bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective and non-selective right bundle pacing for the diagnosis of bundle branch reentry ventricular tachycardia
Authors: Nageh Maged F , Murdock Robert
Published: July 2023

Aims and background

Bundle branch reentry ventricular tachycardia (BBRVT) can be seen in patients with conduction disease. In this report, we describe the use of conduction system pacing for its diagnosis.

Methods and results

BBRVT was induced in two patients with infra-nodal conduction disease. Bundle branch reentry ventricular tachycardia with a left bundle branch block morphology was observed in the first patient (type A), whereas the second patient had a right bundle branch block morphology (type C).

The diagnosis of BBRVT was confirmed in both patients by ventriculo-atrial dissociation, and the interdependence of the conduction system and the ventricular tachycardia cycle length variations.

Selective and non-selective RB pacing was observed in the two patients during apical right ventricular pacing for entrainment of BBRVT with evidence of manifest entrainment with non-selective RB capture in the first patient, and concealed entrainment by selective RB capture in the second patient. Other criteria for entrainment including a short post-pacing interval at the right bundle pacing site were noted.

Conclusion

Right bundle pacing is feasible in patients with BBRVT and may be a helpful manoeuver for the diagnosis of BBRVT.
A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection
Authors: Weller Benjamin , Lin Chung-Wen , Pogoutse Oxana , Sauer Mayra , Marin-de la Rosa Nora , Strobel Alexandra , Young Veronika , Knapp Jennifer J , Rayhan Ashyad , Falter Claudia , Kim Dae-Kyum , Roth Frederick P , Falter-Braun Pascal
Published: July 2023

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.
Analysis of reconstructed multisource and multiscale 3-D digital rocks based on the cycle-consistent generative adversarial network method
Authors: Yan Weichao , Chi Peng , Golsanami Naser , Sun Jianmeng , Xing Huilin , Li Sanzhong , Dong Huaimin
Published: July 2023

Digital rock physics (DRP) is important for characterizing the pore characteristics and petrophysical parameters of rocks from a microscopic perspective. Among the digital rock reconstruction methods, the most widely used is the computer tomography (CT) scan method. However, the pore structure of rocks has multiscale features, and CT scan images with a single resolution cannot completely describe the pore structure characteristics of rocks. In this paper, we analysed reconstructed multisource and multiscale 3-D digital rocks based on the cycle-consistent generative adversarial network (CycleGAN) method. This method fully integrates the advantages of the large field of view of low-resolution images and the high-precision features of high-resolution images. To investigate the performance of the method, two sequences of CT scan images of a sandstone (sample A) and a carbonate rock (sample B) collected from oilfields were studied. Moreover, due to the high resolution of scanning electron microscope (SEM) images, we also constructed 3-D digital rocks with different resolutions of the Berea sandstone based on the combination of CT scan images and SEM images. Finally, the statistical properties and absolute permeabilities were calculated to evaluate the accuracies of reconstructed multisource and multiscale 3-D digital rocks. The results show that the reconstructed multiscale digital rocks based on the CycleGAN method have good accuracy in terms of statistical properties and petrophysical properties. Considering the computational cost and computational accuracy, for high- and low-resolution CT scan images and CT scan images with SEM images as training image data sources, we suggest that the resolution of the reconstructed multiscale digital cores is 4–8 times and 4–16 times higher than that of the low-resolution CT scan images, respectively. The findings of our research will be helpful in gaining insight into the petrophysical properties of heterogeneous rocks.
Doctors for the people? The problematic distribution of rural service doctors in Ecuador
Authors: Romero-Alvarez Daniel , López-Cevallos Daniel F , Torres Irene
Published: July 2023

