gebhart/patrepeval huggingface dataset:
The Pharmacogenetics of Type 2 Diabetes: A Systematic Review (2014)

We found evidence of pharmacogenetic interactions for metformin, sulfonylureas, repaglinide, thiazolidinediones, and acarbose consistent with their pharmacokinetics and pharmacodynamics. While high-quality controlled studies with prespecified analyses are still lacking, our results bring the promise of personalized medicine in diabetes one step closer to fruition.
Pulmonary immunity and immunopathology: lessons from respiratory syncytial virus (2008)

Respiratory syncytial virus (RSV) is the leading cause of severe respiratory disease in infants and is an important source of morbidity and mortality in the elderly and immunocompromised. This review will discuss the humoral and cellular adaptive immune responses to RSV infection and how these responses are shaped in the immature immune system of the infant and the aged environment of the elderly. Furthermore, we will provide an overview of our current understanding of the role the various arms of the adaptive immune response play in mediating the delicate balance between the successful elimination of the virus from the host and the induction of immunopathology. Efficacious immunization against RSV remains a high priority within the field and we will highlight recent advances made in vaccine design.
Pharmacokinetic properties of IB1001, an investigational recombinant factor IX, in patients with haemophilia B: repeat pharmacokinetic evaluation and sialylation analysis (2012)

IB1001 trenacog alfa is an investigational recombinant factor IX (FIX) for the treatment and prevention of bleeding in individuals with haemophilia B. To compare the pharmacokinetics (PK) of IB1001 with nonacog alfa in individuals with haemophilia B and to assess the relationship between sialylation and PK of IB1001 (NCT00768287). A randomized, double-blind, non-inferiority, cross-over study conducted in participants aged ≥ 12 years weighing ≥ 40 kg, with severe or moderately severe haemophilia B (FIX activity ≤ 2 IU dL (-1) ). PK parameters were derived using observed FIX concentration levels and actual PK sampling times, and repeated in a subset of participants who had received IB1001 prophylaxis for 4-18 months. A retrospective analysis was conducted in subgroups according to the sialylation levels of IB1001 (50.8, 57.8-59.0%, or 71.7%). In the 32 adolescent and adult males evaluated, there were no clinically meaningful differences in PK parameters between those receiving IB1001 75 IU kg(-1) or nonacog alfa. The lower limit of the one-sided 95% confidence interval for the ratio of AUC(0-t) and AUC(0-∞) (IB1001/nonacog alfa) was 0.90, establishing non-inferiority. Terminal phase half-lives were similar (29.7 ± 18.2 h for IB1001 and 33.4 ± 21.2 h for nonacog alfa). The PK results were stable for up to 18 months of IB1001 exposure; the impact of sialylation levels was not clinically meaningful. There were no clinically meaningful PK differences between IB1001 and nonacog alfa. IB1001 was well tolerated and without safety concerns. The non-inferiority of IB1001 to nonacog alfa supports IB1001 becoming a useful alternative recombinant agent for the management of haemophilia B.
ChemInform Abstract: Asymmetric Syntheses of β‐Phenylalanine, α‐Methyl‐β‐ phenylalanines, and Derivatives. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Reactions of some dicarbonyl compounds. Part III. Oxidation of some β-diketones with alkaline hydrogen peroxide (1975)

Oxidation of β-diketones (R1CO·CR2R3·COR4) with alkaline hydrogen peroxide affords two types of acid depending upon the nature of R2 and R3. Where both of these are H, the products are R1CO2H, R4CO2H, and formic acid, which suffers further oxidation. Where R2 is alkyl, the products are R1CO2H, R2CO2H, R4CO2H, and R1R2CH·CO2H and/or R2R4CH·CO2H. Where both R2 and R4 are alkyl, the products are R1R2R3C·CO2H and R4CO2H, and R2R3R4C·CO2H and R1CO2H, and this constitutes a useful source of trisubstituted acetic acids. The mechanisms of these reactions are discussed, and an additional oxidative side-reaction of two 2-alkyl-1,3-diketones is described.
An extended relationship for the characterization of Young's modulus and Poisson's ratio of tunable polyacrylamide gels (2006)

