bluuebunny/crossref_metadata_2025_split huggingface dataset:
TP53-associated early breast cancer: new observations from a large cohort
Authors: Sandoval Renata L , Bottosso Michele , Tianyu Li , Polidorio Natalia , Bychkovsky Brittany L , Verret Benjamin , Gennari Alessandra , Cahill Sophie , Achatz Maria Isabel , Caron Olivier , Imbert-Bouteille Marion , Noguès Catherine , Mawell Kara N , Fortuno Cristina , Spurdle Amanda B , Tayob Nabihah , Andre Fabrice , Garber Judy E 
Published: April 2024

Abstract

Background
A recent large, well-annotated international cohort of patients with Li-Fraumeni syndrome and early-stage breast cancer was examined for shared features.

Methods
This multicenter cohort study included women with a germline TP53 pathogenic or likely pathogenic variant and nonmetastatic breast cancer diagnosed between 2002 and 2022. Clinical and genetic data were obtained from institutional registries and clinical charts. Descriptive statistics were used to summarize proportions, and differences were assessed using χ2 or Wilcoxon rank sum tests. Metachronous contralateral breast cancer risk, radiation-induced sarcoma risk, and recurrence-free survival were analyzed using the Kaplan-Meier methodology.

Results
Among 227 women who met study criteria, the median age of first breast cancer diagnosis was 37 years (range = 21-71), 11.9% presented with bilateral synchronous breast cancer, and 18.1% had ductal carcinoma in situ only. In total, 166 (73.1%) patients underwent mastectomies, including 67 bilateral mastectomies as first breast cancer surgery. Among those patients with retained breast tissue, the contralateral breast cancer rate was 25.3% at 5 years. Among 186 invasive tumors, 72.1% were stages I to II, 48.9% were node negative, and the most common subtypes were hormone receptor-positive/HER2-negative (40.9%) and hormone receptor positive/HER2 positive (34.4%). At a median follow-up of 69.9 months (interquartile range = 32.6-125.9), invasive hormone receptor–positive/HER2-negative disease had the highest recurrence risk among the subtypes (5-year recurrence-free survival = 61.1%, P = .001). Among those who received radiation therapy (n = 79), the 5-year radiation-induced sarcoma rate was 4.8%.

Conclusion
We observed high rates of ductal carcinoma in situ, hormone receptor–positive, and HER2-positive breast cancers, with a worse outcome in the hormone receptor–positive/HER2-negative luminal tumors, despite appropriate treatment. Confirmation of these findings in further studies could have implications for breast cancer care in those with Li-Fraumeni syndrome.
Identification of hub genes involved in gibberellin-regulated elongation of coleoptiles of rice seeds germinating under submerged conditions
Authors: Hu Yunfei , Ma Mingqing , Zhao Wenlong , Niu Pengwei , Li Rongbai , Luo Jijing 
Published: April 2024

Abstract
Rapid elongation of coleoptiles from rice seeds to reach the water surface enables plants to survive submergence stress and therefore plays a crucial role in allowing direct seeding in rice cultivation. Gibberellin (GA) positively influences growth in rice, but the molecular mechanisms underlying its regulation of coleoptile elongation under submerged conditions remain unclear. In this study, we performed a weighted gene co-expression network analysis to conduct a preliminarily examination of the mechanisms. Four key modules were identified with high correlations to the GA regulation of submergence tolerance. The genes within these modules were mainly involved in the Golgi apparatus and carbohydrate metabolic pathways, suggesting their involvement in enhancing submergence tolerance. Further analysis of natural variation revealed that the specific hub genes Os03g0337900, Os03g0355600, and Os07g0638400 exhibited strong correlations with subspecies divergence of the coleoptile elongation phenotype. Consistent with this analysis, mutation of Os07g0638400 resulted in a lower germination potential and a stronger inhibition of coleoptile elongation under submerged conditions. The hub genes identified in this study provide new insights into the molecular mechanisms underlying GA-dependent tolerance to submergence stress in rice, and a potential basis for future modification of rice germplasm to allow for direct seeding.
Accounting for photosystem I photoinhibition sheds new light on seasonal acclimation strategies of boreal conifers
Authors: Grebe Steffen , Porcar-Castell Albert , Riikonen Anu , Paakkarinen Virpi , Aro Eva-Mari 
Published: April 2024