Primary health care is at the core of health systems that aim to ensure equitable health outcomes. With an estimated 36% of rural population, Ecuador has a service year programme (created in 1970) for recently graduated doctors to provide primary care services in rural and remote communities. However, little has been done to monitor or evaluate the programme since its inception. The aim of this study was to assess Ecuador’s rural medical service implementation with a focus on equitable distribution of doctors across the country. For this purpose, we analysed the distribution of all doctors, including rural service doctors, in health-care facilities across rural and remote areas of Ecuador in the public sector at the canton level for 2015 and 2019, by level of care (primary, secondary and tertiary). We used publicly available data from the Ministry of Public Health, the Ecuadorian Institute of Social Security and the Peasant Social Security. Our analyses show that two of every three rural service doctors are concentrated at the secondary level, while almost one in five rural service doctors, at the tertiary level. Moreover, cantons concentrating most rural service doctors were in the country’s major urban centres (Quito, Guayaquil, Cuenca). To our knowledge, this is the first quantitative assessment of the mandatory rural service year in Ecuador in its five-decade existence. We provide evidence of gaps and inequities impacting rural communities and present decision makers with a methodology for placement, monitoring and support of the rural service doctors programme, provided that legal and programmatic reforms come into place. Changing the programme’s approach would be more likely to fulfill the intended goals of rural service and contribute to strengthening primary health care.
Loss of collagen gene expression in the notochord of the tailless tunicate Molgula occulta
Authors: Popsuj Sydney , Di Gregorio Anna , Swalla Billie J , Stolfi Alberto
Published: July 2023

Synopsis

In tunicates, several species in the Molgulidae family have convergently lost the tailed, swimming larval body plan, including the morphogenesis of the notochord, a major chordate-defining trait. Through the comparison of tailless M. occulta and a close relative, the tailed species M. oculata, we show that notochord-specific expression of the Collagen Type I/II Alpha (Col1/2a) gene appears to have been lost specifically in the tailless species. Using CRISPR/Cas9-mediated mutagenesis in the tailed laboratory model tunicate Ciona robusta, we demonstrate that Col1/2a plays a crucial role in the convergent extension of notochord cells during tail elongation. Our results suggest that the expression of Col1/2a in the notochord, although necessary for its morphogenesis in tailed species, is dispensable for tailless species. This loss is likely a result of the accumulation of cis-regulatory mutations in the absence of purifying selective pressure. More importantly, the gene itself is not lost, likely due to its roles in other developmental processes, including during the adult stage. Our study further confirms the Molgulidae as an interesting family in which to study the evolutionary loss of tissue-specific expression of indispensable genes.
Spatial distributional shifts and associated body condition changes of haddock (Melanogrammus aeglefinus) following population expansion
Authors: Jónsdóttir I G , Björnsson B , Ragnarsson S Á , Elvarsson B Þ , Sólmundsson J
Published: July 2023

Temperature fluctuations impact the distribution of various marine fish species and typically result in distributional changes, seeing either a geographical expansion or, possibly, a retraction. Survival and fitness in the new habitat depend, however, on the species’ adaptability capacity. Here, we describe changes in geographical distribution of Icelandic haddock (Melanogrammus aeglefinus) based on annual survey data for a 38-year period, 1985–2022. Most of the stock is in the warm waters off the south and west coasts of Iceland (south area), but a small proportion in colder water masses off the north and east coasts (north area). Due to high recruitment, density increased greatly in both areas in the years 2001–2005. Haddock density was usually higher in the south area in 1985–2004, in the north area in 2005–2014, but similar in both areas in 2015–2022. Haddock condition was found to be influenced by both temperature and haddock density. Density-dependent factors influenced haddock mean weight, which dropped considerable during times of high haddock density. Capelin was of great importance as a diet, especially in the south, where stomach fullness decreased considerably when capelin was not a part of the diet. Food availability seems to be highly variable between the two areas but more stable in the north, where fluctuations in capelin fullness were small. Even though favourable environmental conditions may result in increased haddock density in the colder waters in the north, lower condition indicates that the northern area may be less suitable for this species.
The Identification of Enteric Fever-Specific Antigens for Population-Based Serosurveillance
Authors: Mylona Elli , Hefele Lisa , Tran Vu Thieu Nga , Trinh Van Tan , Nguyen Ngoc Minh Chau , Tran Tuan Anh , Karkey Abhilasha , Dongol Sabina , Basnyat Buddha , Voong Vinh Phat , Ho Ngoc Dan Thanh , Russell Paula , Charles Richelle C , Parry Christopher M , Baker Stephen
Published: July 2023

Background

Enteric fever, caused by Salmonella enterica serovars Typhi and Paratyphi A, is a major public health problem in low- and middle-income countries. Moderate sensitivity and scalability of current methods likely underestimate enteric fever burden. Determining the serological responses to organism-specific antigens may improve incidence measures.

