gebhart/patrepeval huggingface dataset:
Methadone and Metabolite Urine Concentrations in Patients Maintained on Methadone (2003)

As regulatory control over methadone maintenance relaxes, the need for methods of monitoring compliance will increase. In community clinics, monitoring would most likely involve immunoassays of outpatients' trough urine specimens. There are no published norms for such data. Therefore, we determined concentrations of methadone in 1093 urine specimens collected thrice weekly in 27 outpatients during up to 17 weeks of observed methadone ingestion (35 to 80 mg/day) using a semiquantitative homogeneous enzyme immunoassay (CEDIA). We used a separate CEDIA assay to measure methadone's main metabolite, 2-ethylidene-3,3-diphenylpyrrolidine (EDDP), which may help detect compliance in fast metabolizers or patients who adulterate samples to simulate compliance. Methadone concentrations were more variable than those of EDDP. Concentrations of methadone were < 100 ng/mL in one specimen, between 100 and 300 ng/mL in 27, and >or= 300 ng/mL in all others. EDPP concentrations were >or= 100 ng/mL in all specimens, suggesting that EDDP should be detectable in urine from compliant patients. Methadone and EDDP concentrations significantly increased with methadone dose and (in one participant with poor clinic attendance) significantly decreased following missed methadone doses. Nevertheless, variability was too great to permit estimation of methadone dose (or detect a single missed administration) from any single specimen.
An Efficient and Automatic Systolic Peak Detection Algorithm for Photoplethysmographic Signals (2014)

Processing of physiological signals often involves detection of peaks and finding intervals between them. Well developed methods are available for Electrocardiogram(ECG) QRS complex detection. However, there are only a few algorithms published for peak detection suitable for pulse wave signals such as arterial pressure wave and photoplethysmographic (PPG) signals. Algorithms for detection of QRS complex in ECG are based on the impulsive character of the signal and are not applicable for pulse wave signals, which are more sinusoidal in nature and the shape varies with age. In this background, a versatile algorithm based on the physiology of the pulse wave is developed to detect the peaks from a pulse wave signal such as PPG. The algorithm combines the technique of moving average of valley-peak differences with an adaptive threshold filtering to detect the systolic peaks. The algorithm is validated against a publicly available validation dataset and achieved a sensitivity of 99.82 and a positive predictivity of 98.88 when compared to expert manual annotations. This algorithm is computationally simple and can be easily implemented in real time processing hardware.
A structure-adaptive piece-wise linear segments representation for time series (2005)

This paper presents a structure-adaptive piece-wise linear segments representation of time series. The 1-th order landmarks are made as the endpoints of the liner segment by computing an error criterion, this algorithm can automatically produce the K piece-wise segments of time series, which can approximate the time series. This representation allows efficient computation of the similar measure. And we present a method of the similar measure, which is designed to be insensitive to noise, shifting, amplitude scaling and time scaling. The k-mean clustering algorithm is run on this representation. The results show that the representation can improve the clustering precision.
A physiologically‐based early warning score for ward patients: the association between score and outcome* (2005)

We analysed the physiological values and early warning score obtained from 1047 ward patients assessed by an intensive care outreach service. Patients were either referred directly from the wards (n = 245, 23.4%) or were routine critical care follow-ups. Decisions were made to admit 135 patients (12.9%) to a critical care area and limit treatment in another 78 (7.4%). An increasing number of physiological abnormalities was associated with higher hospital mortality (p < 0.0001) ranging from 4.0% with no abnormalities to 51.9% with five or more. An increasing early warning score was associated with more intervention (p < 0.0001) and higher hospital mortality (p < 0.0001). For patients with scores above one (n = 660), decisions to admit to a critical care area or limit treatment were taken in 200 (30.3%). Scores of all physiological variables except temperature contributed to the need for intervention and all variables except temperature and heart rate were associated with hospital mortality.
Heterodimerization of thyroid hormone (TH) receptor with H-2RIIBP (RXR beta) enhances DNA binding and TH-dependent transcriptional activation. (1992)