Abstract
The photosynthetic acclimation of boreal evergreen conifers is controlled by regulatory and photoprotective mechanisms that allow conifers to cope with extreme environmental changes. However, the underlying dynamics of photosystem II (PSII) and photosystem I (PSI) remain unresolved. Here, we investigated the dynamics of PSII and PSI during the spring recovery of photosynthesis in Pinus sylvestris and Picea abies using a combination of chlorophyll a fluorescence, P700 difference absorbance measurements, and quantification of key thylakoid protein abundances. In particular, we derived a new set of PSI quantum yield equations, correcting for the effects of PSI photoinhibition. Using the corrected equations, we found that the seasonal dynamics of PSII and PSI photochemical yields remained largely in balance, despite substantial seasonal changes in the stoichiometry of PSII and PSI core complexes driven by PSI photoinhibition. Similarly, the previously reported seasonal up-regulation of cyclic electron flow was no longer evident, after accounting for PSI photoinhibition. Overall, our results emphasize the importance of considering the dynamics of PSII and PSI to elucidate the seasonal acclimation of photosynthesis in overwintering evergreens. Beyond the scope of conifers, our corrected PSI quantum yields expand the toolkit for future studies aimed at elucidating the dynamic regulation of PSI.
Biofilm-producing Escherichia coli O104:H4 overcomes bile salts toxicity by expressing virulence and resistance proteins
Authors: Machado Maxsueli Aparecida Moura , Chapartegui-González Itziar , Castro Vinicius Silva , Figueiredo Eduardo Eustáquio de Souza , Conte-Junior Carlos Adam , Torres Alfredo G 
Published: April 2024

Abstract
We investigated bile salts’ ability to induce phenotypic changes in biofilm production and protein expression of pathogenic Escherichia coli strains. For this purpose, 82 pathogenic E. coli strains isolated from humans (n = 70), and animals (n = 12), were examined for their ability to form biofilms in the presence or absence of bile salts. We also identified bacterial proteins expressed in response to bile salts using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-electrophoresis) and liquid chromatography-mass spectrometry (LC-MS/MS). Lastly, we evaluated the ability of these strains to adhere to Caco-2 epithelial cells in the presence of bile salts. Regarding biofilm formation, two strains isolated from an outbreak in Republic of Georgia in 2009 were the only ones that showed a high and moderate capacity to form biofilm in the presence of bile salts. Further, we observed that those isolates, when in the presence of bile salts, expressed different proteins identified as outer membrane proteins (i.e. OmpC), and resistance to adverse growth conditions (i.e. F0F1, HN-S, and L7/L12). We also found that these isolates exhibited high adhesion to epithelial cells in the presence of bile salts. Together, these results contribute to the phenotypic characterization of E. coli O104: H4 strains.
Using CHROMagar™ STEC medium exclusively does not recover all clinically relevant Shiga toxin-producing Escherichia coli in Aotearoa, New Zealand
Authors: Rivas Lucia , Duncan David , Wang Jing , Miller Hilary , Wright Jackie 
Published: April 2024

Abstract
Diagnostic laboratories in Aotearoa, New Zealand (NZ) refer cultures from faecal samples positive for Shiga toxin genes to the national Enteric Reference Laboratory for isolation of Shiga toxin-producing Escherichia coli (STEC) for epidemiological typing. As there was variation in the culture media being referred, a panel of 75 clinical isolates of STEC, representing 28 different serotypes, was used to assess six commercially available media and provide guidance to clinical laboratories. Recommendations were subsequently tested for a 3-month period, where STEC isolations and confirmations were assessed by whole genome sequencing analysis against the culture media referred. CHROMagar™ STEC (CH-STEC; CHROMagar Microbiology, Paris, France) or CH-STEC plus cefixime-tellurite sorbitol MacConkey agar was confirmed inferior to CH-STEC plus blood agar with vancomycin, cefsulodin, and cefixime (BVCC). The former resulted in fewer STEC types (n = 18) being confirmed compared to those from a combination of CH-STEC and BVCC (n = 42). A significant (P &lt; .05) association with an STEC’s ability to grow on CH-STEC and the presence of the ter gene cluster, and eae was observed. Culturing screen positive STEC samples onto both CH-STEC and BVCC ensures a consistently higher recovery of STEC from all clinical samples in NZ than CH-STEC alone.
Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T
Authors: Louie Tiffany S , Kumar Anil , Bini Elisabetta , Häggblom Max M 
Published: April 2024

