gebhart/patrepeval huggingface dataset:
New antimicrobials in the management of cystic fibrosis (2002)

The chronic Pseudomonas aeruginosa lung infection in cystic fibrosis (CF) is a biofilm 1 characterized by (i) the mucoid phenotype producing an abundance of alginate in vitro and in the patients, (ii) microcolonies surrounded by alginate in sputum and in post-mortem investigations and bacteria staying on the surface of the airways as an endobronchiolitis without spreading to the blood or to other organs, (iii) high levels of antibodies against alginate and other P. aeruginosa antigens, and (iv) resistance to the patients' defence mechanisms and to antibiotic treatment. xygen radicals produced by the inflammatory response (polmorphonuclear leucocytes; PMNs) induce mutations leading to the alginate production that is so characteristic of P. aeruginosa biofilm infection in CF. 2 Quorum sensing is also involved in mature biofilm formation in vitro and in vivo. The biofilm mode of growth is the survival strategy of environmental bacteria such as P. aeruginosa, and alginate biofilms are also protected against antibiotics and against the immune response in the lungs of the patient.
Hyaluronan–Carbon Nanotube Derivatives: Synthesis, Conjugation with Model Drugs, and DOSY NMR Characterization (2011)

Abstract Carbon nanotube (CNTs) derivatives are nowadays under thorough investigation as biomedically interesting materials. In this paper we describe a method for the preparation of water‐soluble CNTs by condensation of the carboxylic groups introduced onto the carbon framework and the primary amine moieties inserted in the naturally occurring biopolymer hyaluronan (HA). The covalent conjugation between CNTs and HA should merge the biocompatibility and further processability of the HA chains with the well‐known cellular penetration properties of the CNT derivatives to produce novel drug delivery platforms. In fact, thanks to the primary amino groups introduced in the HA chains, HA–CNT derivatives can be further covalently modified with model drugs like ibuprofen and methotrexate. We describe also the monitoring of all the CNT derivatization steps by diffusion‐ordered NMR spectroscopy (DOSY), a technique that allows fast and reliable characterization of these novel derivatives.
Interactive high-dimensional index for large Chinese calligraphic character databases (2007)

The large numbers of Chinese calligraphic scripts in existence are valuable part of the Chinese cultural heritage. However, due to the shape complexity of these characters, it is hard to employ existing techniques to effectively retrieve and efficiently index them. In this article, using a novel shape-similarity- based retrieval method in which shapes of calligraphic characters are represented by their contour points extracted from the character images, we propose an interactive partial-distance-map (PDM)- based high-dimensional indexing scheme which is designed specifically to speed up the retrieval performance of the large Chinese calligraphic character databases effectively. Specifically, we use the approximate minimal bounding sphere of a query character and utilize users' relevance feedback to refine the query gradually. Comprehensive experiments are conducted to testify the efficiency and effectiveness of this method. In addition, a new k -NN search called Pseudo k -NN (P k -NN) search is presented to better facilitate the PDM-based character retrieval.
Thin Layer Chromatography (1987)

Introduction: Historical Development from Paper Chromatography, General Experimental Arrangements Stationary Phase: Adsorbants, High Performance Thin Layer Chromatography Practical Techniques: Spotting of Plates, Preparation of Solvent Tanks, Methods of Plate Development, Visualisation Applications: Qualitative TLC, Quantitative TLC, Preparative TLC, Advantages and Disadvantages of TLC.
Four‐dimensional MRI using three‐dimensional radial sampling with respiratory self‐gating to characterize temporal phase‐resolved respiratory motion in the abdomen (2015)

We demonstrated the feasibility of the proposed 4D-MRI technique to characterize abdominal respiratory motion, which may provide valuable information for radiotherapy planning.
Using Triplex-Forming Oligonucleotide Probes for the Reagentless, Electrochemical Detection of Double-Stranded DNA (2010)

