bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chiral single photons from deterministic quantum emitter arrays via proximity coupling to van der Waals ferromagnets
Authors: Liu Na , Xiao Licheng , Fu Shichen , Ma Yichen , Liu Song , Chen Siwei , Hone James , Yang Eui-Hyeok , Strauf Stefan 
Published: July 2023

Abstract
Chiral single photons are highly sought to enhance encoding capacities or enable propagation-dependent routing in nonreciprocal devices. Unfortunately, most semiconductor quantum emitters (QEs) produce only linear polarized photons unless external magnets are applied. Magnetic proximity coupling utilizing 2D ferromagnets promises to make bulky external fields obsolete. Here we directly grow Fe-doped MoS2 (Fe:MoS2) via chemical vapor deposition that displays pronounced hard ferromagnetic properties even in monolayer form. This approach with monolayer ferromagnets enables full utilization of the strain from the pillar stressor to form QE in WSe2 deterministically. The Fe:MoS2/WSe2 heterostructures display strong hysteretic magneto-response and high-purity chiral single photons with a circular polarization degree of 92 ± 1% (74% average) without external magnetic fields. Furthermore, the chiral single photons are robust against uncontrolled twist-angle and external stray-fields. This ability to manipulate quantum states and transform linear polarized photons into high-purity chiral photons on-chip enables nonreciprocal device integration in quantum photonics.
Spatial and temporal distribution of HCHO and its pollution sources based on satellite remote sensing: a case study of the Yangtze River Economic Belt
Authors: Huang Cheng , Ju Tianzhen , Geng Tunyang , Fan Jiachen , Peng Shuai , Xia Xuhui , Niu Xiaowen 
Published: July 2023

Abstract
In recent years, with the acceleration of industrialization and the expansion of urban scale, air pollution including formaldehyde (HCHO) becomes more and more serious. In order to study HCHO pollution in the Yangtze River Economic Belt (YEB), the temporal and spatial evolution of atmospheric HCHO and its influencing factors were analyzed by using the Ozone Monitoring Instrument (OMI) during 2012–2021. The results showed that the concentration of YEB HCHO column was unevenly distributed, with high values concentrated in Anhui, Jiangsu, Yunnan and Hubei provinces. During the past 10 years, the concentration of YEB HCHO column varied between 10.28 and 17.19 × 1015 molec cm−2, and the lowest concentration of HCHO column was 13.16 × 1015 molec cm−2 in 2015. However, it reached the peak value in 2018 (14.93 × 1015 molec cm−2). In natural sources, normalized vegetation index (NDVI) and leaf area index (LAI) had greater influence on YEB HCHO, and the correlation was −0.91 ∼ 0.97 and −0.9 ∼ 0.95, respectively. The positive correlation area between HCHO and Mean annual temperature (MAT) reached 93%. The contribution of high-intensity human activity areas to HCHO cannot be underestimated. Industrial and civil sources have great influence on HCHO. In addition, the potential source of HCHO in Shanghai is affected by local emission sources, trans-regional potential sources, northwest air mass and ocean airflow.
Reformulation of traditional Iranian food (Doeeneh) using probiotics: Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus acidophilus LA-5, Lacticaseibacillus rhamnosus LGG, and inulin and its effect on diabetic and non-diabetic rats
Authors: AziziShafa Mahdi , Akhondzadeh Basti Afshin , Sharifan Anousheh , Khanjari Ali 
Published: July 2023

Abstract

Objectives
The purposes of this study were to produce novel formulations of Doeeneh using three probiotic strains and different inulin ratios and to investigate the survival of probiotics. Likewise, the effect of Doeeneh on the biological properties of non-diabetic and diabetic rats was also evaluated.

Materials and Methods
Doeeneh, composed of milk and wheat bulgur, was enriched with different proportions of inulin and fermented by Bifidobacterium animalis subsp. lactis BB-12 (B), Lactobacillus acidophilus LA-5 (A), Lacticaseibacillus rhamnosus LGG (R), and their co-cultures. The physicochemical and sensory properties and probiotics viability were investigated for 14 d. Diabetes was induced in albino rats by administration of alloxan monohydrate (150 mg/kg i.p.). Changes in weight and blood glucose were measured weekly, and food and water consumption were measured daily; total cholesterol and triglycerides were measured after 35 d by a biochemical kit.

Results
The increased proportion of high-degree of polymerization inulin decreased pH and increased acidity. However, a higher concentration of inulin applied to Doeeneh resulted in a slower decrease in pH value. This result can show the buffering effect of inulin in Doeeneh as well; changes in pH were slow over time due to the presence of the buffering compounds. Therefore, the probiotics’ survival was in the standard range even in the inulin-free sample. Likewise, the Doeeneh sample containing 5% inulin (SABR3) considerably reduced the levels of blood glucose, total cholesterol, and triglyceride in diabetic rats. Moreover, the diabetic rats fed Doeeneh demonstrated less weight loss and food/water intake than the control.

