The effect of reionization on direct measurements of the mean free path

Recent measurements of the ionizing photon mean free path (MFP) based on composite quasar spectra may point to a late end to reionization at $z<6$. These measurements are challenging, however, because they rely on assumptions about the proximity zones of the quasars in the analysis. For example, some of the $z\sim 6$ quasars in the composite might have been close to large-scale regions where reionization was still ongoing ("neutral islands"), and it is unclear how this would affect the measurements. We address the question here with mock MFP measurements from radiative transfer simulations. We find that, even in the presence of neutral islands, the inferred MFP tracks to within $30 \%$ the true attenuation scale of the spatially averaged IGM, which includes opacity from both the ionized medium and the islands. During reionization, this scale is always shorter than the MFP in the ionized medium. The inferred MFP is sensitive at the $< 50\%$ level to assumptions about the quasar environments and lifetimes for realistic models. We demonstrate that future analyses with improved data may require explicitly modeling the effects of neutral islands on the composite spectra, and we outline a method for doing this. Lastly, we quantify the effects of neutral islands on Lyman-series transmission, which has been modeled with optically thin simulations in previous MFP analyses. Neutral islands can suppress transmission at $\lambda_{\rm rest} < 912$ \r{A} significantly, up to a factor of 2 for $z_{\rm qso} = 6$ in a plausible reionization scenario, owing to absorption by many closely spaced lines as quasar light redshifts into resonance. However, the suppression is almost entirely degenerate with the spectrum normalization, thus does not significantly bias the inferred MFP.Comment: 11 pages, 8 figures, submitted to MNRA

Identification and Validation of Two Novel Prognostic lncRNAs in Kidney Renal Clear Cell Carcinoma

Background/Aims: Kidney renal clear cell carcinoma (KIRC) is one of the most fatal malignancies due to late diagnosis and poor treatment. To improve its prognosis, a screening for molecular biomarkers of KIRC is urgently needed. Long non-coding RNAs (lncRNAs) play important roles in tumorigenesis and prognosis of cancers. However, it is not clear whether lncRNAs can be used as molecular biomarkers in predicting the survival of KIRC patients. Methods: In this study, our aim was to identify lncRNAs/mRNAs signatures and their prognostic values in KIRC. The aberrant expression profile of mRNAs and lncRNAs in 529 KIRC tissues and 72 adjacent non-tumor pancreatic tissues were obtained from the Cancer Genome Atlas (TCGA). A weighted gene co-expression network analysis (WGCNA) of two key lncRNAs was constructed. We constructed an aberrant lncRNA-mRNA-miRNA ceRNA network in CESC. In addition, Gene Ontology (GO) and KEGG pathway analysis were performed. Results: Using lncRNA/mRNA expression profiling data, the overall analysis revealed that two novel lncRNA signatures (DNM1P35 and MIR155HG) and several mRNAs were found to be significantly correlated with KIRC patient’s overall analysis. Based on the target gene of the two lncRNA in co-expression network, the GO and KEGG analysis were also performed. A dysregulated lncRNA-related ceRNA network was also observed. Conclusion: These results suggested that the two novel lncRNAs signatures may act as independent prognostic biomarkers for predicting the survival of KIRC patient

Investigation of the shape transferability of nanoscale multi-tip diamond tools in the diamond turning of nanostructures

In this article, the shape transferability of using nanoscale multi-tip diamond tools in the diamond turning for scale-up manufacturing of nanostructures has been demonstrated. Atomistic multi-tip diamond tool models were built with different tool geometries in terms of the difference in the tip cross-sectional shape, tip angle, and the feature of tool tip configuration, to determine their effect on the applied forces and the machined nano-groove geometries. The quality of machined nanostructures was characterized by the thickness of the deformed layers and the dimensional accuracy achieved. Simulation results show that diamond turning using nanoscale multi-tip tools offers tremendous shape transferability in machining nanostructures. Both periodic and non-periodic nano-grooves with different cross-sectional shapes can be successfully fabricated using the multi-tip tools. A hypothesis of minimum designed ratio of tool tip distance to tip base width (L/Wf) of the nanoscale multi-tip diamond tool for the high precision machining of nanostructures was proposed based on the analytical study of the quality of the nanostructures fabricated using different types of the multi-tip tools. Nanometric cutting trials using nanoscale multi-tip diamond tools (different in L/Wf) fabricated by focused ion beam (FIB) were then conducted to verify the hypothesis. The investigations done in this work imply the potential of using the nanoscale multi-tip diamond tool for the deterministic fabrication of period and non-periodic nanostructures, which opens up the feasibility of using the process as a versatile manufacturing technique in nanotechnology