Methods

Plasma samples were collected from blood culture-confirmed enteric fever patients, blood culture-negative febrile patients over the course of 3 months, and afebrile community controls. A panel of 17 Salmonella Typhi and Paratyphi A antigens was purified and used to determine antigen-specific antibody responses by indirect ELISAs.

Results

The antigen-specific longitudinal antibody responses were comparable between enteric fever patients, patients with blood culture-negative febrile controls, and afebrile community controls for most antigens. However, we found that IgG responses against STY1479 (YncE), STY1886 (CdtB), STY1498 (HlyE), and the serovar-specific O2 and O9 antigens were greatly elevated over a 3-month follow up period in S. Typhi/S. Paratyphi A patients compared to controls, suggesting seroconversion.

Conclusions

We identified a set of antigens as good candidates to demonstrate enteric fever exposure. These targets can be used in combination to develop more sensitive and scalable approaches to enteric fever surveillance and generate invaluable epidemiological data for informing vaccine policies.

Clinical Trial Registration

ISRCTN63006567.
Prior Herpes Simplex Virus Infection and the Risk of Herpes Zoster
Authors: Harbecke Ruth , Oxman Michael N , Selke Stacy , Ashbaugh Mark E , Lan Kristine F , Koelle David M , Wald Anna
Published: July 2023

Background

The incidence of herpes zoster (HZ) has increased in the United States concurrent with decrease in herpes simplex virus (HSV) prevalence. We hypothesized that lack of HSV-elicited cross-reactive immunity to varicella-zoster virus (VZV) results in an increased risk of HZ. Using specimens from the placebo arm of the Shingles Prevention Study, we investigated whether persons who develop HZ are less likely to have prior HSV infection than persons who do not develop HZ, and whether HZ is less severe in persons with HSV than in HSV seronegative persons.

Methods

We conducted a nested case-control (1:2) study comparing the seroprevalence of HSV-1 and HSV-2 in cases (persons with polymerase chain reaction-confirmed HZ) to age-, sex-, and health-matched controls (persons without HZ).

Results

Sera from 639 study participants (213 cases and 426 controls) yielded definitive HSV antibody results and were analyzed. Overall, HSV seropositivity rate was 75%. HSV seronegativity was significantly higher in HZ cases than controls (30.5% vs 22.3%; P = .024), with a 55% higher risk of HZ in HSV seronegative than HSV seropositive participants. HSV seropositivity was associated with more severe HZ (P = .021).

Conclusions

Our study demonstrated that prior infection with HSV partly protects against HZ.
Political Visual Literacy
Authors: Galai Yoav
Published: July 2023

Visual politics is a fast-growing field and much of it is focused on images that inspire criticism. This tendency results in a lack of attention to oppressive visual practices. A political visual literacy approaches all visual practices as being layered with different “visual truths” that were developed in response to political commitments over time. These “visual truths” inflected visual practices in ways that may outlive the political settings in which they were first articulated. Most important of these is the desire to capture human difference that framed the development of visual technologies and is still embedded in a range of visual practices. The methodology I develop here links a conjunctural analysis of visual tools and practices and the visual truths implicated in them with their operationalisation by actors as cultural tools through the framework of mediated action. I develop this approach by interrogating two layered and harmful visual practices: the White-centrism of visual technologies and the racialised origins of transphobic visualities in automatic gender recognition technology.
Antimicrobial efficiency of chlorine dioxide and its potential use as anti-SARS-CoV-2 agent: mechanisms of action and interactions with gut microbiota
Authors: Peredo-Lovillo Audry , Romero-Luna Haydee Eliza , Juárez-Trujillo Naida , Jiménez-Fernández Maribel
Published: July 2023

