Miracle-dz/UniFAR-FTUs huggingface dataset:
Further Characterization of Chlamydia pneumoniae Specific Monoclonal Antibodies

Studies using monoclonal antibodies have demonstrated species‐specific reactivities with Chlamydia pneumoniae. In this study, further characterization of C. pneumoniae specific monoclonal antibodies TT‐205 and RR‐402 and description of C. pneumoniae specific antibodies prepared against other isolates are presented. TT‐205 and RR‐402 were shown to neutralize infectivity. Neutralization in cell culture was specific and enhanced by complement. Attempts to characterize the reactive antigen by immunoblotting, immunoaffinity chromatography and radioimmunoprecipitation were unsuccessful, probably due to difficulties in solubilizing the immunoreactive epitope without denaturing it. Recognition of the determinant by the monoclonal antibodies is labile to physical and chemical treatments suggesting that the reactive epitope is conformational.
Nicotine Metabolite Ratio Predicts Smoking Topography and Carcinogen Biomarker Level

Background: Variability in smoking behavior is partly attributable to heritable individual differences in nicotine clearance rates. This can be assessed as the ratio of the metabolites cotinine and 3′-hydroxycotinine (referred to as the nicotine metabolism ratio; NMR). We hypothesized that faster NMR would be associated with greater cigarette puff volume and higher levels of total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), a carcinogen biomarker. Methods: Current smokers (n = 109) smoked one of their preferred brand cigarettes through a smoking topography device and provided specimens for NMR and total NNAL assays. Results: Faster nicotine metabolizers (third and fourth quartiles versus first quartile) based on the NMR exhibited significantly greater total puff volume and total NNAL; the total puff volume by daily cigarette consumption interaction was a significant predictor of total NNAL level. Conclusion: A heritable biomarker of nicotine clearance predicts total cigarette puff volume and total NNAL. Impact: If validated, the NMR could contribute to smoking risk assessment in epidemiologic studies and potentially in clinical practice. Cancer Epidemiol Biomarkers Prev; 20(2); 234–8. 2011 AACR.
Functions of parent-child reminiscing about emotionally negative events

Parent-child reminiscing about negative experiences influences children's developing “emotional self-concept”, which comprises three interrelated functions: self-defining (this is the kind of emotional person I am), self-in-relation (this is how I express and share my emotions with others), and coping (this is how I cope with and resolve negative emotion). In this study, we examined how 70 mostly white, middle-class mothers discuss three negative experiences (fear, anger, and sadness) with their 4-year-old children. Conversations about fear elaborate on the facts of the event and emotional resolutions, thus focusing on coping. Conversations about sadness contain evaluative feedback and emotional resolutions, thus focusing on self-in-relation and coping. Finally, conversations about anger highlight the emotional state itself, thus focusing on self-definition. Mothers are also more elaborative and more evaluative with daughters than with sons, and place emotional events in a more interpersonal context with daughters than sons. Thus girls may be forming a more elaborated and more interpersonal emotional self-concept than boys.
Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162‐bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well‐supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human‐mediated stock transfers, parsimony‐network‐based nested‐clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre‐dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter‐ and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.
Decadal mass balance of the antarctic ice sheet and its contribution to global sea level rise

We analyzed Antarctic ice sheet elevation change (dH/dt) from 1992-2002 using nearly 307 million elevation change measurements from ERS-1 and ERS-2 satellite radar altimeter data covering an area of about 8.5 million km2. Ten-year elevation change time series were constructed for 1,500 local regions, 22 drainage basins, East and West Antarctica, and the continent as a whole (north of 81.6degS). Almost all basins in East Antarctica were found to have long-term dH/dt trends that fell within plusmn3 cm/yr. In West Antarctica the long-term dH/dt trends varied from -9 cm/yr to +22 cm/yr occur over basin scales. Despite these significant spatial variations, both the East and West Antarctic ice sheets, and the continent as a whole are very close to a state of overall mass balance. The average elevation change for the Antarctic continent from 1992-2002 was found to be 1.4plusmn0. 2 cm/yr. Considering decadal accumulation variability, this translates to a net sink of fresh water of 42plusmn23 Gt/yr. The Antarctic continent's decadal contribution to global sea level change is estimated to be -0.12plusmn0.07 mm/yr, which is very close to zero. The plusmn0.07 mm/yr error is a three-fold reduction in uncertainty compared to the most recent best estimate for the Antarctic ice sheet
Quantitative Analysis of Translesion DNA Synthesis across a Benzo[a]pyrene-Guanine Adduct in Mammalian Cells

