gebhart/patrepeval huggingface dataset:
[Pre-analytical problems on assay conditions for blood midkine]. (2008)

We have established the assay conditions of midkine (MK) measurement, the reference intervals and evaluation for clinical significance of blood MK measurement. MK is a kind of cytokines and basic protein which is a heparin-binding growth factor of various cells. The increase of MK expression suggests a prognostic value in early stage on cancers or inflammation. But significant problems in the MK measurement are alterations resulting from standing time and temperature instability after blood collection. Assay of MK was performed with solid phase human MK immunoassay recently developed sensitive enzyme linked immunosorbent method. The assay condition of MK was required to be separated immediately after blood sampling within 24 hrs at 4 degrees C or within 2 hrs at room temperature-standing. Plasma sample obtained with EDTA-2Na or citric acid-Na, and serum obtained from plain tube container showed good results. Linearity was obtained up to 1500 pg/ml and repeatability and reproducibility were within 10% as CV%. The recovery of MK was 101.1+/-3.8% with 10 specimens ranged 97-105%. Addition of interfering substances showed no effect on assay results when hemoglobin, EDTA-Na, citrate and turbidity check, but conjugated bilirubin (over 0.68 mmol/l) and gave negative errors within 10% in the assay results and heparin gave negative errors. The reference interval was 550 +/- 160 pg/ml in healthy individuals serum.
The use of neutrons in cancer therapy: a historical perspective through the modern era. (1997)

The fields of boron neutron capture therapy (BNCT) and fast neutron radiotherapy are surveyed starting with the early clinical work that began shortly after the discovery of the neutron by Chadwick in 1932. The evolution of each field is described and the current status in regards to accepted clinical indications and ongoing research areas summarized. BNCT remains a research area but a discussion is given of current efforts to design and construct non-reactor-based epithermal neutron sources to deploy this technology to major medical centers if the clinical research proves successful. Fast neutron radiotherapy is a mature field with selected clinical indications for locally advanced salivary gland tumors and inoperable sarcomas of bone and soft tissue. The current status of clinical trials for locally advanced prostate cancer and other tumors is reviewed. Ongoing areas of research in the field of fast neutron radiotherapy are described.
Characterization of the knob domain of the adenovirus type 5 fiber protein expressed in Escherichia coli (1994)

The adenovirus fiber protein is used for attachment of the virus to a specific receptor on the cell surface. Structurally, the protein consists of a long, thin shaft that protrudes from the vertex of the virus capsid and terminates in a globular domain termed the knob. To verify that the knob is the domain which interacts with the cellular receptor, we have cloned and expressed the knob from adenovirus type 5 together with a single repeat of the shaft in Escherichia coli. The protein was purified by conventional chromatography and functionally characterized for its interaction with the adenovirus receptor. The recombinant knob domain bound about 4,700 sites per HeLa cell with an affinity of 3 x 10(9) M-1 and blocked adenovirus infection of human cells. Antibodies raised against the knob also blocked virus infection. By gel filtration and X-ray diffraction analysis of protein crystals, the knob was shown to consist of a homotrimer of 21-kDa subunits. The results confirm that the trimeric knob is the ligand for attachment to the adenovirus receptor.
Attenuation of Leukocytes Sequestration by Carbon Monoxide-Releasing Molecules: Liberated Carbon Monoxide in the Liver of Thermally Injured Mice (2007)

