managed," it is no surprise that America's cities are dying. During the last three decades, American urban growth policy was directed to suburban growth. Government encouraged exodus from the metropolis through: deep subsidies for highways, utilities, and open space; housing finance, particularly in the form of tax deductions for mortgage interest and real property taxes; and subsidized Veteran's Administration loans and Federal Housing Administration mortgage insurance. Leaving the city in search of suburban values, the affluent were followed by industry in search of greener locations, retail establishments that favor malls, and restaurants and entertainment outlets looking for secure locations. Thus, the economic base from which taxes are generated to fund public services was transferred to the suburbs.
Anatomical and Functional Assessment of Brown Adipose Tissue by Magnetic Resonance Imaging (2012)

Brown adipose tissue (BAT) is the primary tissue responsible for nonshivering thermogenesis in mammals. The amount of BAT and its level of activation help regulate the utilization of excessive calories for thermogenesis as opposed to storage in white adipose tissue (WAT) which would lead to weight gain. Over the past several years, BAT activity in vivo has been primarily assessed by positron emission tomography-computed tomography (PET-CT) scan using 2-[18F]-fluoro-2-deoxy-D-glucose (18F-FDG) to measure glucose utilization associated with BAT mitochondrial respiration. In this study, we demonstrate the feasibility of mapping and estimating BAT volume and metabolic function in vivo in rats at a 9.4T magnetic resonance imaging (MRI) scanner using sequences available from clinical MR scanners. Based on the morphological characteristics of BAT, we measured the volume distribution of BAT with MRI sequences that have strong fat-water contrast. We also investigated BAT volume by utilizing spin-echo MRI sequences. The in vivo MRI-estimated BAT volumes were correlated with direct measurement of BAT mass from dissected samples. Using MRI, we also were able to map hemodynamic responses to changes in BAT metabolism induced pharmacologically by β3-adrenergic receptor agonist, CL-316,243 and compare this to BAT activity in response to CL-316,243 assessed by PET 18F-FDG. In conclusion, we demonstrate the feasibility of measuring BAT volume and function in vivo using routine MRI sequences. The MRI measurement of BAT volume is consistent with quantitative measurement of the tissue ex vivo.
Catheter Ablation to Maintain Sinus Rhythm (2012)

O ver the past 12 years, catheter ablation of atrial fibrilla- tion (AF) has emerged from being a novel, largely unproven procedure to its role today as a very commonly performed procedure for treatment of patients with symptomatic AF. The objective of the present report is to provide a state-of-the-art review of the techniques, outcomes, and complications of catheter ablation of AF. Three main topic areas will be discussed. First, I will review the current approaches for and outcomes of AF ablation. Second, I will identify and briefly review areas in the field of AF ablation about which less is known and that remain active areas for research. Third, I will briefly review the current status of a number of emerging technologies, approaches, and tools that are being developed with the aim of improving the outcomes of AF ablation. Finally, I will conclude by sharing with you my perspective on the indications for AF ablation.
Prospects for rational approaches to anthelmintic discovery (1996)

Rational approaches to anthelmintic discovery include the design of screens for compounds directed at specific proteins in helminths that are pharmacologically distinguishable from their vertebrate homologues. The existence of several anthelmintics that selectively target the neuromusculature of helminths (e.g. levamisole, ivermectin, praziquantel, metrifonate), together with recent basic research in helminth physiology, have contributed to the recognition that neurobiology distinguishes these organisms from their vertebrate hosts. In this survey, we focus on mechanism-based screening and its application to anthelmintic discovery, with particular emphasis on targets in the neuromusculature of helminths. Few of these proteins have been exploited in chemotherapy. However, recent studies in comparative pharmacology and molecular biology, including the C. elegans genome project, have provided insights on potential new targets and, in some cases, molecular probes useful for their incorporation in mechanism-based screens.
Synthesis and Photodynamic Activities of Silicon 2,3-Naphthalocyanine Derivatives (1994)

