bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-body urea kinetics and functional roles of urea transporters and aquaporins in urea secretion into the rumen in sheep fed diets varying in crude protein content and corn grain processing method
Authors: Burns Kaitlin S , Penner Gregory B , Hogan Natacha S , Mutsvangwa Timothy 
Published: August 2024

Abstract
The objectives were to determine the effects of dietary crude protein (CP) content and corn grain processing on whole-body urea kinetics and the functional roles of urea transporter-B (UT-B) and aquaporins (AQP) in serosal-to-mucosal urea flux (Jsm-urea) in ovine ruminal epithelia. Thirty-two Rideau-Arcott ram lambs were blocked by bodyweight into groups of 4 and then randomly allocated within blocks to 1 of 4 diets (n = 8) in a 2 × 2 factorial design. Dietary factors were CP content (11% [LP] vs. 16% [HP]) and corn grain processing (whole-shelled [WSC] vs. steam-flaked [SFC] corn). Whole-body urea kinetics and N balance were determined using 4-d continuous intrajugular infusions of [15N15N]-urea with concurrent collections of urine and feces with four blocks of lambs (n = 4). After 23 d on diets, lambs were killed to collect ruminal epithelia for mounting in Ussing chambers to determine Jsm-urea and the measurement of mRNA abundance of UT-B and AQP. Serosal and mucosal additions of phloretin and NiCl2 were used to inhibit UT-B- and AQP-mediated urea transport, respectively. Lambs fed HP had a greater (P &lt; 0.01) N intake (29.4 vs. 19.1 g/d) than those fed LP; however, retained N (g/d or % of N intake) was not different. As a % of N intake, lambs fed SFC tended (P = 0.09) to have a lower N excretion (72.2 vs. 83.5%) and a greater N retention (27.8 vs. 16.6%) compared to those fed WSC. Endogenous urea-N production (UER) was greater in lambs fed HP compared to those fed LP (29.9 vs. 20.6 g/d; P = 0.02), whereas urea-N secreted into the gut (GER; g/d) and urea-N used for anabolic purposes (UUA; g/d) were similar. Lambs fed LP tended (P = 0.05) to have greater GER:UER (0.78 vs. 0.66) and UUA:GER (0.23 vs. 0.13) ratios, and a greater Jsm-urea (144.7 vs. 116.1 nmol/[cm2 × h]; P = 0.07) compared to those fed HP. Lambs fed SFC tended to have a lower NiCl2-insensitive Jsm-urea (117.4 vs. 178.4 nmol/[cm2 × h]; P = 0.09) and had a lower phloretin-insensitive Jsm-urea (87.1 vs. 143.1 nmol/[cm2 × h]; P = 0.02) compared to those fed WSC. The mRNA abundance of UT-B (0.89 vs. 1.07; P = 0.08) and AQP-3 (0.90 vs. 1.05; P = 0.07) tended to be lower in lambs fed SFC compared to those fed WSC. Overall, reducing CP content tended to increase the GER:UER ratio with no changes in the expression or function of UT-B and AQP. Although corn grain processing had no effects on GER, feeding SFC increased the portion of urea secretion into the rumen that was mediated via UT-B and AQP.
External Validation of a Commercial Artificial Intelligence Algorithm on a Diverse Population for Detection of False Negative Breast Cancers
Authors: Plimpton S Reed , Milch Hannah , Sears Christopher , Chalfant James , Hoyt Anne , Fischer Cheryce , Hsu William , Joines Melissa 
Published: August 2024

Abstract

Objective
There are limited data on the application of artificial intelligence (AI) on nonenriched, real-world screening mammograms. This work aims to evaluate the ability of AI to detect false negative cancers not detected at the time of screening when reviewed by the radiologist alone.

Methods
A commercially available AI algorithm was retrospectively applied to patients undergoing screening full-field digital mammography (FFDM) or digital breast tomosynthesis (DBT) at a single institution from 2010 to 2019. Ground truth was established based on 1-year follow-up data. Descriptive statistics were performed with attention focused on AI detection of false negative cancers within these subsets.

Results
A total of 26 694 FFDM and 3183 DBT examinations were analyzed. Artificial intelligence was able to detect 7/13 false negative cancers (54%) in the FFDM cohort and 4/10 (40%) in the DBT cohort on the preceding screening mammogram that was interpreted as negative by the radiologist. Of these, 4 in the FFDM cohort and 4 in the DBT cohort were identified in breast densities of C or greater. False negative cancers detected by AI were predominantly luminal A invasive malignancies (9/11, 82%). Artificial intelligence was able to detect these false negative cancers a median time of 272 days sooner in the FFDM cohort and 248 days sooner in the DBT cohort compared to the radiologist.