Steroid/TH receptors mediate transcriptional induction of promoters containing hormone response elements (HREs) through an unclear mechanism that involves receptor binding to both hormone and a HRE. Here we demonstrate that both HRE binding and the transcriptional inducing activities of one member of this family, TH receptor, were markedly enhanced by heterodimerization with H-2RIIBP, a non-TH-binding member of the steroid hormone receptor superfamily. H-2RIIBP, the mouse homologue of human retinoic acid-related receptor, was shown to form stable heterodimers with the TH receptor either in solution or when bound to a TH response element. The results presented indicate that it might be necessary for the TH receptor or other members of this superfamily to have specific partners for heterodimer formation to elicit maximal hormone-specific gene regulation from particular HREs.
Molecular cloning of an allene oxide synthase: a cytochrome P450 specialized for the metabolism of fatty acid hydroperoxides. (1993)

Allene oxide synthases convert lipoxygenase-derived fatty acid hydroperoxides to unstable allene epoxides. In plants, an allene oxide is a precursor of the growth regulator jasmonic acid. Previously, we showed that an allene oxide synthase from flaxseed has the spectral properties of a cytochrome P450. The relationship to the P450 gene family is now established from the primary structure deduced from the cDNA. The encoded protein of 536 amino acids has segments at the C terminus that match certain well conserved regions in cytochrome P450s. The heme-binding cysteine is recognizable at position 489. However, there are unprecedented modifications in this region, with substitution of two of the three most highly conserved amino acids. Also very unusual is the absence of a conserved threonine that normally helps form the O2-binding pocket in cytochrome P450s. Notably, O2 is not involved in the allene oxide synthase reaction and, furthermore, the enzyme is known to have a weak interaction with CO. While allene oxide synthases are usually described as microsomal, the flax cDNA encodes a 58-amino acid signal sequence characteristic of a mitochondrial or chloroplast transit peptide. Therefore, the enzyme is a type I P450 and most likely is located in chloroplasts. Overall, the flax allene oxide synthase has < or = 25% identity to other P450s; it belongs to a newly discovered gene family, to be designated CYP74. The flaxseed enzyme is prototypical of this family of enzymes that remain to be characterized in plants and animals.
Effects of ezetimibe on hypercholesterolemia in the lipid profile in patients with metabolic syndrome: Zenith Trial (2013)

Ezetimibe may be more effective in patients with high cholesterol absorption than in patients with low cholesterol absorption. This prospective study was performed to evaluate the effect of ezetimibe on hypercholesterolemia in patients with metabolic syndrome (MetS). 81 patients with hypercholesterolemia in the presence or absence of MetS (MetS or non-MetS group) initially received ezetimibe (10 mg/day). In both groups, the levels of total cholesterol (TC), triglyceride, low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C) and the ratio of LDL-C to HDL-C (L/H) significantly decreased with treatment. A ratio of lathosterol to TC (lathosterol/TC) in the MetS group was significantly higher than that in the non-MetS group before treatment. Lathosterol/TC significantly increased after treatment in both groups, and campesterol/TC and sitosterol/TC significantly decreased. The non-MetS group, but not the MetS group, showed a significant increase in cholesterol/TC after treatment. Finally, we divided all of the patients into two groups (responders and non-responders) according to the percent changes in LDL-C after treatment. Male gender (p = 0.037), the presence of MetS (p = 0.026) and lower levels of L/H (p = 0.006) were independent factors that predicted a response to ezetimibe. The lipid-lowering effect of ezetimibe in MetS was comparable to that in non-MetS. Treatment with ezetimibe may be effective in males with MetS and relatively lower levels of L/H.
Immunization Against Active Ghrelin Using Virus-Like Particles for Obesity Treatment (2013)