Replication across unrepaired DNA lesions in mammalian cells is effected primarily by specialized, low fidelity DNA polymerases. We studied translesion DNA synthesis (TLS) across a benzo[a]pyrene-guanine (BP-G) adduct, a major mutagenic DNA lesion generated by tobacco smoke. This was done using a quantitative assay that measures TLS indirectly, by measuring the recovery of gapped plasmids transfected into cultured mammalian cells. Analysis of PolK+/+ mouse embryo fibroblasts (MEFs) showed that TLS across the BP-G adduct occurred with an efficiency of 48 ± 4%, which is an order of magnitude higher than in Escherichia coli. In PolK–/– MEFs, bypass was 16 ± 1%, suggesting that at least two-thirds of the BP-G adducts in MEFs were bypassed exclusively by polymerase κ (polκ). In contrast, polη was not required for bypass across BP-G in a human XP-V cell line. Analysis of misinsertion specificity across BP-G revealed that bypass was more error-prone in MEFs lacking polκ. Expression of polκ from a plasmid introduced into PolK–/– MEFs restored both the extent and fidelity of bypass across BP-G. Polκ was not required for bypass of a synthetic abasic site. In vitro analysis demonstrated efficient bypass across BP-G by both polκ and polη, suggesting that the biological role of polκ in TLS across BP-G is due to regulation of TLS and not due to an exclusive ability to bypass this lesion. These results indicate that BP-G is bypassed in mammalian cells with relatively high efficiency and that polκ bypasses BP-G in vivo with higher efficiency and higher accuracy than other DNA polymerases.
[Male infertility with severe oligospermatism and azoospermia treated by Bushen Shengjing Decoction combined with intracytoplasmic sperm injection].

OBJECTIVE To observe the pregnancy promoting effect of Bushen Shengjing Decoction (BSSJD) combined with intracytoplasmic sperm injection (ICSI) in treating male infertility with severe oligospermatism and azoospermia (SOA). METHODS ICSI were applied on 164 patients, among them, the 82 assigned to the TCM group were treated with additionally by BSSJD before injection for 2-3 months, and the other 82 assigned to the control group received ICSI alone. The density, motility, viability and deformity of sperm; semen level of reactive oxygen species (ROS); number of eggs retrieved, M II eggs and mean transplanted fetus; rates of fertilization, cleavage, available embryo and clinical pregnancy in the two groups were observed and compared. RESULTS Compared with those in the control group, the density, motility and viability of sperm were higher, the deformity rate and ROS level were lower in the TCM group respectively (P<0.05). Moreover, higher rates of fertilization and clinical pregnancy were also shown in the TCM group (P<0.05). CONCLUSION BSSJD has the effects of decreasing semen level of ROS and improving the quality of sperm. It is also helpful for the natural fertilization ability of patients with SOA and raise the viability of their sperm to increase the ovarian fertilization rate and clinical pregnancy rate in ICSI cycles.
Transceiver Design for Nonconcurrent Two-Way MIMO AF Relaying With QoS Guarantees