Chlorine dioxide (ClO2) is a disinfectant gas with strong antifungal, antibacterial, and antiviral activities. Applied on hard, non-porous surfaces as an aqueous solution or gas, the ClO2 exerts antimicrobial activity through its interaction and destabilization of cell membrane proteins, as well as through DNA/RNA oxidation, triggering cell death. As for viruses, the ClO2 promotes protein denaturalization mechanisms, preventing the union between the human cells and the viral envelope. Currently, ClO2 has been pointed out as a potential anti-SARS-CoV-2 clinical treatment for use in humans with the ability to oxidize the cysteine residues in the spike protein of SARS-CoV-2, inhibiting the subsequent binding with the Angiotensin-converting enzyme type 2 receptor, located in the alveolar cells. Orally administered ClO2 reaches the gut tract and exacerbates the symptoms of COVID-19, generating a dysbiosis with gut inflammation and diarrhea as side effects, and once absorbed, produces toxic effects including methemoglobinemia and hemoglobinuria, which can trigger respiratory diseases. These effects are dose-dependent and may not be entirely consistent between individuals since the gut microbiota composition is highly heterogeneous. However, to support the use of ClO2 as an anti-SARS-CoV-2 agent, further studies focused on its effectiveness and safety both in healthy and immunocompromised individuals, are needed.
Final Price Neglect in Multi-Product Promotions: How Non-Integrated Price Reductions Promote Higher-Priced Products
Authors: Jia He (Michael) , Huang Yunhui , Zhang Qiang , Shi Zhengyu , Zhang Ke
Published: July 2023

Price reductions take either an integrated form (e.g., a discount shown directly on the price tag) or a non-integrated form (e.g., a discount contained in a coupon sent to consumers and thus separate from the price tag). This research examines how non-integrated versus integrated promotions influence choices among vertically differentiated products. Under an integrated promotion (e.g., $10 off) applicable to multiple products (e.g., original list prices: $50 vs. $30), consumers directly compare these products’ post-promotion final prices displayed on their price tags (after a reduction of $10: $40 vs. $20). In contrast, under a non-integrated promotion of the same monetary value, consumers simply compare these products’ original list prices ($50 vs. $30) and neglect their post-promotion final prices, which require calculations. The list prices ($50 vs. $30; relative to the final prices: $40 vs. $20) as a basis for price comparison reduce the perceived price difference between these products. Consequently, a non-integrated promotion (compared to an integrated promotion) increases consumers’ choice of higher-priced products. A series of experiments (N = 5,187) demonstrate this effect and support the final price neglect mechanism. Furthermore, although attenuated, this effect still emerges for price reductions of a smaller magnitude or in a percent-off format.
The role of personal and impersonal relational contracts on partner selection and efficiency
Authors: Muñoz-Herrera Manuel , Reuben Ernesto
Published: July 2023

In this article, we use a laboratory experiment to study the effects of relational contracts on market efficiency in environments with different degrees of contract enforceability and market competition. By exogenously varying the communication protocol, we create relational contracts that are more personal or impersonal. On the one hand, personal relational contracts improve efficiency by promoting trust and coordination. On the other hand, impersonal relational contracts increase efficiency by facilitating the severance of trading relationships when more productive competitors enter the market. Therefore, the overall effect on market efficiency depends on the relative importance of competition and agreement enforceability (JEL D91, L22, L14).
Care ethics, needs-recognition, and teaching encounters
Authors: Seton Bennett Pip
Published: July 2023