We sought to determine whether the CO-releasing molecules, ie, liberated CO, attenuates the leukocytes sequestration in the liver of thermally injured mice. Sixty-five mice were assigned to five groups in three respective experiments. In each experiment, mice in sham group (n = 7) and sham + CORM-2 group (n = 7) were underwent sham thermal injury, whereas mice in burn group (n = 7) received 15% TBSA full-thickness thermal injury, mice in burn + CORM-2 group (n = 7) underwent the same thermal injury with the immediate administration of CORM-2 (8 mg/kg intravenously), and mice in burn + DMSO group (n = 7) underwent the same thermal injury with an immediate 160 microl-bolus injection of 0.5% dimethyl sulfoxide/saline. Polymorphonuclear leucocyte (PMN) accumulation (assessed by the myeloperoxidase assay) was assessed in mice liver. Activation of nuclear factor kappa B (NF-kappaB) and the expression levels of ICAM-1 and VCAM-1 in liver were assessed. In an in vitro experiment, sinusoidal endothelial cells (SECs) isolated from the liver of normal mice were stimulated by experimental mice serum (50% v/v) for 4 hours. Subsequently, the adhesion of PMNs to SECs was assessed. In addition, the number and states (rolling or stationary) of leukocytes in liver were observed by intravital microscopy. Treatment of thermally injured mice with CORM-2 attenuated PMN accumulation and prevented activation of NF-kappaB in the liver, which was accompanied by a decrease of the expression of ICAM-1 and VCAM-1. In parallel, PMNs adhesion to SECs stimulated by CORM-2-treated thermally injured mice serum was markedly decreased. Intravital microscopy showed that the stationary leukocytes in thermally injured mice liver were significantly reduced by treatment of CORM-2. CORM-released CO attenuates leukocytes sequestration in the liver of burn mice by interfering with NF-kappaB activation, protein expression of ICAM-1 and VCAM-1, and therefore suppressing endothelial cells proadhesive phenotype.
Epstein–Barr virus-transforming protein latent infection membrane protein 1 activates transcription factor NF-κB through a pathway that includes the NF-κB-inducing kinase and the IκB kinases IKKα and IKKβ (1998)

The Epstein-Barr virus oncoprotein latent infection membrane protein 1 (LMP1) is a constitutively aggregated pseudo-tumor necrosis factor receptor (TNFR) that activates transcription factor NF-kappaB through two sites in its C-terminal cytoplasmic domain. One site is similar to activated TNFRII in associating with TNFR-associated factors TRAF1 and TRAF2, and the second site is similar to TNFRI in associating with the TNFRI death domain interacting protein TRADD. TNFRI has been recently shown to activate NF-kappaB through association with TRADD, RIP, and TRAF2; activation of the NF-kappaB-inducing kinase (NIK); activation of the IkappaB alpha kinases (IKKalpha and IKKbeta); and phosphorylation of IkappaB alpha. IkappaB alpha phosphorylation on Ser-32 and Ser-36 is followed by its degradation and NF-kappaB activation. In this report, we show that NF-kappaB activation by LMP1 or by each of its effector sites is mediated by a pathway that includes NIK, IKKalpha, and IKKbeta. Dominant negative mutants of NIK, IKKalpha, or IKKbeta substantially inhibited NF-kappaB activation by LMP1 or by each of its effector sites.
Molecular Regulation of β-Lactam Biosynthesis in Filamentous Fungi (1998)

The most commonly used beta-lactam antibiotics for the therapy of infectious diseases are penicillin and cephalosporin. Penicillin is produced as an end product by some fungi, most notably by Aspergillus (Emericella) nidulans and Penicillium chrysogenum. Cephalosporins are synthesized by both bacteria and fungi, e.g., by the fungus Acremonium chrysogenum (Cephalosporium acremonium). The biosynthetic pathways leading to both secondary metabolites start from the same three amino acid precursors and have the first two enzymatic reactions in common. Penicillin biosynthesis is catalyzed by three enzymes encoded by acvA (pcbAB), ipnA (pcbC), and aatA (penDE). The genes are organized into a cluster. In A. chrysogenum, in addition to acvA and ipnA, a second cluster contains the genes encoding enzymes that catalyze the reactions of the later steps of the cephalosporin pathway (cefEF and cefG). Within the last few years, several studies have indicated that the fungal beta-lactam biosynthesis genes are controlled by a complex regulatory network, e. g., by the ambient pH, carbon source, and amino acids. A comparison with the regulatory mechanisms (regulatory proteins and DNA elements) involved in the regulation of genes of primary metabolism in lower eukaryotes is thus of great interest. This has already led to the elucidation of new regulatory mechanisms. Furthermore, such investigations have contributed to the elucidation of signals leading to the production of beta-lactams and their physiological meaning for the producing fungi, and they can be expected to have a major impact on rational strain improvement programs. The knowledge of biosynthesis genes has already been used to produce new compounds.
Single doses of Panax ginseng (G115) reduce blood glucose levels and improve cognitive performance during sustained mental activity (2005)

