Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel NAT2 haplotyping using allele-specific sequencing.

BACKGROUND NAT2 is a common metabolizer of many clinical drugs. NAT2 haplotyping requires a complex procedure. Allele-specific PCR followed by direct sequencing or cloning sequencing are common methods used for haplotyping. However, these common methods require labor-intensive procedures. Allele-specific sequencing was designed for haplotyping of the NAT2 gene. MATERIALS & METHODS Using rapid DNA polymerase with high fidelity, we amplified the NAT2 coding region of genomic DNA for direct sequencing, allele-specific sequencing and for the cloning of genomic DNA from 307 healthy Korean subjects. Direct sequencing analysis of the 870-bp coding region of NAT2 was performed in order to search 11 of the most common SNPs. For cases who were heterozygous for two or more SNPs and whose haplotypes were not determined by direct sequencing, we performed sequencing analysis using the allele-specific sequencing primer for one specified allele. We performed cloning-sequencing analysis for confirmation of the haplotyping results of allele-specific sequencing. RESULTS Homozygotes for SNPs, heterozygotes for one SNP and heterozygotes for two or more SNPs were 142 (46.3%), six (2.0%) and 259 (51.8%) cases, respectively. There was 100% concordance between the results of NAT2 haplotyping using allele-specific sequencing and cloning sequencing of 65 cases that were heterozygous for two or more SNPs in 307 samples. For cases that were homozygous for the SNPs by direct sequencing, the haplotypes of NAT2 were clearly determined by cloning sequencing. CONCLUSION We have developed a novel method for NAT2 haplotyping using allele-specific sequencing, which could be an innovative and reliable method for NAT2 haplotyping.
Learning visual forward models to compensate for self-induced image motion

Predicting the sensory consequences of an agent's own actions is considered an important skill for intelligent behavior. In terms of vision, so-called visual forward models can be applied to learn such predictions. This is no trivial task given the high-dimensionality of sensory data and complex action spaces. In this work, we propose to learn the visual consequences of changes in pan and tilt of a robotic head using a visual forward model based on Gaussian processes and SURF correspondences. This is done without any assumptions on the kinematics of the system or requirements on calibration. The proposed method is compared to an earlier work using accumulator-based correspondences and Radial Basis function networks. We also show the feasibility of the proposed method for detection of independent motion using a moving camera system. By comparing the predicted and actual captured images, image motion due to the robot's own actions and motion caused by moving external objects can be distinguished. Results show the proposed method to be preferable from the earlier method in terms of both prediction errors and ability to detect independent motion.
Bimodal run distribution in a northern population of sockeye salmon (Oncorhynchus nerka): life history and genetic analysis on a temporal scale

Life history variation and genetic differentiation were analysed in sockeye salmon in Klukshu River, Yukon Canada over 7 years (1994–2000). Sockeye salmon return to the Klukshu River in two distinct runs, with a small ‘early run’ in June–August, and a larger ‘late run’ in August–September. A maximum likelihood test for clusters indicated that the return frequency distribution was bimodal in all the years analysed. Life history differences (fork length, sex ratio, age at maturity, fresh‐ and saltwater residency times) were found between the early and late runs; however, inconsistent patterns suggest that environmental effects outweigh, or strongly interact with, genetic effects for the life history characters evaluated. Analysis of variation at eight microsatellite loci showed that the early and late runs are genetically differentiated in all years examined (exact test). FST estimates between runs within years were significantly greater than zero (range: 0.018–0.041) for all years except one (0.004). The genetic variance explained by early vs. late runs (2.27%) was twice the variance among years (1.16%) based on analysis of molecular variance. Our neighbour‐joining tree showed early and late runs generally clustering separately, indicating higher gene flow among the early or late run fish across years relative to between‐run gene flow. Two years did not fit the general clustering pattern; although the early and late runs in 1995 and 2000 were genetically differentiated, they clustered separately from the rest of the groups. We cannot offer a definitive explanation for these anomalies; however, an analysis of possible cryptic population structure in early and late runs indicated that at least a few fish strayed between the runs in each year, and the highest rate of mixing was in 1995 and 2000. Our data indicate that the runs are at least partially reproductively isolated as a result of temporal and/or spatial isolating mechanisms. Such reproductive isolation has important implications for conservation and management of the Klukshu sockeye salmon, and make them an evolutionarily interesting group because of parallels with incipient speciation.
Lateralized automatic auditory processing of phonetic versus musical information: A PET study