The relationship between IGM Lyman-alpha opacity and galaxy density near the end of reionization

Observed scatter in the Lyman-alpha opacity of quasar sightlines at $z<6$ has motivated measurements of the correlation between Ly$\alpha$ opacity and galaxy density, as models that predict this scatter make strong and sometimes opposite predictions for how they should be related. Our previous work associated two highly opaque Ly$\alpha$ troughs at $z\sim5.7$ with a deficit of Lyman-$\alpha$ emitting galaxies (LAEs). In this work, we survey two of the most highly transmissive lines of sight at this redshift, towards the $z=6.02$ quasar SDSS J1306+0356 and the $z=6.17$ quasar PSO J359-06. We find that both fields are underdense in LAEs within 10 $h^{-1}$ Mpc of the quasar sightline, somewhat less extensive than underdensities associated with Ly$\alpha$ troughs. We combine our observations with three additional fields from the literature, and find that while fields with extreme opacities are generally underdense, moderate opacities span a wider density range. The results at high opacities are consistent with models that invoke UV background fluctuations and/or late reionization to explain the observed scatter in IGM Ly$\alpha$ opacities. There is tension at low opacities, however, as the models tend to associate lower IGM Ly$\alpha$ opacities with higher densities. Although the number of fields surveyed is still small, the low-opacity results may support a scenario in which the ionizing background in low-density regions increases more rapidly than some models suggest after becoming ionized. Elevated gas temperatures from recent reionization may also be making these regions more transparent.Comment: 20 pages, 17 figures. Accepted to Ap

The mean free path of ionizing photons at 5 &lt; z &lt; 6: evidence for rapid evolution near reionization

The mean free path of ionizing photons, λmfp, is a key factor in the photoionization of the intergalactic medium (IGM). At z ≳ 5, however, λmfp may be short enough that measurements towards QSOs are biased by the QSO proximity effect. We present new direct measurements of λmfp that address this bias and extend up to z ∼ 6 for the first time. Our measurements at z ∼ 5 are based on data from the Giant Gemini GMOS survey and new Keck LRIS observations of low-luminosity QSOs. At z ∼ 6 we use QSO spectra from Keck ESI and VLT X-Shooter. We measure λmfp=9.09+1.62−1.28 proper Mpc and 0.75+0.65−0.45 proper Mpc (68 per cent confidence) at z = 5.1 and 6.0, respectively. The results at z = 5.1 are consistent with existing measurements, suggesting that bias from the proximity effect is minor at this redshift. At z = 6.0, however, we find that neglecting the proximity effect biases the result high by a factor of two or more. Our measurement at z = 6.0 falls well below extrapolations from lower redshifts, indicating rapid evolution in λmfp over 5 < z < 6. This evolution disfavours models in which reionization ended early enough that the IGM had time to fully relax hydrodynamically by z = 6, but is qualitatively consistent with models wherein reionization completed at z = 6 or even significantly later. Our mean free path results are most consistent with late reionization models wherein the IGM is still 20 per cent neutral at z = 6, although our measurement at z = 6.0 is even lower than these models prefer