We consider a cellular system with amplify-and-forward (AF) nonconcurrent two-way relaying (ncTWR), where a base station serves a transmit-only user and a receive-only user. Most of the state-of-the-art transceiver designs for AF multiple-input multiple-output (MIMO) ncTWR optimize a system-wide objective function subject to the transmit power constraints. Transceiver designs that incorporate quality-of-service (QoS) constraints are not well investigated in ncTWR literature. In this paper, we design a MIMO AF transceiver that maximizes weighted sum-rate (WSR) while guaranteeing the QoS constraints that are cast as per-stream rate required by two ncTWR users. The WSR maximization is a nonconvex problem due to its nonconvex objective. We solve this problem by separately approximating the objective at low and high signal-to-noise ratios (SNRs), with each approximation cast as a geometric program. With extensive numerical evaluations, we first demonstrate the improved performance of the proposed transceiver over existing designs without QoS constraints. We later investigate the effect of QoS constraints on the system WSR.
VPAC1 is a cellular neuroendocrine receptor expressed on T cells that actively facilitates productive HIV-1 infection

Objective A lack of productive HIV-1 infection of Kit225 compared to Jurkat T cells, despite similar levels of CD4 and HIV-1 chemokine co-receptors, was found to correlate with the expression of vasoactive intestinal peptide/pituitary adenylate cyclase activating polypeptide receptor-1 (VPAC1). We therefore examined a role for this seven-transmembrane G protein-coupled neuroendocrine receptor in modulating HIV-1 infection. Methods Reverse transcription–PCR was used to show the level of VPAC1 expression in different T-cell lines. A signal-blocking antibody to VPAC1 was used to examine its inhibiting effect on HIV-1 infection. Transfection of VPAC1 cDNA in both sense and anti-sense orientation was used to assess the role of VPAC1 in HIV-1 infection. HIV-1 infection was monitored by gag p24 ELISA using HIV-1IIIB or by luciferase activity using pseudo envelope-typed HXB2-NL4-3-luciferase. Analysis of HIV-1 gag DNA and 2-LTR circles was utilized to examine a possible mechanism for the effect of VPAC1. Results Using VPAC1 signal blocking antibody, we showed that up to 80% of productive infection with HIV-1IIIB was inhibited. We also demonstrated that HIV-1 gp120 has sequence similarity to the natural ligand for VPAC1 and postulate that it can activate this receptor directly. Transfection of VPAC1 cDNA in the anti-sense orientation resulted in a significant loss, up to 50% of productive infection. In contrast, transfection of cells with VPAC1 in the sense orientation increased the productive infection by more than 15-fold and caused a profound increase in syncytium formation. Furthermore, stimulation of VPAC1 on primary cells facilitated in vitro infection with HIV-1 HXB2-NL4-3. Analysis of HIV-1 gag DNA indicated that VPAC1 does not affect viral entry; however, cells that show negligible expression of VPAC1 may not be productively infected as indicated by a lack of 2-LTR circle formation. Conclusion We have discovered a cellular receptor, VPAC1, that is a novel and potent facilitator of HIV-1 infection and thus, is a potentially important new target for therapeutic intervention.
Metabolic Flux Analysis of Plastidic Isoprenoid Biosynthesis in Poplar Leaves Emitting and Nonemitting Isoprene1[W]

Isoprene biosynthesis demands a huge carbon flux through the plastidic isoprenoid pathway, and the concentration of its immediate precursor modulates this flux. The plastidic 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway is one of the most important pathways in plants and produces a large variety of essential isoprenoids. Its regulation, however, is still not well understood. Using the stable isotope 13C-labeling technique, we analyzed the carbon fluxes through the MEP pathway and into the major plastidic isoprenoid products in isoprene-emitting and transgenic isoprene-nonemitting (NE) gray poplar (Populus × canescens). We assessed the dependence on temperature, light intensity, and atmospheric [CO2]. Isoprene biosynthesis was by far (99%) the main carbon sink of MEP pathway intermediates in mature gray poplar leaves, and its production required severalfold higher carbon fluxes compared with NE leaves with almost zero isoprene emission. To compensate for the much lower demand for carbon, NE leaves drastically reduced the overall carbon flux within the MEP pathway. Feedback inhibition of 1-deoxy-d-xylulose-5-phosphate synthase activity by accumulated plastidic dimethylallyl diphosphate almost completely explained this reduction in carbon flux. Our data demonstrate that short-term biochemical feedback regulation of 1-deoxy-d-xylulose-5-phosphate synthase activity by plastidic dimethylallyl diphosphate is an important regulatory mechanism of the MEP pathway. Despite being relieved from the large carbon demand of isoprene biosynthesis, NE plants redirected only approximately 0.5% of this saved carbon toward essential nonvolatile isoprenoids, i.e. β-carotene and lutein, most probably to compensate for the absence of isoprene and its antioxidant properties.
Physical activity assessed with three different methods and the Framingham Risk Score on 10-year coronary heart disease risk.