Conclusion
Artificial intelligence was able to detect cancers at the time of screening that were missed by the radiologist. Prospective studies are needed to evaluate the synergy of AI and the radiologist in real-world settings, especially on DBT examinations.
Collimation principles of a hollow X-ray microbeam for high-contrast cytoplasm irradiation
Authors: Cheng Qinqin , Zhao Ruifeng , Wang Xiaowa , Wang Xufei 
Published: August 2024

Abstract
A Monte Carlo simulation was used to assess the performance of a collimated hollow X-ray microbeam for subcellular cytoplasm irradiation. A high-Z coaxial collimation structure with an inner core for nucleus shielding was investigated. Two key performances, the extraction efficiency (cytoplasm dose per unit incident fluence) and the dose contrast (cytoplasm-to-nucleus dose ratio), were evaluated regarding the influences of the material, geometry and physical arrangements of the collimator, target dish and incident beam source. Simulation results demonstrate that a gold coaxial structure with a practical collimation geometry of a 1-mm length, 10-μm inner diameter and 200-μm outer diameter, with the top exit closely attached (with a minimized air gap) to the bottom of a cell dish with a 3-μm thick Mylar film is recommended for cytoplasm irradiation of adherent mammalian cells. For a synchrotron source in the energy range &lt; 10 keV, a dose contrast of approximately 100 can be achieved. For a bremsstrahlung source &lt;30-kV tube voltage, a dose contrast of approximately 50–100 can still be achieved. General principles are summarized with further explanations of the performance of the hollow X-ray microbeam.
Dosimetric impact of calibration coefficients determined using linear accelerator photon and electron beams for ionization chamber in an on-site dosimetry audit
Authors: Tani Kensuke , Wakita Akihisa , Tohyama Naoki , Fujita Yukio 
Published: August 2024

Abstract
This study aimed to clarify the dosimetric impact of calibration beam quality for calibration coefficients of the absorbed dose to water for an ionization chamber in an on-site dosimetry audit. Institution-measured doses of 200 photon and 184 electron beams were compared with the measured dose using one year data before and after the calibration of the ionization chamber used. For photon and electron reference dosimetry, the agreements of the institution-measured dose against two measured doses in this audit were evaluated using the calibration coefficients determined using 60Co (${N}_{D,\mathrm{w},{}^{60}\mathrm{Co}}$) and linear accelerator (linac) (${N}_{D,\mathrm{w},Q}$) beams. For electron reference dosimetry, the agreement of two institution-measured doses against the measured dose was evaluated using${N}_{D,\mathrm{w},Q}$. Institution-measured doses were evaluated using direct- and cross-calibration coefficients. For photon reference dosimetry, the mean differences and standard deviation (SD) of institution-measured dose against the measured dose using ${N}_{D,\mathrm{w},{}^{60}\mathrm{Co}}$ and ${N}_{D,\mathrm{w},Q}$ were −0.1% ± 0.4% and −0.3% ± 0.4%, respectively. For electron reference dosimetry, the mean differences and SD of institution-measured dose using the direct-calibration coefficient against the measured dose using ${N}_{D,\mathrm{w},{}^{60}\mathrm{Co}}$ and ${N}_{D,\mathrm{w},Q}$ were 1.3% ± 0.8% and 0.8% ± 0.8%, respectively. Further, the mean differences and SD of institution-measured dose using the cross-calibration coefficient against the measured dose using ${N}_{D,\mathrm{w},Q}$ were −0.1% ± 0.6%. For photon beams, the dosimetric impact of introducing calibration coefficients determined using linac beams was small. For electron beams, it was larger, and the measured dose using ${N}_{D,\mathrm{w},Q}$ was most consistent with the institution-measured dose, which was evaluated using a cross-calibration coefficient.
Impact of neoadjuvant androgen deprivation therapy on toxicity in intensity-modulated radiation therapy for prostate cancer
Authors: Serizawa Itsuko , Kozuka Takuyo , Soyano Takashi , Sasamura Kazuma , Kamima Tatsuya , Kunogi Hiroaki , Numao Noboru , Yamamoto Shinya , Yonese Junji , Yoshioka Yasuo 
Published: August 2024

