bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the likelihood of the 21-cm power spectrum with simulation-based inference
Authors: Prelogović David , Mesinger Andrei 
Published: July 2023

ABSTRACT
Observations of the cosmic 21-cm power spectrum (PS) are starting to enable precision Bayesian inference of galaxy properties and physical cosmology, during the first billion years of our Universe. Here we investigate the impact of common approximations about the likelihood used in such inferences, including: (i) assuming a Gaussian functional form; (ii) estimating the mean from a single realization; and (iii) estimating the (co)variance at a single point in parameter space. We compare ‘classical’ inference that uses an explicit likelihood with simulation-based inference (SBI) that estimates the likelihood from a training set. Our forward models include: (i) realizations of the cosmic 21-cm signal computed with 21cmFAST by varying ultraviolet (UV) and X-ray galaxy parameters together with the initial conditions; (ii) realizations of the telescope noise corresponding to a $1000 \, \mathrm{h}$ integration with the low-frequency component of the Square Kilometre Array (SKA1-Low); and (iii) the excision of Fourier modes corresponding to a foreground-dominated horizon ‘wedge’. We find that the 1D PS likelihood is well described by a Gaussian accounting for covariances between wave modes and redshift bins (higher order correlations are small). However, common approaches of estimating the forward-modelled mean and (co)variance from a random realization or at a single point in parameter space result in biased and overconstrained posteriors. Our best results come from using SBI to fit a non-Gaussian likelihood with a Gaussian mixture neural density estimator. Such SBI can be performed with up to an order of magnitude fewer simulations than classical, explicit likelihood inference. Thus SBI provides accurate posteriors at a comparably low computational cost.
Time delay induced by plasma in strong lens systems
Authors: Bisnovatyi-Kogan Gennady S , Tsupko Oleg Yu 
Published: July 2023

ABSTRACT
If the gravitational lens is surrounded by non-homogeneous plasma, in addition to the vacuum gravitational deflection, chromatic refraction occurs. Also, the speed of signal propagation decreases compared to a vacuum. In this article, we investigate analytically the time delay in the case of gravitational lensing in plasma, focusing on strong lens systems. We take into account the following contributions: geometric delay due to trajectory bending in the presence of both gravity and plasma; potential delay of the ray in the gravitational field of the lens; dispersion delay in the plasma due to decrease in the speed of light signal in the medium. We consider the singular isothermal sphere as a model of a gravitational lens and the arbitrary spherically symmetric distribution of surrounding plasma. For this scenario, plasma corrections for the time delay between two images are found in a compact analytical form convenient for estimates.
Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation
Authors: Guzman Carlos , Duttke Sascha , Zhu Yixin , De Arruda Saldanha Camila , Downes Nicholas L , Benner Christopher , Heinz Sven 
Published: July 2023

Abstract
Cis-regulatory elements (CREs) can be classified by the shapes of their transcription start site (TSS) profiles, which are indicative of distinct regulatory mechanisms. Massively parallel reporter assays (MPRAs) are increasingly being used to study CRE regulatory mechanisms, yet the degree to which MPRAs replicate individual endogenous TSS profiles has not been determined. Here, we present a new low-input MPRA protocol (TSS-MPRA) that enables measuring TSS profiles of episomal reporters as well as after lentiviral reporter chromatinization. To sensitively compare MPRA and endogenous TSS profiles, we developed a novel dissimilarity scoring algorithm (WIP score) that outperforms the frequently used earth mover's distance on experimental data. Using TSS-MPRA and WIP scoring on 500 unique reporter inserts, we found that short (153 bp) MPRA promoter inserts replicate the endogenous TSS patterns of ∼60% of promoters. Lentiviral reporter chromatinization did not improve fidelity of TSS-MPRA initiation patterns, and increasing insert size frequently led to activation of extraneous TSS in the MPRA that are not active in vivo. We discuss the implications of our findings, which highlight important caveats when using MPRAs to study transcription mechanisms. Finally, we illustrate how TSS-MPRA and WIP scoring can provide novel insights into the impact of transcription factor motif mutations and genetic variants on TSS patterns and transcription levels.
Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data
Authors: Wang Ruo Han , Wang Jianping , Li Shuai Cheng 
Published: July 2023