Abstract
Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.
Safety and pharmacokinetics of antifungal agent VT-1598 and its primary metabolite, VT-11134, in healthy adult subjects: phase 1, first-in-human, randomized, double-blind, placebo-controlled study of single-ascending oral doses of VT-1598
Authors: Gu Kenan , Spitz Robert , Hammett Erin , Jaunarajs Anna , Ghazaryan Varduhi , Garvey Edward P , Degenhardt Thorsten 
Published: April 2024

Abstract
VT-1598 is a novel fungal CYP51 inhibitor and 1-tetrazole-based antifungal drug candidate with improved selectivity minimizing off-target binding to and inhibition of human CYP450 enzymes. Data are presented from this first clinical study in the evaluation of the safety and pharmacokinetic (PK) of single ascending doses of 40, 80, 160, 320, and 640 mg VT-1598, comprising a 160 mg cohort in both fasting and fed states. Eight healthy adults per dose were randomized to receive either oral VT-1598 or placebo (3:1). Over the dose range, exposures were with relatively high variation. The maximum plasma concentrations (Cmax) for VT-1598 were 31.00–279.4 ng/ml and for its primary metabolite, VT-11134, were 27.80–108.8 ng/ml. The plasma area under the concentration–time curve to the last measurable concentration (AUC0–last) for VT-1598 were 116.1–4507 ng*h/ml, and for VT-11134 were 1140–7156 ng*h/ml. The dose proportionality was inconclusive based on the results of the power model. The peak concentration time (Tmax) was 4–5 h for VT-1598 and for VT-11134. Half-life was 103–126 h for VT-11134. After food intake, Cmax of VT-1598 increased by 44% (geometric mean ratio (GMR), 1.44; 90%CI [0.691, 2.19]) and AUC0–last by 126% (GMR, 2.26; 90%CI [1.09, 3.44]), while exposure of VT-11134 was decreased 23% for Cmax (GMR, 0.77; 90%CI [0.239, 1.31]) and unchanged for AUC0–last (GMR, 1.02; 90%CI [0.701, 1.33]). Neither VT-1598 nor VT-11134 were detected in urine. No serious adverse events (AEs) or AEs leading to early termination were observed. The safety and PK profiles of VT-1598 support its further clinical development.
Aflatoxin profiles of Aspergillus flavus isolates in Sudanese fungal rhinosinusitis
Authors: Zhou Shaoqin , Ismail Mawahib A I , Aimanianda Vishukumar , de Hoog G Sybren , Kang Yingqian , Ahmed Sarah A 
Published: April 2024

Abstract
Aspergillus flavus is a commonly encountered pathogen responsible for fungal rhinosinusitis (FRS) in arid regions. The species is known to produce aflatoxins, posing a significant risk to human health. This study aimed to investigate the aflatoxin profiles of A. flavus isolates causing FRS in Sudan. A total of 93 clinical and 34 environmental A. flavus isolates were studied. Aflatoxin profiles were evaluated by phenotypic (thin-layer and high-performance chromatography) and genotypic methods at various temperatures and substrates. Gene expression of aflD and aflR was also analyzed. A total of 42/93 (45%) isolates were positive for aflatoxin B1 and AFB2 by HPLC. When the incubation temperature changed from 28°C to 36°C, the number of positive isolates decreased to 41% (38/93). Genetic analysis revealed that 85% (79/93) of clinical isolates possessed all seven aflatoxin biosynthesis-associated genes, while 27% (14/51) of non-producing isolates lacked specific genes (aflD/aflR/aflS). Mutations were observed in aflS and aflR genes across both aflatoxin-producers and non-producers. Gene expression of aflD and aflR showed the highest expression between the 4th and 6th days of incubation on the Sabouraud medium and on the 9th day of incubation on the RPMI (Roswell Park Memorial Institute) medium. Aspergillus flavus clinical isolates demonstrated aflatoxigenic capabilities, influenced by incubation temperature and substrate. Dynamic aflD and aflR gene expression patterns over time enriched our understanding of aflatoxin production regulation. The overall findings underscored the health risks of Sudanese patients infected by this species, emphasizing the importance of monitoring aflatoxin exposure.
SN 2015da: late-time observations of a persistent superluminous Type IIn supernova with post-shock dust formation
Authors: Smith Nathan , Andrews Jennifer E , Milne Peter , Filippenko Alexei V , Brink Thomas G , Kelly Patrick L , Yuk Heechan , Jencson Jacob E 
Published: April 2024