Abstract
This study aimed to compare toxicities, prostate volume and dosimetry, between patients who underwent intensity-modulated radiation therapy (IMRT) combined with ≥3 months of neoadjuvant androgen deprivation therapy (NADT) and those without NADT for prostate cancer. In total, 449 patients with intermediate- and high-risk prostate cancer received 78 Gy IMRT in 39 fractions, of which 129 were treated without any ADT (non-ADT group) and 320 with NADT ≥3 months (NADT group). Adverse events and dose-volume indices were compared between the two groups retrospectively. The NADT group had a lower rate of acute grade 2 gastrointestinal (GI) toxicities (17% vs 25%, P = 0.063) and late grade 2 GI toxicities (P = 0.055), including a significantly lower rate of late grade 2 rectal hemorrhage (P = 0.033), compared with the non-ADT group. There were no cases of late grade 3 or higher GI toxicities. The average volume of the prostate in the NADT group was 38% smaller than that in the non-ADT group (43.7 vs 27.0 cm3, P &lt; 0.001). Bladder V40Gy and V50Gy, and rectum V40Gy, V50Gy, V60Gy and V70Gy were significantly smaller in the NADT group. In the NADT group, no significant difference was observed in adverse events or dosimetry between the subgroups with NADT ≥12 and &lt;12 months. Acute and late rectal toxicities were reduced by NADT within ≥3 months in accordance with reduced prostate volume and improved rectal dosimetry. This suggests a merit of administering neoadjuvant ADT ≥3 months for reducing rectal toxicities.
Craniospinal irradiation for leptomeningeal metastasis of solid tumors: survival analysis and prognostic factors
Authors: Takeda Kazuya , Umezawa Rei , Yamamoto Takaya , Takahashi Noriyoshi , Jingu Keiichi 
Published: August 2024

Abstract
We conducted a study to examine the treatment outcomes and prognostic factors for patients who underwent craniospinal irradiation (CSI) for leptomeningeal metastasis of solid tumors. This retrospective study included patients who received CSI for leptomeningeal metastasis at a single institute between 2010 and 2021. Data from clinical records and the radiation information system were obtained and analyzed. A total of 25 patients were included in the study. Eighteen patients (72%) completed the scheduled CSI. The median overall survival (OS) period was 4.8 months (95% confidence interval (CI): 3.2–10.0 months). Symptom relief was achieved in four out of 23 symptomatic patients (17%). Non-hematological adverse events occurred in 12 patients (48%), with 1 patient (4%) developing Grade 3 bacterial meningitis and the other patients having Grade 1–2 events. Twenty patients (80%) had hematological adverse events of Grade 3 or higher. Grade 4 hematologic toxicities occurred in 3 patients (12%) due to neutropenia and in 11 patients (44%) due to lymphopenia. In multivariate Cox regression analysis, the systemic immune-inflammation index (SII) was identified as the only significant parameter for predicting OS. The median OS periods for patients with SII &lt; 607 and SII ≥ 607 were 6.1 and 2.1 months, respectively (P = 0.003). In conclusion, this study showed the treatment outcomes of CSI for leptomeningeal metastasis of solid tumors. It was shown that a high baseline SII was associated with shorter OS after CSI. The findings will contribute to the evaluation of prognosis after CSI.
Molecular epidemiological investigation of Cryptococcus spp. isolated from cats in Japan using multi-locus sequence typing
Authors: Omura Miki , Komori Aya , Tamura Takashi , Han Hock Siew , Kano Rui , Makimura Koichi 
Published: August 2024

Abstract
Cryptococcosis is an important fungal infection for both humans and cats, but molecular epidemiological studies on strains isolated from cats are limited. We conducted multi-locus sequence typing analysis and antifungal susceptibility testing of 14 Cryptococcus spp. strains from domestic cats in Japan and one strain isolated from a cat in Singapore. All 14 strains from domestic cats in Japan were identified as Cryptococcus neoformans molecular type VNI. The sequence types (STs) included eight cases of ST5, five cases of ST31, and one novel ST. VNI ST5 is the most frequently isolated strain in Japanese patients as well, while there are no records of VNI ST31 being isolated from Japanese patients. The Singaporean cat strain was identified as C. gattii VGIIb (C. deuterogattii), ST7. We compared these results with strains previously reported to have been isolated from cats. This comparison suggested that molecular types of Cryptococcus spp. isolated from cats may differ depending on the country. In the antifungal susceptibility testing of C. neoformans, one strain each exceeded the epidemiological cutoff value (ECV) for amphotericin B and 5-fluorocytosine, while two strains exceeded the ECV for fluconazole. This study reveals the molecular epidemiology of Cryptococcus spp. isolated from cats with cryptococcosis in Japan. It suggests that investigating Cryptococcus spp. carried by cats, which share close living environments with humans, may contribute to the health of both cats and human populations.
ALMA follow-up of ~3000 red-Herschel galaxies: the nature of extreme submillimetre galaxies
Authors: Quirós-Rojas Marianela , Montaña Alfredo , Zavala Jorge A , Aretxaga Itziar , Hughes David H 
Published: August 2024