Substrates with tunable mechanical properties are crucial for the study of cellular processes, and polyacrylamide gels (PAGs) are frequently used in this context. Several experimental techniques have been proposed to obtain the mechanical properties of PAGs. However, the range of the considered Poisson's ratio values remains quite large and no attempt has been made to propose an analytical relationship allowing the estimation of PAG Young's modulus when both bis-acrylamide and acrylamide concentrations are known. In order to complete the actual knowledge on the mechanical properties of PAGs, we took benefit of our original method based on the micropipette aspiration technique (Boudou et al., J. Biomech. 2006) for characterizing gels made with concentrations in the range 0.02% < or =[Bis]< or =0.20% and 3% < or =[Acry]< or =10%. We found that the PAGs Young's modulus varies nonlinearly with the acrylamide amount. Moreover, our study validates the quasi-incompressibility hypothesis usually made in studies using PAGs (mean Poisson's ratio of 0.480+/-0.012). More generally, and in agreement with data published by other groups, we propose an original nonlinear mathematical relationship allowing the computation of Young's modulus of PAG for any given acrylamide and bis-acrylamide amounts taken in the range of values we considered.
Dependence of the lethal effect of pore-forming haemolysins of Gram-positive bacteria on cytolytic activity (2006)

Among bacterial haemolysins, cholesterol-dependent cytolysins (CDCs) produced by various Gram-positive bacteria are known to exhibit a lethal activity in mice. In this study, recombinant CDCs of streptolysin O, pneumolysin, ivanolysin O, listeriolysin O and several listeriolysin O mutants were constructed and the relationship between cytolytic activity and the lethal activity of each recombinant protein in mice was examined. Specific activity for cytolysis was determined by a quantitative haemolytic assay. Each protein was injected intravenously into mice and the lethal activity was evaluated by measuring the time until death of the mice. The four full-length CDC proteins exhibited lethal activity and their activities were highly proportional to their cytolytic activities. Inhibition of haemolytic activity resulted in the loss of lethal activity and non-haemolytic mutants of listeriolysin O did not exhibit any lethal activity. These data clearly indicate that the lethal effect of CDC proteins is dependent on the cytolytic activity.
Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. (1997)

Staphylococcus aureus has long been recognized as an important pathogen in human disease. Due to an increasing number of infections caused by methicillin-resistant S. aureus (MRSA) strains, therapy has become problematic. Therefore, prevention of staphylococcal infections has become more important. Carriage of S. aureus appears to play a key role in the epidemiology and pathogenesis of infection. The ecological niches of S. aureus are the anterior nares. In healthy subjects, over time, three patterns of carriage can be distinguished: about 20% of people are persistent carriers, 60% are intermittent carriers, and approximately 20% almost never carry S. aureus. The molecular basis of the carrier state remains to be elucidated. In patients who repeatedly puncture the skin (e.g., hemodialysis or continuous ambulatory peritoneal dialysis [CAPD] patients and intravenous drug addicts) and patients with human immunodeficiency virus (HIV) infection, increased carriage rates are found. Carriage has been identified as an important risk factor for infection in patients undergoing surgery, those on hemodialysis or CAPD, those with HIV infection and AIDS, those with intravascular devices, and those colonized with MRSA. Elimination of carriage has been found to reduce the infection rates in surgical patients and those on hemodialysis and CAPD. Elimination of carriage appears to be an attractive preventive strategy in patients at risk. Further studies are needed to optimize this strategy and to define the groups at risk.
Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter (2001)