Bis(tert-butyldimethylsiloxy)- (7), bis(dimethylthexylsiloxy)- (8), bis(tri-n-hexylsiloxy)- (9), and bis(dimethyloctadecylsiloxy)silicon 2,3-naphthalocyanines (10) were prepared via substitution of the bis(hydroxy) precursor with the corresponding chlorosilane ligands and characterized by spectroscopic and combustion analyses. They show strong absorption around 780 nm where tissues exhibit optimal transparency. Compounds 7-10 are capable of producing singlet oxygen. They are relatively photostable although less stable than the analogous phthalocyanine, i.e., the bis-(dimethylthexylsiloxy)silicon phthalocyanine (12). They were evaluated as potential photosensitizers for the photodynamic therapy (PDT) of cancer in vitro against V-79 cells and in vivo against the EMT-6 tumor in Balb/c mice. In vitro all four dyes showed limited phototoxicity combined with substantial dark toxicity. Surprisingly, in vivo (i.v., 0.1 mumol/kg, 24 h prior to the photoirradiation of the tumor with 780-nm light, 190 mW/cm2, 400 J/cm2) all dyes induced tumor regression in at least 50% of mice whereas compound 8 gave a complete tumor response in 80% of mice without apparent systemic toxicity at doses as high as 10 mumol/kg. At 24 h postinjection, compound 8 showed a favorable tumor to muscle ratio of 7, assuring minimal damage to the healthy tissue surrounding the tumor during PDT. Our data confirm the potential of silicon naphthalocyanines as far-red-shifted photosensitizers for the PDT of cancer and indicate the importance of the selection of the two axial silicon ligands for optimal photodynamic efficacy.
Diagnostic criteria for schwannomatosis (2005)

The neurofibromatoses are a diverse group of genetic conditions that share a predisposition to the development of tumors of the nerve sheath. Schwannomatosis is a recently recognized third major form of neurofibromatosis (NF) that causes multiple schwannomas without vestibular tumors diagnostic of NF2. Patients with schwannomatosis represent 2.4 to 5% of all patients requiring schwannoma resection and approximately one third of patients with schwannomatosis have anatomically localized disease with tumors limited to a single limb or segment of spine. Epidemiologic studies suggest that schwannomatosis is as common as NF2, but that familial occurrence is inexplicably rare. Patients with schwannomatosis overwhelmingly present with pain, and pain remains the primary clinical problem and indication for surgery. Diagnostic criteria for schwannomatosis are needed for both clinicians and researchers, but final diagnostic certainly will await the identification of the schwannomatosis locus itself.
α-fetoprotein monitoring in chinese patients with chronic hepatitis B virus infection: Role in the early detection of hepatocellular carcinoma (1989)

Two hundred ninety patients (203 men, 87 women), age 7 to 74 years (mean: 39.1 years), with chronic hepatitis B virus infection, were prospectively followed for a period of 1 to 4 years to determine the value of alpha-fetoprotein monitoring in the early detection of hepatocellular carcinoma. At presentation, 66% of the patients were asymptomatic, 19% had chronic hepatitis and 15% had established cirrhosis. Forty-four (15%) patients had elevated alpha-fetoprotein levels on one or more occasions during the study period. Twenty patients with normal alpha-fetoprotein levels at presentation developed elevated alpha-fetoprotein levels during the course of follow-up, whereas 24 patients had elevated alpha-fetoprotein levels at presentation. Six (14%) of these 44 patients (five men and one woman), age 23 to 66 years, had persistent or progressive increase in alpha-fetoprotein levels and were confirmed to have hepatocellular carcinoma. In four patients, the alpha-fetoprotein levels were below 500 ng per ml at the time of tumor localization. Only three patients had resectable tumors. All six patients would have been missed if alpha-fetoprotein screening was restricted to men above the age of 40 with cirrhosis and anti-HBe. Of the remaining 38 patients, elevation in alpha-fetoprotein levels in 18 patients was associated with exacerbations of the underlying liver disease and/or significant changes in level of hepatitis B virus replication, but in 20 patients, no apparent cause could be identified. The elevation in AFP levels exceeded 200 ng per ml in 26% and persisted beyond 6 months in 15% of these patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Functional expression of CD134 by neutrophils (2004)