Care ethics takes as central the discerning of needs in those being cared for and attempts to meet those needs. Perceptive caring agents are more likely to be able to identify needs in those for whom they are caring. The identification of needs is no small matter, not least in teaching encounters. This paper modestly proposes that at least some of the needs a caring agent should attempt to meet are a function of the identity of the patient of caring action. Taking Nel Noddings’ account of care ethics as representative, I present it in outline. This leads to the needs-identification problematic. Following this I turn to Soran Reader’s account of needs. I interpret this to offer what I designate as identity as ‘what-ness’. Such an understanding of identity-based needs is a starting point for the caring agent but a more nuanced account, of identity as ‘who-ness’, is argued to be preferable. Identity as ‘who-ness’, as expressed in Paul Ricoeur’s work, advances the discussion, culminating in his concept of the ‘capable human being’. Having brought this aspect of Ricoeur’s thought into conversation with care ethics, I offer an account of identity-based needs conducive to the broader aims of the care ethical project. Finally, I consider what this bolstered account of care ethics might say about a brief and illustrative teaching encounter.
Cluster extent inference revisited: quantification and localisation of brain activity
Authors: Goeman Jelle J , Górecki Paweł , Monajemi Ramin , Chen Xu , Nichols Thomas E , Weeda Wouter
Published: July 2023

Cluster inference based on spatial extent thresholding is a popular analysis method multiple testing in spatial data, and is frequently used for finding activated brain areas in neuroimaging. However, the method has several well-known issues. While powerful for finding regions with some activation, the method as currently defined does not allow any further quantification or localisation of signal. In this paper, we repair this gap. We show that cluster-extent inference can be used (1) to infer the presence of signal in any region of interest and (2) to quantify the percentage of activation in such regions. These additional inferences come for free, i.e. they do not require any further adjustment of the alpha-level of tests, while retaining full family-wise error control. We achieve this extension of the possibilities of cluster inference by embedding the method into a closed testing procedure, and solving the graph-theoretic k-separator problem that results from this embedding. We demonstrate the usefulness of the improved method in a large-scale application to neuroimaging data from the Neurovault database.
Endometrioma causing recurrent small bowel obstruction in a virgin abdomen—a case report and literature review
Authors: Chiu Tricia , Niranjan Nithya , FitzGerald Kate
Published: July 2023

There has been a modest number of cases of bowel obstruction secondary to endometriosis reported. Delays in diagnoses can cause significant morbidity to patients. We describe the case of a 45-year-old female with a 2-year history of recurrent small bowel obstructions (SBOs) without a history of abdominal surgery. She underwent multiple computed tomography scans, and a magnetic resonance enterography, which queried possible terminal ileitis secondary to Crohn’s fibro-stenosing disease or a Meckel’s diverticulum. Colonoscopy up to TI was normal. Elective laparoscopy showed a cicatrizing small bowel mass in her distal ileum ~15 cm from the TI, which was resected. There were no other findings. Histopathological testing revealed endometriosis. At 2-month post-resection, she remains symptom-free and was referred to gynaecology. Endometriosis causing bowel obstruction should be considered early in female patients, especially those with virgin abdomens. Timely elective laparoscopy is a safe and effective way of diagnosing and treating small bowel obstruction, avoiding an emergency procedure.
The Silence of the Bride: A Fatimid marriage contract on silk
Authors: Alrudainy Reem , Tillier Mathieu , Vanthieghem Naïm
Published: July 2023

Marriage contracts and divorce deeds are of particular importance for historians, as they provide clues about both social practices and gender relations. In this article, we offer an edition of a noteworthy document from Dār al-āthār al-islāmiyya in Kuwait, which, beyond its remarkable aesthetic quality, offers a testimony to marriage and divorce practices in a bourgeois milieu of the Egyptian capital during the late Fatimid period. More than a micro-history, this document adds a new piece to the picture of matrimonial dynamics in medieval Egypt, which were often more subtle than previously understood. Patriarchal authority did not prevent a father from deploying all sorts of strategies to protect his daughter in marriage and guarantee her a certain amount of autonomy. In accordance with some jurists’ recommendations, which were based on a Prophetic hadith, the father did not marry off his daughter without first obtaining her tacit permission. Finally, the document preserves the memory of a marital crisis in the seventh year of marriage, during which the husband repudiated his wife before rapidly taking her back.
Intraventricular neurocysticercosis in a migrant from Honduras
Authors: Maldonado-Barrueco Alfredo , Utrilla Cristina , Hernández-González Ana , Perteguer María J , Díaz-Pollán Beatriz , Untoria-Tabares Yeray , Díaz-Menéndez Marta , Falces-Romero Iker , Gutiérrez-Arroyo Almudena , García-Rodríguez Julio , Montero-Vega Dolores
Published: July 2023