Conclusions
Traditional foods and their preparation methods are a suitable target for the development of health-oriented products, and functional food with nutraceutical capabilities can be designed and produced based on them.
Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche
Authors: Carr Erin C , Barton Quin , Grambo Sarah , Sullivan Mitchell , Renfro Cecile M , Kuo Alan , Pangilinan Jasmyn , Lipzen Anna , Keymanesh Keykhosrow , Savage Emily , Barry Kerrie , Grigoriev Igor V , Riekhof Wayne R , Harris Steven D 
Published: July 2023

Abstract
Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primar yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.
Existence of Solutions on the Critical Hyperbola for a Pure Lane–Emden System with Neumann Boundary Conditions
Authors: Pistoia Angela , Schiera Delia , Tavares Hugo 
Published: July 2023

Abstract
We study the following Lane–Emden system: $$\begin{align*} & -\Delta u=|v|^{q-1}v \quad \ \textrm{in}\ \Omega, \qquad -\Delta v=|u|^{p-1}u \quad \ \textrm{in}\ \Omega, \qquad u_{\nu}=v_{\nu}=0 \quad \ \textrm{on}\ \partial \Omega, \end{align*}$$with $\Omega $ a bounded regular domain of ${\mathbb{R}}^{N}$, $N \ge 4$, and exponents $p, q$ belonging to the so-called critical hyperbola $1/(p+1)+1/(q+1)=(N-2)/N$. We show that, under suitable conditions on $p, q$, least-energy (sign-changing) solutions exist, and they are classical. In the proof we exploit a dual variational formulation, which allows to deal with the strong indefinite character of the problem. We establish a compactness condition which is based on a new Cherrier-type inequality. We then prove such condition by using as test functions the solutions to the system in the whole space and performing delicate asymptotic estimates. If $N \ge 5$, $p=1$, the system above reduces to a biharmonic equation, for which we also prove existence of least-energy solutions. Finally, we prove some partial symmetry and symmetry-breaking results in the case $\Omega $ is a ball or an annulus.
Prevotella and Gardnerella Are Associated With Treatment Failure Following First-line Antibiotics for Bacterial Vaginosis
Authors: Plummer Erica L , Sfameni Amelia M , Vodstrcil Lenka A , Danielewski Jennifer A , Murray Gerald L , Fehler Glenda , Fairley Christopher K , Garland Suzanne M , Chow Eric P F , Hocking Jane S , Bradshaw Catriona S 
Published: July 2023

Abstract

Background
Bacterial vaginosis (BV) is a common vaginal dysbiosis that often recurs following first-line antibiotics. We investigated if vaginal microbiota composition was associated with BV recurrence.

Methods
We analyzed samples and data from 121 women who participated in 3 published trials evaluating novel interventions for improving BV cure, including concurrent antibiotic treatment of regular sexual partners (RSPs). Women diagnosed with BV received first-line antibiotics and self-collected vaginal swabs pretreatment and the day after finishing antibiotics (immediately posttreatment). 16S rRNA gene sequencing was performed on vaginal samples. Logistic regression explored associations between BV recurrence and features of the vaginal microbiota pre- and posttreatment.

Results
Sixteen women (13% [95% confidence interval {CI}, 8%–21%]) experienced BV recurrence within 1 month of treatment. Women with an untreated RSP were more likely to experience recurrence than women with no RSP (P = .008) or an RSP who received treatment (P = .011). A higher abundance of Prevotella pretreatment (adjusted odds ratio [AOR], 1.35 [95% CI, 1.05–1.91]) and Gardnerella immediately posttreatment (AOR, 1.23 [95% CI, 1.03–1.49]) were associated with increased odds of BV recurrence.

Conclusions
Having specific Prevotella spp prior to recommended treatment and persistence of Gardnerella immediately posttreatment may contribute to the high rates of BV recurrence. Interventions that target these taxa are likely required to achieve sustained BV cure.
Enhancing performance of electron holography with mathematical and machine learning–based denoising techniques
Authors: Anada Satoshi , Nomura Yuki , Yamamoto Kazuo 
Published: July 2023