ABSTRACT
We present photometry and spectroscopy of the slowly evolving superluminous Type IIn supernova (SN) 2015da. SN 2015da is extraordinary for its very high peak luminosity, and also for sustaining a high luminosity for several years. Even at 8 yr after explosion, SN 2015da remains as luminous as the peak of a normal SN II-P. The total radiated energy integrated over this time period (with no bolometric correction) is at least $1.6 \times 10^{51}$ erg (or 1.6 FOE). Including a mild bolometric correction, adding kinetic energy of the expanding cold dense shell of swept-up circumstellar material (CSM), and accounting for asymmetry, the total explosion kinetic energy was likely 5–10 FOE. Powering the light curve with CSM interaction requires an energetic explosion and 20 M$_{\odot }$ of H-rich CSM, which in turn implies a massive progenitor system $\gt $30 M$_{\odot }$. Narrow P Cyg features show steady CSM expansion at 90 km s$^{-1}$, requiring a high average mass-loss rate of $\sim$0.1 M$_{\odot }$ yr$^{-1}$ sustained for two centuries before explosion (although ramping up toward explosion time). No current theoretical model for single-star pre-SN mass-loss can account for this. The slow CSM, combined with broad wings of H $\alpha$ indicating H-rich material in the unshocked ejecta, disfavours a pulsational pair instability model for the pre-SN mass-loss. Instead, violent pre-SN binary interaction is a likely culprit. Finally, SN 2015da exhibits the characteristic asymmetric blueshift in its emission lines from shortly after peak until the present epoch, adding another well-studied superluminous SNe IIn with unambiguous evidence of post-shock dust formation.
NSCs from groups to clusters: a catalogue of dwarf galaxies in the Shapley supercluster and the role of environment in galaxy nucleation
Authors: Zanatta Emílio , Sánchez-Janssen Rubén , de Souza Rafael S , Chies-Santos Ana L , Blakeslee John P 
Published: April 2024

ABSTRACT
Nuclear star clusters (NSCs) are dense star clusters located at the centre of galaxies spanning a wide range of masses and morphologies. Analysing NSC occupation statistics in different environments provides an invaluable window into investigating early conditions of high-density star formation and mass assembly in clusters and group galaxies. We use HST/ACS deep imaging to obtain a catalogue of dwarf galaxies in two galaxy clusters in the Shapley supercluster: the central cluster Abell 3558 and the northern Abell 1736a. The Shapley region is an ideal laboratory to study nucleation as it stands as the highest mass concentration in the nearby Universe. We investigate the NSC occurrence in quiescent dwarf galaxies as faint as MI = −10 mag and compare it with all other environments where nucleation data is available. We use galaxy cluster/group halo mass as a proxy for the environment and employ a Bayesian logistic regression framework to model the nucleation fraction (fn) as a function of galaxy luminosity and environment. We find a notably high fn in Abell 3558: at MI ≈ −13.1 mag, half the galaxies in the cluster host NSCs. This is higher than in the Virgo and Fornax clusters but comparable to the Coma Cluster. On the other hand, the fn in Abell 1736a is relatively lower, comparable to groups in the local volume. We find that the probability of nucleation varies with galaxy luminosity remarkably similarly in galaxy clusters. These results reinforce previous findings of the important role of the environment in NSC formation/growth.
Generic gravito-magnetic clock effects
Authors: Li Kaye Jiale , Wu Kinwah , Younsi Ziri , Teixeira Joana , Singh Dinesh 
Published: April 2024

