Constructing confidence intervals for selected parameters

In large-scale problems, it is common practice to select important parameters by a procedure such as the Benjamini and Hochberg procedure and construct confidence intervals (CIs) for further investigation while the false coverage-statement rate (FCR) for the CIs is controlled at a desired level. Although the well-known BY CIs control the FCR, they are uniformly inflated. In this paper, we propose two methods to construct shorter selective CIs. The first method produces shorter CIs by allowing a reduced number of selective CIs. The second method produces shorter CIs by allowing a prefixed proportion of CIs containing the values of uninteresting parameters. We theoretically prove that the proposed CIs are uniformly shorter than BY CIs and control the FCR asymptotically for independent data. Numerical results confirm our theoretical results and show that the proposed CIs still work for correlated data. We illustrate the advantage of the proposed procedures by analyzing the microarray data from a HIV study.

DNA methylation markers in the diagnosis and prognosis of common leukemias

The ability to identify a specific type of leukemia using minimally invasive biopsies holds great promise to improve the diagnosis, treatment selection, and prognosis prediction of patients. Using genome-wide methylation profiling and machine learning methods, we investigated the utility of CpG methylation status to differentiate blood from patients with acute lymphocytic leukemia (ALL) or acute myelogenous leukemia (AML) from normal blood. We established a CpG methylation panel that can distinguish ALL and AML blood from normal blood as well as ALL blood from AML blood with high sensitivity and specificity. We then developed a methylation-based survival classifier with 23 CpGs for ALL and 20 CpGs for AML that could successfully divide patients into high-risk and low-risk groups, with significant differences in clinical outcome in each leukemia type. Together, these findings demonstrate that methylation profiles can be highly sensitive and specific in the accurate diagnosis of ALL and AML, with implications for the prediction of prognosis and treatment selection.

Spatiotemporal dynamics of a reaction-diffusion model of pollen tube tip growth

A reaction-diffusion model is proposed to describe the mechanisms underlying the spatial distributions of ROP1 and calcium on the pollen tube tip. The model assumes that the plasma membrane ROP1 activates itself through positive feedback loop, while the cytosolic calcium ions inhibit ROP1 via a negative feedback loop. Furthermore it is proposed that lateral movement of molecules on the plasma membrane are depicted by diffusion. It is shown that bistable or oscillatory dynamics could exist even in the non-spatial model, and stationary and oscillatory spatiotemporal patterns are found in the full spatial model which resemble the experimental data of pollen tube tip growth.

Clinical analysis of Chinese anti-low-density-lipoprotein-receptor-associated protein 4 antibodies in patients with myasthenia gravis

BACKGROUND AND PURPOSE

Low-density-lipoprotein-receptor-associated protein 4 (LRP4) autoantibodies have recently been detected in myasthenia gravis (MG), but little is known about the clinical characteristics associated with this serological type. In this study, the clinical features of Chinese patients with anti-LRP4 antibody-positive MG were characterized.

METHODS

A total of 2172 MG serum samples were collected from patients in various parts of China. An enzyme-linked immunosorbent assay was used to detect acetylcholine receptor (AChR) antibody and titin antibody, and cell-based assays were used to detect muscle-specific kinase antibody and LRP4 antibody. Clinical data for patients with MG were collected from different provinces in China.

RESULTS

In total, 16 (0.8%) patients with LRP4-MG were found amongst 2172 total patients, including three patients with AChR/LRP4-MG. Additionally, 13 (2.9%) patients with LRP4-MG were found amongst 455 patients with double seronegative MG. The ratio of males to females for these 13 patients was 1:1.6, and 53.8% patients were children. A total of 91.7% of cases exhibited initial ocular involvement, and 58.3% of cases exhibited simple eye muscle involvement. Responses to acetylcholinesterase inhibitors and prednisone were observed.

CONCLUSION

The expanded sample confirmed that the positive rate of LRP4 antibodies in China is lower than that in western countries. Our results highlighted the differences between LRP4-MG and other antibody groups. Children and female patients with LRP4-MG have a higher prevalence, often involving the ocular muscles and limb muscles. The clinical symptoms are mild, and satisfactory responses to treatment are often achieved.

Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling

MOTIVATION

Subspecies identification is one of the most critical issues in microbiome studies, as it is directly related to their functions in response to the environmental stress and their feedbacks. However, identification of subspecies remains a challenge largely due to the small variation between different strains within the same species. Accurate identification of subspecies primarily relies on variant identification and categorization through microbiome data. However, current SNP calling and subspecies identification for microbiome data remain underdeveloped.

RESULTS

In this work, we have proposed Strain-GeMS for subspecies identification from microbiome data, based on solid statistical model for SNP calling, as well as optimized procedure for subspecies identification. Results on simulated, ab initio and in vivo datasets have shown that Strain-GeMS could always generate more accurate results compared with other subspecies identification methods.