Abstract
Single-cell sequencing technology enables the simultaneous capture of multiomic data from multiple cells. The captured data can be represented by tensors, i.e. the higher-rank matrices. However, the existing analysis tools often take the data as a collection of two-order matrices, renouncing the correspondences among the features. Consequently, we propose a probabilistic tensor decomposition framework, SCOIT, to extract embeddings from single-cell multiomic data. SCOIT incorporates various distributions, including Gaussian, Poisson, and negative binomial distributions, to deal with sparse, noisy, and heterogeneous single-cell data. Our framework can decompose a multiomic tensor into a cell embedding matrix, a gene embedding matrix, and an omic embedding matrix, allowing for various downstream analyses. We applied SCOIT to eight single-cell multiomic datasets from different sequencing protocols. With cell embeddings, SCOIT achieves superior performance for cell clustering compared to nine state-of-the-art tools under various metrics, demonstrating its ability to dissect cellular heterogeneity. With the gene embeddings, SCOIT enables cross-omics gene expression analysis and integrative gene regulatory network study. Furthermore, the embeddings allow cross-omics imputation simultaneously, outperforming current imputation methods with the Pearson correlation coefficient increased by 3.38–39.26%; moreover, SCOIT accommodates the scenario that subsets of the cells are with merely one omic profile available.
IgA nephropathy in adults—treatment standard
Authors: Gleeson Patrick J , O'Shaughnessy Michelle M , Barratt Jonathan 
Published: July 2023

ABSTRACT
Immunoglobulin A nephropathy (IgAN) is the most common primary form of glomerular disease worldwide and carries a high lifetime risk of kidney failure. The underlying pathogenesis of IgAN has been characterized to a sub-molecular level; immune complexes containing specific O-glycoforms of IgA1 are central. Kidney biopsy remains the gold-standard diagnostic test for IgAN and histological features (i.e. MEST-C score) have also been shown to independently predict outcome. Proteinuria and blood pressure are the main modifiable risk factors for disease progression. No IgAN-specific biomarker has yet been validated for diagnosis, prognosis or tracking response to therapy.
There has been a recent resurgence of investigation into IgAN treatments. Optimized supportive care with lifestyle interventions and non-immunomodulatory drugs remains the backbone of IgAN management. The menu of available reno-protective medications is rapidly expanding beyond blockade of the renin–angiotensin–aldosterone system to include sodium-glucose cotransporter 2 and endothelin type A receptor antagonism. Systemic immunosuppression can further improve kidney outcomes, although recent randomized controlled trials have raised concerns regarding infectious and metabolic toxicity from systemic corticosteroids. Studies evaluating more refined approaches to immunomodulation in IgAN are ongoing: drugs targeting the mucosal immune compartment, B-cell promoting cytokines and the complement cascade are particularly promising.
We review the current standards of treatment and discuss novel developments in pathophysiology, diagnosis, outcome prediction and management of IgAN.
Quantized anomalous Hall resistivity achieved in molecular beam epitaxy-grown MnBi2Te4 thin films
Authors: Bai Yunhe , Li Yuanzhao , Luan Jianli , Liu Ruixuan , Song Wenyu , Chen Yang , Ji Peng-Fei , Zhang Qinghua , Meng Fanqi , Tong Bingbing , Li Lin , Jiang Yuying , Gao Zongwei , Gu Lin , Zhang Jinsong , Wang Yayu , Xue Qi-Kun , He Ke , Feng Yang , Feng Xiao 
Published: July 2023

ABSTRACT
The intrinsic magnetic topological insulator MnBi2Te4 provides a feasible pathway to the high-temperature quantum anomalous Hall (QAH) effect as well as various novel topological quantum phases. Although quantized transport properties have been observed in exfoliated MnBi2Te4 thin flakes, it remains a big challenge to achieve molecular beam epitaxy (MBE)-grown MnBi2Te4 thin films even close to the quantized regime. In this work, we report the realization of quantized anomalous Hall resistivity in MBE-grown MnBi2Te4 thin films with the chemical potential tuned by both controlled in situ oxygen exposure and top gating. We find that elongated post-annealing obviously elevates the temperature to achieve quantization of the Hall resistivity, but also increases the residual longitudinal resistivity, indicating a picture of high-quality QAH puddles weakly coupled by tunnel barriers. These results help to clarify the puzzles in previous experimental studies on MnBi2Te4 and to find a way out of the big difficulty in obtaining MnBi2Te4 samples showing quantized transport properties.
Screening for Latent Tuberculosis Infection in Solid Organ Transplant Recipients to Predict Active Disease: A Systematic Review and Meta-Analysis of Diagnostic Studies
Authors: Yahav Dafna , Gitman Melissa R , Margalit Ili , Avni Tomer , Leeflang Mariska M G , Husain Shahid 
Published: July 2023

Abstract

Background
This is a systematic review and meta-analysis of diagnostic test accuracy studies to assess the predictive value of both tuberculin skin test (TST) and interferon-gamma release assays (IGRA) for active tuberculosis (TB) among solid organ transplantation (SOT) recipients.

