gebhart/patrepeval huggingface dataset:
Molecular cloning and expression in Escherichia coli of the glycoprotein gene of VHS virus, and immunization of rainbow trout with the recombinant protein (1993)

The gene encoding the envelope glycoprotein of a recent Danish isolate of a salmonid rhabdovirus, viral haemorrhagic septicaemia virus (VHSV) has been cloned and sequenced at the cDNA level. When compared with the deduced sequence of a French isolate of VHSV, it was noted that there were 13 amino acid substitutions in the Danish virus. Amino acid homologies with the glycoprotein of a North American salmonid rhabdovirus (infectious haematopoietic necrosis virus) indicate a high degree of structural similarity between the two fish rhabdovirus glycoproteins. Results from partial enzymatic deglycosylation of the viral protein indicate that all four NXT/S sites found in the sequence are N-glycosylated in the virus. The glycoprotein, without the N-terminal leader sequence and C-terminal hydrophobic anchor segment, was expressed in Escherichia coli as a factor Xa protease-cleavable fusion protein. The purified and renatured viral part of the recombinant protein was able to elicit VHSV-specific antibodies and neutralizing antibody activity in serum when injected into rainbow trout.
Generating daily activity schedules for households using Genetic Algorithms (2005)

One way of making activity-based travel analysis operational for transport planning is multiagent micro-simulation. Modeling activity and trip generation based on individual and social characteristics are central steps in this method. The model presented here generates complete daily activity schedules based on the structure of a household and its members’ activity agendas. The model assumes that the household is another basic decision-making unit for travel demand aside from individual mobility needs. Results of the model are schedules containing complete information about activity type and sequence, locations, and means of transportation, as well as activity start times and durations. The generated schedules are the outcome of a probabilistic optimisation using genetic algorithms. This iterative method improves solutions found in a random search according to the specification of a fitness criterion, which equals utility here. It contains behavioural assumptions about individuals as well as the household level. Individual utility is derived from the number of activities and their respective durations. It is reduced by costs of travelling, waiting times, and environmental as well as social constraints. The household level is represented directly by the utility of joint activities, and indirectly by allocation of activities and means of transportation to household members. The paper presents initial tests with a three-person household, detailing resulting schedules, and discussing run time experiences. A sensitivity analysis of the joint utility parameter impact is also included.
Systemic lupus erythematosus: demographics, prognosis, and outcome. (1997)

Systemic lupus erythematosus (SLE) is a systemic autoimmune disorder with an annual incidence of 50 to 70/million and a prevalence of 500/million population. The highest incidence is observed in women aged 20 to 40 years. The clinical manifestations of SLE are remarkably heterogeneous. Major organ system involvement may occur in the heart, lungs, kidneys, and central nervous system and is responsible for most of the mortality and morbidity caused by the disease. Complications of drug treatment, in particular corticosteroid side effects, contribute to longterm morbidity. The major causes of death are directly related to the disease and include acute vascular neurologic events, renal failure, cardiovascular or pulmonary involvement, infection, and coronary artery disease.
Autonomous in Situ Analysis and Real-Time Chemical Detection Using a Backpack Miniature Mass Spectrometer: Concept, Instrumentation Development, and Performance (2014)

A major design objective of portable mass spectrometers is the ability to perform in situ chemical analysis on target samples in their native states in the undisturbed environment. The miniature instrument described here is fully contained in a wearable backpack (10 kg) with a geometry-independent low-temperature plasma (LTP) ion source integrated into a hand-held head unit (2 kg) to allow direct surface sampling and analysis. Detection of chemical warfare agent (CWA) simulants, illicit drugs, and explosives is demonstrated at nanogram levels directly from surfaces in near real time including those that have complex geometries, those that are heat-sensitive, and those bearing complex sample matrices. The instrument consumes an average of 65 W of power and can be operated autonomously under battery power for ca. 1.5 h, including the initial pump-down of the manifold. The maximum mass-to-charge ratio is 925 Th with mass resolution of 1-2 amu full width at half-maximun (fwhm) across the mass range. Multiple stages of tandem analysis can be performed to identify individual compounds in complex mixtures. Both positive and negative ion modes are available. A graphical user interface (GUI) is available for novice users to facilitate data acquisition and real-time spectral matching.
NMR and mutagenesis evidence for an I domain allosteric site that regulates lymphocyte function-associated antigen 1 ligand binding (2000)

