Miracle-dz/UniFAR-FTUs huggingface dataset:
Leeway and constraints in the forced evolution of a regulatory RNA helix.

The start of the coat protein gene of RNA phage MS2 adopts a well‐defined hairpin structure of 12 bp (including one mismatch) in which the start codon occupies the loop position. An earlier expression study using partial MS2 cDNA clones had indicated that the stability of this hairpin is important for gene expression. For every ‐1.4 kcal/mol increase in stability a 10‐fold reduction in coat protein was obtained. Destabilizations beyond the wild‐type value did not affect expression. These results suggested that the hairpin was tuned in the sense that it has the highest stability still compatible with maximal ribosome loading. Employing an infectious MS2 cDNA clone, we have now tested the prediction that the delta G 0 of the coat protein initiator helix is set at a precise value. We have introduced stabilizing and destabilizing mutations into this hairpin in the intact phage and monitored their evolution to viable species. By compensatory mutations, both types of mutants quickly revert along various pathways to wild‐type stability, but not to wild‐type sequence. As a rule the second‐site mutations do not change the encoded amino acids or the Shine‐Dalgarno sequence. The return of too strong hairpins to wild‐type stability can be understood from the need to produce adequate supplies of coat protein. The return of unstable hairpins to wild‐type stability is not self‐evident and is presently not understood. The revertants provide an evolutionary landscape of slightly suboptimal phages, that were stable at least for the duration of the experiment (approximately 20 infection cycles). (ABSTRACT TRUNCATED AT 250 WORDS)
Calibration of the isomer shift for the 77.34 keV transition in 197Au using the full-potential linearized augmented plane-wave method.

The isomer shift calibration constant has been calculated for the 77.34 keV Mossbauer transition connecting the ground state of the (197)Au nucleus with the first excited state of this nucleus. The full-potential linearized augmented plane-wave method was used in the fully relativistic approach, albeit without taking into account the spin-orbit coupling. The final assignment of the calibration constant was based on calculations performed for AuCN, AuCl(3), AuBr(3), KAuCl(4), KAuBr(4), and metallic gold. It is found that the calibration constant takes on the following value alpha = +0.0665(4) mm s(-1) a.u. (3). The error quoted is due to the linear regression fit, and the real error might be as large as 10%. The spectroscopic electric quadrupole moment for the ground state of the (197)Au nucleus was calculated as the by-product. It was found that this moment equals Q(g) = +0.566(1)b in fair agreement with the accepted value based on the muonic hyperfine spectroscopy results. The error quoted is again due to the linear regression fit and the real error might be as large as 10%. The final assignment of the value for the quadrupole moment is based on the calculations for the following compounds: AuCl, AuBr, AuI, AuCN, and AuMn(2). Results for the magnetically ordered Au(2)Mn were applied to determine the sign of the quadrupole moment.
Interleukin-6 delays neutrophil apoptosis.

BACKGROUND Neutrophil (PMN) apoptosis promotes the phagocytosis of PMNs without inciting an inflammatory response or local cytotoxic effect. This is important in the normal resolution of inflammatory processes and the control of tissue injury. Conversely, a delay in PMN apoptosis may facilitate PMN-mediated organ dysfunction by extending PMN functional integrity at an inflammatory site. Elevated circulating and tissue levels of interleukin-6 (IL-6) have been associated with postinjury organ dysfunction, and IL-6 appears to augment PMN cytotoxic functions. Therefore, we hypothesized that IL-6 delays PMN apoptosis, thereby enhancing PMN-mediated cytotoxicity. METHODS Neutrophils isolated from healthy human donors were incubated for 24 hours in enriched RPMI 1640 cell culture medium at 37 degrees C in 5% carbon dioxide. Subgroups were incubated with IL-6, heat-denatured IL-6, or buffer alone. Apoptosis was assessed morphologically using acridine orange-ethidium bromide stain, and biochemically by DNA gel electrophoresis. Functional capacity of PMNs was assessed by superoxide generation after activation with phorbol myristate acetate or platelet-activating factor plus formyl-methionyl-leucyl-phenylalanine. RESULTS Treatment with IL-6 resulted in a greater population of surviving (nonapopototic) PMNs after 24 hours. In addition, the IL-6-treated population produced more superoxide after 24 hours than did the untreated or heat-denature IL-6-treated groups, after either activating stimulus. CONCLUSIONS Interleukin-6 delays PMN apoptosis, resulting in a larger population of surviving PMNs with a greater collective capacity for superoxide production. This could potentially facilitate PMN-mediated tissue injury and may be a mechanism whereby IL-6 contributes to organ dysfunction.
Expression Profile of MicroRNAs in Gram-Negative Bacterial Sepsis