The XQR-30 Metal Absorber Catalog: 778 Absorption Systems Spanning 2 < z < 6.5

Intervening metal absorption lines in the spectra of z > 6 quasars are fundamental probes of the ionization state and chemical composition of circumgalactic and intergalactic gas near the end of the reionization epoch. Large absorber samples are required to robustly measure typical absorber properties and to refine models of the synthesis, transport, and ionization of metals in the early Universe. The "Ultimate XSHOOTER legacy survey of quasars at z~5.8-6.6" (XQR-30) has obtained high signal-to-noise spectra of 30 luminous quasars, nearly quadrupling the existing sample of 12 high quality z~6 quasar spectra. We use this unprecedented sample to construct a catalog of 778 systems showing absorption in one or more of MgII (360 systems), FeII (184), CII (46), CIV (479), SiIV (127), and NV (13) which span 2 < z < 6.5. This catalog significantly expands on existing samples of z > 5 absorbers, especially for CIV and SiIV which are important probes of the ionizing photon background at high redshift. The sample is 50% (90%) complete for rest-frame equivalent widths W > 0.03AA (0.09AA). We publicly release the absorber catalog along with completeness statistics and a Python script to compute the absorption search path for different ions and redshift ranges. This dataset is a key legacy resource for studies of enriched gas from the era of galaxy assembly to cosmic noon, and paves the way for even higher redshift studies with the James Webb Space Telescope and 30m-class telescopes.Comment: 29 pages and 14 figures including 2 appendices. Accepted for publication in MNRAS. The metal absorber catalogue can be downloaded from https://github.com/XQR-30/Metal-catalogue. Contents unchanged from v1 apart from change to author lis

The fraction and kinematics of broad absorption line quasars across cosmic time

Luminous quasars are powerful targets to investigate the role of feedback from supermassive black-holes (BHs) in regulating the growth phases of BHs themselves and of their host galaxies, up to the highest redshifts. Here we investigate the cosmic evolution of the occurrence and kinematics of BH-driven outflows, as traced by broad absorption line (BAL) features, due to the C IV ionic transition. We exploit a sample of 1935 quasars quasars at $z=2.1-6.6$ with bolometric luminosity log($L_{\rm bol}/$erg s$^{-1})\gtrsim46.5$, drawn from the Sloan Digital Sky Survey and from the X-shooter legacy survey of Quasars at Reionisation (XQR-30). We consider rest-frame optical bright quasars to minimise observational biases due to quasar selection criteria. We apply a homogeneous BAL identification analysis, based on employing composite template spectra to estimate the quasar intrinsic emission. We find a BAL quasar fraction close to 20\% at $z\sim2-4$, while it increases to almost 50\% at $z\sim6$. The velocity and width of the BAL features also increase at $z\gtrsim4.5$. We exclude that the redshift evolution of the BAL properties is due to differences in terms of quasar luminosity and accretion rate. These results suggest significant BH feedback occurring in the 1 Gyr old Universe, likely affecting the growth of BHs and, possibly, of their host galaxies, as supported by models of early BH and galaxy evolution.Comment: Accepted for publication in Ap

Measuring the photo-ionization rate, neutral fraction and mean free path of HI ionizing photons at 4.9≤z≤6.04.9 \leq z \leq 6.0 from a large sample of XShooter and ESI spectra

We measure the mean free path ($\lambda_{\rm mfp,HI}$), photo-ionization rate ($\langle \Gamma_{\rm HI} \rangle$) and neutral fraction ($\langle f_{\rm HI} \rangle$) of hydrogen in 12 redshift bins at $4.85<z<6.05$ from a large sample of moderate resolution XShooter and ESI QSO absorption spectra. The fluctuations in ionizing radiation field are modeled by post-processing simulations from the Sherwood suite using our new code ''EXtended reionization based on the Code for Ionization and Temperature Evolution'' (EX-CITE). EX-CITE uses efficient Octree summation for computing intergalactic medium attenuation and can generate large number of high resolution $\Gamma_{\rm HI}$ fluctuation models. Our simulation with EX-CITE shows remarkable agreement with simulations performed with the radiative transfer code Aton and can recover the simulated parameters within $1\sigma$ uncertainty. We measure the three parameters by forward-modeling the Ly$\alpha$ forest and comparing the effective optical depth ($\tau_{\rm eff, HI}$) distribution in simulations and observations. The final uncertainties in our measured parameters account for the uncertainties due to thermal parameters, modeling parameters, observational systematics and cosmic variance. Our best fit parameters show significant evolution with redshift such that $\lambda_{\rm mfp,HI}$ and $\langle f_{\rm HI} \rangle$ decreases and increases by a factor $\sim 6$ and $\sim 10^{4}$, respectively from $z \sim 5$ to $z \sim 6$. By comparing our $\lambda_{\rm mfp,HI}$, $\langle \Gamma_{\rm HI} \rangle$ and $\langle f_{\rm HI} \rangle$ evolution with that in state-of-the-art Aton radiative transfer simulations and the Thesan and CoDa-III simulations, we find that our best fit parameter evolution is consistent with a model in which reionization completes by $z \sim 5.2$.Comment: 30 pages (+14 pages appendices), 14 figures (+18 figures appendices); submitted to MNRAS; Main results are summarized in Fig. 10, Fig. 11 and Table