We report a reagentless, electrochemical sensor for the detection of double-stranded DNA targets that employs triplex-forming oligonucleotides (TFOs) as its recognition element. These sensors are based on redox-tagged TFO probes strongly chemisorbed onto an interrogating gold electrode. Upon the addition of the relevant double-stranded DNA target, the probe forms a rigid triplex structure via reverse Hoogsteen base pairing in the major groove. The formation of the triplex impedes contact between the probe's redox moiety and the interrogating electrode, thus signaling the presence of the target. We first demonstrated the proof of principle of this approach by using a well-characterized 22-base polypurine TFO sequence that readily detects a synthetic, double-stranded DNA target. We then confirmed the generalizability of our platform with a second probe, a 19-base polypyrimidine TFO sequence that targets a polypurine tract (PPT) sequence conserved in all HIV-1 strains. Both sensors rapidly and specifically detect their double-stranded DNA targets at concentrations as low as ~10 nM and are selective enough to be employed directly in complex sample matrices such as blood serum. Moreover, to demonstrate real-world applicability of this new sensor platform, we have successfully detected unpurified, double-stranded PCR amplicons containing the relevant conserved HIV-1 sequence.
Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection (2001)

In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In contrast, in mammals, while nonequal use of alternative codons is observed, the bias is attributed to the background variance in nucleotide concentrations, reflected in the similar nucleotide composition of flanking noncoding and exonic third sites. However, a systematic examination of the covariants of codon usage controlling for background nucleotide content has yet to be performed. Here we present a new method to measure codon bias that corrects for background nucleotide content and apply this to 2396 human genes. Nearly all (99%) exhibit a higher amount of codon bias than expected by chance. The patterns associated with selectively driven codon bias are weakly recovered: Broadly expressed genes have a higher level of bias than do tissue-specific genes, the bias is higher for genes with lower rates of synonymous substitutions, and certain codons are repeatedly preferred. However, while these patterns are suggestive, the first two patterns appear to be methodological artifacts. The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans.
Cloning and characterization of the gsk gene encoding guanosine kinase of Escherichia coli (1995)

The Escherichia coli gsk gene encoding guanosine kinase was cloned from the Kohara gene library by complementation of the E. coli gsk-1 mutant allele. The cloned DNA fragment was sequenced and shown to encode a putative polypeptide of 433 amino acids with a molecular mass of 48,113 Da. Minicell analysis established the subunit M(r) as 43,500. Primer extension analysis indicated the presence of an adequate Pribnow box and suggested that the transcript contained a 110-base leader sequence. Strains harboring the gsk gene on multicopy plasmids overexpressed both guanosine and inosine kinase activities. N-terminal sequence and amino acid composition analyses of the 43,500-M(r) polypeptide band confirmed the correct reading frame assignment and the identity of this band as the gsk gene product. Comparison of the amino acid sequence with the protein database revealed similarity to regions of other mononucleotide-utilizing enzymes.
Cyc: toward programs with common sense (1990)

Cyc is a bold attempt to assemble a massive knowledge base (on the order of 10 8 axioms) spanning human consensus knowledge. This article examines the need for such an undertaking and reviews the authos' efforts over the past five years to begin its construction. The methodology and history of the project are briefly discussed, followed by a more developed treatment of the current state of the representation language used (epistemological level), techniques for efficient inferencing and default reasoning (heuristic level), and the content and organization of the knowledge base.
Anrukinzumab, an anti-interleukin 13 monoclonal antibody, in active UC: efficacy and safety from a phase IIa randomised multicentre study (2015)

ClinicalTrials.gov number NCT01284062.
Role of focal adhesion kinase in integrin signaling (1997)

