bluuebunny/crossref_metadata_2025 huggingface dataset:
GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
Authors: Chang Daniel , Gupta Vinod K , Hur Benjamin , Cunningham Kevin Y , Sung Jaeyun
Published: January 2023

We recently introduced the Gut Microbiome Wellness Index (GMWI), a stool metagenome-based indicator for assessing health by determining the likelihood of disease given the state of one’s gut microbiome. The calculation of our wellness index depends on the relative abundances of health-prevalent and health-scarce species. Encouragingly, GMWI has already been utilized in various studies focusing on differences in the gut microbiome between cases and controls. Herein, we introduce the GMWI-webtool, a user-friendly browser application that computes GMWI, health-prevalent/-scarce species’ relative abundances, and α-diversities from stool shotgun metagenome taxonomic profiles. Users of our interactive online tool can visualize their results and compare them side-by-side with those from our pooled reference dataset of metagenomes, as well as export data in.csv format and high-resolution figures.

Availability and implementation

GMWI-webtool is freely available here: https://gmwi-webtool.github.io/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data
Authors: St-Pierre Julien , Oualkacha Karim , Bhatnagar Sahir Rai
Published: January 2023

Motivation

Sparse regularized regression methods are now widely used in genome-wide association studies (GWAS) to address the multiple testing burden that limits discovery of potentially important predictors. Linear mixed models (LMMs) have become an attractive alternative to principal components (PCs) adjustment to account for population structure and relatedness in high-dimensional penalized models. However, their use in binary trait GWAS rely on the invalid assumption that the residual variance does not depend on the estimated regression coefficients. Moreover, LMMs use a single spectral decomposition of the covariance matrix of the responses, which is no longer possible in generalized linear mixed models (GLMMs).

Results

We introduce a new method called pglmm, a penalized GLMM that allows to simultaneously select genetic markers and estimate their effects, accounting for between-individual correlations and binary nature of the trait. We develop a computationally efficient algorithm based on penalized quasi-likelihood estimation that allows to scale regularized mixed models on high-dimensional binary trait GWAS. We show through simulations that when the dimensionality of the relatedness matrix is high, penalized LMM and logistic regression with PC adjustment fail to select important predictors, and have inferior prediction accuracy compared to pglmm. Further, we demonstrate through the analysis of two polygenic binary traits in a subset of 6731 related individuals from the UK Biobank data with 320K SNPs that our method can achieve higher predictive performance, while also selecting fewer predictors than a sparse regularized logistic lasso with PC adjustment.

Availability and implementation

Our Julia package PenalizedGLMM.jl is publicly available on github: https://github.com/julstpierre/PenalizedGLMM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Anex vivoovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates
Authors: Zhang Jiyang , Goods Brittany A , Pattarawat Pawat , Wang Yingzheng , Haining Tessa , Zhang Qiang , Shalek Alex K , Duncan Francesca E , Woodruff Teresa K , Xiao Shuo
Published: January 2023

Ovulation is an integral part of women’s menstrual cycle and fertility. Understanding the mechanisms of ovulation has broad implications for the treatment of anovulatory diseases and the development of novel contraceptives. Now, few studies have developed effective models that both faithfully recapitulate the hallmarks of ovulation and possess scalability. We established a three-dimensional encapsulated in vitro follicle growth (eIVFG) system that recapitulates folliculogenesis and produces follicles that undergo ovulation in a controlled manner. Here, we determined whether ex vivo ovulation preserves molecular signatures of ovulation and demonstrated its use in discovering novel ovulatory pathways and nonhormonal contraceptive candidates through a high-throughput ovulation screening. Mature murine follicles from eIVFG were induced to ovulate ex vivo using human chorionic gonadotropin and collected at 0, 1, 4, and 8 hours post-induction. Phenotypic analyses confirmed key ovulatory events, including cumulus expansion, oocyte maturation, follicle rupture, and luteinization. Single-follicle RNA-sequencing analysis revealed the preservation of ovulatory genes and dynamic transcriptomic profiles and signaling. Soft clustering identified distinct gene expression patterns and new pathways that may critically regulate ovulation. We further used this ex vivo ovulation system to screen 21 compounds targeting established and newly identified ovulatory pathways. We discovered that proprotein convertases activate gelatinases to sustain follicle rupture and do not regulate luteinization and progesterone secretion. Together, our ex vivo ovulation system preserves molecular signatures of ovulation, presenting a new powerful tool for studying ovulation and anovulatory diseases as well as for establishing a high-throughput ovulation screening to identify novel nonhormonal contraceptives for women.
Differential responsiveness of spermatogonia to retinoic acid dictates precocious differentiation but not meiotic entry during steady-state spermatogenesis
Authors: Johnson Taylor A , Niedenberger Bryan A , Kirsanov Oleksandr , Harrington Ellen V , Malachowski Taylor , Geyer Christopher B
Published: January 2023