The leukocyte integrin, lymphocyte function-associated antigen 1 (LFA-1) (CD11a/CD18), mediates cell adhesion and signaling in inflammatory and immune responses. To support these functions, LFA-1 must convert from a resting to an activated state that avidly binds its ligands such as intercellular adhesion molecule 1 (ICAM-1). Biochemical and x-ray studies of the Mac-1 (CD11b/CD18) I domain suggest that integrin activation could involve a conformational change of the C-terminal alpha-helix. We report the use of NMR spectroscopy to identify CD11a I domain residues whose resonances are affected by binding to ICAM-1. We observed two distinct sites in the CD11a I domain that were affected. As expected from previous mutagenesis studies, a cluster of residues localized around the metal ion-dependent adhesion site (MIDAS) was severely perturbed on ICAM-1 binding. A second cluster of residues distal to the MIDAS that included the C-terminal alpha-helix of the CD11a I domain was also affected. Substitution of residues in the core of this second I domain site resulted in constitutively active LFA-1 binding to ICAM-1. Binding data indicates that none of the 20 substitution mutants we tested at this second site form an essential ICAM-1 binding interface. We also demonstrate that residues in the I domain linker sequences can regulate LFA-1 binding. These results indicate that LFA-1 binding to ICAM-1 is regulated by an I domain allosteric site (IDAS) and that this site is structurally linked to the MIDAS.
Peptide Mimicry of Adenocarcinoma-Associated Carbohydrate Antigens (1997)

Carbohydrate antigens have been identified as significant antigens in many human tumors either by analyzing antibodies in patients' sera or by using monoclonal antibodies of either mouse or human origin. Three carbohydrate epitopes present on cancer-associated mucins [sialyl-Lewis A (SLA), sialyl-Lewis X (SLX), and sialyl-Tn (STn)] may have functional significance in metastasis. Subsequently, these antigens are considered as targets for active specific immunotherapy. Carbohydrates, as T-cell-independent antigens, often elicit diminished immune responses. To overcome this drawback, carbohydrates are typically coupled to protein carriers to elicit immunoglobulin G (IgG) responses as opposed to low-affinity IgM responses, which often times accompanies carbohydrate-based immunizations. In addition, some complex carbohydrates are difficult to synthesize. This latter aspect is further magnified if one considers that clustering of epitopes on neoglycoproteins must be emulated in the synthesis process, leading to multiple presentation or tandem repeats of the synthetic carbohydrate immunogen. Here, we examine the hypothesis that peptides that mimic carbohydrates might be developed to induce immune responses that target and mediate the killing of tumor cells, particularly breast cancer cells in an adjuvant-type setting. We have found that carbohydrate-mimicking peptides retain carbohydrate-like conformations, inducing anti-carbohydrate immune responses against breast tumor cells and mediating their killing by a complement-dependent mechanism.
Sodium carboxyl‐methyl‐cellulose dressings in the management of deep ulcerations of diabetic foot (2001)

Carboxyl-methyl-cellulose dressings were shown to be safe, effective and well tolerated in the management of non-ischaemic, non-infected deep diabetic foot ulcers.
MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes (2000)

MADS-box genes encode transcriptional regulators involved in diverse aspects of plant development. Here we describe the cloning and mRNA spatio-temporal expression patterns of five new MADS-box genes from Arabidopsis: AGL16, AGL18, AGL19, AGL27 and AGL31. These genes will probably become important molecular tools for both evolutionary and functional analyses of vegetative structures. We mapped our data and previous expression patterns onto a new MADS-box phylogeny. These analyses suggest that the evolution of the MADS-box family has involved a rapid and simultaneous functional diversification in vegetative as well as reproductive structures. The hypothetical ancestral genes had broader expression patterns than more derived ones, which have been co-opted for putative specialized functions as suggested by their expression patterns. AGL27 and AGL31, which are closely related to the recently described flowering-time gene FLC (previously AGL25), are expressed in most plant tissues. AGL19 is specifically expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. AGL18, which is most similar in sequence to the embryo-expressed AGL15 gene, is expressed in the endosperm and in developing male and female gametophytes, suggesting a role for AGL18 that is distinct from previously characterized MADS-box genes. Finally, AGL16 RNA accumulates in leaf guard cells and trichomes. Our new phylogeny reveals seven new monophyletic clades of MADS-box sequences not specific to flowers, suggesting that complex regulatory networks involving several MADS-box genes, similar to those that control flower development, underlie development of vegetative structures.
Toward Efficient Binders for Li-Ion Battery Si-Based Anodes: Polyacrylic Acid (2010)

