Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of anion-exchange and steric-exclusion HPLC assays of mouse plasma lipoproteins Published, JLR Papers in Press, March 16, 2005. DOI 10.1194/jlr.D500002-JLR200

We compared two HPLC methods (anion exchange [AE] and steric exclusion [SE]) for analysis of mouse lipoprotein profiles by determining coefficients of variability (CVs) under varying conditions. CVs for AE and SE were comparable on fresh samples. There was an inverse relationship between subfraction curve area and CV [r = −0.65 (AE) and −0.50 (SE)], consistent with the interpretation that as curve area decreased, error variance increased and signal-to-noise ratio decreased. Sample storage did not affect SE. In contrast, with AE, alterations in measured lipoproteins were apparent after storage, including a decrease in the HDL subfraction [66.8% (baseline) vs. 15.9% (1 week); P < 0.01] and an increase in areas under LDL and VLDL peaks. Concomitant with decreasing HDL area, reproducibility deteriorated with the duration of storage. Analysis of the effects of decreasing sample injectate volume to <25 μl on SE lipoprotein subfractions revealed that areas under LDL and VLDL peaks decreased and persisted as volume was decreased further. Areas under all lipoprotein subfractions measured with either AE or SE were linearly correlated with the amount of cholesterol [r = 0.69 (AE) and 0.87 (SE)]. Both AE and SE yield reproducible, accurate, and rapid measurements of lipoproteins from small amounts of serum. AE yields more sensitive, high-amplitude, well-defined peaks that can be easily distinguished and necessitates the use of smaller sample volumes compared with SE, but sample storage causes alterations in the chromatogram. SE appears better suited to serial analyses involving stored samples.
Validation of Referral Guidelines for Women With Pelvic Masses

OBJECTIVE: Guidelines for referring women with pelvic masses suspicious for ovarian cancers to gynecologic oncologists have been published jointly by Society of Gynecologic Oncologists (SGO) and the American College of Obstetricians and Gynecologists (ACOG). They are based on patient age, CA 125 level, physical findings, imaging study results, and family history. Although the guidelines are evidence-based, their predictive value in distinguishing cancers from benign masses is unknown. METHODS: Chart review for factors included in the guidelines of surgically evaluated women with pelvic masses at 7 tertiary care centers during a 12-month interval was performed. This information was used to estimate the predictive values of the SGO and ACOG guidelines in identifying patients with malignant pelvic masses. RESULTS: A total of 1,035 patients were identified, including 318 (30.7%) with primary malignancies of the ovary, fallopian tube, or peritoneum. Seventy-seven were younger than 50 years old (premenopausal group), and 240 were 50 years old or older (postmenopausal group). Fifty additional patients (4.8%) had cancers metastatic to the ovaries, and the remaining 667 (64.4%) had benign masses. The referral guidelines captured 70% of the ovarian cancers in the premenopausal group and 94% of the ovarian cancers in the postmenopausal group. The positive predictive value was 33.8% for the premenopausal group and 59.5% for the postmenopausal group, whereas the negative predictive values were more than 90% for both groups. Elevated CA 125 level was the single best predictor of malignancy in both groups. CONCLUSION: The SGO and ACOG referral guidelines effectively separate women with pelvic masses into 2 risk categories for malignancy. This distinction permits a rational approach for referring high-risk patients to a gynecologic oncologist for management. LEVEL OF EVIDENCE: III
B Cells Help Alloreactive T Cells Differentiate Into Memory T Cells

B cells are recognized as effector cells in allograft rejection that are dependent upon T cell help to produce alloantibodies causing graft injury. It is not known if B cells can also help T cells differentiate into memory cells in the alloimmune response. We found that in B‐cell‐deficient hosts, differentiation of alloreactive T cells into effectors was intact whereas their development into memory T cells was impaired. To test if B cell help for T cells was required for their continued differentiation into memory T cells, activated T cells were sorted from alloimmunized mice and transferred either with or without B cells into naïve adoptive hosts. Activated T cells cotransferred with B cells gave rise to more memory T cells than those transferred without B cells and upon recall, mediated accelerated rejection of skin allografts. Cotransfer of B cells led to increased memory T cells by enhancing activated CD4 T‐cell proliferation and activated CD8 T‐cell survival. These results indicate that B cells help alloreactive T‐cell differentiation, proliferation and survival to generate optimal numbers of functional memory T cells.
Space charge and soil ionization: an electro-kinetic approach

