bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitivity of principal components to system changes in the presence of non-stationarity
Authors: Bette Henrik M , Schreckenberg Michael , Guhr Thomas
Published: October 2023

Non-stationarity affects the sensitivity of change detection in correlated systems described by sets of measurable variables. We study this by projecting onto different principal components. Non-stationarity is modeled as multiple normal states that exist in the system even before a change occurs. The studied changes occur in mean values, standard deviations or correlations of the variables. Monte Carlo simulations are performed to test the sensitivity for change detection with and without knowledge about non-stationarity for different system dimensions and numbers of normal states. A comparison clearly shows that knowledge about the non-stationarity of the system greatly improves change detection sensitivity for all principal components. This improvement is largest for those components that already provide the greatest possibility for change detection in the stationary case. We illustrate our results with an example using real traffic flow data, in which we detect a weekend and a bank holiday start as anomalies.
Optimisation via encodings: a renormalisation group perspective
Authors: Klemm Konstantin , Mehta Anita , Stadler Peter F
Published: October 2023

Difficult, in particular NP-complete, optimization problems are traditionally solved approximately using search heuristics. These are usually slowed down by the rugged landscapes encountered, because local minima arrest the search process. Cover-encoding maps were devised to circumvent this problem by transforming the original landscape to one that is free of local minima and enriched in near-optimal solutions. By definition, these involve the mapping of the original (larger) search space into smaller subspaces, by processes that typically amount to a form of coarse-graining. In this paper, we explore the details of this coarse-graining using formal arguments, as well as concrete examples of cover-encoding maps, that are investigated analytically as well as computationally. Our results strongly suggest that the coarse-graining involved in cover-encoding maps bears a strong resemblance to that encountered in renormalisation group schemes. Given the apparently disparate nature of these two formalisms, these strong similarities are rather startling, and suggest deep mathematical underpinnings that await further exploration.
All-dielectric terahertz metasurfaces for arbitrary linear polarization detection
Authors: Xu Wenhui , Li Hui , Xu Hang , Tan Qi , Song Chunyu , Yao Jianquan
Published: October 2023

The polarization state, an intrinsic property of electromagnetic waves, plays a key role in determining the mechanism of light–matter interactions. Recently, the bulky elements for evaluating polarization states have been miniaturized by using metasurfaces. However, determining arbitrary linear polarization (LP) states from vortex beams generated by metasurfaces is quite challenging. Here, a general design of all-silicon quasi-periodic arrays based on polarization multiplexing technology is proposed, which can be used for the detection of arbitrary incident LP state. By embedding independent helical phase profiles in two orthogonal LP channels, the generated interference spot at the predesigned focal plane is resolvable in a proper polarized direction. Benefiting from the establishment of a parametric theoretical model, the evolution of the incident polarization can be determined using key parameters defined on the pixelated focal plane. The proposed method can flexibly determine the polarization state of incident terahertz waves, which has great potential in remote sensing, high-resolution imaging, and data communication.
Simultaneous nonlinear spectral broadening and temporal contrast enhancement of ultrashort pulses in a multi-pass cell
Authors: Kaur Jaismeen , Daniault Louis , Cheng Zhao , Tourneur Oscar , Tcherbakoff Olivier , Réau Fabrice , Hergott Jean-François , Lopez-Martens Rodrigo
Published: October 2023

We study both numerically and experimentally the use of two third-order nonlinear temporal filtering techniques, namely nonlinear ellipse rotation and cross-polarized wave generation, for simultaneous nonlinear spectral broadening and temporal contrast enhancement of mJ energy, 30 fs titanium:sapphire laser pulses in a multi-pass cell. In both cases, a contrast enhancement greater than 3 orders of magnitude is observed, together with record high conversion efficiencies. Careful balancing of nonlinearity and dispersion inside the multi-pass cell helps tune the spectral broadening process and control the post-compressed pulse duration for specific applications.
Global epidemiology of actinic keratosis in the general population: a systematic review and meta-analysis
Authors: George Christopher D , Lee Truelian , Hollestein Loes M , Asgari Maryam M , Nijsten Tamar
Published: October 2023

Background

Actinic keratosis (AK) is a common dermatological condition, and among the most common dermatological diagnoses in older populations. Although the prevalence of AK depends on demographic and environmental factors, little is known about the global context of AK.

Objectives

To provide a comprehensive and updated analysis of the global prevalence rate and incidence of AK in the general population through a systematic review and meta-analysis, and – through subgroup analyses – to identify high-risk phenotypes, demographic and lifestyle risk factors and regional variations in disease prevalence.