Ghrelin is a gut hormone that stimulates food intake. In physiological conditions, ghrelin plasma levels rise with fasting and decrease after meals. Obese individuals have low fasting ghrelin levels that rise after food restriction, which is pointed out as a reason for the difficulty in maintaining weight loss. Some bariatric surgery procedures prevent rise in ghrelin levels with weight loss and this has been hypothesised to contribute to the long-term success of the treatment. The main goal of this study was to develop a safe and effective anti-ghrelin vaccine for obesity, through the chemical conjugation of ghrelin with a virus like particle, namely NS1 protein tubules from the Bluetongue Virus (BTV) using a hetero-bifunctional cross linker. Male adult C57BL/6 mice, with a normal weight and with diet-induced obesity (DIO), were randomized into six weight matched groups (n=6/group) and each group of mice received three intra-peritoneal injections with two weeks intervals, containing either 75 μg of ghrelin- NS1 immunoconjugate, 75 μg of NS1 or PBS. Our data show that immunized animals present increasing titres of anti-ghrelin antibodies, while their cumulative food intake significantly decreased and energy expenditure was significantly enhanced, although there were no significative changes in body weight.Vaccinated DIO mice also displayed significant decrease of NPY gene expression in the basal hypothalamus reflecting a decrease in central orexigenic signals. This study suggests that this anti-ghrelin vaccine has a positive impact on energy homeostasis and may be an additional therapeutical tool to be used with diet and exercise for obesity treatment.
Development and application of an excitation ratiometric optical pH sensor for bioprocess monitoring (2008)

The development of a fluorescent excitation ratiometric pH sensor (AHQ-PEG) using a novel allylhydroxyquinolinium (AHQ) derivative copolymerized with polyethylene glycol dimethacrylate (PEG) is described. The AHQ-PEG sensor film is shown to be suitable for real-time, noninvasive, continuous, online pH monitoring of bioprocesses. Optical ratiometric measurements are generally more reliable, robust, inexpensive, and insensitive to experimental errors such as fluctuations in the source intensity and fluorophore photobleaching. The sensor AHQ-PEG in deionized water was shown to exhibit two excitation maxima at 375 and 425 nm with a single emission peak at 520 nm. Excitation spectra of AHQ-PEG show a decrease in emission at the 360 nm excitation and an increase at the 420 nm excitation with increasing pH. Accordingly, the ratio of emission at 420:360 nm excitation showed a maximum change between pH 5 and 8 with an apparent pK(a) of 6.40. The low pK(a) value is suitable for monitoring the fermentation of most industrially important microorganisms. Additionally, the AHQ-PEG sensor was shown to have minimal sensitivity to ionic strength and temperature. Because AHQ is covalently attached to PEG, the film shows no probe leaching and is sterilizable by steam and alcohol. It shows rapid (approximately 2 min) and reversible response to pH over many cycles without any photobleaching. Subsequently, the AHQ-PEG sensor film was tested for its suitability in monitoring the pH of S. cereviseae (yeast) fermentation. The observed pH using AHQ-PEG film is in agreement with a conventional glass pH electrode. However, unlike the glass electrode, the present sensor is easily adaptable to noninvasive monitoring of sterilized, closed bioprocess environments without the awkward wire connections that electrodes require. In addition, the AHQ-PEG sensor is easily miniaturized to fit in microwell plates and microbioreactors for high-throughput cell culture applications.
Joint source-channel coding of binary sources with side information at the decoder using IRA codes (2004)

We use systematic irregular repeat accumulate (IRA) codes as source-channel codes for the transmission of an equiprobable memoryless binary source with side information at the decoder. A special case of this problem is joint source-channel coding for a nonequiprobable memoryless binary source. The theoretical limits of this problem are given by combining the Slepian-Wolf theorem, the source entropy in the special case, with the channel capacity. The approach is based on viewing the correlation between the binary source output and the side information as a separate channel or an enhancement of the original channel. The joint source-channel encoding, decoding and code design procedures are explained in detail. The simulated performance results are better than the recently published solutions using turbo codes and very close to the theoretical limit.
Nucleotide sequence of a cloned duck hepatitis B virus genome: comparison with woodchuck and human hepatitis B virus sequences (1984)

The nucleotide sequence of an EcoRI duck hepatitis B virus (DHBV) clone was elucidated by using the Maxam and Gilbert method. This sequence, which is 3,021 nucleotides long, was compared with the two previously analyzed hepatitis B-like viruses (human and woodchuck). From this comparison, it was shown that DHBV is derived from an ancestor common to the two others but has a slightly different genomic organization. There was no intergenic region between genes 5 and 8, which were fused into a single open reading frame in DHBV. Genes for the surface and core proteins were assigned to open reading frames 7 and 5/8. Amino acid comparisons showed some structural relationship between gene 6 product and avian reverse transcriptase, suggesting either evolution from a common ancestor or convergence to some particular structure to fulfill a specific function. This should be correlated with the synthesis of an RNA intermediate during DNA replication. This is also taken as an argument in favor of the hypothesis that gene 6 codes for the DNA polymerase that is found within the virion. DNA sequence comparison also showed that the two mammalian hepatitis B viruses are more homologous to each other than they are to DHBV, indicating that DHBV starts to evolve on its own earlier than the two other viruses, as do birds compared with mammals. From this it is proposed that the viruses evolved in a fashion parallel to the species they infect.
The use of live attenuated Salmonella for oral vaccination. (1994)