This paper proposes an electro-kinetic model of soil ionization for concentrated electrodes submitted to impulse currents. This approach allows a better understanding of the dynamic response of earth rods. Since current density attains a sufficient value around the electrode, ionization appears in the soil and produces a transient reduction of the grounding resistance. Experimental results, obtained under well-controlled conditions in laboratory, indicate that the injected energy is the most important parameter in the transient resistance reduction, rather than the crest value of impulse currents. The meaning of this resistance reduction is interpreted by the electro-kinetic model that calculates the resistance-time variation by computing the energy required to arrange a distribution of space charge around the electrode. A practical conclusion of this energy-depending interpretation for grounding electrodes, is that with ionization it would be attended a significant and durable reduction of the transient resistance for long impulse currents.
STAT-1 Mediates the Stimulatory Effect of IL-10 on CD14 Expression in Human Monocytic Cells1

IL-10, an anti-inflammatory cytokine, has been shown to exhibit stimulatory functions including CD14 up-regulation on human monocytic cells. CD14-mediated signaling following LPS stimulation of monocytic cells results in the synthesis of proinflammatory cytokines. Our results show that LPS-induced CD14 expression on monocytic cells may be mediated by endogenously produced IL-10. To investigate the molecular mechanism by which IL-10 enhances CD14 expression, both human monocytes and the promyelocytic HL-60 cells were used as model systems. IL-10 induced the phosphorylation of PI3K and p42/44 ERK MAPK. By using specific inhibitors for PI3K (LY294002) and ERK MAPKs (PD98059), we demonstrate that LY294002 either alone or in conjunction with PD98059 inhibited IL-10-induced phosphorylation of STAT-1 and consequently CD14 expression. However, IL-10-induced STAT-3 phosphorylation remained unaffected under these conditions. Finally, STAT-1 interfering RNA inhibited IL-10-induced CD14 expression. Taken together, these results suggest that IL-10-induced CD14 up-regulation in human monocytic cells may be mediated by STAT-1 activation through the activation of PI3K either alone or in concert with the ERK MAPK.
Efficiency of the Tax System: A Marginal Excess Burden Analysis

This paper analyses the efficiency of the Australian tax system using CGETAX, a large-scale, long-run CGE model designed for tax policy analysis. This follows an analysis with CGETAX of an Australian Government proposal to reduce the corporate tax rate from 30 to 25 per cent in Murphy (2016a) and Murphy(2016b) and an Australian Treasury Working Paper on the efficiency of certain taxes (Cao et al., 2015). This paper begins by uses a highly stylised version of CGETAX to provide a theoretical analysis of the efficiency of major taxes, applicable to advanced, open economies in general. The Stylised model, like CGETAX, allows for imperfect competition and models the disincentive effects of taxes on labour supply, the capital-to-labour ratio, and the choice between present and future consumption. Of the major taxes, company income tax is found to be least efficient, with a marginal excess burden of 139 cents per additional dollar of tax revenue. For open economies the literature finds that company tax is among the most inefficient of taxes because it suppresses labour supply and the capital to labour ratio and leads to profit shifting to lower taxed jurisdictions. For Australia, company tax is even more inefficient because of its above-normal company tax rate and the erosion of the final revenue yield through the system of franking credits.
Influence of Distribution of Animals between Dose Groups on Estimated Benchmark Dose and Animal Welfare for Continuous Effects

The benchmark dose (BMD) approach is increasingly used as a preferred approach for dose–effect analysis, but standard experimental designs are generally not optimized for BMD analysis. The aim of this study was to evaluate how the use of unequally sized dose groups affects the quality of BMD estimates in toxicity testing, with special consideration of the total burden of animal distress. We generated continuous dose–effect data by Monte Carlo simulation using two dose–effect curves based on endpoints with different shape parameters. Eighty‐five designs, each with four dose groups of unequal size, were examined in scenarios ranging from low‐ to high‐dose placements and with a total number of animals set to 40, 80, or 200. For each simulation, a BMD value was estimated and compared with the “true” BMD. In general, redistribution of animals from higher to lower dose groups resulted in an improved precision of the calculated BMD value as long as dose placements were high enough to detect a significant trend in the dose–effect data with sufficient power. The improved BMD precision and the associated reduction of the number of animals exposed to the highest dose, where chemically induced distress is most likely to occur, are favorable for the reduction and refinement principles. The result thereby strengthen BMD‐aligned design of experiments as a means for more accurate hazard characterization along with animal welfare improvements.
A multicenter study on the use of pulsed low-intensity direct current for healing chronic stage II and stage III decubitus ulcers.

BACKGROUND AND DESIGN Pulsed low-intensity direct current (300 to 600 microA) has been used in a double-blind placebo multicenter study in the treatment of stage II and stage III chronic decubitus ulcers. RESULTS Seventy-four ulcers were treated in four centers. Forty-three patients were selected for the experimental group, and 31 control subjects used the sham instrument (placebo group). In the treated group, 25 ulcers (58%) healed in 8 weeks, whereas in the placebo group, only one ulcer (3%) healed and most ulcers increased in size. Statistical analysis, based on surface area and ulcer depth before and after treatment, showed that low-intensity direct current had a significant influence on the healing rates for these ulcers (P < .0001). Experiments with guinea pigs (n = 10) showed that pulsed low-intensity direct current caused a rapid calcium flux in the epidermis. CONCLUSIONS Pulsed low-intensity direct current represents a useful approach for the treatment of stage II and stage III chronic decubitus ulcers by increasing the healing rate. The growth of fibroblasts and keratinocytes may be enhanced by pulsed low-intensity direct current due to changes in calcium homeostasis.
Frequencies contributing to functional connectivity in the cerebral cortex in "resting-state" data.