BACKGROUND Physical activity (PA) protects against coronary heart disease (CHD) by favorably altering several CHD risk factors. In order to best understand the true nature of the relationship between PA and CHD, the impact different PA assessment methods have on the relationships must first be clarified. The purpose of this study was to examine associations between the Framingham Risk Score on 10-year estimated risk of CHD (10-year CHD risk) and three different PA assessment methods. MATERIAL/METHODS Female (n=143) and male (n=155) adults wore activity monitors and recorded PA in logs during a seven-day period after which they completed a seven-day PA recall and had CHD risk factors assessed. The 10-year CHD risk was calculated from the CHD risk factors. RESULTS Multiple regression analyses showed 10-year CHD risk was negatively associated with physical activity measured by the activity monitor (p<0.05) but not the log or recall in women. In men, significant inverse relationships between 10-year CHD risk and physical activity measured by the activity monitor and recall were observed. The log was not significantly associated with 10-year CHD risk in men. CONCLUSIONS The results of this study concur with previous research in that PA is associated with the risk of developing CHD; however, the findings clearly suggest that it is important to consider the PA assessment method when interpreting this relationship.
Impaired Migration in the Rostral Migratory Stream But Spared Olfactory Function after the Elimination of Programmed Cell Death in Bax Knock-Out Mice

Rats and mice exhibit neurogenesis of olfactory bulb (OB) interneurons throughout adulthood. To homeostatically maintain stable neuron numbers, it is necessary to continuously remove a subset of OB neurons by programmed cell death (PCD). Here we demonstrate that Bax is critical for the elimination of OB neurons by showing that Bax-KO mice exhibit greatly reduced PCD in the OB. Despite the reduction of PCD, however, proliferation of progenitors and the size of the OB were virtually unaffected in Bax-knock-out (KO) mice. However, reducing PCD by Bax deletion affected the migration of a subset of adult-produced neurons by the disruption of glial tube formation as well as by premature detachment of neuroblasts from the migratory chain. Rescued cells aberrantly remained in the subventricular zone (SVZ)-rostral migratory stream (RMS), in which they differentiated into calretinin+ or GABA-expressing interneurons. Because of the migratory deficit, OB cell homeostasis involving new cell entry and PCD (neuronal turnover) was virtually absent in adult Bax-KO mice. Despite this, Bax-KO mice exhibited normal olfactory behaviors such as odor discrimination and olfactory memory which are thought to be influenced by adult neurogenesis. These results demonstrate that PCD is involved in the regulation of RMS migration and differentiation after OB neurogenesis, but that animals maintain normal olfactory function in the absence of PCD.
Application of biostatistics in research by teaching faculty and final-year postgraduate students in colleges of modern medicine: A cross-sectional study

Context: Biostatistics is well recognized as an essential tool in medical research, clinical decision making, and health management. Deficient basic biostatistical knowledge adversely affects research quality. Surveys on this issue are uncommon in the literature. Aims: To study the use of biostatistics in research by teaching faculty and postgraduate students from colleges of modern medicine. Settings and Design: Cross-sectional study in colleges of modern medicine. Materials and Methods: A pretested proforma was used to collect information about the use of biostatistics by teaching faculty and final-year postgraduate students from colleges of modern medicine. The study period was 6 months. Statistical Analysis: Chi-square test, Spearman rank correlation coefficient, and multivariate analysis were used for analysis of data. Results: With this questionnaire, the maximum possible score for appropriate use of biostatistics in research was 20. The range of scores obtained by the study subjects was 1–20 and the median was 11. Appropriate use of biostatistics was independent of sex, designation, and education (P>.05). Spearman coefficient showed low—but significant—correlation between the score and the number of papers presented and published (P=.002 and P=.000, respectively). Conclusions: The study showed that nearly half of the respondents were not using statistics appropriately in their research. There was also lack of awareness about the need for applying statistical methods from the stage of planning itself.
The influence of genetic polymorphisms of cytochrome P450 3A5 and ABCB1 on starting dose- and weight-standardized tacrolimus trough concentrations after kidney transplantation in relation to renal function