Single doses of the traditional herbal treatment Panax ginseng have recently been shown to elicit cognitive improvements in healthy young volunteers. The mechanisms by which ginseng improves cognitive performance are not known. However, they may be related to the glycaemic properties of some Panax species. Using a double-blind, placebo-controlled, balanced crossover design, 30 healthy young adults completed a 10 min test battery at baseline, and then six times in immediate succession commencing 60 min after the day's treatment (placebo, 200mg G115 or 400mg G115). The 10 min battery comprised a Serial Threes subtraction task (2 min); a Serial Sevens task (2 min); a Rapid Visual Information Processing task (5 min); then a 'mental fatigue' visual analogue scale. Blood glucose was measured prior to each day's treatment, and before, during and after the post-dose completions of the battery. Both the 200mg and 400mg treatments led to significant reductions in blood glucose levels at all three post-treatment measurements (p 0.005 in all cases). The most notable behavioural effects were associated with 200mg of ginseng and included significantly improved Serial Sevens subtraction task performance and significantly reduced subjective mental fatigue throughout all (with the exception of one time point in each case) of the post-dose completions of the 10 min battery (p 0.05). Overall these data suggest that Panax ginseng can improve performance and subjective feelings of mental fatigue during sustained mental activity. This effect may be related to the acute gluco-regulatory properties of the extract.
Toward dynamic recalibration and three-dimensional reconstruction in a structured light system (2007)

We present a method for dynamic recalibration and 3D reconstruction via a structured light system. Assuming that the light planes cast from the digital light projector have been calibrated off-line, we show that the focal length, aspect ratio, and all motion parameters of the camera can be determined on-line. Then the 3D reconstruction can be carried out by either a traditional triangulation method or a more efficient transformation-based method. In the latter method, a single image is sufficient for the whole process of calibration and reconstruction. Thus a hand-held camera can be used. Computer simulation and real data experiments were carried out to validate the method.
Generalized Louvain method for community detection in large networks (2011)

In this paper we present a novel strategy to discover the community structure of (possibly, large) networks. This approach is based on the well-know concept of network modularity optimization. To do so, our algorithm exploits a novel measure of edge centrality, based on the κ-paths. This technique allows to efficiently compute a edge ranking in large networks in near linear time. Once the centrality ranking is calculated, the algorithm computes the pairwise proximity between nodes of the network. Finally, it discovers the community structure adopting a strategy inspired by the well-known state-of-the-art Louvain method (henceforth, LM), efficiently maximizing the network modularity. The experiments we carried out show that our algorithm outperforms other techniques and slightly improves results of the original LM, providing reliable results. Another advantage is that its adoption is naturally extended even to unweighted networks, differently with respect to the LM.
Cloning and sequence analysis of cDNAs for human high molecular weight and low molecular weight prekininogens. Primary structures of two human prekininogens. (1985)

cDNA sequences for both human high molecular weight (HMW) and low molecular weight (LMW) prekininogens have been isolated by molecular cloning and determined by sequence analysis. The sequence determination together with the S1 nuclease mapping and RNA blot-hybridization analyses indicate that human HMW and LMW prekininogen mRNAs share an identical sequence throughout the 5'-untranslated region and the protein-coding region up to the sequence encoding the 12 amino acids distal to the bradykinin sequence, and the two mRNAs then completely diverge from each other. The signal peptide, the heavy chain (H chain), and the bradykinin moiety, which are common between the two prekininogens, consist of 18, 362, and 9 amino acids, respectively, while the light chains (L chains) of the HMW and LMW prekininogens are composed of 255 and 38 amino acids, respectively. All 17 cysteine residues present in the human and bovine H chains are located at exactly equivalent positions, indicating that the human H chain, like the bovine counterpart, can form 8 loop structures, each connected by two adjacent cysteine residues. The L chains of human and bovine kininogens differ in the protein lengths as well as in some amino acids crucial for the processing of the kininogens by kallikrein. Based upon this finding, we have discussed the molecular basis for the different modes of processing of human and bovine HMW kininogens and for the different kinetics of contact activation reactions exhibited by the two HMW kininogens.
Ionic liquid pretreatment of cellulosic biomass: Enzymatic hydrolysis and ionic liquid recycle (2010)