Methods

A systematic search of Embase, MEDLINE, Web of Science and Google Scholar was performed on 20 May 2022. Two reviewers independently screened and assessed the quality of each study using a validated critical appraisal checklist. Epidemiological measurements (e.g. prevalence) from individual studies performed in the general population were then pooled in a random-effects meta-analysis. Subgroup analyses (i.e. population age, geographical region, occupation, sex and study quality) were conducted.

Results

Of the 65 articles that made it through the full-text screening, 60 reported a point prevalence. A meta-analysis of these articles yielded an overall point prevalence of 14% [95% confidence interval (CI) 14–15]. In further analyses, the calculated prevalence rate varied depending on subgroup. The pooled incidence rate from the seven eligible studies analysed was 1928 per 100 000 person-years (PY; 95% CI −439 to 4294).

Conclusions

This comprehensive meta-analysis provides an updated global prevalence rate of AK of 14%, indicating a significant worldwide disease burden. The incidence rate of AK was found to be 1928 per 100 000 PY, emphasizing a growing public health concern. However, high heterogeneity among studies suggests that various factors influence the AK prevalence rate, necessitating further research to understand the observed differences.
Individuals with Darier disease have an increased risk of suicide and self-injurious behaviours
Authors: Cederlöf Martin , Jebril William , Larsson Henrik , Curman Philip , Bachar-Wikström Etty , Wikström Jakob D
Published: October 2023

In a large population-based registry study of 935 patients in Sweden with Darier disease, we show that patients with the disease display significantly increased risks of suicide and self-injurious behaviours.
International patterns and trends in the incidence of melanoma and cutaneous squamous cell carcinoma, 1989–2020
Authors: Olsen Catherine M , Pandeya Nirmala , Ragaini Bruna S , Neale Rachel E , Whiteman David C
Published: October 2023

Background

Cutaneous squamous cell carcinoma (cSCC) and melanoma have different associations with sun exposure.

Objectives

To compare trends in the incidence rates of cSCC and melanoma, to provide insight into changing patterns of exposure to ultraviolet radiation (UVR).

Methods

We compared trends in the incidence of cSCC and melanoma in seven susceptible populations residing at mid-to-high latitudes: Finland, Norway, Sweden, Denmark, Scotland, the Netherlands and Tasmania (Australia). We fitted Joinpoint models to describe trends in age-standardized incidence rates for melanoma and cSCC and calculated the average annual percentage rate of change for the period 1989–2020 (1989–2018 for Tasmania). We calculated the incident rate ratio (IRR) as the ratio of the age-standardized rates (European Standard Population) for cSCC to melanoma and conducted age–period–cohort modelling to compare age, period and cohort effects.

Results

The ratio of cSCC-to-melanoma incidence increased with proximity to the equator and over time. In the most recent time period, the incidence of cSCC was higher than the incidence of melanoma for men and women in all seven populations. While the ratio of cSCC-to-melanoma incidence was higher for men vs. women, in most countries the cSCC-to-melanoma IRR increased over time to a greater extent in women than in men. Melanoma incidence was higher among younger people and cSCC incidence was higher among older people; the age at which the incidence of cSCC overtook the incidence of melanoma was progressively younger with proximity to the equator.

Conclusions

Despite concerted international efforts to preserve the ozone layer over the past four decades resulting in significant reductions in surface ultraviolet B at mid-latitudes, the incidence of skin cancer, particularly cSCC, continues to rise in those regions. Our findings are consistent with a stronger association with age-associated cumulative sun exposure for cSCC vs. melanoma and suggest that women are currently receiving greater UV radiation exposure than in the past.
Endovascular arch repair of anastomotic aneurysm and pseudoaneurysm in patients after open repair of the ascending aorta and aortic arch: a case series
Authors: Becker Daniel , Stana Jan , Prendes Carlota F , Konstantinou Nikolaos , Öz Tugce , Pichlmaier Maximilian , Peterss Sven , Tsilimparis Nikolaos
Published: October 2023

OBJECTIVES

The aim of the study was to investigate the outcomes of branched endovascular arch repair (b-TEVAR) with a custom-made double- or triple-branched arch endograft in patients with distal anastomotic aneurysms after open repair of the ascending aorta or proximal arch replacement.

METHODS

Retrospective analysis was conducted of all consecutive patients with anastomotic aneurysms after open surgical repair involving the ascending aorta and/or aortic arch treated with b-TEVAR. All patients were treated with a custom-made double or triple inner-branched arch endograft. Study end points were technical success, 30-day and follow-up mortality/morbidity and re-interventions.