Methods
Medline, Embase, and the CENTRAL databases were searched from 1946 until June 30, 2022. Two independent assessors extracted data from studies. Sensitivity analyses were performed to investigate the effect of studies with high or low risk of bias. Methodological quality of each publication was assessed using QUADAS-2.

Results
A total of 43 studies (36 403 patients) with patients who were screened for latent TB infection (LTBI) and who underwent SOT were included: 18 were comparative and 25 noncomparative (19 TST, 6 QuantiFERON-TB Gold In-Tube [QFT-GIT]). For IGRA tests taken together, positive predictive value (PPV) and negative predictive value (NPV) were 1.2% and 99.6%, respectively. For TST, PPV was 2.13% and NPV was 95.5%. Overall, PPV is higher when TB burden is higher, regardless of test type, although still low in absolute terms. Incidence of active TB was similar between studies using LTBI prophylaxis (mean incidence 1.22%; 95% confidence interval [CI], .2179–2.221) and those not using prophylaxis (mean incidence 1.045%; 95% CI, 0.2731–1.817; P = .7717). Strengths of this study include the large number of studies available from multiple different countries; limitations include absence of gold standard for diagnosis of latent TB and low incidence of active TB.

Conclusions
We found both TST and IGRA had a low PPV and high NPV for the development of active TB posttransplant. Further studies are needed to better understand how to prevent active TB in the SOT population.
Stigma and Social Determinants of Health Associated With Fidelity to Guideline-Concordant Therapy in Patients With Breast Cancer Living With and Without HIV in Botswana
Authors: Martei Yehoda M , Obasohan Modesty , Mokokwe Lebogang , Ralefala Tlotlo , Mosepele Mosepele , Gross Robert , Barg Frances K 
Published: July 2023

Abstract

Background
Patients with breast cancer in sub-Saharan Africa (SSA) experience a disproportionate burden of mortality. Fidelity to treatment guidelines, defined as receiving optimal dose and frequency of prescribed treatments, improves survival. We sought to identify patient factors associated with treatment fidelity and how this may differ for people with HIV (PWH) and breast cancer.

Methods
We conducted a qualitative study of women who initiated outpatient treatment for stages I-III breast cancer in Botswana, with deviance sampling of high- and low-fidelity patients. One-on-one interviews were conducted using semi-structured guides informed by the Theory of Planned Behavior. The sample size was determined by thematic saturation. Transcribed interviews were double coded with an integrated analytic approach.

Results
We enrolled 15 high- and 15 low-fidelity participants from August 25, 2020 to December 15, 2020, including 10 PWH (4 high, 6 low fidelity). Ninety-three percent had stage III disease. Barriers to treatment fidelity included stigma, social determinants of health (SDOH), and health system barriers. Acceptance and de-stigmatization, peer and other social support, increased knowledge and self-efficacy were identified as facilitators. The COVID-19 pandemic amplified existing socioeconomic stressors. Unique barriers and facilitators identified by PWH included intersectional stigma, and HIV and cancer care integration, respectively.

Conclusion
We identified multilevel modifiable patient and health system factors associated with fidelity. The facilitators provide opportunities for leveraging existing strengths within the Botswana context to design implementation strategies to increase treatment fidelity to guideline-concordant breast cancer therapy. However, PWH experienced unique barriers, suggesting that interventions to address fidelity may need to be tailored to specific comorbidities.
IQ domain-containing protein ZmIQD27 modulates water transport in maize
Authors: Li Haiyan , Xie Jun , Gao Yongmeng , Wang Xuemei , Qin Li , Ju Wei , Roberts Jeremy A , Cheng Beijiu , Zhang Xuebin , Lu Xiaoduo 
Published: July 2023

Abstract
Plant metaxylem vessels provide physical support to promote upright growth and the transport of water and nutrients. A detailed characterization of the molecular network controlling metaxylem development is lacking. However, knowledge of the events that regulate metaxylem development could contribute to the development of germplasm with improved yield. In this paper, we screened an EMS-induced B73 mutant library, which covers 92% of maize (Zea mays) genes, to identify drought-sensitive phenotypes. Three mutants were identified, named iqd27-1, iqd27-2, and iqd27-3, and genetic crosses showed that they were allelic to each other. The causal gene in these 3 mutants encodes the IQ domain-containing protein ZmIQD27. Our study showed that defective metaxylem vessel development likely causes the drought sensitivity and abnormal water transport phenotypes in the iqd27 mutants. ZmIQD27 was expressed in the root meristematic zone where secondary cell wall deposition is initiated, and loss-of-function iqd27 mutants exhibited a microtubular arrangement disorder. We propose that association of functional ZmIQD27 with microtubules is essential for correct targeted deposition of the building blocks for secondary cell wall development in maize.
Photosystem II monomeric antenna CP26 plays a key role in nonphotochemical quenching in Chlamydomonas
Authors: Cazzaniga Stefano , Kim Minjae , Pivato Matteo , Perozeni Federico , Sardar Samim , D’Andrea Cosimo , Jin EonSeon , Ballottari Matteo 
Published: July 2023