Ionic liquids (ILs) are promising solvents for the pretreatment of biomass as certain ILs are able to completely solubilize lignocellulose. The cellulose can readily be precipitated with an anti-solvent for further hydrolysis to glucose, but the anti-solvent must be removed for the IL to be recovered and recycled. We describe the use of aqueous kosmotropic salt solutions to form a three-phase system that precipitates the biomass, forming IL-rich and salt-rich phases. The phase behavior of [Emim][Ac] and aqueous phosphate salt systems is presented, together with a process for recycling the [Emim][Ac] and enzymatically hydrolyzing the cellulose. This process reduces the amount of water to be evaporated from recycled IL, permitting efficient recycle of the IL. Material balances on the process, with multiple recycles of the [Emim][Ac], quantify the major components from a Miscanthus feedstock through the pretreatment, separation, and enzymatic hydrolysis steps. A more rapid and higher yielding conversion of cellulose to glucose is obtained by use of the three-phase system as compared to the cellulose obtained from biomass pretreated with IL and precipitated with water. The addition of a kosmotropic salt during the precipitation results in partial delignification of the biomass, which makes the substrate more accessible, enhancing the enzymatic hydrolysis.
Effect of Pramlintide on Weight in Overweight and Obese Insulin‐Treated Type 2 Diabetes Patients (2004)

These findings support further evaluation of the weight-lowering potential of pramlintide in obese patients with type 2 diabetes.
Coupling of Monoclonal Antibodies with Enzymes (2003)

As an outgrowth of the experience obtained from the chemical modification of proteins, a series of techniques to crosslink different proteins chemically has been developed in the last two decades. The conjugation of enzymes to antibodies, particularly to monoclonal antibodies (MAbs), has allowed the universal application of immunological techniques to histochemistry, cytochemistry, quantitative assays (e.g., enzyme-linked immunosorbent assay [ELISA]), and cytogenetics.
Human IgA-binding Peptides Selected from Random Peptide Libraries (2012)

Phage display system is a powerful tool to design specific ligands for target molecules. Here, we used disulfide-constrained random peptide libraries constructed with the T7 phage display system to isolate peptides specific to human IgA. The binding clones (A1-A4) isolated by biopanning exhibited clear specificity to human IgA, but the synthetic peptide derived from the A2 clone exhibited a low specificity/affinity (K(d) = 1.3 μm). Therefore, we tried to improve the peptide using a partial randomized phage display library and mutational studies on the synthetic peptides. The designed Opt-1 peptide exhibited a 39-fold higher affinity (K(d) = 33 nm) than the A2 peptide. An Opt-1 peptide-conjugated column was used to purify IgA from human plasma. However, the recovered IgA fraction was contaminated with other proteins, indicating nonspecific binding. To design a peptide with increased binding specificity, we examined the structural features of Opt-1 and the Opt-1-IgA complex using all-atom molecular dynamics simulations with explicit water. The simulation results revealed that the Opt-1 peptide displayed partial helicity in the N-terminal region and possessed a hydrophobic cluster that played a significant role in tight binding with IgA-Fc. However, these hydrophobic residues of Opt-1 may contribute to nonspecific binding with other proteins. To increase binding specificity, we introduced several mutations in the hydrophobic residues of Opt-1. The resultant Opt-3 peptide exhibited high specificity and high binding affinity for IgA, leading to successful isolation of IgA without contamination.
Noninvasive prenatal diagnosis of common aneuploidies by semiconductor sequencing (2014)