ABSTRACT Bacterial lipopolysaccharide (LPS) is an effective trigger of the inflammatory response during infection with gram-negative bacilli (GNB), which implicates the pathogenesis of sepsis and septic shock. MicroRNAs (miRNAs) are shown to have a significant role in the fine-tuning of toll-like receptor (TLR)–mediated inflammatory response. We profiled miRNA expression levels in peripheral leukocytes of GNB urosepsis patients and compared them with those of healthy controls. We further explored the regulatory mechanism of endotoxin-responsive miRNAs in TLR and cytokine signaling by using human monocytic cell line (THP-1 cells) treated with LPS antigen stimulation. The expression of two miRNAs, that is, let-7a (P < 0.001) and miR-150 (P < 0.001), were confirmed to be significantly downregulated in GNB urosepsis patients compared with healthy controls. The expression of let-7a is first to be identified as a biomarker of GNB sepsis. By using an in vitro model with the human monocytic cell line, we demonstrated that LPS stimulation downregulated the THP-1 cell expression of let-7a. The downregulation of let-7a is correlated with the induced expression of cytokine-inducible Src homology 2–containing protein without change in cytokine-inducible Src homology 2–containing protein mRNA levels in THP-1 cells via TLR signaling pathway activation. Moreover, gain of function by overexpression of let-7a revealed that let-7a significantly decreased tumor necrosis factor-&agr; and interleukin-1&bgr; production in response to LPS. Reduced let-7a and miR-150 levels in peripheral leukocytes correlate with GNB urosepsis patients. Furthermore, let-7a is relevant to the regulation of TLR-mediated innate immune response.
CCR6-deficient mice have impaired leukocyte homeostasis and altered contact hypersensitivity and delayed-type hypersensitivity responses.

CCR6 expression in dendritic, T, and B cells suggests that this beta-chemokine receptor may regulate the migration and recruitment of antigen-presenting and immunocompetent cells during inflammatory and immunological responses. Here we demonstrate that CCR6-/- mice have underdeveloped Peyer's patches, in which the myeloid CD11b+ CD11c+ dendritic-cell subset is not present in the subepithelial dome. CCR6-/- mice also have increased numbers in T-cell subpopulations within the intestinal mucosa. In 2,4-dinitrofluorobenzene-induced contact hypersensitivity (CHS) studies, CCR6-/- mice developed more severe and more persistent inflammation than wild-type (WT) animals. Conversely, in a delayed-type hypersensitivity (DTH) model induced with allogeneic splenocytes, CCR6-/- mice developed no inflammatory response. The altered responses seen in the CHS and DTH assays suggest the existence of a defect in the activation and/or migration of the CD4(+) T-cell subsets that downregulate or elicit the inflammation response, respectively. These findings underscore the role of CCR6 in cutaneous and intestinal immunity and the utility of CCR6-/- mice as a model to study pathologies in these tissues. This article was published online in advance of the print edition. The date of publication is available from the JCI website, http://www.jci. org.
Osteoblasts lacking the vitamin D receptor display enhanced osteogenic potential in vitro