Studies of the pathogenesis of Salmonella at the molecular level have led to the identification of several classes of genes that are involved in survival in the host. This has led to the availability of a panel of attenuating lesions which are now being used to develop several rationally attenuated strains which are being evaluated as oral vaccines against human and animal salmonellosis. Much effort has been directed towards the development of a more efficacious single dose oral typhoid vaccine and there are now several candidates in Phase 1 studies. The successful development of a genetically defined oral typhoid vaccine will not only be a major step forward in the control of typhoid but will pave the way for development of practical human vaccines based on using the strain to deliver heterologous antigens to the human immune system. We have concentrated on developing a single dose oral tetanus vaccine based on constructing strains expressing fragment C (a non-toxic immunogenic protein derived from tetanus toxin). Several different promotors have been used for controlling the expression of fragment C and these have been introduced into double aro mutants of S. typhimurium and compared for their ability to elicit protective immune responses in mice. This work has demonstrated that it is possible to protect mice against tetanus toxin challenge after a single oral dose of one of these recombinant Salmonella strains. Analogous hybrid S. typhi double aro mutants have now been constructed for potential use in humans.
A distinct type of sialyl Lewis X antigen defined by a novel monoclonal antibody is selectively expressed on helper memory T cells (1993)

A subset of human helper memory T cells is known to adhere to E-selectin expressed on cytokine-activated endothelial cells. However, sialyl Lex antigen, the carbohydrate ligand for E-selectin, has been hardly detectable on these cells, at least when typical anti-sialyl Lex antibodies were used for detection. One of the MoAbs (2F3, IgM), which we raised against a chemically synthesized sialyl Lex glycolipid preparation, is found to react selectively to CD4+ CD45RObright+ CD45RA- helper memory T cells among peripheral lymphocytes in healthy individuals. The specificity of the antibody is in clear contrast to that of the hitherto reported typical anti-sialyl Lex antibodies FH-6 and SNH-3. These classical anti-sialyl Lex antibodies were known to react to a subset of natural killer (NK) cells, but were not reactive with any particular subset of resting peripheral T or B cells of healthy individuals if the cells were not activated. On the other hand, the newly generated 2F3 antibody specifically reacted to helper memory T cells, and did not react to NK cells, B cells, or any T cells other than helper memory T cells. When tested against the sialyl Lex-active glycolipid antigen, the reactivity of 2F3 was not significantly different from that of the classical anti-sialyl Lex antibodies. But when tested against oligosaccharides prepared from cellular glycoproteins, 2F3 detected a distinct set of O-linked oligosaccharides, which were not reactive to the classical anti-sialyl Lex antibodies. Our results suggest that various molecular species of sialyl Lex antigens are present on carbohydrate side chains of cellular glycoproteins, and that helper memory T cells express a distinct type of sialyl Lex antigen that is defined by 2F3 but is not efficiently detected by other typical anti-sialyl Lex antibodies. Among cultured lymphocytic leukemia cells, the adult T-cell leukemia (ATL) cells preferentially expressed the 2F3-defined antigen, and acute lymphocytic leukemia cells rarely expressed the antigen. The cultured ATL cells expressing the 2F3-defined antigen showed a clear E-selectin-dependent adhesion to cytokin-activated endothelial cells, and the 2F3-defined sialyl Lex antigen served as a ligand for E-selectin as ascertained by the clear inhibition of adhesion with the 2F3 antibody.(ABSTRACT TRUNCATED AT 400 WORDS)
[Clinical significance of galactosyltransferase associated with tumor (GAT), a new tumor marker for ovarian cancer--with special reference to the discrimination between ovarian cancer and endometriosis]. (1994)