Massively parallel sequencing (MPS) of cell-free fetal DNA from maternal plasma has revolutionized our ability to perform noninvasive prenatal diagnosis. This approach avoids the risk of fetal loss associated with more invasive diagnostic procedures. The present study developed an effective method for noninvasive prenatal diagnosis of common chromosomal aneuploidies using a benchtop semiconductor sequencing platform (SSP), which relies on the MPS platform but offers advantages over existing noninvasive screening techniques. A total of 2,275 pregnant subjects was included in the study; of these, 515 subjects who had full karyotyping results were used in a retrospective analysis, and 1,760 subjects without karyotyping were analyzed in a prospective study. In the retrospective study, all 55 fetal trisomy 21 cases were identified using the SSP with a sensitivity and specificity of 99.94% and 99.46%, respectively. The SSP also detected 16 trisomy 18 cases with 100% sensitivity and 99.24% specificity and 3 trisomy 13 cases with 100% sensitivity and 100% specificity. Furthermore, 15 fetuses with sex chromosome aneuploidies (10 45,X, 2 47,XYY, 2 47,XXX, and 1 47,XXY) were detected. In the prospective study, nine fetuses with trisomy 21, three with trisomy 18, three with trisomy 13, and one with 45,X were detected. To our knowledge, this is the first large-scale clinical study to systematically identify chromosomal aneuploidies based on cell-free fetal DNA using the SSP and provides an effective strategy for large-scale noninvasive screening for chromosomal aneuploidies in a clinical setting.
Alkoxyalkyl Esters of ( S )-9-[3-Hydroxy-2-(Phosphonomethoxy)Propyl]Adenine Are Potent Inhibitors of the Replication of Wild-Type and Drug-Resistant Human Immunodeficiency Virus Type 1 In Vitro (2006)

(S)-9-[3-Hydroxy-2-(phosphonomethoxy)propyl]adenine [(S)-HPMPA], is an effective broad-spectrum antiviral against many DNA viruses but has been reported to be inactive against human immunodeficiency virus (HIV). We synthesized several alkoxyalkyl esters of (S)-HPMPA and now report that hexadecyloxypropyl-(S)-HPMPA [HDP-(S)-HPMPA] and octadecyloxyethyl-(S)-HPMPA [ODE-(S)-HPMPA]had 50% effective concentrations of 0.4 to 7.0 nanomolar and were nearly fully active against HIV variants having reverse transcriptase mutations M184V and K103N and against a zidovudine-resistant variant with mutations D67N, K70R, T215Y, and K219Q. Resistance to HDP-(S)-HPMPA and ODE-(S)-HPMPA was noted for a mutant with mutation K65R. HDP-(S)-HPMPA is also active against herpes simplex virus type 1, human cytomegalovirus, hepatitis B virus, adenoviruses, and orthopoxviruses and is worthy of further evaluation as a possibly therapy for HIV infection.
Cellulose Nanopaper Structures of High Toughness (2008)

Cellulose nanofibrils offer interesting potential as a native fibrous constituent of mechanical performance exceeding the plant fibers in current use for commercial products. In the present study, wood nanofibrils are used to prepare porous cellulose nanopaper of remarkably high toughness. Nanopapers of different porosities and from nanofibrils of different molar mass are prepared. Uniaxial tensile tests are performed and structure-property relationships are discussed. The high toughness of highly porous nanopaper is related to the nanofibrillar network structure and high mechanical nanofibril performance. Also, molar mass correlates with tensile strength. This indicates that nanofibril fracture controls ultimate strength. Furthermore, the large strain-to-failure means that mechanisms, such as interfibril slippage, also contributes to inelastic deformation in addition to deformation of the nanofibrils themselves.
Identification and characterization of nuclear matrix-attachment regions in the human serpin gene cluster at 14q32.1 (1999)

Matrix-attachment regions (MARs) are DNA elements that are defined by their abilities to bind to isolated nuclear matrices in vitro. The DNA sequences of different matrix-binding elements vary widely. The locations of some MARs at the ends of chromatin loops suggest that they may represent boundaries of individual chromatin domains. As such, MARs may play important roles in regulating transcription and chromatin structure. As a first step towards assessing the roles of MARs in these processes, we assayed DNA sequences from the human serine protease inhibitor (serpin) gene cluster at 14q32.1 for matrix-binding activity in vitro. This approximately 150 kb region contains the cell-specific genes encoding alpha1-anti-trypsin (alpha1AT) and corticosteroid-binding globulin (CBG), as well as an antitrypsin-related sequence termed ATR. A DNase I-hypersensitive site (DHS) map of the locus has recently been described. We report here that the alpha1AT-ATR-CBG region contains five distinct MARs. There is a strong matrix-binding element approximately 16 kb upstream of alpha1AT; three MARs are between ATR and CBG and one MAR is within the CBG gene itself. These MARs were matrix-associated in all cell types examined. DNA sequencing indicated that the serpin MARs contained predominantly repetitive DNA, although the types of DNA repeats differed among the MARs.