AVAILABILITY AND IMPLEMENTATION

Strain-GeMS is available at: https://github.com/HUST-NingKang-Lab/straingems.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Impact of Modifiable Risk Factors on Bone Loss During Periodontal Maintenance

Objectives:

The aim of this study was to analyze modifiable patient risk factors from dental chart histories and radiographs for progressive mild-moderate periodontitis during periodontal maintenance (PM).

Methods and Materials:

Bitewing radiographs of 442 elderly periodontal maintenance patients were taken before and after two years of periodontal maintenance. Each progressive periodontitis (PP) patient (with at least one site of posterior interproximal bone loss of ≥2 mm, n=71) was matched to a periodontitis stable (PS) patient (no sites with bone loss, n=71) of the same gender and age (±five years) to control for these variables and was compared for measurements of general patient (medical history, smoking, hygiene and compliance habits) and tooth-related (bone loss, overhangs, interproximal dimensions) factors at baseline. Fisher exact and t-tests were used to compare groups.

Results:

While the elderly PM patients with mild-moderate periodontitis were generally stable, 71 of 442 were PP patients. No significant differences from PS patients were observed at baseline with regard to the systemic factors measured. However, the PP group had less cementoenamel junction to bone length (bone loss p<0.0001) and more interproximal width (2.3±1.0 mm) than did the PS group (1.7±0.6 mm, p=0.0016). This was reflected in more open sites without adjacent tooth contact in PP (42% vs 15%, p=0.0006).

Conclusions:

In the short term, systemic and behavior factors are of limited value in identifying mild-moderate periodontitis patients on PM at increased risk of bone loss. However, interproximal width and lack of adjacent tooth contacts are related to the likelihood of losing interproximal bone during periodontal maintenance, suggesting the need for restorative therapy.

Vegetarians have a lower fasting insulin level and higher insulin sensitivity than matched omnivores: A cross-sectional study

BACKGROUND AND AIMS

Potential associations of vegetarian diet patterns with fasting insulin (FI) and insulin sensitivity remain unclear. We aimed to investigate whether vegetarian diets were associated with FI and insulin sensitivity in a cross-sectional study in Chinese vegetarians and matched omnivores and then to test whether it is independent of body mass index (BMI).

METHODS AND RESULTS

This study included 279 vegetarians (73 vegans, 206 lacto-ovo-vegetarians) and 279 age- and sex-matched omnivores. Fasting blood glucose (FG) and FI concentrations were measured, and β-cell function (HOMA-β) and insulin resistance index (HOMA-IR) were used to evaluate insulin sensitivity. All blood glucose and insulin sensitivity indices were naturally log-transformed, and multiple-linear regression was used to determine the association between vegetarian diet patterns and insulin sensitivity after adjusting for confounders including BMI, visceral fat area, physical activity, sedentary time, income, alcohol consumption, and daily dietary intakes of macronutrients. Compared to omnivores, both vegan diet [β = -0.25, 95% CI: (-0.38, -0.14)] and lacto-ovo-vegetarian diet [β = -0.10, 95% CI: (-0.18, -0.01)] were negatively associated with HOMA-IR after adjusting for BMI. Vegan diet remained negatively associated with FI [β = -0.16, 95% CI: (-0.30, -0.01)] and HOMA-IR [β = -0.17, 95% CI: (-0.32, -0.03)] after adjusting for all confounders.

CONCLUSION

Vegetarian diet, especially vegan diet, is negatively associated with FI and IR, independent of BMI.

The molecular chaperone sigma 1 receptor mediates rescue of retinal cone photoreceptor cells via modulation of NRF2

Sigma 1 receptor (Sig1R), a putative molecular chaperone, has emerged as a novel therapeutic target for retinal degenerative disease. Earlier studies showed that activation of Sig1R via the high-affinity ligand (+)-pentazocine ((+)-PTZ) induced profound rescue of cone photoreceptor cells in the rd10 mouse model of retinitis pigmentosa; however the mechanism of rescue is unknown. Improved cone function in (+)-PTZ-treated mice was accompanied by reduced oxidative stress and normalization of levels of NRF2, a transcription factor that activates antioxidant response elements (AREs) of hundreds of cytoprotective genes. Here, we tested the hypothesis that modulation of NRF2 is central to Sig1R-mediated cone rescue. Activation of Sig1R in 661W cone cells using (+)-PTZ induced dose-dependent increases in NRF2-ARE binding activity and NRF2 gene/protein expression, whereas silencing Sig1R significantly decreased NRF2 protein levels and increased oxidative stress, although (+)-PTZ did not disrupt NRF2-KEAP1 binding. In vivo studies were conducted to investigate whether, in the absence of NRF2, activation of Sig1R rescues cones. (+)-PTZ was administered systemically for several weeks to rd10/nrf2+/+ and rd10/nrf2-/- mice. Through post-natal day 42, cone function was significant in rd10/nrf2+/+, but minimal in rd10/nrf2-/- mice as indicated by electroretinographic recordings using natural noise stimuli, optical coherence tomography and retinal histological analyses. Immunodetection of cones was limited in (+)-PTZ-treated rd10/nrf2-/-, though considerable in (+)-PTZ-treated rd10/nrf2+/+mice. The data suggest that Sig1R-mediated cone rescue requires NRF2 and provide evidence for a previously-unrecognized relationship between these proteins.