Integrins are the major cell surface receptors for extracellular matrix molecules, which play critical roles in a variety of biological processes. Focal adhesion kinase has recently been established as a key component of the signal transduction pathways triggered by integrins. Aggregation of FAK with integrins and cytoskeletal proteins in focal contacts has been proposed to be responsible for FAK activation and autophosphorylation by integrins in cell adhesion. This may be achieved by FAK interaction with talin or other cytoskeletal proteins that in turn associate with the cytoplasmic domain of integrin beta subunits. Autophosphorylation of FAK at Y397 leads to its association with Src, resulting in activation of both kinases. The activated FAK/Src complex acts on potential substrates tensin, paxillin and p130cas. Besides cytoskeletal regulation, FAK phosphorylation and/or binding to paxillin and p130cas may trigger downstream activation of MAP kinase by the adoptor protein Crk. Src association with FAK may also lead to its phosphorylation of other sites on FAK, including a binding site for Grb2. Cell adhesion-dependent association of FAK and Grb2 may provide a mechanism by which MAP kinase is activated in cell adhesion. PI 3-kinase has also been shown to bind FAK in a cell adhesion-dependent manner at the major autophosphorylation site Y397. This association could lead to activation of PI 3-kinase and its downstream effectors. Recent results from a number of different approaches have shown that integrin signaling through FAK leads to increased cell migration on fibronectin as well as potentially regulating cell proliferation and survival.
Relationship between non‐localized tail states and carrier transport in amorphous oxide semiconductor, In–Ga–Zn–O (2008)

Abstract The relationship between non‐localized tail states and carrier transport in transparent amorphous oxide semiconductor, In–Ga–Zn–O (a‐IGZO), was investigated. It was found that the energy width ( E 0 ) of the non‐localized tail states varied from &lt;7 meV to 20 meV depending on the film deposition conditions (i.e. film quality). At carrier concentrations of ∼10 19 cm –3 , Hall mobilities larger than 10 cm 2 (V s) –1 were obtained for the high‐quality films, while they were only several cm 2 (V s) –1 for low‐quality films that have large E 0 values ∼20 meV. However, even for low‐quality films, the E 0 value decreased from 20 meV to 7 meV and their Hall mobilities were increased from ∼1 cm 2 to &gt;10 cm 2 (V s) –1 by post thermal annealing at ≥300 °C. These observations indicate that structural relaxation associated with electron transport starts from ∼300 °C, which is much lower than the crystallization temperature (∼520 °C). This situation is similar to the case of amorphous metals. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
TGF-β Receptors and Signalling Mechanisms (1998)

Transforming growth factor-beta (TGF-beta) is the founding member of a large superfamily of related growth and differentiation factors that include bone morphogenetic proteins and activins. TGF-beta signals through two related transmembrane ser/thr kinase receptors, the type I and type II receptors. Signalling is initiated when the ligand binds to the type II receptor which is followed by recruitment of the type I receptor into a heteromeric complex. Within the complex the type II receptor transphosphorylates and activates the type I receptor kinase which targets downstream signalling components of the pathway. Proteins related to the Drosophila gene Mothers against dpp (MAD) are critical downstream substrates of the type I kinase. The vertebrate members of the MAD-related family, termed Smad2 and Smad3, interact specifically with the TGF-beta type I receptor and are phosphorylated on the last two serines of a conserved C-terminal SSXS motif. This phosphorylation induces association between these receptor-regulated Smads and Smad4 followed by translocation of the heteromeric complex to the nucleus. In the nucleus, heteromeric complexes of Smads can interact with DNA and with specific DNA binding transcription factors to elicit gene responses to TGF-beta. Thus TGF-beta signalling involves a direct pathway from the cell surface receptors to the nucleus. Recently, a novel mechanism to negatively regulate TGF-beta signalling was described that involves another class of MADR proteins. These anti-MADR proteins potently inhibit TGF-beta signalling by functioning as direct antagonists of the TGF-beta receptor type I kinase domain.
Adhesion, Invasion, and Agglutination Mediated by Two Trimeric Autotransporters in the Human Uropathogen Proteus mirabilis (2010)