The foundation of mammalian spermatogenesis is provided by undifferentiated spermatogonia, which comprise of spermatogonial stem cells (SSCs) and transit-amplifying progenitors that differentiate in response to retinoic acid (RA) and are committed to enter meiosis. Our laboratory recently reported that the foundational populations of SSCs, undifferentiated progenitors, and differentiating spermatogonia are formed in the neonatal testis in part based on their differential responsiveness to RA. Here, we expand on those findings to define the extent to which RA responsiveness during steady-state spermatogenesis in the adult testis regulates the spermatogonial fate. Our results reveal that both progenitor and differentiating spermatogonia throughout the testis are capable of responding to exogenous RA, but their resulting fates were quite distinct—undifferentiated progenitors precociously differentiated and proceeded into meiosis on a normal timeline, while differentiating spermatogonia were unable to hasten their entry into meiosis. This reveals that the spermatogonia responding to RA must still complete the 8.6 day differentiation program prior to their entry into meiosis. Addition of exogenous RA enriched testes with preleptotene and pachytene spermatocytes one and two seminiferous cycles later, respectively, supporting recent clinical studies reporting increased sperm production and enhanced fertility in subfertile men on long-term RA analog treatment. Collectively, our results reveal that a well-buffered system exists within mammalian testes to regulate spermatogonial RA exposure, that exposed undifferentiated progenitors can precociously differentiate, but must complete a normal-length differentiation program prior to entering meiosis, and that daily RA treatments increased the numbers of advanced germ cells by directing undifferentiated progenitors to continuously differentiate.
Spontaneous activity in cortical neurons is stereotyped and non-Poisson
Authors: Swindale Nicholas V , Spacek Martin A , Krause Matthew , Mitelut Catalin
Published: January 2023

Neurons fire even in the absence of sensory stimulation or task demands. Numerous theoretical studies have modeled this spontaneous activity as a Poisson process with uncorrelated intervals between successive spikes and a variance in firing rate equal to the mean. Experimental tests of this hypothesis have yielded variable results, though most have concluded that firing is not Poisson. However, these tests say little about the ways firing might deviate from randomness. Nor are they definitive because many different distributions can have equal means and variances. Here, we characterized spontaneous spiking patterns in extracellular recordings from monkey, cat, and mouse cerebral cortex neurons using rate-normalized spike train autocorrelation functions (ACFs) and a logarithmic timescale. If activity was Poisson, this function should be flat. This was almost never the case. Instead, ACFs had diverse shapes, often with characteristic peaks in the 1–700 ms range. Shapes were stable over time, up to the longest recording periods used (51 min). They did not fall into obvious clusters. ACFs were often unaffected by visual stimulation, though some abruptly changed during brain state shifts. These behaviors may have their origin in the intrinsic biophysics and dendritic anatomy of the cells or in the inputs they receive.
Letting leaders spontaneously emerge yields better creative outcomes and higher leader–follower interbrain synchrony during creative group communication
Authors: He Yingyao , Wang Xinyue , Lu Kelong , Hao Ning
Published: January 2023