Chemical Abundance of z~6 Quasar Broad-Line Regions in the XQR-30 Sample

The elemental abundances in the broad-line regions of high-redshift quasars trace the chemical evolution in the nuclear regions of massive galaxies in the early universe. In this work, we study metallicity-sensitive broad emission-line flux ratios in rest-frame UV spectra of 25 high-redshift (5.8 < z < 7.5) quasars observed with the VLT/X-shooter and Gemini/GNIRS instruments, ranging over $\log(M_{\rm{BH}}/M_{\odot})= 8.4-9.8$ in black hole mass and $\log(L_{\rm{bol}}/\rm{erg\, s}^{-1})= 46.7-47.7$ in bolometric luminosity. We fit individual spectra and composites generated by binning across quasar properties: bolometric luminosity, black hole mass, and blueshift of the \civ\, line, finding no redshift evolution in the emission-line ratios by comparing our high-redshift quasars to lower-redshift (2.0 < z < 5.0) results presented in the literature. Using Cloudy-based locally optimally-emitting cloud photoionisation model relations between metallicity and emission-line flux ratios, we find the observable properties of the broad emission lines to be consistent with emission from gas clouds with metallicity that are at least 2-4 times solar. Our high-redshift measurements also confirm that the blueshift of the CIV emission line is correlated with its equivalent width, which influences line ratios normalised against CIV. When accounting for the CIV blueshift, we find that the rest-frame UV emission-line flux ratios do not correlate appreciably with the black hole mass or bolometric luminosity.Comment: MNRAS accepted, 24 pages, 17 figures, 4 table

Mini percutaneous nephrolithotomy is a noninferior modality to standard percutaneous nephrolithotomy for the management of 20-40 mm renal calculi: A Multicenter randomized controlled trial

Background: High quality of evidence comparing mini percutaneous nephrolithotomy (mPNL) with standard percutaneous nephrolithotomy (sPNL) for the treatment of larger-sized renal stones is lacking. Objective: To compare the efficacy and safety of mPNL and sPNL for the treatment of 20–40 mm renal stones. Design, setting, and participants: A parallel, open-label, and noninferior randomized controlled trial was performed at 20 Chinese centers (2016–2019). The inclusion criteria were patients 18–70 yr old, with normal renal function, and 20–40 mm renal stones. Intervention: Percutaneous nephrolithotomy PNL was performed using either 18 F or 24 F percutaneous nephrostomy tracts. Outcome measurements and statistical analysis: The primary outcome was the one-session stone-free rate (SFR). The secondary outcomes included operating time, visual analog pain scale (VAS) score, blood loss, complications as per the Clavien-Dindo grading system, and length of hospitalization. Results and limitations: The 1980 intention-to-treat patients were randomized. The mPNL group achieved a noninferior one-session SFR to the sPNL group by the one-side noninferiority test (0.5% [difference], p < 0.001). The transfusion and embolization rates were comparable; however, the sPNL group had a higher hemoglobin drop (5.2 g/l, p < 0.001). The sPNL yielded shorter operating time (–2.2 min, p = 0.008) but a higher VAS score (0.8, p < 0.001). Patients in the sPNL group also had longer hospitalization (0.6 d, p < 0.001). There was no statistically significant difference in fever or urosepsis occurrences. The study's main limitation was that only 18F or 24F tract sizes were used. Conclusions: Mini mPNL achieves noninferior SFR outcomes to sPNL, but with reduced bleeding, less postoperative pain, and shorter hospitalization. Patient summary: We evaluated the surgical outcomes of percutaneous nephrolithotomy using two different sizes of nephrostomy tracts in a large population. We found that the smaller tract might be a sensible alternative for patients with 20–40 mm renal stones. This multicenter, parallel, open-label, and noninferior randomized controlled trial showed that mini percutaneous nephrolithotomy achieved noninferior stone-free rate with advantages of reduced blood loss, less postoperative pain, and shorter hospitalization. Mini percutaneous nephrolithotomy should be considered a sensible alternative treatment of 20–40 mm renal stones.grants from high-level development funding of Guangzhou Medical Universit