ABSTRACT
We present the analysis of over 3000 red-Herschel sources ($S_{\mathrm{250\, \mu m}}\lt S_{\mathrm{350\, \mu m}}\lt S_{\mathrm{500\, \mu m} }$) using public data from the ALMA archive and the Herschel-ATLAS survey. This represents the largest sample of red-Herschel sources with interferometric follow-up observations to date. The high ALMA angular resolution and sensitivity ($\theta _{\rm FWHM}\sim$1 arcsec; $\sigma _{1.3\mathrm{\, mm}}\sim 0.17$ mJy beam$^{-1}$) allow us to classify the sample into individual sources, multiple systems, and potential lenses and/or close mergers. Interestingly, even at this high angular resolution, 73 per cent of our detections are single systems, suggesting that most of these galaxies are isolated and/or post-merger galaxies. For the remaining detections, 20 per cent are classified as multiple systems, 5 per cent as lenses and/or mergers, and 2 per cent as low-z galaxies or active galactic nuclei. Combining the Herschel/SPIRE and ALMA photometry, these galaxies are found to be extreme and massive systems with a median star formation rate of $\sim$1500 $\mathrm{M_{\odot }\, yr^{-1}}$ and molecular gas mass of $M_{\mathrm{gas}}\sim 10^{11}$ $\mathrm{M_{\odot }}$. The median redshift of individual sources is $z\approx 2.8$, while the likely lensed systems are at $z\approx 3.3$, with redshift distributions extending to $z\sim 6$. Our results suggest a common star formation mode for extreme galaxies across cosmic time, likely triggered by close interactions or disc-instabilities, and with short depletion times consistent with the starburst-type population. Moreover, all galaxies with $S_{\mathrm{1.3mm}}\ge 13$ mJy are gravitationally amplified which, similar to the established $S_{500\mathrm{ \, \mu m}}\gt 100$ mJy threshold, can be used as a simple criterion to identify gravitationally lensed galaxies.
The physical mechanism of the streaming instability
Authors: Magnan Nathan , Heinemann Tobias , Latter Henrik N 
Published: August 2024

ABSTRACT
The main hurdle of planet formation theory is the metre-scale barrier. One of the most promising ways to overcome it is via the streaming instability (SI). Unfortunately, the mechanism responsible for the onset of this instability remains mysterious. It has recently been shown that the SI is a Resonant Drag Instability (RDI) involving inertial waves. We build on this insight and clarify the physical picture of how the SI develops, while bolstering this picture with transparent mathematics. Like all RDIs, the SI is built on a feedback loop: in the ‘forward action’, an inertial wave concentrates dust into clumps; in the ‘backward reaction’, those drifting dust clumps excite an inertial wave. Each process breaks into two mechanisms, a fast one and a slow one. At resonance, each forward mechanism can couple with a backward mechanism to close a feedback loop. Unfortunately, the fast-fast loop is stable, so the SI uses the fast-slow and slow-fast loops. Despite this last layer of complexity, we hope that our explanation will help understand how the SI works, in which conditions it can grow, how it manifests itself, and how it saturates.
Searching for the imprints of AGN feedback on the Lyman alpha forest around luminous red galaxies
Authors: Khaire Vikram , Hu Teng , Hennawi Joseph F , Burchett Joseph N , Walther Michael , Davies Frederick 
Published: August 2024