RESULTS

Between 2018 and 2022, 10 patients were treated with custom-made double- or triple-branched thoracic endovascular aortic repair due to anastomotic aneurysms after open ascending aorta and/or proximal aortic arch replacement. Eight patients received a triple and 2 a double arch-branched endograft. Eight cases were performed electively and 2 urgently for contained rupture. Technical success was achieved in 9 cases (90%). All elective patients survived. Two patients treated due to contained ruptures expired. Within 30 postoperative days, 1 transient ischaemic attack occurred. No early endograft-related re-interventions were necessary. The median follow-up was 20 months. One patient died 2 months after discharge due to sepsis caused by pneumonia. No further deaths or endograft-related re-interventions were observed.

CONCLUSIONS

Endovascular aortic arch repair with double or triple inner-branched arch endograft for anastomotic aneurysms after open ascending and/or proximal arch replacement is technically feasible and a promising alternative in a patient cohort unfit for surgery.
Enhancing the interpretation of genetic observations in KCNQ1 in unselected populations: relevance to secondary findings
Authors: Novelli Valeria , Faultless Trent , Cerrone Marina , Care Melanie , Manzoni Martina , Bober Sara L , Adler Arnon , De-Giorgio Fabio , Spears Danna , Gollob Michael H
Published: October 2023

Aims

Rare variants in the KCNQ1 gene are found in the healthy population to a much greater extent than the prevalence of Long QT Syndrome type 1 (LQTS1). This observation creates challenges in the interpretation of KCNQ1 rare variants that may be identified as secondary findings in whole exome sequencing.

This study sought to identify missense variants within sub-domains of the KCNQ1-encoded Kv7.1 potassium channel that would be highly predictive of disease in the context of secondary findings.

Methods and results

We established a set of KCNQ1 variants reported in over 3700 patients with diagnosed or suspected LQTS sent for clinical genetic testing and compared the domain-specific location of identified variants to those observed in an unselected population of 140 000 individuals. We identified three regions that showed a significant enrichment of KCNQ1 variants associated with LQTS at an odds ratio (OR) >2: the pore region, and the adjacent 5th (S5) and 6th (S6) transmembrane (TM) regions. An additional segment within the carboxyl terminus of Kv7.1, conserved region 2 (CR2), also showed an increased OR of disease association. Furthermore, the TM spanning S5–Pore–S6 region correlated with a significant increase in cardiac events.

Conclusion

Rare missense variants with a clear phenotype of LQTS have a high likelihood to be present within the pore and adjacent TM segments (S5–Pore–S6) and a greater tendency to be present within CR2. This data will enhance interpretation of secondary findings within the KCNQ1 gene. Further, our data support a more severe phenotype in LQTS patients with variants within the S5–Pore–S6 region.
Vesicle-enriched secretomes alter bacterial competitive abilities and are drivers of evolution in microbial communities
Authors: Warsi Omar M , Gedda Lars , Edwards Katarina , Andersson Dan I
Published: October 2023

Microbial membrane vesicles can carry compounds that inhibit bacterial growth, but how they impact the fitness of the vesicle-producing bacterial species and influence community dynamics remain unexplored questions. To address these questions, we examined the effect of vesicle-enriched secretomes (VESs) in different single-species and multi-species systems. Effects of VESs on single-species growth dynamics were determined for nine bacterial species belonging to four genera (Escherichia, Salmonella, Pseudomonas and Bacillus) in nutrient-rich and poor growth media. Results showed both species-specific and nutrient-dependent effects of the VESs on bacterial growth. The strongest antagonistic effects were observed for VES isolated from the natural isolates of E. coli, while those isolated from P. aeruginosa PA14 affected the highest number of species. We further demonstrated that these VESs altered the competitive abilities of the species involved in two-species (S. Typhimurium LT2 and S. arizonae) and three-species systems (E. coli, S. Typhimurium LT2 and B. subtilis). Finally, using experimental evolution we showed that different bacterial species could rapidly acquire mutations that abrogated the antagonistic effects of VESs. This study demonstrates how VESs can contribute in shaping microbial communities, both by increasing the competitive ability of a given bacterial species and as a driver of genetic adaptation.
An ecosystemic view on refugee mental health care: on caring environments and their interaction
Authors: Klapprott Felix , Saleh Ebtesam A , Kluge Ulrike
Published: October 2023

Despite the burden of mental health problems among refugees, knowledge about mental health care for this group is limited. In this context, the comprehensive discussion is important because care is more than professional care, but takes place in everyday situations and between different groups of people. In this study, we look at expert views (based on profession and lived experience) on caring environments concerning refugees’ mental health on different system levels. These levels include the individual level, family level, community level and the society. Additionally, we aimed to understand how these system levels interact. We conducted interviews with 11 psychotherapists from Germany and 12 participants who fled from Arabic-speaking countries to Germany. We analyzed transcripts following Braun and Clarke’s reflexive thematic analysis. Interviewees shared ideas on how society in general (e.g. increase acceptance), professional actors (e.g. be sensitive about cultural differences), other refugees (e.g. exchange information), family/friends (e.g. provide emotional help) and refugees with mental health problems themselves (e.g. be open to involve others) could provide care. Participants provided examples of how system levels interacted, for example when legal norms made care among family members harder. The interactions between different system levels point to a multidisciplinary approach towards mental health care for refugees and call for building expert networks instead of viewing refugee mental health as a medical, psychiatric issue alone. To improve the mental health of refugees, different societal actors should keep in mind the interactions across different system levels and exchange their respective expert knowledge.
Entire Curves Producing Distinct Nevanlinna Currents
Authors: Xie Song-Yan
Published: October 2023