Fimbriae of the human uropathogen Proteus mirabilis are the only characterized surface proteins that contribute to its virulence by mediating adhesion and invasion of the uroepithelia. PMI2122 (AipA) and PMI2575 (TaaP) are annotated in the genome of strain HI4320 as trimeric autotransporters with "adhesin-like" and "agglutinating adhesin-like" properties, respectively. The C-terminal 62 amino acids (aa) in AipA and 76 aa in TaaP are homologous to the translocator domains of YadA from Yersinia enterocolitica and Hia from Haemophilus influenzae. Comparative protein modeling using the Hia three-dimensional structure as a template predicted that each of these domains would contain four antiparallel beta sheets and that they formed homotrimers. Recombinant AipA and TaaP were seen as ∼28 kDa and ∼78 kDa, respectively, in Escherichia coli, and each also formed high-molecular-weight homotrimers, thus supporting this model. E. coli synthesizing AipA or TaaP bound to extracellular matrix proteins with a 10- to 60-fold-higher level of affinity than the control strain. Inactivation of aipA in P. mirabilis strains significantly (P < 0.01) reduced the mutants' ability to adhere to or invade HEK293 cell monolayers, and the functions were restored upon complementation. A 51-aa-long invasin region in the AipA passenger domain was required for this function. E. coli expressing TaaP mediated autoagglutination, and a taaP mutant of P. mirabilis showed significantly (P < 0.05) more reduced aggregation than HI4320. Gly-247 in AipA and Gly-708 in TaaP were indispensable for trimerization and activity. AipA and TaaP individually offered advantages to P. mirabilis in a murine model. This is the first report characterizing trimeric autotransporters in P. mirabilis as afimbrial surface adhesins and autoagglutinins.
Efficient gene delivery targeted to the brain using a transferrin‐conjugated polyethyleneglycol‐modified polyamidoamine dendrimer (2007)

The blood-brain barrier (BBB) poses great difficulties for gene delivery to the brain. To circumvent the BBB, we investigated a novel brain-targeting gene vector based on the nanoscopic high-branching dendrimer, polyamidoamine (PAMAM), in vitro and in vivo. Transferrin (Tf) was selected as a brain-targeting ligand conjugated to PAMAM via bifunctional polyethyleneglycol (PEG), yielding PAMAM-PEG-Tf. UV and nuclear magnetic resonance (NMR) spectroscopy were used to evaluate the synthesis of vectors. The characteristics and biodistribution of gene vectors were evaluated by fluorescent microscopy, flow cytometry, and a radiolabeling method. The transfection efficiency of vector/DNA complexes in brain capillary endothelial cells (BCECs) was evaluated by fluorescent microscopy and determination of luciferase activity. The potency of vector/DNA complexes was evaluated by using frozen sections and measuring tissue luciferase activity in Balb/c mice after i.v. administration. UV and NMR results demonstrated the successful synthesis of PAMAM-PEG-Tf. This vector showed a concentration-dependent manner in cellular uptake study and a 2.25-fold brain uptake compared with PAMAM and PAMAM-PEG in vivo. Transfection efficiency of PAMAM-PEG-Tf/DNA complex was much higher than PAMAM/DNA and PAMAM-PEG/DNA complexes in BCECs. Results of tissue expression experiments indicated the widespread expression of an exogenous gene in mouse brain after i.v. administration. With a PAMAM/DNA weight ratio of 10:1, the brain gene expression of the PAMAM-PEG-Tf/DNA complex was approximately 2-fold higher than that of the PAMAM/DNA and PAMAM-PEG/DNA complexes. These results suggested that PAMAM-PEG-Tf can be exploited as a potential nonviral gene vector targeting to brain via noninvasive administration.
[Hereditary prolonged QT interval (Romano-Ward syndrome) in a female patient with non-elective cesarean section]. (1992)