AbstractElectron holography is a useful tool for analyzing functional properties, such as electromagnetic fields and strains of materials and devices. The performance of electron holography is limited by the ‘shot noise’ inherent in electron micrographs (holograms), which are composed of a finite number of electrons. A promising approach for addressing this issue is to use mathematical and machine learning–based image-processing techniques for hologram denoising. With the advancement of information science, denoising methods have become capable of extracting signals that are completely buried in noise, and they are being applied to electron microscopy, including electron holography. However, these advanced denoising methods are complex and have many parameters to be tuned; therefore, it is necessary to understand their principles in depth and use them carefully. Herein, we present an overview of the principles and usage of sparse coding, the wavelet hidden Markov model and tensor decomposition, which have been applied to electron holography. We also present evaluation results for the denoising performance of these methods obtained through their application to simulated and experimentally recorded holograms. Our analysis, review and comparison of the methods clarify the impact of denoising on electron holography research.
Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer
Authors: Grimes Susan M , Kim Heon Seok , Roy Sharmili , Sathe Anuja , Ayala Carlos I , Bai Xiangqi , Almeda-Notestine Alison F , Haebe Sarah , Shree Tanaya , Levy Ronald , Lau Billy T , Ji Hanlee P 
Published: July 2023

Abstract
In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.
Model Complexity, Expectations, and Asset Prices
Authors: Molavi Pooya , Tahbaz-Salehi Alireza , Vedolin Andrea 
Published: July 2023

Abstract
This paper analyses how limits to the complexity of statistical models used by market participants can shape asset prices. We consider an economy in which the stochastic process that governs the evolution of economic variables may not have a simple representation, and yet, agents are only capable of entertaining statistical models with a certain level of complexity. As a result, they may end up with a lower-dimensional approximation that does not fully capture the intertemporal complexity of the true data-generating process. We first characterize the implications of the resulting departure from rational expectations and relate the extent of return and forecast-error predictability at various horizons to the complexity of agents’ models and the statistical properties of the underlying process. We then apply our framework to study violations of uncovered interest rate parity in foreign exchange markets. We find that constraints on the complexity of agents’ models can generate return predictability patterns that are simultaneously consistent with the well-known forward discount and predictability reversal puzzles.
Integrating Disaster Management Into Curricula: A Successful Collaboration With Community Partners
Authors: Gibson Terri L. , Davis Kathy , Smith Ann L. 
Published: July 2023

Abstract
Millions of people are killed annually in disasters, and even more are injured, displaced, and in need of emergency assistance. Communities continue to need nurses who can respond effectively during times of disaster. A one-credit course was developed to provide a collaborative and engaging approach to prepare students for disaster and mass casualty situations. Student evaluation responses regarding all segments of the course indicate satisfaction and quality learning. The course prepared and qualified students to volunteer for a community service organization and provide community-based care.
Effective Postoperative Surveillance Protocol after Thoracoscopic Esophagectomy Focusing on Symptoms in Patients with Esophageal Cancer
Authors: Tajima Kohei , Koyanagi Kazuo , Ozawa Soji , Kazuno Akihito , Yamamoto Miho , Shoji Yoshiaki , Yatabe Kentaro , Kanamori Kohei , Zhao Hongbo , Mori Masaki 
Published: July 2023

BACKGROUND:
The optimal postoperative surveillance protocol after esophagectomy for patients with esophageal cancer has still not been established. We investigated the risk factors for recurrence of esophageal cancer to devise an appropriate surveillance protocol. We focused on the appearance and worsening of symptoms to determine if additional imaging examinations should be performed.

STUDY DESIGN:
We enrolled 416 patients with esophageal and esophagogastric junctional cancer who had undergone thoracoscopic esophagectomy at Tokai University Hospital. Outpatient visits for the patients are usually scheduled at least 4 times per year with CT imaging and blood biochemical examination. We evaluated the time to recurrence after esophagectomy, especially the correlation of this parameter with the appearance and worsening of symptoms during the postoperative outpatient follow-up.

RESULTS:
Of the 416 patients, recurrence occurred in 127 patients (30.5%). The median time to recurrence was 6 months after esophagectomy; recurrence occurred within 24 months in 112 patients (88%), and 51 of these patients (40%) developed some new symptom(s) (symptomatic group) before the diagnosis of recurrence. The number of patients who developed recurrence within 6 months was significantly higher in the symptomatic group compared with that in the asymptomatic group (66.7% vs 46.0%, p = 0.02). The overall survival in the symptomatic group was significantly shorter than that in the asymptomatic group (p < 0.001).