Previous positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) studies show that during attentive listening, processing of phonetic information is associated with higher activity in the left auditory cortex than in the right auditory cortex while the opposite is true for musical information. The present PET study determined whether automatically activated neural mechanisms for phonetic and musical information are lateralized. To this end, subjects engaged in a visual word classification task were presented with phonetic sound sequences consisting of frequent (P = 0.8) and infrequent (P = 0.2) phonemes and with musical sound sequences consisting of frequent (P = 0.8) and infrequent (P = 0.2) chords. The phonemes and chords were matched in spectral complexity as well as in the magnitude of frequency difference between the frequent and infrequent sounds (/e/ vs. /o/; A major vs. A minor). In addition, control sequences, consisting of either frequent (/e/; A major) or infrequent sounds (/o/; A minor) were employed in separate blocks. When sound sequences consisted of intermixed frequent and infrequent sounds, automatic phonetic processing was lateralized to the left hemisphere and musical to the right hemisphere. This lateralization, however, did not occur in control blocks with one type of sound (frequent or infrequent). The data thus indicate that automatic activation of lateralized neuronal circuits requires sound comparison based on short‐term sound representations. Hum. Brain Mapping 10:74–79, 2000. © 2000 Wiley‐Liss, Inc.
Maturational differences in hyperoxic AP-1 activation in rat lung.

Immature organisms (neonates; <12 h old) have vastly differing responses to hyperoxic injury than adults. A common feature of hyperoxic gene regulation is involvement of activator protein (AP)-1. We evaluated lung AP-1 binding as well as that of the AP-1 subunit proteins c-Fos, c-Jun, phosphorylated c-Jun, Jun B, and Jun D after exposure to >95% O(2) for 3 days. Unlike adults, neonates showed no increased AP-1 binding in hyperoxia despite a high affinity of the AP-1 binding complexes for phosphorylated c-Jun and Jun D as demonstrated by supershift of these antibodies with the AP-1 complexes. Moreover, neonatal lungs exhibited two distinguishable AP-1 binding complexes, whereas adult lungs had one. In neonates, sequential immunoprecipitation revealed that the lower AP-1 complex was composed of proteins from both the Fos and Jun families, whereas the upper complex consisted of Jun family proteins, with predominance of Jun D. In adults, the single AP-1 complex appeared to involve other Fos or non-Fos or non-Jun family proteins as well. Neonatal lungs showed a higher level of Jun B and Jun D immunoreactive proteins in both air and hyperoxia compared with those in adult lungs. These results suggest that significant maturational differences in lung AP-1 complexes exist and that these may explain transcriptional differences in hyperoxic gene regulation.
Identification of the PRMT1v1 and PRMT1v2 specific interactomes by quantitative mass spectrometry in breast cancer cells

Arginine methylation is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). The PRMT1 gene generates at least seven distinct alternatively spliced isoforms (PRMT v1–v7), which together contribute a significant portion of the cellular arginine methylome. The distinct biochemical and biological functions of these PRMT1 isoforms have not been well characterized. Previously we have shown that while both PRMT1v1 and PRMT1v2 are overexpressed in breast cancer cells, PRMT1v2 specifically promotes breast cancer cell survival and invasion. These isoforms also have distinct subcellular localizations, PRMT1v1 is mainly nuclear and PRMT1v2 cytosolic. To gain further knowledge into their isoform‐specific roles within cells we used a SILAC‐based quantitative affinity purification/MS approach to identify their individual protein interactomes in breast cancer cells. This analysis has uncovered distinct interactomes for PRMT1v1 and PRMT1v2. Consistent with their distinct subcellular localizations, PRMT1v1 enriched a mainly nuclear protein interactome, while PRMT1v2 enriched predominantly cytoplasmic interactors from whole‐cell extracts. Furthermore, these interactomes revealed that PRMT1v1 has a role in regulating gene expression, while PRMT1v2 functions in cytoskeletal dynamics. These results highlight the unique functions of these isoforms and the distinct roles they may play within cells, with potential implications for breast cancer and other diseases.
Inhibition of myeloid cell differentiation in cancer: the role of reactive oxygen species