BACKGROUND AND PURPOSE In subjects performing no specific cognitive task ("resting state"), time courses of voxels within functionally connected regions of the brain have high cross-correlation coefficients ("functional connectivity"). The purpose of this study was to measure the contributions of low frequencies and physiological noise to cross-correlation maps. METHODS In four healthy volunteers, task-activation functional MR imaging and resting-state data were acquired. We obtained four contiguous slice locations in the "resting state" with a high sampling rate. Regions of interest consisting of four contiguous voxels were selected. The correlation coefficient for the averaged time course and every other voxel in the four slices was calculated and separated into its component frequency contributions. We calculated the relative amounts of the spectrum that were in the low-frequency (0 to 0.1 Hz), the respiratory-frequency (0.1 to 0.5 Hz), and cardiac-frequency range (0.6 to 1.2 Hz). RESULTS For each volunteer, resting-state maps that resembled task-activation maps were obtained. For the auditory and visual cortices, the correlation coefficient depended almost exclusively on low frequencies (<0.1 Hz). For all cortical regions studied, low-frequency fluctuations contributed more than 90% of the correlation coefficient. Physiological (respiratory and cardiac) noise sources contributed less than 10% to any functional connectivity MR imaging map. In blood vessels and cerebrospinal fluid, physiological noise contributed more to the correlation coefficient. CONCLUSION Functional connectivity in the auditory, visual, and sensorimotor cortices is characterized predominantly by frequencies slower than those in the cardiac and respiratory cycles. In functionally connected regions, these low frequencies are characterized by a high degree of temporal coherence.
Diabetes mellitus and periodontal diseases.

BACKGROUND The purpose of this review is to provide the reader with practical knowledge concerning the relationship between diabetes mellitus and periodontal diseases. Over 200 articles have been published in the English literature over the past 50 years examining the relationship between these two chronic diseases. Data interpretation is often confounded by varying definitions of diabetes and periodontitis and different clinical criteria applied to prevalence, extent, and severity of periodontal diseases, levels of glycemic control, and complications associated with diabetes. METHODS This article provides a broad overview of the predominant findings from research published in English over the past 20 years, with reference to certain "classic" articles published prior to that time. RESULTS This article describes current diagnostic and classification criteria for diabetes and answers the following questions: 1) Does diabetes affect the risk of periodontitis, and does the level of metabolic control of diabetes have an impact on this relationship? 2) Do periodontal diseases affect the pathophysiology of diabetes mellitus or the metabolic control of diabetes? 3) What are the mechanisms by which these two diseases interrelate? and 4) How do people with diabetes and periodontal disease respond to periodontal treatment? CONCLUSIONS Diabetes increases the risk of periodontal diseases, and biologically plausible mechanisms have been demonstrated in abundance. Less clear is the impact of periodontal diseases on glycemic control of diabetes and the mechanisms through which this occurs. Inflammatory periodontal diseases may increase insulin resistance in a way similar to obesity, thereby aggravating glycemic control. Further research is needed to clarify this aspect of the relationship between periodontal diseases and diabetes.
The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet

Abstract The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses, we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores. As a valuable resource for the improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation.
Reliability and Validity of the Greek Version of the Derogatis Psychiatric Rating Scale (DPRS)

Background: The aim of this paper is to report on the Greek version of the Derogatis Psychiatric Rating Scale (DPRS) and its validity and reliability when administered to a Greek sample. The DPRS is a clinician-rated measure of psychiatric symptoms with nine basic and eight complementary symptom dimensions and a Global Pathology Index. Method: The DPRS was translated into Greek and administered to 161 psychiatric patients and healthy volunteers. Its validity was assessed against the Semi-structured Clinical Interview (SCID) and the Symptoms Checklist-90-Revised (SCL-90-R). The inter-rater reliability and test-retest reliability were also evaluated for each symptom dimension. Results: All the symptom dimensions of the DPRS, except euphoria, have concurrent validity with the SCID on the relevant symptom dimensions diagnoses set by the interview. At the cut-off point 2/3 the DPRS has a sensitivity of 98% and a specificity of 74% in indicating active psychiatric patients. The symptom dimensions of the DPRS also have strong correlations with the relevant dimensions of SCL-90-R. The range for inter-rater reliability was from 0.48 to 0.88, the range for test-retest reliability was from 0.25 to 0.85, and the internal consistency was 0.90. Conclusion: The Greek version of the DPRS has acceptable psychometric properties, rendering it a useful screening instrument of global psychopathology as well as a multidimensional measure of some basic psychiatric symptoms.
Intraindividual Reproducibility of Blood Pressure Surge upon Rising after Nighttime Sleep and Siesta