CD134 (OX40) is a member of the tumor necrosis factor (TNF) receptor superfamily expressed on activated T cells. Here, we show that human peripheral blood neutrophils express CD134. Activation of CD134 by soluble CD134 ligand (OX40 ligand/gp34) resulted in delayed caspase-3 activation and consequently in delayed neutrophil apoptosis in vitro. Moreover, CD134 ligand, like G-CSF, maintained anti-apoptotic Mcl-1 levels and inhibited cleavage of the pro-apoptotic Bcl-2 family members Bid and Bax in these cells, suggesting that CD134-mediated signals block apoptosis pathways proximal to mitochondria activation. In conclusion, CD134 regulates neutrophil survival, suggesting that this molecule does not only contribute to adaptive but also to innate immune responses.
Apoptotic neutrophils in the circulation of patients with glycogen storage disease type 1b (GSD1b) (2003)

Glycogen storage disease type 1b (GSD1b) is a rare autosomal recessive disorder characterized by hypoglycemia, hepatomegaly, and growth retardation, and associated-for unknown reasons- with neutropenia and neutrophil dysfunction. In 5 GSD1b patients in whom nicotin-amide adenine dinucleotide phosphate-oxidase activity and chemotaxis were defective, we found that the majority of circulating granulocytes bound Annexin-V. The neutrophils showed signs of apoptosis with increased caspase activity, condensed nuclei, and perinuclear clustering of mitochondria to which the proapoptotic Bcl-2 member Bax had translocated already. Granulocyte colony-stimulating factor (G-CSF) addition to in vitro cultures did not rescue the GSD1b neutrophils from apoptosis as occurs with G-CSF-treated control neutrophils. Moreover, the 2 GSD1b patients on G-CSF treatment did not show significantly lower levels of apoptotic neutrophils in the bloodstream. Current understanding of neutrophil apoptosis and the accompanying functional demise suggests that GSD1b granulocytes are dysfunctional because they are apoptotic.
Development of a Quantitative Real-Time Detection Assay for Hepatitis B Virus DNA and Comparison with Two Commercial Assays (2000)

A highly reproducible and sensitive real-time detection assay based on TaqMan technology was developed for the detection of hepatitis B virus (HBV) DNA and compared with two commercially available assays. The assay was validated with the Viral Quality Control panel, which also includes EUROHEP HBV DNA standards. This real-time PCR detection system had a dynamic range of 373 to 10(10) genome copies per ml and showed an excellent correlation with both the commercial HBV Digene Hybrid Capture II microplate assay (Digene Diagnostics) and the HBV MONITOR assay (Roche Diagnostics). To demonstrate its clinical utility, four chronically HBV-infected patients treated with lamuvidine were monitored using the three different assays. From the results we concluded that this assay is an excellent alternative for monitoring of HBV-infected patients in routine diagnostics and clinical practice, enabling the analysis of a large dynamic range of HBV DNA in a single, undiluted sample.
Leukocyte-endothelial interaction and capillary perfusion in ischemia/reperfusion of the rat cremaster muscle. (1991)