It is well established that tumor growth is associated with accumulation of immature myeloid cells (ImC). They play an important role in tumor‐associated immune suppression. ImC accumulate not only in tumor‐bearing hosts but also in immunized, tumor‐free hosts or hosts infected with bacterial pathogens. The kinetics of ImC in these mice is different. If in tumor‐bearing mice, the number of ImC continues to increase with tumor progression in tumor‐free mice after an initial spike, it decreases to the control level. Here, we have investigated the mechanisms of ImC accumulation in tumor‐bearing hosts by comparing differentiation of ImC obtained from tumor‐free and tumor‐bearing mice. In the presence of appropriate growth factors, ImC isolated from tumor‐free mice quickly differentiated in vitro into mature dendritic cells (DC), macrophages, and granulocytes. In contrast, differentiation of ImC from tumor‐bearing mice was significantly delayed. Similar results were obtained in vivo after adoptive transfer of ImC into naïve, congeneic mice. ImC transferred into tumor‐bearing recipients failed to differentiate into DC or macrophages. ImC from tumor‐bearing mice had significantly higher levels of reactive oxygen species (ROS) than ImC obtained from tumor‐free mice. Hydrogen peroxide (H2O2) but not superoxide radical anions was found to be the major part of this increased ROS production. In vitro experiments demonstrated that scavenging of H2O2 with catalase induced differentiation of ImC from tumor‐bearing mice into macrophages. Thus, this is a first demonstration that tumors may prevent differentiation of antigen‐presenting cells by increasing the level of endogenous H2O2 in immature myeloid cells.
Effect of negative pressure wound therapy followed by tissue flaps for deep sternal wound infection after cardiovascular surgery: propensity score matching analysis.

OBJECTIVES Deep sternal wound infection (DSWI) after cardiovascular surgery via median sternotomy remains a severe complication associated with a drastic decrease in the quality of life. We assessed the risk factors for in-hospital death caused by DSWI and the available treatments for DSWI. METHODS Between January 1991 and August 2015, we retrospectively reviewed 73 patients (51 males and 22 females, mean age 67.5 ± 10.3 years) who developed DSWI after cardiovascular surgery via median sternotomy. Pathogenic bacteria mainly comprised methicillin-resistant Staphylococcus aureus (MRSA) (49.3%). Fifteen patients (20.5%) died in hospital with DSWI. Treatment of DSWI consisted of open daily irrigation (up to 2006) or negative pressure wound therapy (NPWT) (2007 onwards), followed by primary closure or reconstruction of tissue flaps. We assessed the risk factors for in-hospital mortality from DSWI by comparing data from the 15 patients who died and the 58 survivors using propensity score matching analysis of the treatments used for DSWI. RESULTS Univariate analysis identified age, use of intra-aortic balloon pumping, prolonged mechanical ventilation, tracheotomy, prolonged intensive care unit stay, postoperative low output syndrome, postoperative myocardial infarction, postoperative renal failure, postoperative use of haemodialysis, postoperative pneumonia, postoperative cerebral disorder, MRSA infection, NPWT and tissue flaps as being associated with in-hospital mortality (P < 0.05). Multivariate analysis identified NPWT (odds ratio, 0.062; 95% confidence interval, 0.004-0.897; P = 0.041) and tissue flaps (odds ratio, 0.022; 95% confidence interval, 0.000-0.960; P = 0.048) as independently associated with reduced in-hospital mortality after DSWI. On comparing 22 patients receiving NPWT with 22 not on NPWT using propensity score matching, patients on NPWT had significantly lower in-hospital mortality than those without NPWT (NPWT vs non-NPWT, 5 vs 36%, P = 0.021). In DSWI infected by MRSA, NPWT significantly reduced the in-hospital mortality caused by DSWI (NPWT vs non-NPWT, 0 vs 52%, P = 0.003). CONCLUSIONS NPWT and tissue flaps may be favourable factors associated with reduced in-hospital mortality attributable to DSWI. NPWT as a bridge therapy to tissue flaps may play a major role in treating DSWI and improve the prognosis for patients with MRSA-infected DSWI.
Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS

Abstract: As new assay methods for quantitative reverse transcription‐polymerase chain reaction (RT‐PCR), such as real time RT‐PCR techniques, approach theoretical limits of per reaction sensitivity, further increments in the sensitivity of measurements of viral load can only be achieved by increasing the amount of input RNA per reaction. We describe a robust, convenient, rapid integrated approach for specimen preparation and real time RT‐PCR assay for plasma simian immunodeficiency virus (SIV) RNA viral load that provides a threshold sensitivity of 10 copy Eq/ml, and tolerates less than optimally processed specimens. The method provides accurate quantitation of viral load for the SIV virus isolates in common use for non‐human primate studies. We demonstrate the utility of the method in sensitively tracking viral load in an animal showing effective control of viral replication to levels below the threshold for quantitation in conventional assays.
Modelling Walleye Population and Its Cannibalism Effect

Walleye is a very common recreational fish in Canada with a strong cannibalism tendency, such that walleyes with larger sizes will consume their smaller counterparts when food sources are limited or a surplus of adults is present. Cannibalism may be a factor promoting population oscillation. As fish reach a certain age or biological stage (i.e. biological maturity), the number of fish achieving that stage is known as fish recruitment. The objective of this thesis is to model the walleye population with its recruitment and cannibalism e↵ect. A matrix population model has been introduced to characterize the walleye population into three di↵erent groups: newborns, juveniles, and adults. A delay di↵erential equation (DDE) model has also been introduced to characterize walleyes into two groups including juveniles and adults. Local and global stabilities of equilibria have been discussed in both models. Furthermore, numerical simulations are present to visualize the e↵ects of both models.
Two levels similarity modelling: A co-clustering approach for image classification

In this work, we introduced a new co-clustering based approach in content based image classification field: the two levels similarity modelling (TLSM) concept. This approach is based on a new images similarity formulation using obtained co-clusters and a wave effect which changes similarity correlations. The obtained results show a real improvement of image recognition accuracy in comparison with obtained accuracy using one of classical co-clustering systems.
PocketSLAM based on the principle of the FootSLAM algorithm

Infrastructureless indoor navigation remains a challenging research area in spite of the fact that multiple low cost sensors suitable for positioning recently became available even in mobile phones. Since Global Navigation Satellite Signals (GNSS) are often unavailable indoors, the use of Inertial Measurement Units (IMUs) seems to be promising for indoor navigation. Auspicious results are available when the sensor is placed on the foot in indoor positioning applications, but still many problems remain when the drift error during stance phases cannot be reduced. An indoor navigation solution is the so called FootSLAM algorithm, where reliable positioning (positioning error below 1 meter in the case of loop closures) is possible assuming that the sensor is fixed on the foot. More recently, another navigation system was proposed where the sensor is located in the pocket of a pedestrian. Since no special fixation or no special shoe is needed, this location of the sensor is more convenient for mass market users. But also this system suffers from a remaining drift that needs to be compensated. In this paper, we propose a combination of the pocket navigation system with the FootSLAM approach and show that it is also possible to reduce the remaining drift with this combination.
Selective cleavage of ErbB4 by G‐protein‐coupled Gonadotropin‐Releasing Hormone Receptor in Cultured Hypothalamic Neurons

Gonadotropin‐releasing hormone (GnRH) is secreted from hypothalamic neurons (GnRH neurons). GnRH neurons have a GnRH receptor belonging to the G‐protein‐coupled receptors. The stimulation of this receptor activates extracellular signal‐regulated kinase (ERK). In the present study, we found that epidermal growth factor receptor (EGFR) and ErbB4 were expressed in immortalized GnRH neurons (GT1‐7 cells). AG1478, a relatively specific inhibitor of the ErbB family, and small interfering RNA (siRNA) for ErbB4 inhibited the GnRH‐induced activation of ERK in GT1‐7 cells, suggesting that EGFR and ErbB4 were necessary for the activation. In addition, GnRH induced the cleavage of ErbB4 and accumulation of an 80‐kDa fragment. After treatment of the cells with 50 nM GnRH for 5 min, about 80% of ErbB4 was cleaved. Biotinylation of cell surface proteins revealed that more than 70% of the cell surface ErbB4 was cleaved by GnRH treatment. A higher concentration and longer treatment were necessary for GnRH to induce ErbB4 cleavage than ERK activation. TAPI‐2, an inhibitor of tumor necrosis factor‐α‐converting enzyme (TACE), and siRNA for TACE inhibited the cleavage of ErbB4, suggesting that TACE was involved. After ErbB4 cleavage, the activation of ERK by neuregulin 1 was almost completely inhibited. These results suggest that the down‐regulation of ErbB4 expression is induced by G‐protein‐coupled receptor stimulation. J. Cell. Physiol. 227: 2492–2501, 2012. © 2011 Wiley Periodicals, Inc.
Glycaemic control, disease duration and beta-cell function in patients with Type 2 diabetes in a Swedish community. Skaraborg Hypertension and Diabetes Project