Si-based Li-ion battery anodes offer specific capacity an order of magnitude beyond that of conventional graphite. However, the formation of stable Si anodes is a challenge because of significant volume changes occurring during their electrochemical alloying and dealloying with Li. Binder selection and optimization may allow significant improvements in the stability of Si-based anodes. Most studies of Si anodes have involved the use of carboxymethylcellulose (CMC) and poly(vinylidene fluoride) (PVDF) binders. Herein, we show for the first time that pure poly(acrylic acid) (PAA), possessing certain mechanical properties comparable to those of CMC but containing a higher concentration of carboxylic functional groups, may offer superior performance as a binder for Si anodes. We further show the positive impact of carbon coating on the stability of the anode. The carbon-coated Si nanopowder anodes, tested between 0.01 and 1 V vs Li/Li+ and containing as little as 15 wt % of PAA, showed excellent stability during the first hundred cycles. The results obtained open new avenues to explore a novel series of binders from the polyvinyl acids (PVA) family.
A study of the difference of wheat and oilseed rape in tolerance to Mn deficiency in the field. (2000)

Under rice wheat or rice oilseed rape cropping system, seven oilseed rape cultivars and two wheat cultivars were used to study the difference of oilseed rape and wheat in tolerance to Mn deficiency. The results demonstrated that oilseed rape was higher tolerance to Mn deficiency than that of wheat in the same Mn deficient soil. Among seven oilseed rape cultivars, five oilseed rape cultivars showed slight Mn deficient symptoms just in seedling bed. After transplanting, all oilseed rape cultivars grew healthily without any Mn deficient symptoms. Compared with the plants in +Mn treatments, the plants of all oilseed rape cultivars in -Mn treatments had no significant differences in leaf color, growth vigour and grain yields in field growth period. The two wheat cultivars in -Mn treatments showed typical Mn deficient symptoms from early tillering stage to ear bearing stage. The grain yields of two wheat cultivars under Mn stress reduced more than 30%. In the Mn deficient soil of rice wheat or rice oilseed rape rotation, relative grain yield of direct sowing oilseed rape was higher than that of transplanting oilseed rape.
Vasopressin pressor hypersensitivity in vasodilatory septic shock (1997)

Landry, Donald W. MD, PhD; Levin, Howard R. MD; Gallant, Ellen M. MD; Seo, Susan BA; D'Alessandro, David MD; Oz, Mehmet C. MD; Oliver, Juan A. MD Author Information
In Vitro Conversion of Propionate to Pyruvate bySalmonella entericaEnzymes:  2-Methylcitrate Dehydratase (PrpD) and Aconitase Enzymes Catalyze the Conversion of 2-Methylcitrate to 2-Methylisocitrate (2001)