This study aimed to investigate how the ways leaders arise (appointed vs. emergent) affect the leader–follower interaction during creative group communication. Hyperscanning technique was adopted to reveal the underlying interpersonal neural correlates using functional near-infrared spectroscopy. Participants were assigned into 3-person groups to complete a creative problem-solving task. These groups were randomly split into conditions of appointed (condition A) and emergent (condition E) leaders. Creative group outcomes were better in condition E, accompanied by more frequent perspective-taking behaviors between leaders and followers. The interpersonal brain synchronization (IBS) increment for leader–follower pairs was significantly higher at the right angular gyrus (rAG), between the rAG and the right supramarginal gyrus (rSMG), and between the right middle temporal gyrus and the right motor cortex in condition E and positively correlated with perspective-taking behaviors between leaders and followers. The graph-based analysis showed higher nodal betweenness of the rAG and the rSMG in condition E. These results indicated the neural coupling of brain regions involved in mentalizing, semantic processing and motor imagery may underlie the dynamic information transmission between leaders and followers during creative group communication.
Patient-reported Outcomes and Disability Are Associated with Histological Disease Activity in Patients with Ulcerative Colitis: Results from the APOLLO Study
Authors: Verstockt Bram , Pouillon Lieven , Ballaux Florence , Jorissen Celine , Hoefkens Eveline , Lembrechts Nikki , Bossuyt Peter
Published: January 2023

Background and Aims

Treating beyond endoscopic remission, aiming for histological remission, is an emerging target in ulcerative colitis [UC]. Patient-reported outcome measurements [PROMs] become increasingly important, but their association with histology is unclear.

Methods

Multiple PROMs were prospectively collected in UC patients undergoing colonoscopy. Mayo endoscopic sub-score [MES] and ulcerative colitis endoscopic index of severity [UCEIS] were determined, as well as the Nancy histological index [NHI] of the most affected area. Endoscopic remission was defined as MES and UCEIS 0, histological remission as NHI 0, and histo-endoscopic mucosal remission [HEMR] as a combination of both.

Results

A total of 109 assessments were collected in 80 patients with endoscopic and HEMR remission rates of 24.8% and 16.5%, respectively. Patients with HEMR had a significantly lower overall inflammatory bowel disease [IBD] disability [p <0.001] and disease activity score [p <0.001] as compared with patients without. In line, NHI correlated with the overall IBD-disk [r = 0.36, p <0.001] and simple clinical colitis activity index [SCCAI] score [r = 0.44, p <0.001]. Many individual components of both differed significantly between patients with and without HEMR. Although the overall accuracy of the IBD-disk [0.78] or SCCAI score [0.83] for HEMR is lower [p <0.005] than the MES or UCEIS [0.95], a cumulative IBD-disk score >35.5 and an SSCAI score >3.5 have a high negative predictive value [98.6% and 100.0%, respectively] to exclude HEMR.

Conclusion

Histo-endoscopic inactive disease is associated with reduced IBD disability, but not with complete absence thereof. PROMs for disability and clinical disease activity cannot fully replace histo-endoscopic findings, and should be considered complementary in patient-centred endpoint discussions. Nevertheless, PROMs have a high negative predictive value to rule out HEMR.
Against Future Generations
Authors: Humphreys Stephen
Published: January 2023

Future generations are invoked in the United Nations Framework Convention on Climate Change, and increasingly often in climate debate, as a locus of responsibility for present generations. In this article, I argue against this framing. I look at the historical context and rhetorical effects of a generational frame for both present and future generations, dwelling in particular on guiding conceptions of sacrifice and legacy as well as on the construction of future scenarios and the practice of future discounting. I conclude that the appeal to future generations obfuscates, rendering a series of critical boundaries diffuse, and, in doing so, abjures concrete urgent existing responsibilities towards those alive today in the same gesture that nominally assumes them for an abstract unformed future.
Professors’ gender biases in assessing applicants for professorships
Authors: Solga Heike , Rusconi Alessandra , Netz Nicolai
Published: January 2023