Differential chromatin structure is one of the hallmarks distinguishing active and inactive genes. For the X-linked human hypoxanthine phosphoribosyltransferase gene (HPRT), this difference in chromatin structure is evident in the differential general DNase I sensitivity and hypersensitivity of the promoter regions on active versus inactive X chromosomes. Here we characterize the nucleosomal organization responsible for the differential chromatin structure of the active and inactive HPRT promoters. The micrococcal nuclease digestion pattern of chromatin from the active allele in permeabilized cells reveals an ordered array of translationally positioned nucleosomes in the promoter region except over a 350-bp region that is either nucleosome free or contains structurally altered nucleosomes. This 350-bp region includes the entire minimal promoter and all of the multiple transcription initiation sites of the HPRT gene. It also encompasses all of the transcription factor binding sites identified by either dimethyl sulfate or DNase I in vivo footprinting of the active allele. In contrast, analysis of the inactive HPRT promoter reveals no hypersensitivity to either DNase I or a micrococcal nuclease and no translational positioning of nucleosomes. Although nucleosomes on the inactive promoter are not translationally positioned, high-resolution DNase I cleavage analysis of permeabilized cells indicates that nucleosomes are rotationally positioned over a region of at least 210 bp on the inactive promoter, which coincides with the 350-bp nuclease-hypersensitive region on the active allele, including the entire minimal promoter. This rotational positioning of nucleosomes is not observed on the active promoter. These results suggest a model in which the silencing of the HPRT promoter during X chromosome inactivation involves remodeling a transcriptionally competent, translationally positioned nucleosomal array into a transcriptionally repressed architecture consisting of rotationally but not translationally positioned nucleosomal arrays.
Mixture-modeling with unsupervised clusters for domain adaptation in statistical machine translation (2012)

In Statistical Machine Translation, in-domain and out-of-domain training data are not always clearly delineated. This paper investigates how we can still use mixture-modeling techniques for domain adaptation in such cases. We apply unsupervised clustering methods to split the original training set, and then use mixture-modeling techniques to build a model adapted to a given target domain. We show that this approach improves performance over an unadapted baseline, and several alternative domain adaptation methods.
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. (1999)

The program is available on-line at the Bielefeld University Bioinformatics Server (BiBiServ) http://bibiserv.TechFak.Uni-Bielefeld.DE/dial ign/
Positional signalling by Hensen’s node when grafted to the chick limb bud (1986)

ABSTRACT Hensen’s node from stage 4 to stage 10 shows polarizing activity when grafted to the anterior margin of the chick limb bud. It can specify additional digits though its action is somewhat attenuated when compared with the effect of a grafted polarizing region. At stage 10 the activity disappears from the node and is found both posterior to the node and in the future wing region of the flank. The ability of Hensen’s node to generate a positional signal suggests that the signal in the limb and early embryo may be similar. The results support the view of the polarizing region as a discrete signalling region.
Lipid and metabolite profiles of human brain tumors by desorption electrospray ionization-MS (2016)

Examination of tissue sections using desorption electrospray ionization (DESI)-MS revealed phospholipid-derived signals that differ between gray matter, white matter, gliomas, meningiomas, and pituitary tumors, allowing their ready discrimination by multivariate statistics. A set of lower mass signals, some corresponding to oncometabolites, including 2-hydroxyglutaric acid and N-acetyl-aspartic acid, was also observed in the DESI mass spectra, and these data further assisted in discrimination between brain parenchyma and gliomas. The combined information from the lipid and metabolite MS profiles recorded by DESI-MS and explored using multivariate statistics allowed successful differentiation of gray matter (n = 223), white matter (n = 66), gliomas (n = 158), meningiomas (n = 111), and pituitary tumors (n = 154) from 58 patients. A linear discriminant model used to distinguish brain parenchyma and gliomas yielded an overall sensitivity of 97.4% and a specificity of 98.5%. Furthermore, a discriminant model was created for tumor types (i.e., glioma, meningioma, and pituitary), which were discriminated with an overall sensitivity of 99.4% and a specificity of 99.7%. Unsupervised multivariate statistics were used to explore the chemical differences between anatomical regions of brain parenchyma and secondary infiltration. Infiltration of gliomas into normal tissue can be detected by DESI-MS. One hurdle to implementation of DESI-MS intraoperatively is the need for tissue freezing and sectioning, which we address by analyzing smeared biopsy tissue. Tissue smears are shown to give the same chemical information as tissue sections, eliminating the need for sectioning before MS analysis. These results lay the foundation for implementation of intraoperative DESI-MS evaluation of tissue smears for rapid diagnosis.
Development and Evaluation of an Epidural Injection Simulator with Force Feedback for Medical Training (2001)