1,25‐Dihydroxyvitamin D plays an important role in the regulation of osteoblast gene expression, regulating the expression of bone matrix proteins as well as that of Runx2, a key regulator of osteoblast differentiation. Studies in mice lacking the vitamin D receptor (VDR) have revealed that the actions of the VDR on the skeleton are not required in the setting of normal mineral ion homeostasis. Since paracrine and endocrine factors can compensate for gene defects in vivo, studies were performed to determine whether ablation of the VDR alters the program of osteoblast differentiation in vitro. Studies in primary calvarial cultures revealed that ablation of the VDR enhanced osteoblast differentiation. The cells from the VDR null mice exhibited an earlier onset and increased magnitude of alkaline phosphatase activity, as well as an earlier and sustained increase in mineralized matrix formation, demonstrating that this enhancement persists throughout the program of osteoblast differentiation. The expression of bone sialoprotein, which enhances mineralization, was also increased in the VDR null cultures. To determine whether the increase in osteoblast differentiation was associated with an increase in the number of osteogenic progenitors, the number of osteoblastic colony forming units (CFU‐OB) was evaluated. There was a twofold increase in the number of CFU‐OB in the cultures isolated from the VDR null mice. Furthermore, the VDR null CFU‐OB demonstrated an earlier onset and higher magnitude of expression of alkaline phosphatase activity when compared to the CFU‐OB from their wild‐type control littermates. These studies demonstrate that the VDR attenuates osteoblast differentiation in vitro and suggest that other endocrine and paracrine factors modulate the effect of the VDR on osteoblast differentiation in vivo. © 2004 Wiley‐Liss, Inc.
Deconstructing the externalizing spectrum: Growth patterns of overt aggression, covert aggression, oppositional behavior, impulsivity/inattention, and emotion dysregulation between school entry and early adolescence

Abstract The purpose of this study was to determine whether five subcomponents of children's externalizing behavior showed distinctive patterns of long-term growth and predictive correlates. We examined growth in teachers' ratings of overt aggression, covert aggression, oppositional defiance, impulsivity/inattention, and emotion dysregulation across three developmental periods spanning kindergarten through Grade 8 (ages 5–13 years). We also determined whether three salient background characteristics, family socioeconomic status, child ethnicity, and child gender, differentially predicted growth in discrete categories of child externalizing symptoms across development. Participants were 543 kindergarten-age children (52% male, 81% European American, 17% African American) whose problem behaviors were rated by teachers each successive year of development through Grade 8. Latent growth curve analyses were performed for each component scale, contrasting with overall externalizing, in a piecewise fashion encompassing three developmental periods: kindergarten–Grade 2, Grades 3–5, and Grades 6–8. We found that most subconstructs of externalizing behavior increased significantly across the early school age period relative to middle childhood and early adolescence. However, overt aggression did not show early positive growth, and emotion dysregulation significantly increased across middle childhood. Advantages of using subscales were most clear in relation to illustrating different growth functions between the discrete developmental periods. Moreover, growth in some discrete subcomponents was differentially associated with variations in family socioeconomic status and ethnicity. Our findings strongly affirmed the necessity of adopting a developmental approach to the analysis of growth in children's externalizing behavior and provided unique data concerning similarities and differences in growth between subconstructs of child and adolescent externalizing behavior.
Comparison of four commercial quantitative HIV-1 assays for viral load monitoring in clinical daily routine

Abstract Background: Quantification of viral load (VL) is standard for monitoring HIV-1 therapy and is crucial before deciding whether to switch or to continue a current antiretroviral regimen. Methods: We compared the performance of the four most widely used commercial viral-load assays, COBAS Amplicor Monitor v1.5, Versant HIV-1 RNA 3.0, Abbott RealTime HIV-1 and Cobas AmpliPrep/Cobas TaqMan HIV-1 (CAP/CTM), in terms of intra- and inter-assay variability, as well as hands-on-time, specificity and ability to quantify group M subtypes. Results: Although linearity and correlation were confirmed for the assays and comparable sensitivity and specificity were verified for genetically diverse HIV-1 subtypes, demonstrating suitability for monitoring of HIV group M isolates, the viral loads obtained showed variations, with a mean difference of 0.1–0.4 log, depending on the system used. Conclusions: Although sensitivity and precision were confirmed for all the systems, differences between them should be taken into account when viral load monitoring of the same person is performed using different systems. Clin Chem Lab Med 2007;45:93–9.
A Coordinated Multipoint Scheduler for Packet Loss Reduction