Erratum: Observation of D^{0} Meson Nuclear Modifications in Au+Au Collisions at sqrt[s_{NN}]=200 GeV [Phys. Rev. Lett. 113, 142301 (2014)]

This corrects the article DOI: 10.1103/PhysRevLett.113.142301.

IL-37 inhibits IL-4/IL-13-induced CCL11 production and lung eosinophilia in murine allergic asthma

BACKGROUND

IL-37 is emerging as an anti-inflammatory cytokine, particularly in innate inflammation. However, the role of IL-37 in Th2-mediated allergic lung inflammation remains uncertain. We sought to determine the role and the underlying mechanisms of IL-37 in the development of house dust mites (HDM)-induced murine asthma model.

METHODS

We examined the effect of IL-37 administration during the sensitization or challenge phase on Th2-mediated allergic asthma induced by inhaled HDM. Cellular source of CCL11 and distribution of IL-37 receptors, IL-18Rα and IL-1R8, were determined in HDM-exposed lungs. Finally, we examined the effect of IL-37 on CCL11 production and STAT6 activation in different primary lung structural cell types upon IL-4/IL-13 stimulation.

RESULTS

IL-37 had no effect on HDM sensitization, but when administrated during the challenge phase, significantly attenuated pulmonary eosinophilia, CCL11 production, and airway hyper-reactivity (AHR). Interestingly, IL-37 treatment had no significant effects on lung infiltrating T cells and Th2 cytokine production. Intranasal co-administration of CCL11 reversed the inhibiting effect of IL-37 on HDM-induced pulmonary eosinophilia and AHR. Furthermore, we demonstrated that CCL11 was primarily expressed by fibroblasts and airway smooth muscle cells (AMSC), while IL-37 receptors by tracheobronchial epithelial cells (TEC). In vitro study showed that IL-37 inhibited IL-4/IL-13-induced STAT6 activation and CCL11 production by fibroblasts and AMSC, which was dependent on its direct action on TEC. Moreover, cell contact was required for the inhibitory effect of IL-37-treated TEC.

CONCLUSIONS

IL-37 attenuates HDM-induced asthma, possibly by inhibiting IL-4/IL-13-induced CCL11 production by fibroblasts and AMSC via its direct act on TEC.

[Clinical application of negative pressure dressing in the full-thickness skin grafting]

Objective: To investigate the effect of different negative pressure of wound negative pressure dressing (NPD) on the survival of full-thickness skin grafts of patients. Methods: One hundred and eleven patients who need skin grafting, conforming to the inclusion criteria were hospitalized in our unit from August 2012 to March 2017, and their clinical data were retrospectively analyzed. Forty-seven patients hospitalized from August 2012 to October 2015 were assigned into traditional treatment group. Sixty-four patients hospitalized from November 2015 to March 2017 were divided into -9.975 kPa negative pressure treatment group (n=34) and -13.300 kPa negative pressure treatment group (n=30). Patients in traditional treatment group received conventional dressing after full-thickness skin grafting. Patients in -9.975 kPa and -13.300 kPa negative pressure treatment groups received -9.975 kPa and -13.300 kPa NPD based on traditional treatment after vacuum sealing, respectively. Dot necrosis area of skin grafts and erosion and escharosis of graft edges of patients in the three groups on post operation day 10 were observed. The percentage of dot necrosis area of skin grafts and occurrence rate of erosion and escharosis of skin graft edges were calculated, respectively. Data were processed with chi-square test, Fisher's exact test, and Kruskal-Wallis H test. Results: Percentages of dot necrosis area of skin grafts of patients in traditional treatment group and -9.975 kPa and -13.300 kPa negative pressure treatment groups were 17.81%, 3.20%, and 3.00%, respectively. Percentage of dot necrosis area of skin grafts of patients in traditional treatment group was significantly higher than that in -9.975 kPa and -13.300 kPa negative pressure treatment groups (Z=-5.770, -4.690, P<0.001). Percentages of dot necrosis area of skin grafts of patients in -9.975 kPa and-13.300 kPa groups were close (Z=-0.619, P>0.05). The occurrence rates of erosion and escharosis of skin graft edges of patients in traditional treatment group and -9.975 kPa and -13.300 kPa negative pressure treatment groups were 78.7% (37/47), 32.4 (11/34), and 36.7% (11/30), respectively. Erosion and escharosis of skin graft edges of patients in -9.975 kPa and -13.300 kPa negative pressure treatment groups were better than those in traditional treatment group (P<0.001). Erosion and escharosis of skin graft edges of patients in -9.975 kPa and -13.300 kPa negative pressure treatment groups were close (P>0.05). Conclusions: The use of -9.975 kPa and -13.300 kPa NPD in skin grafts after full-thickness skin grafting significantly diminishes the occurrence rates of dot necrosis area of skin grafts and erosion and escharosis of graft edges.