We report in Madrid (Spain) a case of intraventricular neurocysticercosis in a migrant from Choluteca (Honduras), which was confirmed by epidemiological, radiological and microbiological criteria.
Spectroscopic Observation and Modeling of Photonic Modes in CeO2 Nanostructures
Authors: Wang Yifan , Yang Shize , Crozier Peter A
Published: July 2023

Photonic modes in dielectric nanostructures, e.g., wide gap semiconductor like CeO2 (ceria), have the potential for various applications such as information transmission and sensing technology. To fully understand the properties of such phenomenon at the nanoscale, electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope was employed to detect and explore photonic modes in well-defined ceria nanocubes. To facilitate the interpretation of the observations, EELS simulations were performed with finite-element methods. The simulations allow the electric and magnetic field distributions associated with different modes to be determined. A simple analytical eigenfunction model was also used to estimate the energy of the photonic modes. In addition, by comparing various spectra taken at different location relative to the cube, the effect of the surrounding environment on the modes could be sensed. This work gives a high-resolution description of the photonic modes' properties in nanostructures, while demonstrating the advantage of EELS in characterizing optical phenomena locally.
Exoplanet spectroscopy with JWST NIRISS: diagnostics and case studies
Authors: Holmberg Måns , Madhusudhan Nikku
Published: July 2023

The JWST is ushering in a new era in remote sensing of exoplanetary atmospheres. Atmospheric retrievals of exoplanets can be highly sensitive to high-precision JWST data. It is, therefore, imperative to characterize the instruments and noise sources using early observations to enable robust characterization of exoplanetary atmospheres using JWST-quality spectra. This work is a step in that direction, focusing on the Near Infrared Imager and Slitless Spectrograph (NIRISS) Single Object Slitless Spectroscopy (SOSS) instrument mode, with a wavelength coverage of 0.6–2.8 $\mu$m and R ∼ 700. Using a custom-built pipeline, JExoRES, we investigate key diagnostics of NIRISS SOSS with observations of two giant exoplanets, WASP-39 b and WASP-96 b, as case studies. We conduct a detailed evaluation of the different aspects of the data reduction and analysis, including sources of contamination, 1/f noise, and system properties such as limb darkening. The slitless nature of NIRISS SOSS makes it susceptible to contamination due to background sources. We present a method to model and correct for dispersed field stars that can significantly improve the accuracy of the observed spectra. In doing so, we also report an empirically determined throughput function for the instrument. We find significant correlated noise in the derived spectra, which may be attributed to 1/f noise, and discuss its implications for spectral binning. We quantify the covariance matrix that would enable the consideration of correlated noise in atmospheric retrievals. Finally, we conduct a comparative assessment of NIRISS SOSS spectra of WASP-39 b reported using different pipelines and highlight important lessons for exoplanet spectroscopy with JWST NIRISS.
Trajectory-based RFI subtraction and calibration for radio interferometry
Authors: Finlay Chris , Bassett Bruce A , Kunz Martin , Oozeer Nadeem
Published: July 2023