Coordinated multipoint (CoMP) is a base station (BS) cooperation technique to boost the signal-to-noise ratio (SNR) of cell-edge users in future generation wireless networks. We propose a fixed weight CoMP downlink scheduler to reduce the packet loss probability (PLP) due to buffer overflow in BSs with finite queues. The CoMP scheduler selects a single BS to serve the associated cell-edge user with the largest weighted SNR. To meet PLP targets, we develop a simple strategy to design the packet transmission time and the scheduling weights of each BS. The network design capitalizes on our new closed-form expression for the PLP that relates three key network parameters: packet arrival rate, packet transmission time, and probability that each BS is scheduled. We compare the proposed fixed weight scheduler with an adaptive weight scheduler that requires instantaneous packet delay information. We show via analysis and simulation that the fixed weight scheduler can achieve a comparable PLP to the adaptive weight scheduler, while reducing communication overheads for the BSs.
Fundamental dynamics based adaptive energy control for cooperative swinging of complex pendulum-like objects

We present an adaptive energy-based controller for cooperative swinging of complex pendulum-like objects by two agents. The complex pendulum-like object has two oscillation degrees of freedom of which one is to be controlled to a goal energy and the other one has to be damped. The closed-loop fundamental dynamics of a simple pendulum are extended to the two-agent pendulum. Based on the fundamental dynamics, a simple adaptive mechanism identifies the natural frequency of the system. An amplitude factor is adapted such that an agent behaves as a leader or a follower. A leader knows the goal energy and controls the system according to desired reference dynamics. A follower either imitates the leader's energy flow or estimates the leader's goal energy. Properties as stability of both leader-follower structures are analyzed analytically based on the fundamental dynamics assumption. The applicability of the control approaches to a complex pendulum-like object is shown in simulation.
Operational risk quantified with spectral risk measures: a refined closed-form approximation

The quantification of operational risk has become an important issue as a result of the new capital charges required by the Basel Capital Accord (Basel II) to cover the potential losses of this type of risk. In this paper, we investigate second-order approximation of operational risk quantified with spectral risk measures (OpSRMs) within the theory of second-order regular variation (2RV) and second-order subexponentiality. The result shows that asymptotically two cases (the fast convergence case and the slow convergence) arise depending on the range of the second-order parameter. We also show that the second-order approximation under 2RV is asymptotically equivalent to the slow convergence case. A number of Monte Carlo simulations for a range of empirically relevant frequency and severity distributions are employed to illustrate the performance of our second-order results. The simulation results indicate that our second-order approximations tend to reduce the estimation errors to a great degree, especially for the fast convergence case, and are able to capture the sub-extremal behavior of OpSRMs better than the first-order approximation. Our asymptotic results have implications for the regulation of financial institutions, and may provide further insights into the measurement and management of operational risk.
Endothelial Nitric Oxide Synthase Lies Downstream From Angiotensin II–Induced Angiogenesis in Ischemic Hindlimb

We assessed the role of angiotensin (Ang) II in ischemia-induced angiogenesis and analyzed the molecular pathways involved in such an effect. Ischemia was produced by unilateral artery femoral occlusion in control, in valsartan-treated (Ang II receptor type I antagonist, 20 mg/kg per day), in Ang II–treated (5 ng/kg per min), and in Ang II and valsartan–treated rats. After 28 days, angiogenesis was assessed by microangiography and capillary density measurement in hindlimbs. The ischemic/nonischemic leg ratio for angiographic score and capillary number increased by 2.6- and 2-fold, respectively, in Ang II–treated rats compared with controls (P <0.01). This was associated with an increase in vascular endothelial growth factor (VEGF; 1.6-fold) and endothelial NO synthase (eNOS; 1.8-fold) protein content within the ischemic leg, assessed by Western blot. Angiotensin type 1 receptor blockade and administration of VEGF neutralizing antibody (2.5 &mgr;g IP, twice a week) in Ang II–treated rats completely prevented such Ang II angiogenic effects. The key role of eNOS was then emphasized by using mice deficient in gene encoding for eNOS. In wild-type mice, Ang II (0.3 mg/kg per min) treatment increased by 1.7- and 1.6-fold the ischemic/nonischemic leg for angiographic score and blood perfusion (assessed by laser Doppler perfusion imaging) ratios, respectively (P <0.01). Conversely, no significant changes were observed in Ang II–treated mice deficient in gene encoding for eNOS. Subhypertensive dose of Ang II enhanced angiogenesis associated with tissue ischemia through angiotensin type 1 receptor activation that involved the VEGF/eNOS-dependent pathway.
Effect of Lens Base Curve on Subjective Comfort and Assessment of Fit with Silicone Hydrogel Continuous Wear Contact Lenses