Performing epidural injections is a complex task that demands a high level of skill and precision from the physician, since an improperly performed procedure can result in serious complications for the patient. The objective of our project is to create an epidural injection simulator for medical training and education that provides the user with realistic feel encountered during an actual procedure. We have used a Phantom haptic interface by SensAble Technologies, which is capable of three-dimensional force feedback, to simulate interactions between the needle and bones or tissues. An additional degree-of-freedom through an actual syringe was incorporated to simulate the "loss of resistance" effect, commonly considered to be the most reliable method for identifying the epidural space during an injection procedure. The simulator also includes a new training feature called "Haptic Guidance" that allows the user to follow a previously recorded expert procedure and feel the encountered forces. Evaluations of the simulator by experienced professionals indicate that the simulation system has considerable potential to become a useful aid in medical training.
Dendritic cells pulsed with RNA encoding allogeneic MHC and antigen induce T cells with superior antitumor activity and higher TCR functional avidity (2009)

Adoptive transfer of T cells expressing transgenic T-cell receptors (TCRs) with antitumor function is a hopeful new therapy for patients with advanced tumors; however, there is a critical bottleneck in identifying high-affinity TCR specificities needed to treat different malignancies. We have developed a strategy using autologous dendritic cells cotransfected with RNA encoding an allogeneic major histocompatibility complex molecule and a tumor-associated antigen to obtain allo-restricted peptide-specific T cells having superior capacity to recognize tumor cells and higher functional avidity. This approach provides maximum flexibility because any major histocompatibility complex molecule and any tumor-associated antigen can be combined in the dendritic cells used for priming of autologous T cells. TCRs of allo-restricted T cells, when expressed as transgenes in activated peripheral blood lymphocytes, transferred superior function compared with self-restricted TCR. This approach allows high-avidity T cells and TCR specific for tumor-associated self-peptides to be easily obtained for direct adoptive T-cell therapy or for isolation of therapeutic transgenic TCR sequences.
Consistent detection of TLS/FUS-ERG chimeric transcripts in acute myeloid leukemia with t(16;21)(p11;q22) and identification of a novel transcript. (1997)

16;21 translocation is a recurrent primary abnormality in acute myeloid leukemia (AML). The genes involved in this translocation are ERG on chromosome 21 and TLS/FUS on chromosome 16. The rearrangement of the two chromosomes forms the TLS/FUS-ERG fusion gene and produces a consistent chimeric transcript on the der (21) chromosome. In this study, we analyzed the clinical characteristics of 19 patients with t(16;21)-AML, including 2 patients who evolved from myelodysplastic syndrome, and detected the chimeric transcripts of the TLS/FUS-ERG fusion gene in the patients during various clinical stages by the reverse transcriptase-polymerase chain reaction (RT-PCR) technique. We found that the patients with t(16;21) are characterized by a relatively younger age (median age, 22 years old), involvement of various subtypes of French-American-British classification and a poor prognosis: 18 of the 19 patients died of the disease (median survival was 16 months). Four types of TLS/FUS-ERG chimeric transcripts including a novel type were noted in the RT-PCR analysis. The novel transcript contained an additional 138 nucleotides consisting of TLS/FUS exon 8 and ERG exons 7 and 8 and had an in-frame fusion. These chimeric transcripts were consistently detectable in the samples obtained not only at diagnosis and relapse but also in short and long complete remission, suggesting that t(16;21)-AML is resistant to conventional chemotherapy. Thus, we recommend that t(16;21) should be monitored by RT-PCR even in clinical remission and the patients should be treated by other more powerful modality like stem-cell transplantation in the first remission.
Herbicidally Active Sulfamoyl Nucleosides (1995)