Abstract
Thermal dissipation of excess excitation energy, called nonphotochemical quenching (NPQ), is 1 of the main photoprotective mechanisms in oxygenic photosynthetic organisms. Here, we investigated the function of the monomeric photosystem II (PSII) antenna protein CP26 in photoprotection and light harvesting in Chlamydomonas reinhardtii, a model organism for green algae. We used CRISPR/Cas9 genome editing and complementation to generate cp26 knockout mutants (named k6#) that did not negatively affect CP29 accumulation, which differed from previous cp26 mutants, allowing us to compare mutants specifically deprived of CP26, CP29, or both. The absence of CP26 partially affected PSII activity, causing reduced growth at low or medium light but not at high irradiances. However, the main phenotype observed in k6# mutants was a more than 70% reduction of NPQ compared to the wild type (Wt). This phenotype was fully rescued by genetic complementation and complemented strains accumulating different levels of CP26, demonstrating that ∼50% of CP26 content, compared to the Wt, was sufficient to restore the NPQ capacity. Our findings demonstrate a pivotal role for CP26 in NPQ induction, while CP29 is crucial for PSII activity. The genetic engineering of these 2 proteins could be a promising strategy to regulate the photosynthetic efficiency of microalgae under different light regimes.
DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica
Authors: Li Mengdi , Ou Mengwei , He Xiaozhou , Ye Hang , Ma Jiayu , Liu Hengzhao , Yang Huijuan , Zhao Peng 
Published: July 2023

Abstract
Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.
How membership in the North Atlantic Treaty Organization transforms public support for war
Authors: Tomz Michael , Weeks Jessica L P , Bansak Kirk 
Published: July 2023

Abstract
How do military alliances affect public support for defending targets of aggression? We studied this question by fielding an experiment on 14,000 voters in 13 member countries of the North Atlantic Treaty Organization (NATO). Our experiment involved a hypothetical scenario in which Russia attacked a target country. We randomly varied the identity of the target (Bosnia, Finland, Georgia, or Sweden), and whether the target was a member of NATO at the time of the attack. We found that voters in every member country were far more willing to use military force to defend each target when the target was in NATO, than when the target was outside the alliance. The expansion of NATO could, therefore, transform European security by altering the likelihood and scale of future wars. We also uncovered important heterogeneity across targets: the benefits of joining NATO were considerably larger for Bosnia and Georgia than for Finland and Sweden, since most voters in NATO countries would defend Finland and Sweden even if they remained outside the alliance. Finally, the effect of NATO was much stronger among voters who perceived NATO as valuable for their own country. Rhetorical attacks on NATO could, therefore, undermine the alliance by eroding the public's willingness to defend other members, whereas rhetoric highlighting the benefits of NATO could bolster defense and deterrence. These findings advance knowledge about the effects of alliances, while also informing policy debates about the value and size of NATO.
Nudging enforcers: how norm perceptions and motives for lying shape sanctions
Authors: Dimant Eugen , Gesche Tobias 
Published: July 2023

AbstractWe conduct three studies, employing diverse methodologies (a behavioral experiment, a vignette experiment, and a norm elicitation experiment), to investigate when and how norm enforcement patterns can be modified using norm interventions in the context of dishonesty. Our preregistered, three-part data collection effort explores the extent to which norm violations are sanctioned, the impact of norm-nudges on punishment behavior, and the connection to norm perception. Using a representative sample of US participants in Study 1, we present robust evidence that norm enforcement is sensitive not only to the magnitude of the observed transgression (i.e. the size of the lie) but also to its consequences (whether the lie addresses or creates payoff inequalities). We also find that norm enforcers respond to norm-nudges conveying social information about actual lying behavior or its social disapproval. The results of a separate vignette experiment in Study 2 are consistent with the results in our behavioral experiment, thus hinting at the generalizability of our findings. To understand the interplay of norms, information about them, and punishment, we examine norm perceptions across different transgressions in Study 3. We find that norm perceptions are malleable and norm-nudges are most effective when preexisting norms are ambiguous. In sum, we show how norm enforcement can be nudged and which factors matter for doing so across various contexts and discuss their policy implications.