Exploiting coumarin-6 as ancillary ligands in 1,10-phenanthroline Ir(iii) complexes: generating triplet photosensitisers with high upconversion capabilities

A series of new Ir(iii) complexes incorporating 3-(2-benzothiazolyl)-7-(diethylamino)coumarin (coumarin 6) and ethynylpyrene (EP) functionalised 1,10-phenanthroline (phen) were developed. [Ir(iii)(coumarin 6)₂(3-EP-phen)](PF₆) (Ir-3) proved to be the most promising material in triplet photosensitising applications. Highly absorbing at λ = 485 nm (ε = 1.31 × 10⁵ M^-1 cm^-1), it exhibits high upconversion and singlet oxygen quantum yields (Φ_UC = 27.5%, Φ_Δ = 81.5%) and an exemplary upconversion capability (η = 3.60 × 10⁶ M^-1 cm^-1).

Mechanisms of sphingosine-1-phosphate-mediated vasoconstriction of rat afferent arterioles

AIM

Sphingosine-1-phosphate (S1P) influences resistance vessel function and is implicated in renal pathological processes. Previous studies revealed that S1P evoked potent vasoconstriction of the pre-glomerular microvasculature, but the underlying mechanisms remain incompletely defined. We postulated that S1P-mediated pre-glomerular microvascular vasoconstriction involves activation of voltage-dependent L-type calcium channels (L-VDCC) and the rho/rho kinase pathway.

METHODS

Afferent arteriolar reactivity was assessed in vitro using the blood-perfused rat juxtamedullary nephron preparation, and diameter was measured during exposure to physiological and pharmacological agents.

RESULTS

Exogenous S1P (10^-9 -10^-5 mol L^-1 ) evoked concentration-dependent vasoconstriction of afferent arterioles. Superfusion with nifedipine, a L-VDCC blocker, increased arteriolar diameter by 39 ± 18% of baseline and significantly attenuated the S1P-induced vasoconstriction. Superfusion with the rho kinase inhibitor, Y-27632, increased diameter by 60 ± 12% of baseline and also significantly blunted vasoconstriction by S1P. Combined nifedipine and Y-27632 treatment significantly inhibited S1P-induced vasoconstriction over the entire concentration range tested. In contrast, depletion of intracellular Ca²⁺ stores with the Ca²⁺ -ATPase inhibitors, thapsigargin or cyclopiazonic acid, did not alter the S1P-mediated vasoconstrictor profile. Scavenging reactive oxygen species (ROS) or inhibition of nicotinamide adenine dinucleotide phosphate oxidase activity significantly attenuated S1P-mediated vasoconstriction.

CONCLUSION

Exogenous S1P elicits potent vasoconstriction of rat afferent arterioles. These data also demonstrate that S1P-mediated pre-glomerular vasoconstriction involves activation of L-VDCC, the rho/rho kinase pathway and ROS. Mobilization of Ca²⁺ from intracellular stores is not required for S1P-mediated vasoconstriction. These studies reveal a potential role for S1P in the modulation of renal microvascular tone.

Exocytosis-coordinated mechanisms for tip growth underlie pollen tube growth guidance

Many tip-growing cells are capable of responding to guidance cues, during which cells precisely steer their growth toward the source of guidance signals. Though several players in signal perception have been identified, little is known about the downstream signaling that controls growth direction during guidance. Here, using combined modeling and experimental studies, we demonstrate that the growth guidance of Arabidopsis pollen tubes is regulated by the signaling network that controls tip growth. Tip-localized exocytosis plays a key role in this network by integrating guidance signals with the ROP1 Rho GTPase signaling and coordinating intracellular signaling with cell wall mechanics. This model reproduces the high robustness and responsiveness of pollen tube guidance and explains the connection between guidance efficiency and the parameters of the tip growth system. Hence, our findings establish an exocytosis-coordinated mechanism underlying the cellular pathfinding guided by signal gradients and the mechanistic linkage between tip growth and guidance.