The role of leukocytes in the decreased perfusion following ischemia in skeletal muscle was examined in the microcirculation of the rat cremaster muscle. The isolated muscle was viewed with an intravital microscope. Diameters of A1 and A2 arterioles and collecting venules were determined hourly. The number of leukocytes rolling along the venular walls was determined from a videotape. Nonischemic (control) rats (n = 10) were observed for 6 hours. The ischemic group (n = 10) was observed for one hour, the iliac and femoral arteries and veins were then clamped for 4 hours, released, and the muscle was observed for another two hours. No change in arteriole or venule diameters occurred in the control group. The diameters of the arterioles in the ischemic group decreased significantly during reperfusion but, the venule diameters did not. There was a significant reduction during reperfusion but, perfused capillaries following ischemia compared to control. There was a small but not significant increase in the number of rolling leukocytes in the ischemic group. The extent of leukocyte rolling in postcapillary venules was found to not correlate with the decrease in capillary perfusion that occurs after ischemia and reperfusion. However, the decrease in capillary flow was associated with reduced arteriole diameters.
A Method for Assessing the Stability of a Membrane Protein (1997)

The integral membrane protein diacylglycerol kinase (DGK) from Escherichia coli has been reversibly unfolded in a protein/detergent/mixed micelle system by varying the molar ratio of n-decyl beta-D-maltoside (DM) and sodium dodecyl sulfate (SDS). Unfolding was monitored by circular dichroism (CD) and ultraviolet (UV) absorbance spectroscopy. When unfolding is monitored by measuring changes in absorbance at 294 nm, two distinct denaturation phases are observed, indicative of a stable intermediate. When CD is used as a conformational probe, the resulting denaturation curve contains only one major transition, which corresponds to the first unfolding phase observed by absorbance changes. The unfolding behavior of several mutant proteins in which the tryptophan residues were selectively replaced made it possible to assign the first unfolding phase to a denaturation event in a cytoplasmic domain and the second phase to denaturation of the membrane-embedded portion of the protein. The denaturation curves fit well to a model which assumes two cooperative transitions and a linear relationship between unfolding free energy and SDS concentration. Extrapolation back to zero denaturant indicates an unfolding free energy of 6 kcal/mol for the cytoplasmic domain and 16 kcal/mol for the transmembrane domain. The high apparent stability of the transmembrane domain could explain the high degree of tolerance to amino acid substitutions seen for DGK and other membrane proteins. The approach described in this paper may be applicable to other membrane protein systems.
The in vivo pharmacological profile of the novel glycoprotein IIb/IIIa antagonist, SK&F 106760. (1994)

The in vivo pharmacological profile of SK&F 106760 [N alpha-acetyl-cyclo(S,S)-cysteinyl-N alpha-methylarginyl-glycyl-aspartyl-penicillamine-amide], a novel, potent glycoprotein IIb/IIIa (GPIIb/IIIa) antagonist has been investigated. In conscious dogs, SK&F 106760 (0.3-3 mg/kg i.v.) produced a dose-related inhibition of ex vivo whole blood platelet aggregation induced by collagen (5 micrograms/ml) with complete inhibition being produced for 5, 90 and 165 min after administration of 0.3, 1 and 3 mg/kg i.v., respectively. Plasma levels of SK&F 106760 were measured by high-performance liquid chromatography after i.v. bolus administration of 1 mg/kg. An initial alpha-disposition phase with a T1/2 of 11 +/- 6 min was followed by a longer terminal beta-elimination phase with a T1/2 of 66 +/- 12 min, which accounted for 79 +/- 9% of the total area under the plasma concentration-time curve. The apparent steady-state volume of distribution was 259 +/- 26 ml/kg and the plasma clearance was 3.4 +/- 0.8 ml/min/kg. The plasma concentration of SK&F 106760 at which collagen-induced ex vivo whole blood aggregation was inhibited by 50% was estimated to be 593 +/- 52 nM. After intraduodenal and intrajejunal administration of 3 mg/kg, SK&F 106760 had a bioavailability of 3 to 6% and produced a peak inhibition of ex vivo platelet aggregation of 40 to 50%. In anesthetized dogs, SK&F 106760 (0.3-3.0 mg/kg i.v.) produced a complete inhibition of platelet-dependent coronary artery thrombosis, with a dose-related duration of action.(ABSTRACT TRUNCATED AT 250 WORDS)