Salmonella enterica serovar Typhimurium LT2 catabolizes propionate through the 2-methylcitric acid cycle, but the identity of the enzymes catalyzing the conversion of 2-methylcitrate into 2-methylisocitrate is unclear. This work shows that the prpD gene of the prpBCDE operon of this bacterium encodes a protein with 2-methylcitrate dehydratase enzyme activity. Homogeneous PrpD enzyme did not contain an iron-sulfur center, displayed no requirements for metal cations or reducing agents for activity, and did not catalyze the hydration of 2-methyl-cis-aconitate to 2-methylisocitrate. It was concluded that the gene encoding the 2-methyl-cis-aconitate hydratase enzyme is encoded outside the prpBCDE operon. Computer analysis of bacterial genome databases identified the presence of orthologues of the acnA gene (encodes aconitase A) in a number of putative prp operons. Homogeneous AcnA protein of S. enterica had strong aconitase activity and catalyzed the hydration of the 2-methyl-cis-aconitate to yield 2-methylisocitrate. The purification of this enzyme allows the complete reconstitution of the 2-methylcitric acid cycle in vitro using homogeneous preparations of the PrpE, PrpC, PrpD, AcnA, and PrpB enzymes. However, inactivation of the acnA gene did not block growth of S. enterica on propionate as carbon and energy source. The existence of a redundant aconitase activity (encoded by acnB) was postulated to be responsible for the lack of a phenotype in acnA mutant strains. Consistent with this hypothesis, homogeneous AcnB protein of S. enterica also had strong aconitase activity and catalyzed the conversion of 2-methyl-cis-aconitate into 2-methylisocitrate. To address the involvement of AcnB in propionate catabolism, an acnA and acnB double mutant was constructed, and this mutant strain cannot grow on propionate even when supplemented with glutamate. The phenotype of this double mutant indicates that the aconitase enzymes are required for the 2-methylcitric acid cycle during propionate catabolism.
A cytosolic sperm factor stimulates repetitive calcium increases and mimics fertilization in hamster eggs (1990)

Microinjection of cytosolic sperm extracts into unfertilized golden hamster eggs caused a series of increases in cytoplasmic free calcium, Ca2+i, and membrane hyperpolarizing responses, HRs. These HRs and Ca2+i transients are similar to those seen during in vitro fertilization of hamster eggs. The sperm factor that is responsible for causing these effects appears to be of high molecular weight and protein based. Injection of sperm factor activated eggs and mimicked fertilization in causing repetitive HRs in the presence of phorbol esters and in sensitizing the egg to calcium-induced calcium release. Since these effects cannot be mimicked by injecting G-protein agonists or calcium-containing solutions, it seems unlikely that a receptor-G-protein signalling system is involved at fertilization. These data instead suggest a novel signal transduction system operates during mammalian fertilization in which a protein factor is transferred from the sperm into the egg cytoplasm after gamete membrane fusion.
The evolving doublecortin (DCX) superfamily (2006)

This study reveals the existence and conservation of multiple members of the DCX superfamily in different species. Sequence analysis combined with expression analysis is likely to be a useful tool to predict correlations between human disease and mouse models. The sub-specialization of some members due to restricted expression patterns and sequence divergence may explain the successful addition of genes to this family throughout evolution.
Induction of a T-cell specific antigen on bone marrow lymphocytes with thymus RNA. (1978)

Expression of a rabbit T-cell specific antigen can be induced on bone marrow lymphocytes following exposure to an RNA extract obtained from the thymuses of young rabbits. The presence of the antigen was demonstrated using goat anti-rabbit T-cell serum in a complement-dependent cytotoxicity assay. The T-cell antigen first appeared 3 h after addition of the thymus RNA to bone marrow cell cultures and the maximum number of cells expressing the T-cell antigen was observed within 24 h. RNA obtained from a source other than the thymus was found to be ineffective in inducing expression of the T-cell antigen. The induction of the antigen appears to be dependent on the presence of intact thymus RNA, as RNase treatment but not trypsin treatment, destroyed the ability of the RNA to induce the T-cell antigen.
An adaptive microwave phased array for targeted heating of deep tumours in intact breast: animal study results (1999)

It has previously been reported in phantoms, that an adaptive radiofrequency phased array can generate deep focused heating distributions without overheating the skin and superficial healthy tissues. The present study involves adaptive microwave phased array hyperthermia tests in animals (rabbits) with and without tumours. The design of the adaptive phased array as applied to the treatment of tumours in intact breast, is described. The adaptive phased array concept uses breast compression and dual-opposing 915 MHz air-cooled waveguide applicators with electronic phase shifters and electric-field feedback, to focus automatically by computer control the microwave radiation in deep tissue. Temperature measurements for a clinical adaptive phased array hyperthermia system demonstrate tissue heating at depth with reduced skin heating.
Bactericidal/permeability-increasing protein has endotoxin-neutralizing activity. (1990)