Recent evidence suggests that women are more likely to be selected for professorships when they apply. This female advantage may be partly due to the widely promoted gender-equality policy of having a substantial female quota in selection committees. Yet, research has rarely considered whether male and female committee members evaluate applicants for professorships differently. We address this research gap based on a large factorial survey experiment with German university professors from different disciplines. We asked these professors to rate how qualified hypothetical applicants are for full professorships and the likelihood of inviting these applicants for a job interview. We find that female applicants have an modest advantage both in their perceived qualifications and in their likelihood of being invited—with no differences between the male and female professors assessing them. Importantly, however, the female advantage in invitation does not apply to highly qualified female applicants but only to female applicants with low and mediocre perceived qualifications—again, there is no difference between male and female professors. Moreover, our analyses do not indicate a Matilda effect, that is, we do not find a co-authorship penalty for female applicants.
Epigenetics and the exposome: DNA methylation as a proxy for health impacts of prenatal environmental exposures
Authors: Colwell Mathia L , Townsel Courtney , Petroff Rebekah L , Goodrich Jaclyn M , Dolinoy Dana C
Published: January 2023

The accumulation of everyday exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual’s early-life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early-life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes later in life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A, and the metal lead, to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and the current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study offering us a unique and powerful way to assess the early-life exposome and its effects across different life stages.
Sensitivities of diffracted PKKPab waves to the velocity structures in the lowermost mantle
Authors: Chen Yulin , Ni Sidao , Zhang Baolong , Zhao Li , Song Xiaodong , Wang Yi
Published: January 2023

Diffractions of PKKPab (${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$) along the core mantle boundary (CMB) have been observed well beyond its cutoff distance in recent studies, making it useful for improving the spatial sampling to constrain the lowermost mantle velocity structures. However, the diffractions of PKKPab waves may occur at one of the three CMB interaction points (core entry, underside reflection and exit), giving rise to uncertainties of the sampling region. Moreover, the sensitivity kernels of the non-geometrical ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ in the lowermost mantle are difficult to obtain with classical ray theory and can be expected to be more complicated than the typical banana-doughnut shape for direct arrivals. In this study, we address these two issues by analysing the finite-frequency delay-time sensitivity kernels of the ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ waves computed by numerical algorithms based on full-wave theory. We find that the diffraction effects for the ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ waves are most significant near their core entry and exit regions. For a dominant period of 1 s, the estimated widths of the first Fresnel zones on the mantle side of these two areas are about 60 km. To further investigate the sensitivities of ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ to different structures in the lowermost mantle, we conduct a series of 1D and 2D high-frequency (∼1 Hz) modelling experiments. Our results show that the travel times and amplitudes of the ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ waves are sensitive to large-scale P-wave anomalies (with Vp perturbations of ± 2 per cent and thicknesses of more than 100 km) and small-scale ultra-low velocity zones (ULVZs; with Vp reduction of 5 per cent or 10 per cent and thickness of tens of kilometers). However, the slownesses of the ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}\ $ waves remain nearly unchanged in the perturbed models. We explain this unexpected result by the differential delay-time sensitivity kernels for stations at similar epicentral distances. Our results demonstrate both the advantages and limitations of the ${\rm{PKKP}}_{{\rm{ab}}}^{{\rm{diff}}}$ waves in studying the structures at the base of the mantle.
Effect of intraoperative haemoadsorption therapy on cardiac surgery for active infective endocarditis with confirmedStaphylococcus aureusbacteraemia
Authors: Haidari Zaki , Leiler Spela , Mamdooh Hazem , Fittkau Matthias , Boss Kristina , Tyczynski Bartosz , Thielmann Matthias , Bagaev Erik , El Gabry Mohamed , Wendt Daniel , Kribben Andreas , Bertsch Thomas , Ruhparwar Arjang , Fischlein Theodor , Kalisnik Jurij Matija
Published: January 2023

OBJECTIVES

Sepsis caused by infective endocarditis (IE), due to Staphylococcus aureus, is associated with significant morbidity and mortality. Blood purification using haemoadsorption (HA) may attenuate the inflammatory response. We investigated the effect of intraoperative HA on postoperative outcomes in S. aureus IE.