Purpose. To study the effect of base curve on subjective comfort of silicone hydrogel extended wear lenses. Methods. Ninety-five subjects were first trial fitted with 8.6-mm base curve lotrafilcon A (Focus Night & Day) lenses and then with 8.4-mm lenses only if poor subjective comfort or poor fit was present. Comfort and fit were assessed after 15 min. Subjects with discomfort or signs of poor fit were then trial fitted with 8.4-mm lenses. Results. Of 190 eyes, 74.2% were fitted with 8.6-mm lenses, and 23.7% required 8.4-mm lenses. Two (2.1%) subjects could not be fitted with either base curve. Mean steep keratometry (K) reading for eyes dispensed with 8.6-mm lenses was 43.88 D and 45.56 D for eyes dispensed in the 8.4-mm lenses (p < 0.001). Conclusions. A clinically useful criterion showing the need for 8.4-mm lenses was steep K of ≥45.50 D; 77% of these eyes required the steeper lens for good comfort and fit. Subjective discomfort with 8.6-mm lenses was also a useful signal for the need of a steeper lens; mean comfort scores for those subjects rose from 6.33 with 8.6-mm lenses to 9.44 with the 8.4-mm lenses for eyes requiring the steeper lens (p < 0.001).
Self-management and biomedical outcomes of a cooking, and exercise program for patients with chronic kidney disease.

BACKGROUND Limited research has been done on integrating cooking and exercise classes into the routine care of chronic kidney disease (CKD) patients. The main purpose of the research was to determine whether the addition of these services would slow the progression of certain CKD parameters. METHODS The study evaluated 5 endpoints, at baseline, 6 months, and 12 months: urinary protein, blood pressure, urinary sodium, glomerular filtration rate, and total cholesterol between 2 groups (control group receiving CKD standard care and experimental group receiving standard care plus cooking and exercise classes). Eighty percent of the experimental group was hypothesized to improve in 4 out of the 5 endpoints versus ≤50% in the control group with a P-value of 0.05. An overall difference of 30% was anticipated between the 2 groups. The research also compared self-efficacy and health status outcomes using a self-management questionnaire. RESULTS Forty randomly assigned patients participated in the study (17 controls and 23 experimental). In the control group, 2 of 17 people improved in at least 4 of the 5 endpoints. In the experimental group, 14 of 23 people improved in at least 4 of the 5 endpoints. CONCLUSIONS Sixty-one percent of experimental subjects showed improvements in 4 of 5 endpoints, showing a significant difference overall when compared with the control group (12% improved in 4 out of 5 endpoints). In looking at the trend in qualitative measures from the comparison of the self-management questionnaire, the overall trend showed more improved answers with the experimental group versus the control group.
Effect of inhibition of the ROCK isoform on RT2 malignant glioma cells.

BACKGROUND Malignant glioma is one of the most intractable diseases in the human body. Rho-kinase (ROCK) is overexpressed and has been proposed as the main cause for the refractoriness of the disease. Since efficacious treatment is required, this study investigated the effect of inhibition of ROCK isoforms. MATERIALS AND METHODS The short hairpin RNA transcription vector was transfected into the RT2 rat glioma cell line and the characteristics of the cells were investigated. The effect of nimustine hydrochloride (ACNU) anti-neoplastic agent on cells was also measured. RESULTS Inhibition of ROCK isoforms did not alter cell growth. Cell cycle analysis revealed that ROCK1 down-regulation reduced the G(0) phase population and ROCK2 down-regulation reduced the G(2)/M phase population. When ROCK1-down-regulated cells were exposed to ACNU, they demonstrated susceptibility to the agent. CONCLUSION The roles of ROCK1 and ROCK2 may be different in glioma cells. Furthermore, the combination of ROCK1 down-regulation and an anti-neoplastic agent may be useful for the therapy of malignant glioma.