The surge in blood pressure (BP) upon rising after waking in the morning has been associated with increased risk of target organ damage and cardiovascular events. The reproducibility of this phenomenon within the same 24-h period was tested in subjects with a siesta during ambulatory BP monitoring by assessing the morning surge (MS) vs. the evening surge (ES) after siesta. Ambulatory BP recordings with reported siesta from hypertensive subjects were analyzed. MS and ES were assessed using four different definitions. The intraindividual reproducibility was assessed using the standard deviation of differences between MS and ES, the concordance correlation coefficient, the coefficient of variation and the agreement between MS and ES in detecting “surgers” among hypertensive subjects (top quartile of the BP surge distribution). A total of 562 ambulatory recordings were analyzed (476 subjects, mean age 54.9±13.2 [SD] years, treated 47%). Average MS (16.3/14.4 mmHg, systolic/diastolic) was higher than ES (13.3/12.1 mmHg, p<0.001) due to higher post-rising BP in the morning (p<0.01). The intraindividual reproducibility was rather poor, with no clear differences among different definitions. However, there was about 70% agreement between MS and ES in the detection of “surgers” (systolic and diastolic, k statistic 0.18). These data suggest that, although the intraindividual reproducibility of the BP surge within the same 24-h period is rather poor, about 70% of the “morning surgers” were also “evening surgers. ” Thus, the BP surge might be an inherent pathophysiological characteristic of the BP behavior of an individual and deserves further investigation.
Targeted Inhibition of Heat Shock Protein 90 Suppresses Tumor Necrosis Factor–&agr; and Ameliorates Murine Intestinal Inflammation

Abstract:Inflammatory bowel diseases are chronic intestinal inflammatory diseases thought to reflect a dysregulated immune response. Although antibody-based inhibition of tumor necrosis factor-&agr; (TNF-&agr;) has provided relief to many inflammatory bowel diseases patients, these therapies are either ineffective in a patient subset or lose their efficacy over time, leaving an unmet need for alternatives. Given the critical role of the heat shock response in regulating inflammation, this study proposed to define the impact of selective inhibition of heat shock protein 90 (HSP90) on intestinal inflammation. Using multiple preclinical mouse models of inflammatory bowel diseases, we demonstrate a potent anti-inflammatory effect of selective inhibition of the HSP90 C-terminal ATPase using the compound novobiocin. Novobiocin-attenuated dextran sulfate sodium-induced colitis and CD45RBhigh adoptive-transfer colitis through the suppression of inflammatory cytokine secretion, including TNF-&agr;. In vitro assays demonstrate that CD4+ T cells treated with novobiocin produced significantly less TNF-&agr; measured by intracellular cytokine staining and by enzyme-linked immunosorbent assay. This corresponded to significantly decreased nuclear p65 translocation by Western blot and a decrease in nuclear factor-&kgr;B luciferase activity in Jurkat T cells. Finally, to verify the anti-TNF action of novobiocin, 20-week-old TNF&Dgr;ARE mice were treated for 2 weeks with subcutaneous administration of novobiocin. This model has high levels of circulating TNF-&agr; and exhibits spontaneous transmural segmental ileitis. Novobiocin treatment significantly reduced inflammatory cell infiltrate in the ileal lamina propria. HSP90 inhibition with novobiocin offers a novel method of inflammatory cytokine suppression without potential for the development of tolerance that limits current antibody-based methods.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools

MOTIVATION Storing, annotating and analyzing variants from next-generation sequencing projects can be difficult due to the availability of a wide array of data formats, tools and annotation sources, as well as the sheer size of the data files. Useful tools, including the GATK, ANNOVAR and BEDTools can be integrated into custom pipelines for annotating and analyzing sequence variants. However, building flexible pipelines that support the tracking of variants alongside their samples, while enabling updated annotation and reanalyses, is not a simple task. RESULTS We have developed variant tools, a flexible annotation and analysis toolset that greatly simplifies the storage, annotation and filtering of variants and the analysis of the underlying samples. variant tools can be used to manage and analyze genetic variants obtained from sequence alignments, and the command-line driven toolset could be used as a foundation for building more sophisticated analytical methods. AVAILABILITY AND IMPLEMENTATION variant tools consists of two command-line driven programs vtools and vtools_report. It is freely available at http://varianttools.sourceforge. net, distributed under a GPL license. CONTACT bpeng@mdanderson.org.