METHODS

Patients with confirmed S. aureus IE undergoing cardiac surgery were included in a dual-centre study between January 2015 and March 2022. Patients treated with intraoperative HA (HA group) were compared to patients not treated with HA (control group). The primary outcome was vasoactive-inotropic score within the first 72 h postoperatively and secondary outcomes were sepsis-related mortality (SEPSIS-3 definition) and overall mortality at 30 and 90 days.

RESULTS

No differences in baseline characteristics were observed between groups (haemoadsorption group, n = 75, control group, n = 55). Significantly decreased vasoactive-inotropic score was observed in the haemoadsorption group at all time points [6 h: 6.0 (0–17) vs 17 (3–47), P = 0.0014; 12 h: 2 (0–8.3) vs 5.9 (0–37), P = 0.0138; 24 h: 0 (0–5) vs 4.9 (0–23), P = 0.0064; 48 h: 0 (0–2.1) vs 0.1 (0–13), P = 0.0192; 72 h: 0 (0) vs 0 (0–5), P = 0.0014]. Importantly, sepsis-related mortality (8.0% vs 22.8%, P = 0.02) and 30-day (17.3% vs 32.7%, P = 0.03) and 90-day overall mortality (21.3% vs 40%, P = 0.03) were also significantly lower with haemoadsorption.

CONCLUSIONS

Intraoperative HA during cardiac surgery for S. aureus IE was associated with significantly lower postoperative vasopressor and inotropic requirements and resulted in lower sepsis-related and overall 30- and 90-day mortality. In this high-risk population, improved postoperative haemodynamic stabilization by intraoperative HA appears to improve survival and should be further tested in future randomized trials.
Indocyanine green clearance predicts outcome in patients undergoing transcatheter valve intervention for severe atrio-ventricular valve regurgitation
Authors: Doldi Philipp Maximilian , Stolz Lukas , Buech Joscha , Saha Shekhar , Weckbach Ludwig , Gmeiner Jonas , Orban Martin , Braun Daniel , Stocker Thomas J , Nabauer Michael , Lange Christian M , Massberg Steffen , Hagl Christian , Hausleiter Jörg
Published: January 2023

OBJECTIVES

Severe mitral regurgitation (MR) and tricuspid regurgitation (TR) aggravate haemodynamic stress leading to congestive heart failure with impaired hepatic function, also known as cardiohepatic syndrome (CHS). Current perioperative risk calculators do not sufficiently consider CHS and serum liver function parameters lack sensitivity to diagnose CHS. Indocyanine green and its elimination (measured by the LIMON® test) represent a dynamic and non-invasive test which correlates with the hepatic function. Nevertheless, its utility in the setting of transcatheter valve repair/replacement (TVR) to predict CHS and outcome remains unknown.

METHODS

We analysed liver function and outcomes of patients undergoing TVR for MR or TR between August 2020 and May 2021 at the Munich University Hospital.

RESULTS

Out of a total of 44 patients treated at the University Hospital of Munich, 21 (48%) were treated for severe MR, 20 (46%) for severe TR and 3 (7%) for both diseases. Procedural success defined as MR/TR ≤2+ was 94% among MR patients and 92% among TR patients. While classical serum liver function parameters did not change after TVR, there was a significant improvement in liver function as assessed by the LIMON® test (P ≤ 0.001). Patients with baseline indocyanine green plasma disappearance rate <12.95%/min showed significantly increased 1-year mortality (hazard ratio: 1.54, 95% confidence interval: 1.05–2.25, P = 0.027) and lower New York Hear Association class improvement (P = 0.05).