Neutrophil granules contain proteins important in host defense against bacterial pathogens. Granule proteins released from activated neutrophils facilitate opsonization, phagocytosis, tissue digestion, and antimicrobial activity. Three similar, if not identical, neutrophil proteins, bactericidal/permeability-increasing protein (BPI), 57,000 m.w. cationic antimicrobial protein, and bactericidal protein have been described that specifically kill gram negative bacteria. Since LPS is a structure common to all gram-negative bacteria, we investigated whether the microbicidal protein BPI affects biologic activity of LPS in vitro. Human neutrophils can be activated both in vitro and in vivo by LPS. Upon stimulation, surface expression of CR1 and CR3 increases markedly. Using flow microfluorimetry, we analyzed surface expression of CR1 and CR3 as a measure of neutrophil stimulation in response to LPS. CR up-regulation on neutrophils was TNF independent, suggesting direct LPS stimulation of neutrophils in this system. Purified BPI completely inhibited CR up-regulation on neutrophils stimulated with both rough and smooth LPS chemotypes at 1.8 to 3.6 nM (100 to 200 ng/ml). By comparison, the polypeptide antibiotic polymyxin B completely inhibited the same dose of LPS at 0.4 nM. The inhibitory activity of BPI appeared to be specific for LPS because neutrophil stimulation by formylated peptide or TNF was unaffected. The specificity of BPI for LPS was further demonstrated by inhibition of LPS activity in the limulus amebocyte lysate assay. Therefore, the role of BPI in infection may not be limited to its microbicidal activity, but it may also regulate the neutrophil response to LPS.
A bifunctional colchicinoid that binds to the androgen receptor (2007)

Castrate-resistant prostate cancer (CRPC) continues to be dependent on the androgen receptor (AR) for disease progression. We have synthesized and evaluated a novel compound that is a conjugate of colchicine and an AR antagonist (cyanonilutamide) designed to inhibit AR function in CRPC. A problem in multifunctional AR-binding compounds is steric hindrance of binding to the embedded hydrophobic AR ligand-binding pocket. Despite the bulky side chain projecting off of the AR-binding moiety, this novel conjugate of colchicine and cyanonilutamide binds to AR with a K(i) of 449 nmol/L. Structural modeling of this compound in the AR ligand-binding domain using a combination of rational docking, molecular dynamics, and steered molecular dynamics simulations reveals a basis for how this compound, which has a rigid alkyne linker, is able to bind to AR. Surprisingly, we found that this compound also binds to tubulin and inhibits tubulin function to a greater degree than colchicine itself. The tubulin-inhibiting activity of this compound increases cytoplasmic AR levels in prostate cancer cells. Finally, we found that this compound has greater toxicity against androgen-independent prostate cancer cells than the combination of colchicine and nilutamide. Together, these data point to several ways of inhibiting AR function in CRPC.
Suppression of apoptosis in normal and neoplastic human B lymphocytes by CD40 ligand is independent of Bcl‐2 induction (1993)

The tendency of isolated germinal center (GC) B cells to undergo apoptosis was suppressed by recombinant cell-bound CD40 ligand (CD40L): after 2 days at 37 degrees C, > 80% of cells remained viable in the presence of CD40L as compared to < 1% in control cultures. CD40L sustained a high rate of DNA synthesis in GC cells and was more effective than monoclonal antibody to CD40 in this regard. Group I Burkitt lymphoma (BL) cell lines induced to undergo apoptosis with anti-immunoglobulin or calcium ionophore were also protected by CD40L. In BL cells, this route of rescue was not accompanied by induction of Bc1-2 protein, the expression of which has been linked to hemopoietic cell survival. Bc1-2 was induced in GC cells responding to CD40L, but its appearance was a relatively late event not reaching significant levels over controls until day 2 of culture. Thus induction of Bc1-2 appears to be secondary to the survival signal imparted by CD40L. These findings are discussed in relation to a potential role for CD40L in supporting B cell tumors in vivo and the discovery that the molecular defect in the X-linked Hyper-IgM syndrome is targeted to the CD40L gene.
The science of vacuum erectile device in penile rehabilitation after radical prostatectomy. (2013)

Current clinical evidences support the safety, tolerability, effectiveness and benefits of early VED therapy after RP. The available basic scientific evidences demonstrate that VED therapy for penile rehabilitation is achieved by increasing arterial inflow, anti-apoptotic, anti-fibrotic and anti-hypoxia mechanisms.