First, inspired by a question of Sibony, we show that in every compact complex manifold $Y$ with certain Oka property, there exists some entire curve $f: \mathbb {C}\rightarrow Y$ generating all Nevanlinna/Ahlfors currents on $Y$, by holomorphic disks $\{f\restriction _{\mathbb {D}(c, r)}\}_{c\in \mathbb {C}, r>0}$. Next, we answer positively a question of Yau, by constructing some entire curve $g: \mathbb {C}\rightarrow X$ in the product $X:=E_{1}\times E_{2}$ of two elliptic curves $E_{1}$ and $E_{2}$, such that by using concentric holomorphic disks $\{g\restriction _{\mathbb {D}_{ r}}\}_{r>0}$ we can obtain infinitely many distinct Nevanlinna/Ahlfors currents proportional to the extremal currents of integration along curves $[\{e_{1}\}\times E_{2}]$, $[E_{1}\times \{e_{2}\}]$ for all $e_{1}\in E_{1}, e_{2}\in E_{2}$ simultaneously. This phenomenon is new, and it shows tremendous holomorphic flexibility of entire curves in large scale geometry.

Dedicated to Julien Duval with admiration
Rethinking resource enclavity in developing countries: Embedding Global Production Networks in gold mining regions
Authors: Hilson Gavin , Hu Yanfei , Hilson Abigail , Owen John R , Lèbre Éléonore , Sauerwein Titus
Published: October 2023

This article explores how the gold mining sector has adapted and evolved in developing countries since the onset of the global pandemic. A major criticism of capital-intensive gold mines has been that they occur as enclaves which fail to catalyze local economic development. Pre-pandemic, the pressure applied by NGOs and donors on gold mining companies to ‘de-enclave’ was steadily building. It has since dissipated, however, because many governments have declared mining an ‘essential’ industry. This decision has further entrenched the sector’s enclavity by justifying companies’ moves to continue operating in isolation and abandon their traditional Corporate Social Responsibility strategies.
Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets
Authors: DeCandia Alexandra L , Adeduro Laura , Thacher Piper , Crosier Adrienne , Marinari Paul , Bortner Robyn , Garelle Della , Livieri Travis , Santymire Rachel , Comizzoli Pierre , Maslanka Michael , Maldonado Jesús E , Koepfli Klaus-Peter , Muletz-Wolz Carly , Bornbusch Sally L
Published: October 2023

The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian’s National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus—all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.
Changes in body size and fertility due to artificial and natural feeding of laboratory common bed bugs (Heteroptera: Cimicidae)
Authors: Sasínková Markéta , Křemenová Jana , Chajma Petr , Bartonička Tomáš , Massino Christian , Otti Oliver , Balvín Ondřej
Published: October 2023

Rearing common bed bugs (Cimex lectularius L.) and other hematophagous insects is essential for basic, medical, and pest-control research. Logistically, acquiring fresh blood can be a challenge, while biologically, the eventual effects of different rearing and blood preparation protocols on bed bug genotype and phenotype pose a risk of biased research results. Using bed bug populations that are either bat- (BL) or human-related (HL), we tested the short- and long-term effects of rearing bugs on live bats or human volunteers, or artificially on CPDA (citrate phosphate dextrose, adenine)-treated blood, measuring meal size, body size, and fertility. We found that artificial feeding did not affect meal size compared with feeding on natural hosts. Long-term rearing across many generations of HL on CPDA-preserved blood led to reduced body size and fertility compared with populations reared on human volunteers. Blood preservatives increased the proportion of sterile eggs even after a single feed. Finally, our results indicated that laboratory reared bed bugs were smaller, regardless of the blood source, than wild bugs. Similar effects of artificial feeding or laboratory rearing alone should be considered in future studies using bed bug cultures to choose an appropriate rearing protocol. With regard to switching between bat and human hosts, HL took smaller meals and BL had lower fertility when fed on bats than when fed on humans. We attribute these results to methodological constrains, specifically the inconsistency of bat feeding, rather than to host specialization. Nevertheless, BL can be easily reared using human blood and artificial feeding systems.
Proton Gradient Regulation 5 is required to avoid photosynthetic oscillations during light transitions
Authors: Degen Gustaf E , Pastorelli Federica , Johnson Matthew P
Published: October 2023