In the Romano-Ward syndrome, an inherited form of abnormally prolonged QT duration is the matter of concern. The frequency-corrected QTc value in the ECG amounts to more than 0.44 s (upper mean value: 0.44 s). Persons suffering from Romano-Ward syndrome are vitally endangered by attacks of arrhythmia, syncope, and cardiac arrest that are triggered or aggravated by stress or certain drugs. In obstetrical anesthesia, attention should be paid to the fetus, which, due to the genetic dominance, will have a 50% probability of having the disorder. A 28-year-old para I was admitted with cervical dilation on her predetermined date of delivery. Romano-Ward syndrome had been diagnosed 10 years earlier; the patient had been free of complaints and had received no treatment. Due to cephalopelvic disproportion and the cardiac syndrome, a primary cesarean section was performed. Following premedication and provision of a beta-blocker, defibrillator, and drugs for resuscitation, intubation anesthesia with methohexital, nitrous oxide, enflurane, and succinylcholine was carried out. The QTc values were pathologically prolonged (0.47 s; 0.48-063 s) during the pre- and intraoperative period. Hemodynamic irregularities did not occur in the perioperative period. The newborn was vital (3,830 g, 50 cm; Apgar scores 10/10/10; umbilical cord pH 7.29). Directly postpartum isolated supraventricular extrasystoles occurred, and the QTc duration increased to 0.51 s. Simultaneous registration of the ECG and phonocardiogram showed premature occurrence of the second cardiac sound, which is typical of Romano-Ward syndrome.
Advances in Imaging of Lymph Flow Disorders (2000)

Conventional oil-contrast lymphography has long been the mainstay for lymphatic imaging. However, the emergence of computed tomography (CT) and magnetic resonance (MR) imaging has severely curtailed its use. Because of recent improvements and refinements, lymphangioscintigraphy now permits high-resolution imaging of peripheral lymphatic vessels and provides insight into lymph flow dynamics. It is indispensable for patients with known or suspected lymphatic circulatory disorders in confirming the diagnosis and delineating the pathogenesis and evolution of lymphedema. In addition, lymphangioscintigraphy helps evaluate lymphatic truncal anatomy and radiotracer transport. It can also be used to evaluate the efficacy of various treatment options designed to facilitate lymph flow or reduce lymph formation. The procedure is essentially noninvasive, can easily be repeated, and does not adversely affect the lymphatic vascular endothelium. MR imaging complements lymphangioscintigraphy in the monitoring and treatment of more complex lymphatic circulatory disorders, whereas CT facilitates catheter-guided percutaneous sclerosis or obliteration of specific lymphangiectasia or lymphangioma syndromes. Ultrasonography has proved useful in the setting of filariasis. Patients with a provisional diagnosis of peripheral lymphatic dysfunction or idiopathic edema should undergo diagnostic lymphangioscintigraphy and, in some cases, MR imaging to verify diagnostic accuracy, pinpoint the specific abnormality, and help guide subsequent therapy.
Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis (2000)

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses. html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-specified primer to the 3' terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms.
Mathematical model for the biodegradation of vocs in trickle bed biofilters (1999)

The objective of this work is to develop a fundamental mathematical model that describes the biodegradation of volatile organic compounds (VOCs) in gas phase trickle-bed biofilters, and to estimate the unknown model parameters. The mathematical model considers a three-phase system (biofilm, water, and gas phase), non-uniform bacterial population, and one limiting substrate. Two pilot-scale trickle-bed biofilters were operated to remove the VOC diethyl ether from a waste gas stream. Experimental results from this system were used to estimate the unknown parameters of the steady-state model: the maximum rate of substrate utilization μ m X f / Y , the Monod constant, K s , and the ether biofilm/water diffusivity ratio, r d . While the value of μ m X f / Y was uniquely determined, the values of K s and r d were highly correlated. High values of the Monod constant and the ether diffusivity in the biofilm gave similar predictions to those corresponding to low values of both parameters. Batch studies were used to estimate the value of K s without mass transfer limitations showing that K s < 1 mg/L=2.6 mg COD/L. Using this information and biofilter operating data the true values of K s and r d were determined.