Aims To examine determinants for glycaemic control in primary care patients with Type 2 diabetes. Methods In a community-based surveillance of primary care patients with Type 2 diabetes, 190 men and 186 women were consecutively identified and examined for cardiovascular risk factors. Insulin resistance and b -cell function were estimated using homeostasis model assessment (HOMA). Good glycaemic control was defined as HbA 1c < 6.5%. Results Following adjustment for age and gender, HbA 1c ‡ 6.5% was associated with duration of diabetes (10.6 vs. 6.4 years, P < 0.001), lower levels of serum insulin (6.3 vs. 8.0 mU/l, P = 0.012), higher serum triglyceride levels (2.0 vs. 1.7 mmol/l, P = 0.002) and impairment of b -cell function (HOMA index 19.5 vs. 45.8, P < 0.001). The association between HbA 1c levels and duration remained with adjustment for age, gender, waist—hip ratio (WHR) and serum triglycerides (odds ratio (OR) for HbA 1c ‡ 6.5% by 5 years diabetes duration = 1.7; 95% confidence interval (CI) 1.4—2.1) but was lost following additional adjustment for b -cell function (OR for HbA 1c ‡ 6.5% = 1.3; 95% CI 0.96— 1.7). In a separate linear regression with b -cell function as the dependent variable there was a significant association with HbA 1c after adjustments for differences in age, gender, WHR, serum triglyceride levels and diabetes duration ( P < 0.001). Conclusions Increasing HbA 1c by time was associated with declining b -cell function. Diabet. Med. 19, 125—129 (2002)
Factors associated with likelihood of horses having a high serum Streptococcus equi SeM-specific antibody titer.

OBJECTIVE To identify factors associated with an increased likelihood that horses would have a serum Streptococcus equi SeM-specific antibody titer > or = 1:1,600. DESIGN Cross-sectional study. ANIMALS 188 healthy client-owned horses. PROCEDURES A single serum sample from each horse was tested for SeM-specific antibody titer with an ELISA. Multivariate logistic regression was used to identify factors associated with having a titer > or = 1:1,600. RESULTS Age, breed, and vaccination status were significantly associated with the likelihood of having a titer > or = 1:1,600. The odds of having a titer > or = 1:1,600 increased by a factor of 1.07 with each 1-year increase in age. Quarter Horses and horses of other breeds were 4.08 times as likely as were Thoroughbreds and warmbloods to have a titer this high. Horses that had previously received an intranasal S equi vaccine were 4.7 times as likely as were horses without any history of vaccination to have a titer this high. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that older horses, horses other than Thoroughbreds and warmbloods, and horses that had been vaccinated with an attenuated-live intranasal S equi vaccine between 1 and 3 years previously had an increased likelihood of having a serum SeM-specific antibody titer > or = 1:1,600.
Challenges associated with the recognition and treatment of depression in older recipients of home care services

ABSTRACT Background: Home care for older adults is a common phenomenon worldwide because it allows older adults to remain in their home environment. Research has shown that depression is frequently found in older recipients of home care services. Nonetheless, it is often poorly recognized and treated. Untreated or poorly treated depression in older home care recipients has been associated with a variety of negative outcomes, including increased morbidity and mortality, greater likelihood of nursing home institutionalization and higher caregiver distress. Methods: The present review outlines some of the challenges associated with appropriate recognition and treatment of depression in older home care recipients. Results: Our review demonstrates that more aggressive management of depressive symptoms and the employment of an interdiciplinary team can result in beneficial outcomes. Conclusions: Further research is needed, especially in the area of psychotherapeutic interventions as these should be flexible enough to meet the unique and evolving needs of this frail population of older adults.