The production of ATP and NADPH by the light reactions of photosynthesis and their consumption by the Calvin–Benson–Bassham (CBB) cycle and other downstream metabolic reactions requires careful regulation. Environmental shifts perturb this balance, leading to photo-oxidative stress and losses in CO2 assimilation. Imbalances in the production and consumption of ATP and NADPH manifest themselves as transient instability in the chlorophyll fluorescence, P700, electrochromic shift, and CO2 uptake signals recorded on leaves. These oscillations can be induced in wild-type plants by sudden shifts in CO2 concentration or light intensity; however, mutants exhibiting increased oscillatory behaviour have yet to be reported. This has precluded an understanding of the regulatory mechanisms employed by plants to suppress oscillations. Here we show that the Arabidopsis pgr5 mutant, which is deficient in Proton Gradient Regulation 5 (PGR5)-dependent cyclic electron transfer (CET), exhibits increased oscillatory behaviour. In contrast, mutants lacking the NADH-dehydrogenase-like-dependent CET are largely unaffected. The absence of oscillations in the hope2 mutant which, like pgr5, lacks photosynthetic control and exhibits high ATP synthase conductivity, ruled out loss of these photoprotective mechanisms as causes. Instead, we observed slower formation of the proton motive force and, by inference, ATP synthesis in pgr5 following environmental perturbation, leading to the transient reduction of the electron transfer chain and photosynthetic oscillations. PGR5-dependent CET therefore plays a major role in damping the effect of environmental perturbations on photosynthesis to avoid losses in CO2 fixation.
Detection of large-scale synchrotron radiation from the molecular envelope of the Sgr B cloud complex at the Galactic centre
Authors: Yusef-Zadeh F , Wardle M , Arendt R , Hewitt J , Hu Y , Lazarian A , Kassim N E , Hyman S , Heywood I
Published: October 2023

We present highly sensitive measurements taken with MeerKAT at 1280 MHz as well as archival Green Bank Telescope (GBT), Murchison Widefield Array, and Very Large Array (VLA) images at 333, 88, and 74 MHz. We report the detection of synchrotron radio emission from the infrared dark cloud associated with the halo of the Sgr B complex on a scale of ∼60 pc. A strong spatial correlation between low-frequency radio continuum emission and dense molecular gas, combined with spectral index measurements, indicates enhanced synchrotron emission by cosmic ray electrons. Correlation of the Fe i 6.4 keV K α line and synchrotron emission provides compelling evidence that the low energy cosmic ray electrons are responsible for producing the K α line emission. The observed synchrotron emission within the halo of the Sgr B cloud complex has a mean spectral index α ∼ −1 ± 1, which gives the magnetic field strength ∼100 µG for cloud densities nH = 104–105 cm−3, and estimated cosmic ray ionization rates between 10−13 and 10−14 s−1. Furthermore, the energy spectrum of primary cosmic ray electrons is constrained to be E−3 ± 1 for typical energies of few hundred MeV. The extrapolation of this spectrum to higher energies is consistent with X-ray and γ-ray emission detected from this cloud. These measurements have important implications on the role that high cosmic ray electron fluxes at the Galactic centre play in production of radio synchrotron emission, the Fe i K α line emission at 6.4 keV, and ∼GeV γ-ray emission throughout the Central Molecular Zone.
Study of the energetic X-ray superflares from the active fast rotator AB doradus
Authors: Didel Shweta , Pandey Jeewan C , Srivastava A K , Singh Gurpreet
Published: October 2023

We present the analyses of intense X-ray flares detected on the active fast rotator AB Dor using observations from the XMM–Newton. A total of 21 flares are detected, and 13 flares are analysed in detail. The total X-ray energy of these flares is found to be in the range of 1034−36 erg, in which the peak flare flux increased up to 34 times from the pre-/post-flaring states for the strongest observed flare. The duration of these flaring events is found to be 0.7 to 5.8 h. The quiescent state X-ray spectra are found to be explained by a three-temperature plasma with average temperatures of 0.29, 0.95, and 1.9 keV, respectively. The temperatures, emission measures, and abundances are found to be varying during the flares. The peak flare temperature was found in the 31–89 MK range, whereas the peak emission measure was 1052.5–54.7 cm−3 . The abundances vary during the flares and increase by a factor of ∼3 from the quiescent value for the strongest detected flare. The variation in individual abundances follows the inverse-FIP effect in quiescent and flare phases. The X-ray light curves of AB Dor are found to exhibit rotational modulation. The semi-loop lengths of the flaring events are derived in the range of 109.9−10.7  cm, whereas the minimum magnetic field to confine the plasma in the flaring loop is estimated between 200 and 700 G.
Can we really pick and choose? Benchmarking various selections of Gaia Enceladus/Sausage stars in observations with simulations
Authors: Carrillo Andreia , Deason Alis J , Fattahi Azadeh , Callingham Thomas M , Grand Robert J J
Published: October 2023