CONCLUSIONS:
We advocate an effective surveillance protocol depending on the appearance and worsening of symptoms to diagnose recurrence of esophageal cancer; we recommend routine imaging examinations every 6 months and clinical outpatient follow-up at even shorter intervals for the first 24 months after esophagectomy.
The evolution of nest site use and nest architecture in modern birds and their ancestors
Authors: Mainwaring Mark C. , Medina Iliana , Tobalske Bret W. , Hartley Ian R. , Varricchio David J. , Hauber Mark E. 
Published: July 2023

The evolution of nest site use and nest architecture in the non-avian ancestors of birds remains poorly understood because nest structures do not preserve well as fossils. Nevertheless, the evidence suggests that the earliest dinosaurs probably buried eggs below ground and covered them with soil so that heat from the substrate fuelled embryo development, while some later dinosaurs laid partially exposed clutches where adults incubated them and protected them from predators and parasites. The nests of euornithine birds—the precursors to modern birds—were probably partially open and the neornithine birds—or modern birds—were probably the first to build fully exposed nests. The shift towards smaller, open cup nests has been accompanied by shifts in reproductive traits, with female birds having one functioning ovary in contrast to the two ovaries of crocodilians and many non-avian dinosaurs. The evolutionary trend among extant birds and their ancestors has been toward the evolution of greater cognitive abilities to construct in a wider diversity of sites and providing more care for significantly fewer, increasingly altricial, offspring. The highly derived passerines reflect this pattern with many species building small, architecturally complex nests in open sites and investing significant care into altricial young.
This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.
Foraging behaviour affects nest architecture in a cross-species comparison of ant nests
Authors: O'Fallon Sean , Drager Kim , Zhao Art , Suarez Andrew , Pinter-Wollman Noa 
Published: July 2023

Animals construct and inhabit nests that can exhibit dramatic intra- and interspecific variation due to differences in behaviour, the biotic and abiotic environment, and evolutionary history. In ants, variation in nest architecture reflects both differences in ecology and in the collective behaviour of the colonies that live in the nests. Each component of the nest (such as depth, and the number, size and connectivity of chambers) reflects selective pressures for different functions, or structural constraints that are imposed by the environment or evolutionary history. To determine potential drivers of nest structure variation in subterranean nests, we performed a meta-analysis of measures of published ant nests to compare different structural elements within and across species. We complemented this survey with 42 nest casts of two closely related species. We quantified nest features that can potentially impact ant foraging behaviour and examined whether phylogeny or foraging strategy are better explanatory variables for the variation we observed. We found that foraging strategy better explained nest features than evolutionary history. Our work reveals the importance of ecology in shaping nest structure and provides an important foundation for future investigations into the selective pressures that have shaped ant nest architecture.This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.
Beak shape and nest material use in birds
Authors: Sheard Catherine , Street Sally E. , Evans Caitlin , Lala Kevin N. , Healy Susan D. , Sugasawa Shoko 
Published: July 2023

The evolution of behaviour can both influence, and be influenced by, morphology. Recent advances in methods and data availability have facilitated broad-scale investigations of physical form and behavioural function in many contexts, but the relationship between animal morphology and object manipulation—particularly objects used in construction—remains largely unknown. Here, we employ a new global database of nest materials used by 5924 species of birds together with phylogenetically informed random forest models to evaluate the link between beak shape and these nest-building materials. We find that beak morphology, together with species diet and access to materials, can predict nest-material use above chance and with high accuracy (68–97%). Much of this relationship, however, is driven by phylogenetic signal and sampling biases. We therefore conclude that while variation in nest material use is linked with that of beak shape across bird species, these correlations are modulated by the ecological context and evolutionary history of these species.This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.
Long-term environmental stability does not erode plasticity in nest building responses to changing ambient conditions
Authors: Chung Meng-Han Joseph , Barber Iain , Head Megan L. 
Published: July 2023

The primary function of animal nests is to protect developing offspring from hostile and fluctuating environments. Animal builders have been shown to adjust nest construction in response to changes in their environment. However, the extent of this plasticity, and its dependence on an evolutionary history of environmental variability, is not well understood. To test whether an evolutionary history with flowing water impacts male ability to adjust nests in response to flow regime, we collected three-spined sticklebacks (Gasterosteus aculeatus) from three lakes and three rivers, and brought them into reproductive condition in controlled laboratory aquaria. Males were then allowed to nest under both flowing and static conditions. Nest building behaviour, nest structure and nest composition were all recorded. In comparison to males building nests under static conditions, males building in flowing water took longer to construct their nests and invested more in nesting behaviour. Moreover, nests built in flowing water contained less material, were smaller, more compact, neater and more elongated than nests built under static conditions. Whether males came from rivers or lakes had little impact on nesting activities, or male capacity to adjust behaviours in response to flow treatment. Our findings suggest that aquatic animals which have experienced a stable environment over a long period of time retain plasticity in nest-building behaviours that allow them to adjust nests to ambient flow conditions. This ability may prove crucial in coping with the increasingly unpredictable flow regimes found in anthropogenically altered waterways and those resulting from global climate change.This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.