ABSTRACT
We explore the potential of using the low-redshift Lyman $\alpha$ (Ly $\alpha$) forest surrounding luminous red galaxies (LRGs) as a tool to constrain active galactic nuclei (AGNs) feedback models. Our analysis is based on snapshots from the Illustris and IllustrisTNG simulations at a redshift of $z=0.1$. These simulations offer an ideal platform for studying the influence of AGN feedback on the gas surrounding galaxies, as they share the same initial conditions and underlying code but incorporate different feedback prescriptions. Both simulations show significant impacts of feedback on the temperature and density of the gas around massive haloes. Following our previous work, we adjusted the UV background in both simulations to align with the observed number density of Ly $\alpha$ lines ($\rm dN/dz$) in the intergalactic medium and study the Ly $\alpha$ forest around massive haloes hosting LRGs, at impact parameters ($r_{\perp }$) ranging from 0.1 to 100 pMpc. Our findings reveal that $\rm dN/dz$, as a function of $r_{\perp }$, is approximately 1.5 to 2 times higher in IllustrisTNG compared to Illustris up to $r_{\perp }$ of $\sim 10$ pMpc. To further assess whether existing data can effectively discern these differences, we search for archival data containing spectra of background quasars probing foreground LRGs. Through a feasibility analysis based on these data, we demonstrate that ${\rm dN/dz} (r_{\perp })$ measurements can distinguish between feedback models of IllustrisTNG and Illustris with a precision exceeding 16$\sigma$. This underscores the potential of ${\rm dN/dz} (r_{\perp })$ measurements around LRGs as a valuable benchmark observation for discriminating between different feedback models.
Exploring the role of the halo-mass function for inferring astrophysical parameters during reionization
Authors: Greig Bradley , Prelogović David , Mirocha Jordan , Qin Yuxiang , Ting Yuan-Sen , Mesinger Andrei 
Published: August 2024

ABSTRACT
Detecting the 21-cm signal at $z\gtrsim 6$ will reveal insights into the properties of the first galaxies responsible for driving reionization. To extract this information, we perform parameter inference with three-dimensional simulations of the 21-cm signal embedded within a Bayesian inference pipeline. Presently, when performing inference, we must choose which sources of uncertainty to sample and which to hold fixed. Since the astrophysics of galaxies is much more uncertain than that of the underlying halo-mass function (HMF), we typically parametrize and model the former while fixing the latter. However, doing so may bias our inference of the galaxy properties. In this work, we explore the consequences of assuming an incorrect HMF and quantify the relative biases on our inferred astrophysical model parameters when considering the wrong HMF. We then relax this assumption by constructing a generalized five parameter HMF model and simultaneously recover it with our underlying astrophysical model. For this, we use 21cmfast and perform simulation-based inference using marginal neural ratio estimation to learn the likelihood-to-evidence ratio with Swyft. Using a mock 1000-h observation of the 21-cm power spectrum from the forthcoming Square Kilometre Array, conservatively assuming foreground wedge avoidance, we find that assuming the incorrect HMF can bias the recovered astrophysical parameters by up to $\sim 3{\!-\!}4\sigma$ even when including independent information from observed luminosity functions. Using our generalized HMF model, although we recover our astrophysical parameters with a factor of $\sim 2{\!-\!}4$ larger marginalized uncertainties, the constraints are unbiased, agnostic to the underlying HMF and therefore more conservative.
Inferring astrophysical parameters using the 2D cylindrical power spectrum from reionization
Authors: Greig Bradley , Prelogović David , Qin Yuxiang , Ting Yuan-Sen , Mesinger Andrei 
Published: August 2024

ABSTRACT
Enlightening our understanding of the first galaxies responsible for driving reionization requires detecting the 21-cm signal from neutral hydrogen. Interpreting the wealth of information embedded in this signal requires Bayesian inference. Parameter inference from the 21-cm signal is primarily restricted to the spherically averaged power spectrum (1D PS) owing to its relatively straightforward derivation of an analytic likelihood function enabling traditional Monte Carlo Markov Chain approaches. However, in recent years, simulation-based inference (SBI) has become feasible which removes the necessity of having an analytic likelihood, enabling more complex summary statistics of the 21-cm signal to be used for Bayesian inference. In this work, we use SBI, specifically marginal neural ratio estimation to learn the likelihood-to-evidence ratio with swyft, to explore parameter inference using the cylindrically averaged 2D PS. Since the 21-cm signal is anisotropic, the 2D PS should yield more constraining information compared to the 1D PS which isotropically averages the signal. For this, we consider a mock 1000 h observation of the 21-cm signal using the Square Kilometre Array and compare the performance of the 2D PS relative to the 1D PS. Additionally, we explore two separate foreground mitigation strategies, perfect foreground removal and wedge avoidance. We find the 2D PS outperforms the 1D PS by improving the marginalized uncertainties on individual astrophysical parameters by up to $\sim 30\!-\!40$ per cent irrespective of the foreground mitigation strategy. Primarily, these improvements stem from how the 2D PS distinguishes between the transverse, $k_{\perp }$, and redshift-dependent, $k_{\parallel }$, information which enables greater sensitivity to the complex reionization morphology.