Large spectroscopic surveys plus Gaia astrometry have shown us that the inner stellar halo of the Galaxy is dominated by the debris of Gaia Enceladus/Sausage (GES). With the richness of data at hand, there are a myriad of ways these accreted stars have been selected. We investigate these GES selections and their effects on the inferred progenitor properties using data constructed from APOGEE and Gaia. We explore selections made in eccentricity, energy-angular momentum (E-Lz), radial action-angular momentum (Jr-Lz), action diamond, and [Mg/Mn]-[Al/Fe] in the observations, selecting between 144 and 1279 GES stars with varying contamination from in-situ and other accreted stars. We also use the Auriga cosmological hydrodynamic simulations to benchmark the different GES dynamical selections. Applying the same observational GES cuts to nine Auriga galaxies with a GES, we find that the Jr-Lz method is best for sample purity and the eccentricity method for completeness. Given the average metallicity of GES (−1.28 < [Fe/H] < −1.18), we use the z = 0 mass–metallicity relationship to find an average $\rm M_{\star }$of ∼4 × 108 M⊙. We adopt a similar procedure and derive $\rm M_{\star }$ for the GES-like systems in Auriga and find that the eccentricity method overestimates the true $\rm M_{\star }$ by ∼2.6 × while E-Lz underestimates by ∼0.7 ×. Lastly, we estimate the total mass of GES to be $\rm 10^{10.5 - 11.1}~{\rm M}_{\odot }$ using the relationship between the metallicity gradient and the GES-to-in-situ energy ratio. In the end, we cannot just ‘pick and choose’ how we select GES stars, and instead should be motivated by the science question.
Disentangling patchy reionization signatures from primordial gravitational waves using CMB E-mode and B-mode polarization
Authors: Jain Divesh , Mukherjee Suvodip , Choudhury Tirthankar Roy
Published: October 2023

The detection of large angular scale B mode in the cosmic microwave background (CMB) polarization signal will open a direct window into not only the primary CMB anisotropies caused by the primordial gravitational waves (PGW) originating in the epoch of inflation, but also the secondary anisotropies imprinted during the epoch of cosmic reionization. The existence of patchiness in the electron density during reionization produces a unique distortion in the CMB B-mode polarization, which can be distinguished from the PGW signal with the aid of spatial frequency modes. In this work, we employ an EB estimator by combining E-mode and B-mode polarization for the τ power spectrum signal generated in a photon-conserving seminumerical reionization model called SCRIPT. We developed a Bayesian framework for the joint detection of the PGW and reionization signal from CMB observations and show the efficacy of this technique for upcoming CMB experiments. We find that, for our model, the τ power spectrum signal effectively tracks the inhomogeneous electron density field, allowing for robust constraints on the patchy B-mode signal. Further, our results indicate that employing the EB estimator for the τ signal will facilitate ground-based CMB-S4 to detect the patchy B-mode signal at approximately ≥2σ confidence level, while observations with space-based PICO will improve this detection to ≥3σ going as high as ≥7σ for extreme reionization models. These findings not only highlight the future potential of these experiments to provide an improved picture of the reionization process but also have important implications towards an unbiased measurement of r.
Exploring dark matter spike distribution around the Galactic centre with stellar orbits
Authors: Shen Zhao-Qiang , Yuan Guan-Wen , Jiang Cheng-Zi , Tsai Yue-Lin Sming , Yuan Qiang , Fan Yi-Zhong
Published: October 2023