Radio interferometry calibration and radio frequency interference (RFI) removal are usually done separately. Here we show that jointly modelling the antenna gains and RFI has significant benefits when the RFI follows precise trajectories, such as for satellites. One surprising benefit is improved calibration solutions, by leveraging the RFI signal itself. We present trajectory-based RFI subtraction and calibration (tabascal), a new algorithm that jointly models the RFI and calibration parameters in visibilities. We test tabascal on simulated MeerKAT calibration observations contaminated by satellite-based RFI. We obtain gain estimates that are both unbiased and up to an order of magnitude better constrained compared to uncontaminated data. When combined with an ad hoc RFI subtraction scheme, tabascal solutions can be further applied to an adjacent target observation: 5 min of calibration data results in an image with about a third the noise achieved when using flagging alone. The recovered flux distribution of RFI subtracted data was on par with uncontaminated data. In contrast, RFI flagging alone resulted in a higher detection threshold and consistent underestimation of source fluxes. For a mean RFI amplitude of 17 Jy, using RFI subtraction leads to less than 1 per cent loss of data compared to 75 per cent data loss from an ideal 3σ flagging algorithm, a very significant increase in data available for science analysis. Although we have examined the case of satellite RFI, tabascal should work for any RFI moving on parametrizable trajectories, relative to the phase centre, such as planes and/or objects fixed to the ground.
Probing bursty star formation by cross-correlating extragalactic background light and galaxy surveys
Authors: Sun Guochao , Lidz Adam , Faisst Andreas L , Faucher-Giguère Claude-André
Published: July 2023

Understanding the star formation rate (SFR) variability and how it depends on physical properties of galaxies is important for developing and testing the theory of galaxy formation. We investigate how statistical measurements of the extragalactic background light (EBL) can shed light on this topic and complement traditional methods based on observations of individual galaxies. Using semi-empirical models of galaxy evolution and SFR indicators sensitive to different star formation time-scales (e.g. H α and ultraviolet continuum luminosities), we show that the SFR variability, quantified by the joint probability distribution of the SFR indicators (i.e. the bivariate conditional luminosity function), can be characterized as a function of galaxy mass and redshift through the cross-correlation between deep, near-infrared maps of the EBL and galaxy distributions. As an example, we consider combining upcoming SPHEREx maps of the EBL with galaxy samples from Rubin Observatory Legacy Survey of Space and Time. We demonstrate that their cross-correlation over a sky fraction of fsky ∼ 0.5 can constrain the joint SFR indicator distribution at high significance up to z ∼ 2.5 for mass-complete samples of galaxies down to $M_{*}\sim 10^9\, {\rm M}_{\odot }$. These constraints not only allow models of different SFR variability to be distinguished, but also provide unique opportunities to investigate physical mechanisms that require large number statistics such as environmental effects. The cross-correlations investigated illustrate the power of combining cosmological surveys to extract information inaccessible from each data set alone, while the large galaxy populations probed capture ensemble-averaged properties beyond the reach of targeted observations towards individual galaxies.
Halo assembly bias from a deep learning model of halo formation
Authors: Lucie-Smith Luisa , Barreira Alexandre , Schmidt Fabian
Published: July 2023

We build a deep learning framework that connects the local formation process of dark matter haloes to the halo bias. We train a convolutional neural network (CNN) to predict the final mass and concentration of dark matter haloes from the initial conditions. The CNN is then used as a surrogate model to derive the response of the haloes’ mass and concentration to long-wavelength perturbations in the initial conditions, and consequently the halo bias parameters following the ‘response bias’ definition. The CNN correctly predicts how the local properties of dark matter haloes respond to changes in the large-scale environment, despite no explicit knowledge of halo bias being provided during training. We show that the CNN recovers the known trends for the linear and second-order density bias parameters b1 and b2, as well as for the local primordial non-Gaussianity linear bias parameter bϕ. The expected secondary assembly bias dependence on halo concentration is also recovered by the CNN: at fixed mass, halo concentration has only a mild impact on b1, but a strong impact on bϕ. Our framework opens a new window for discovering which physical aspects of the halo’s Lagrangian patch determine assembly bias, which in turn can inform physical models of halo formation and bias.
Exploring the likelihood of the 21-cm power spectrum with simulation-based inference
Authors: Prelogović David , Mesinger Andrei
Published: July 2023

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

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

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

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

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.
Enhancing wireless sensing via a target-mounted intelligent reflecting surface
Authors: Shao Xiaodan , Zhang Rui
Published: July 2023

This perspective paper proposes a new wireless sensing approach by mounting Intelligent Reflecting Surface (IRS) on the target, namely target-mounted IRS, to assist in the detection of the target.
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

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

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

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.