We examined GAT, a newly developed tumor marker, in serum samples collected from 1,503 females in six institutions: 387 healthy females, 1,052 patients with gynecological diseases including 311 ovarian cancers, and 64 with nongynecological diseases. Based on the mean value + 2 SD for the healthy females, the cut-off value was set at 16 U/ml. The positive rate of GAT was 2.6% for the healthy females, 7.1% for patients with benign ovarian tumor, 5.6% for those with endometriosis, 47.9% for those with ovarian cancers, 9.3% for those with cervical cancer, and 13.3% for those with endometrial cancer. The false-positive rate of GAT for endometriosis was very low compared with that of the other markers such as CA 125, CA 602, CA 54/61, CA 72-4, STN, SLX examined in this study. The positive predictive value between ovarian cancer and endometriosis was the highest with GAT among the evaluated markers. In the cases in which the CA 125 (CA 602) value is relatively low, discrimination between ovarian cancer and endometriosis is difficult, because these cases include many patients with endometriosis. GAT showed the highest positive predictive value in such cases, so GAT proved to play a complementary role with CA 125 (CA 602). Combination assay with GAT and CA 54/61/CA 72-4/STN or SLX showed higher diagnostic efficiency between ovarian cancer and endometriosis. These results suggest the usefulness of GAT for discrimination between ovarian cancer and endometriosis.
The number of ribosomal RNA genes in Mycobacterium lepraemurium (1987)

Southern hybridization of Mycobacterium lepraemurium DNA with 16S, 23S, 5S rRNA from Mycobacterium bovis BCG was carried out. It was concluded that M. lepraemurium may possess a minimum set of rRNA genes and tRNA genes were linked to genes for 5S and 23S rRNA genes.
Comparative Pathogenicity of Nine US Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Isolates in a Five-Week-Old Cesarean-Derived, Colostrum-Deprived Pig Model (1996)

One hundred forty-six 5-week- old cesarean-derived, colostrum-deprived (CDCD) pigs were inoculated intranasally with 1 of 9 US porcine reproductive and respiratory syndrome virus (PRRSV) isolates. Differences were found in severity of clinical respiratory disease, rectal temperatures (P < or = 0.001), gross lung lesions (P < or = 0.001), and microscopic lung lesions (P < or = 0.05). Gross lung lesions were generally most severe 10 days postinoculation and were distributed primarily in the cranial, middle, and accessory lobes and ventromedial portion of the caudal lung lobes. Mean gross lung lesion scores estimating the percentage of lung affected by pneumonia at 10 days postinoculation ranged from 16.7% +/- 2.8% (mean +/- SEM, n = 10) for isolate ISU-51 to 62.4% +/- 5.7% (n = 10) for isolate ISU-28. Microscopic lung lesions were characterized by hyperplastic and hypertrophied type 2 pneumocytes, septal infiltration by mononuclear cells, and accumulation of necrotic alveolar exudate. Lymph node follicular hyperplasia and focal necrosis was seen with all 9 isolates. This CDCD pig model was useful for demonstration of significant differences in pathogenicity among US PRRSV isolates. This difference in pathogenicity may help explain the variation of severity of clinical disease observed in field outbreaks of porcine reproductive and respiratory syndrome and should provide for meaningful comparison of PRRSV genotypes.
Production and characterization of monoclonal antibodies specific to multi‐ubiquitin chains of polyubiquitinated proteins (1994)

Polyubiquitinated proteins tagged with multi-ubiquitin chains are substrates preferred by the 26 S proteasome (a ubiquitin/ATP-dependent proteolytic complex). Here, we developed a simple method for the efficient preparation of polyubiquitinated proteins which are degraded by the 26 S proteasome in an ATP-dependent manner. Our efficient method enabled us to produce ten monoclonal antibodies that recognized the multi-ubiquitin chains of the polyubiquitinated proteins, but not free ubiquitin or the protein moieties. Eight of the antibodies recognized only the multi-ubiquitin chains of the polyubiquitinated proteins, while the other two antibodies cross-reacted with mono-ubiquitin and methyl-ubiquitin, both of which are linked to proteins via an isopeptide bond, as well as with the multi-ubiquitin chains. Thus these antibodies are novel and useful tools for the identification and quantification of polyubiquitinated proteins in various cells and tissues under physiological and pathological conditions.