Precise measurements of the stellar orbits around Sagittarius A* have established the existence of a supermassive black hole (SMBH) at the Galactic centre (GC). Due to the interplay between the SMBH and dark matter (DM), the DM density profile in the innermost region of the Galaxy, which is crucial for the DM indirect detection, is still an open question. Among the most popular models in the literature, the theoretical spike profile proposed by Gondolo & Silk (GS hereafter) is well adopted. In this work, we investigate the DM spike profile using updated data from the Keck and Very Large Telescope (VLT) telescopes considering that the presence of such an extended mass component may affect the orbits of the S-stars in the GC. We examine the radius and slope of the generalized Navarro–Frenk–White (NFW) spike profile, analyse the Einasto spike, and discuss the influence of DM annihilation on the results. Our findings indicate that an initial slope of γ ≳ 0.92 for the generalized NFW spike profile is ruled out at a 95 per cent confidence level. Additionally, the spike radius Rsp larger than 21.5 pc is rejected at 95 per cent probability for the Einasto spike with α = 0.17, which also contradicts the GS spike model. The constraints with the VLT/GRAVITY upper limits are also projected. Although the GS NFW spike is well constrained by the Keck and VLT observation of S2, an NFW spike with a weak annihilation cusp may still be viable, as long as the DM annihilation cross-section satisfies $\left\langle \sigma v \right\rangle \gtrsim 7.7\times 10^{-27}~{\rm cm^3\, s^{-1}} (m_{\rm DM}/100~{\rm GeV})$ at 95 per cent level.
NIGHT: A compact, near-infrared, high-resolution spectrograph to survey helium in exoplanet systems
Authors: Farret Jentink C , Bourrier V , Lovis C , Allart R , Chazelas B , Lendl M , Dumusque X , Pepe F
Published: October 2023

Among highly irradiated exoplanets, some have been found to undergo significant hydrodynamic expansion traced by atmospheric escape. To better understand these processes in the context of planetary evolution, we propose NIGHT (the Near-Infrared Gatherer of Helium Transits). NIGHT is a high-resolution spectrograph dedicated to surveying and temporally monitoring He i triplet absorption at 1083 nm in stellar and planetary atmospheres. In this paper, we outline our scientific objectives, requirements, and cost-efficient design. Our simulations, based on previous detections and modelling using the current exoplanet population, determine our requirements and survey targets. With a spectral resolution of 70 000 on a 2-m telescope, NIGHT can accurately resolve the helium triplet and detect 1 per cent peak absorption in 118 known exoplanets in a single transit. Additionally, it can search for 3σ temporal variations of 0.4 per cent in 66 exoplanets in-between two transits. These are conservative estimates considering the ongoing detections of transiting planets amenable to atmospheric characterization. We find that instrumental stability at 40 m s−1, less stringent than for radial velocity monitoring, is sufficient for transmission spectroscopy in He i. As such, NIGHT can utilize mostly off-the-shelf components, ensuring cost-efficiency. A fibre-fed system allows for flexibility as a visitor instrument on a variety of telescopes, making it ideal for follow-up observations after JWST or ground-based detections. Over a few years of surveying, NIGHT could offer detailed insights into the mechanisms shaping the hot Neptune desert and close-in planet population by significantly expanding the statistical sample of planets with known evaporating atmospheres. First light is expected in 2024.
Characterization of acetonitrile ice irradiated by X-rays employing the procoda code – II. Desorption processes
Authors: Carvalho G A , Pilling S , Gerasimenko S
Published: October 2023

In this work, we focus on the study of radiation-induced desorption processes that occurred in acetonitrile ice irradiated by broad-band X-rays (6 eV to 2 keV) monitored by Fourier transform infrared spectroscopy at different radiation fluences. In a previous work, we used the procoda code to derive the chemical evolution of the ice. Here, we have observed that the acetonitrile desorbed column density is at least two orders of magnitude larger than the desorbed column densities of daughter or granddaughter molecular species at chemical equilibrium stage. This indicates that total desorption column density is mainly governed by the father molecule, as also previously hypothesized in experimental studies. This occurs basically because the acetonitrile column density is larger than the other ones. In particular, at chemical equilibrium acetonitrile desorption column density represents almost 98 per cent of the total, while it is close to 1  per cent for H, CN, and CH2, the species with larger molecular desorption percentages at chemical equilibrium. Another derived quantity is what we called intrinsic desorption rate, which is a number per second for individual species. Some of the larger intrinsic desorption rates were 6.2 × 10−6 (CH3CN), 6.2 × 10−6 (CN), 5.7 × 10−6 (H), 5.7 × 10−6 (CH2), and 4.4 × 10−6 (C2N2). These results help to put constraints in astrochemical models and can also be useful to clarify some astronomical radio observations.
Effect of graded levels of selenium supplementation as selenite on expression of selenosugars, selenocysteine, and other selenometabolites in rat liver
Authors: Bierla Katarzyna , Szpunar Joanna , Lobinski Ryszard , Sunde Roger A
Published: October 2023