ABSTRACT
General relativity predicts that two counter-orbiting clocks around a spinning mass differ in the time required to complete the same orbit. The difference in these two values for the orbital period is generally referred to as the gravito-magnetic (GM) clock effect. It has been proposed to measure the GM clock effect using atomic clocks carried by satellites in prograde and retrograde orbits around the Earth. The precision and stability required for satellites to accurately perform this measurement remains a challenge for current instrumentation. One of the most accurate clocks in the Universe is a millisecond pulsar, which emits periodic radio pulses with high stability. Timing of the pulsed signals from millisecond pulsars has proven to be very successful in testing predictions of general relativity and the GM clock effect is potentially measurable in binary systems. In this work, we derive the generic GM clock effect by considering a slowly spinning binary system on an elliptical orbit, with both arbitrary mass ratio and arbitrary spin orientations. The spin–orbit interaction introduces a perturbation to the orbit, causing the orbital plane to precess and nutate. We identify several different contributions to the clock effects: the choice of spin supplementary condition and the observer-dependent definition of a full revolution and ‘nearly identical’ orbits. We discuss the impact of these subtle definitions on the formula for GM clock effects and show that most of the existing formulae in the literature can be recovered under appropriate assumptions.
Pulsation phases and mode identification of tidally excited oscillations in fourteen Kepler Heartbeat Stars
Authors: Li Min-Yu , Qian Sheng-Bang , Zhu Li-Ying , Guo Zhao , Liao Wen-Ping , Zhao Er-Gang , Shi Xiang-Dong , Li Fu-Xing , Sun Qi-Bin 
Published: April 2024

ABSTRACT
Tidally excited oscillations (TEOs) in Heartbeat Stars (HBSs) are an essential probe of the internal properties of the systems, but their potential has yet to be fully exploited. Based on the orbital parameters of TEO candidates from our previous works, we identify the pulsation phases and amplitudes of TEOs in 14 Kepler HBSs. Most pulsation phases of most systems can be explained by the dominant being l = 2, m = 0, or ±2 spherical harmonic, assuming that the spin and orbital axes are aligned, and the pulsations are adiabatic and standing waves. The largest deviation (&gt;6σ) occurs in KIC 8459354, which can be explained by the spin-orbit misalignment, and KIC 5877364 has a similar scenario. For KIC 11122789, almost half of the harmonics show large deviations; we cautiously suggest that these harmonics may not be considered TEO candidates. A similar scenario also exists in KIC 6290740. This phases and mode identification approach can also be used inversely to verify the TEO candidates derived by the Fourier analysis. Furthermore, the harmonics with large deviations (&gt;2σ) in KIC 4377638, KIC 5090937, and KIC 11403032 can be expected to be travelling waves rather than standing waves. In addition, we also suggest that the apsidal motion could cause large deviations in TEO phases from theoretical values.
Enabling unsupervised discovery in astronomical images through self-supervised representations
Authors: Mohale Koketso , Lochner Michelle 
Published: April 2024

ABSTRACT
Unsupervised learning, a branch of machine learning that can operate on unlabelled data, has proven to be a powerful tool for data exploration and discovery in astronomy. As large surveys and new telescopes drive a rapid increase in data size and richness, these techniques offer the promise of discovering new classes of objects and of efficient sorting of data into similar types. However, unsupervised learning techniques generally require feature extraction to derive simple but informative representations of images. In this paper, we explore the use of self-supervised deep learning as a method of automated representation learning. We apply the algorithm Bootstrap Your Own Latent to Galaxy Zoo DECaLS images to obtain a lower dimensional representation of each galaxy, known as features. We briefly validate these features using a small supervised classification problem. We then move on to apply an automated clustering algorithm, demonstrating that this fully unsupervised approach is able to successfully group together galaxies with similar morphology. The same features prove useful for anomaly detection, where we use the framework astronomaly to search for merger candidates. While the focus of this work is on optical images, we also explore the versatility of this technique by applying the exact same approach to a small radio galaxy data set. This work aims to demonstrate that applying deep representation learning is key to unlocking the potential of unsupervised discovery in future data sets from telescopes such as the Vera C. Rubin Observatory and the Square Kilometre Array.