The isolation of the herbicidal nucleoside 2-chloro-5′-0-sulfamoyl-adenosine 1 was reported. Its relation to other herbicidal nucleosides was described. Two new and direct synthetic routes to 1 were established and a number of derivatives were prepared. Herbicidal activity was found in analogs structurally close to 1. An in vitro toxicological screen was applied to these compounds.
Contribution of Exogenous Genetic Elements to the Group A Streptococcus Metagenome (2007)

Variation in gene content among strains of a bacterial species contributes to biomedically relevant differences in phenotypes such as virulence and antimicrobial resistance. Group A Streptococcus (GAS) causes a diverse array of human infections and sequelae, and exhibits a complex pathogenic behavior. To enhance our understanding of genotype-phenotype relationships in this important pathogen, we determined the complete genome sequences of four GAS strains expressing M protein serotypes (M2, M4, and 2 M12) that commonly cause noninvasive and invasive infections. These sequences were compared with eight previously determined GAS genomes and regions of variably present gene content were assessed. Consistent with the previously determined genomes, each of the new genomes is approximately 1.9 Mb in size, with approximately 10% of the gene content of each encoded on variably present exogenous genetic elements. Like the other GAS genomes, these four genomes are polylysogenic and prophage encode the majority of the variably present gene content of each. In contrast to most of the previously determined genomes, multiple exogenous integrated conjugative elements (ICEs) with characteristics of conjugative transposons and plasmids are present in these new genomes. Cumulatively, 242 new GAS metagenome genes were identified that were not present in the previously sequenced genomes. Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. Two large ICEs, designated 2096-RD.2 (63 kb) and 10750-RD.2 (49 kb), have multiple genes encoding resistance to antimicrobial agents, including tetracycline and erythromycin, respectively. Also resident on these ICEs are three genes encoding inferred extracellular proteins of unknown function, including a predicted cell surface protein that is only present in the genome of the serotype M12 strain cultured from a patient with acute poststreptococcal glomerulonephritis. The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, and population genomics.
A 750mV 15kHz 1/f Noise Corner 51dBm IIP2 Direct-Conversion Front-End for GSM in 90nm CMOS (2006)

A direct-conversion front-end using a highly linear mixer is implemented in 90nm CMOS. The front-end shows 15kHz 1/f noise corner, 51dBm IIP2, 31.5dB gain, 3.5dB NF, and draws 15mA from 0.75 V
Vascular endothelial growth factor (VEGF) - part 1: in physiology and pathophysiology. (2011)

Angiogenesis is an important component of many physiological processes, such as the female sexual cycle, placenta formation, the processes of growth and differentiation of tissues, and reparative processes including wound healing, fracture repair, and liver regeneration. The formation of new blood vessels during angiogenesis and vasculogenesis allows the growth and functioning of multicellular organisms. Pathological angiogenesis most commonly occurs in ischaemic, inflammatory and neoplastic diseases. Conditions in the pathogenesis of which angiogenesis plays an important role are sometimes labelled angiogenic diseases. To date, a number of pro-and anti-angiogenic factors have been defined. VEGF is the only specific mitogen for endothelial cells. It stimulates their growth and inhibits apoptosis, increases vascular permeability in many tissues, promotes vasculogenesis and angiogenesis. VEGF signalling activity in relation to the cell is dependent on having its specific membrane receptors (Flt-1, KDR, Flt-4). Angiogenesis plays a protective role in ischaemic heart disease and myocardial infarction. Angiogenesis extends life for patients after a stroke. Most of the facts about physiological angiogenesis are derived from studies into liver regeneration as a result of an acute injury or partial hepatectomy. Pathological hepatic angiogenesis occurs in the course of inflammation, fibrosis, hypoxia, and during tumourogenesis. There is interesting data relating to liver steatosis and obesity.
Complement and Bacteria: Chemistry and Biology in Host Defense (1984)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More