Abstract Background: Cytochrome P450 3A5 (CYP3A5) and ABCB1 polymorphisms have been shown to influence tacrolimus (Tc) blood concentrations in the stable phase after organ transplantation. We hypothesized that Tc pharmacokinetics may be affected by genetic mutations subsequent to starting doses. Methods: We retrospectively analyzed data from a cohort of 59 kidney transplant recipients, in whom CYP3A5 (intron 3) and ABCB1 (exons 12, 21 and 26) genotypes were correlated to dose- and weight-standardized Tc trough concentrations obtained after initial Tc doses. Renal function, expressed as glomerular filtration rate (GFR) (MDRD equation), on days 7 and 14 after transplantation was evaluated and its relationship with Tc concentrations was analyzed. Results: Dose- and weight-standardized Tc trough concentrations were lower in patients carrying the CYP3A5 *1 allele (p<0.01). There was no statistically significant association with ABCB1 polymorphisms. In a multivariate analysis, both the presence of at least one CYP3A5 *1 allele (p=0.006) and age at the time of transplantation (p=0.010) were significant independent variables affecting Tc trough blood concentrations standardized to the first dosages (model r2=0.23). GFR was not affected by Tc concentrations. Conclusions: Prospective trials are needed to prove that a genetic approach to Tc pharmacokinetics and its related side effects during the early period after grafting may improve patient outcome. Clin Chem Lab Med 2006;44:1192–8.
Characterization of Dental Nociceptive Neurons

Selective blockade of nociceptive neurons can be achieved by the delivery of permanently charged sodium channel blockers through the pores of nociceptive ion channels. To assess the feasibility of this application in the dental area, we investigated the electrophysiological and neurochemical characteristics of nociceptive dental primary afferent (DPA) neurons. DPA neurons were identified within trigeminal ganglia labeling with a retrograde fluorescent dye applied to the upper molars of adult rats. Electrophysiological studies revealed that the majority of dental primary afferent neurons showed characteristics of nociceptive neurons, such as sensitivity to capsaicin and the presence of a hump in action potential. Immunohistochemical analysis revealed a large proportion of DPA neurons to be IB4-positive and to express TRPV1 and P2X3. Single-cell RT-PCR revealed mRNA expression of various nociceptive channels, including the temperature-sensitive TRPV1, TRPA1, TRPM8 channels, the extracellular ATP receptor channels P2X2 and P2X3, as well as the nociceptor-specific sodium channel, NaV1.8. In conclusion, DPA neurons have the electrophysiological characteristics of nociceptors and express several nociceptor-specific ion channels. Analysis of these data may assist in the search for a new route of entry for the delivery of membrane-impermeant local anesthetics. Abbreviations: AP, action potential; DiI, 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate; DPA, dental primary afferent; FITC, fluorescein 5(6)-isothiocyanate; IB4, isolectin-B4; RT-PCR, reverse-transcription polymerase chain-reaction; TRP, transient receptor potential.
Fecal microbiota transplantation through mid‐gut for refractory Crohn's disease: Safety, feasibility, and efficacy trial results

The gut microbiota plays a pivotal role in the intestinal diseases. Fecal microbiota transplantation (FMT) might be a rescue therapy for refractory inflammatory bowel disease. This study aimed to evaluate the safety, feasibility, and efficacy of FMT through mid‐gut for refractory Crohn's disease (CD).