Using high pressure liquid chromatography (HPLC) coupled with selenium-specific inductively coupled plasma mass spectrometry (ICP–MS) and molecule specific (Orbitrap MS/MS) detection, we previously found that far more selenium (Se) is present as selenosugar (seleno-N-acetyl galactosamine) in Se-adequate turkey liver than is present as selenocysteine (Sec) in true selenoproteins, and that selenosugars account for half of the Se in high-Se turkey liver. To expand these observations to mammals, we studied Se metabolism in rats fed graded levels of selenite from 0 to 5 μg Se/g for 4 wk. In Se-adequate (0.24 μg Se/g) rats, 43% of liver Se was present as Sec, 32% was present as selenosugars, and 22% as inorganic Se bound to protein. In liver of rats fed 5 μg Se/g as selenite, the quantity of Sec remained at the Se-adequate plateau (11% of total Se), 22% was present as low molecular weight (LMW) selenosugars with substantial additional selenosugars linked to protein, but 64% was present as inorganic Se bound to protein. No selenomethionine was found at any level of selenite supplementation. Below the Se requirement, Se is preferentially incorporated into Sec-selenoproteins. Above the dietary Se requirement, selenosugars become by far the major LMW water soluble Se species in liver, and levels of selenosugar-decorated proteins are far higher than Sec-selenoproteins, making these selenosugar-decorated proteins the major Se-containing protein species in liver with high Se supplementation. This accumulation of selenosugars linked to cysteines on proteins or the build-up of inorganic Se bound to protein may underlie Se toxicity at the molecular level.
‘SAXS-osmometer’ method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state
Authors: Villanueva Valencia José Ramón , Li Dong , Casjens Sherwood R , Evilevitch Alex
Published: October 2023

We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA–DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins
Authors: Martin Vincentius , Zhuang Farica , Zhang Yuning , Pinheiro Kyle , Gordân Raluca
Published: October 2023

Cooperative DNA-binding by transcription factor (TF) proteins is critical for eukaryotic gene regulation. In the human genome, many regulatory regions contain TF-binding sites in close proximity to each other, which can facilitate cooperative interactions. However, binding site proximity does not necessarily imply cooperative binding, as TFs can also bind independently to each of their neighboring target sites. Currently, the rules that drive cooperative TF binding are not well understood. In addition, it is oftentimes difficult to infer direct TF–TF cooperativity from existing DNA-binding data. Here, we show that in vitro binding assays using DNA libraries of a few thousand genomic sequences with putative cooperative TF-binding events can be used to develop accurate models of cooperativity and to gain insights into cooperative binding mechanisms. Using factors ETS1 and RUNX1 as our case study, we show that the distance and orientation between ETS1 sites are critical determinants of cooperative ETS1–ETS1 binding, while cooperative ETS1–RUNX1 interactions show more flexibility in distance and orientation and can be accurately predicted based on the affinity and sequence/shape features of the binding sites. The approach described here, combining custom experimental design with machine-learning modeling, can be easily applied to study the cooperative DNA-binding patterns of any TFs.
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse
Authors: Huang Xuemei , Song Chao , Zhang Guorui , Li Ye , Zhao Yu , Zhang Qinyi , Zhang Yuexin , Fan Shifan , Zhao Jun , Xie Liyuan , Li Chunquan
Published: October 2023

Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF–target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF–target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.
AGIDB: a versatile database for genotype imputation and variant decoding across species
Authors: Zhang Kaili , Liang Jiete , Fu Yuhua , Chu Jinyu , Fu Liangliang , Wang Yongfei , Li Wangjiao , Zhou You , Li Jinhua , Yin Xiaoxiao , Wang Haiyan , Liu Xiaolei , Mou Chunyan , Wang Chonglong , Wang Heng , Dong Xinxing , Yan Dawei , Yu Mei , Zhao Shuhong , Li Xinyun , Ma Yunlong
Published: October 2023

The high cost of large-scale, high-coverage whole-genome sequencing has limited its application in genomics and genetics research. The common approach has been to impute whole-genome sequence variants obtained from a few individuals for a larger population of interest individually genotyped using SNP chip. An alternative involves low-coverage whole-genome sequencing (lcWGS) of all individuals in the larger population, followed by imputation to sequence resolution. To overcome limitations of processing lcWGS data and meeting specific genotype imputation requirements, we developed AGIDB (https://agidb.pro), a website comprising tools and database with an unprecedented sample size and comprehensive variant decoding for animals. AGIDB integrates whole-genome sequencing and chip data from 17 360 and 174 945 individuals, respectively, across 89 species to identify over one billion variants, totaling a massive 688.57 TB of processed data. AGIDB focuses on integrating multiple genotype imputation scenarios. It also provides user-friendly searching and data analysis modules that enable comprehensive annotation of genetic variants for specific populations. To meet a wide range of research requirements, AGIDB offers downloadable reference panels for each species in addition to its extensive dataset, variant decoding and utility tools. We hope that AGIDB will become a key foundational resource in genetics and breeding, providing robust support to researchers.
dbAPIS: a database of

a

nti-

p

rokaryotic

i

mmune

s

ystem genes
Authors: Yan Yuchen , Zheng Jinfang , Zhang Xinpeng , Yin Yanbin
Published: October 2023

Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.