CONCLUSIONS

Especially in the context of the recently stressed importance of a careful patient selection prior to the interdisciplinary treatment of valvular heart disease, the LIMON® test may provide further real-time information on the patients’ cardiohepatic injury and prognosis.
Liquid Legitimacy: Lessons on Military Violence from the Israeli Occupation in the West Bank
Authors: Gazit Nir , Grassiani Erella
Published: January 2023

During the past decades, militaries have increasingly used force against civilians and armed adversaries in operational settings other than war. Theories about legitimacy for the use of military force often focus on macro variables such as international law, government policy, and structural political contingencies. The strength of such theories in explaining military violence during conventional wars notwithstanding, this article argues that they fail to explain the legitimization of the use of force in situations that cannot be categorized as “classic” warfare, where institutional and international norms seem to fade, rational calculations become unclear, and governments often do not hold themselves accountable for soldiers’ violent behavior. When such conflicts linger, they often develop into situations in which sovereignty is fragmented and statehood is limited in ways that further undermine institutional legitimacy. Using the accounts of Israeli soldiers deployed in the occupied Palestinian territories in the last two decades, this article broadens the analytical perspective on military violence's legitimacy by depicting its micromechanisms and local factors. In doing so, it identifies three clusters of factors: emotions, space and time, and informal organizational culture. We posit that, during intense friction between soldiers and civilians in the context of prolonged occupation, the structural variables and formal powers that typically dictate the use of force give way to more fluctuating dynamics that shape the patterns of military violence and, ultimately, influence its legitimacy.
Iconoclasm, Speculative Realism, and Sympathetic Magic
Authors: Rich Sara A , Bartholomew Sarah
Published: January 2023

In the current American iconoclash, certain monuments are subject to vandalism and municipal removal from their pedestals. Phrases such as “the erasure of history” and “damnatio memoriae” point to concerns that iconoclasm is an attempt to censor history or even remove certain individuals from public memory altogether. Because these phrases beckon the past, this wave of iconoclasm calls for a close examination of previous image-breaking to establish motives. Drawing first from art history, we analyze Byzantine iconoclasm and anxieties over the nature of icons’ power, before contextualizing these findings within image destruction from the Paleolithic to the present day. Each comparison is suggestive of an enduring aesthetic principle: that what appears inanimate is not always inert. Next, drawing from cultural anthropology, we argue that principles of sympathetic magic are at the heart of contemporary iconoclasms, but not in the way media outlets often suggest. Instead, the fear of history’s erasure betrays a deeply rooted equivalence between the representation and the represented. In perceiving their fates as shared, sympathetic magic is seen to persist in the way humans create, interpret, and desecrate images. We conclude with the speculative realist proposition that iconoclasm can produce new, original artworks, which carries implications for the autonomy of art and its distribution between artist and artwork.
Comb Cell Structure and Morphological Characteristics of the Chinese Honey Bee, Apis cerana cerana (Hymenoptera: Apidae), Under Successive Generations
Authors: Hu Xiaoling , Meng Qingxin , Zhi Dandan , Deng Shangkao , Zhao Wenzheng , Tian Yakai , Gong Xueyang , Dong Kun
Published: January 2023

This study investigated the changes in comb cell structure and external morphological characteristics of the Chinese honey bee under ten successive generations to determine the optimal time to replace the old combs. Accordingly, ten Chinese honey bee experimental colonies were established, and natural combs were constructed for continuous rearing of workers for 1–10 generations. The brood comb thickness, brood cell structure, birth weight, and morphological characteristics of workers were determined. Pearson correlation analyses between brood comb structure and morphological characteristics of workers were carried out. The results revealed that under ten successive generations, the color of the brood comb deepens from white or light yellow to brown and finally to black. Also, concerning the brood cell shape, the cell base changes from the three-rhomboid structure to the hemisphere, and the cell body changes from the hexagonal prism structure to the cylinder. The brood cell depth increases with an increase in brood comb thickness. The cell volume reduces with the hexagonal cell’s decreasing inner circumference side length, and diameter. A smaller cell volume leads to a decrease in the birth weight and body size of the worker, in addition, the Chinese honey bee has gnawed off the comb cells that have been cultivated for eight generations. This study suggests that the combs of Chinese honey bees should be replaced after eight generations to improve colony strength and production performance.
Baseline Susceptibility and Evidence of Resistance to Acetamiprid in Gill’s Mealybug, Ferrisia gilli Gullan (Hemiptera: Pseudococcidae)
Authors: Bansal Raman , Hunter Wayne B , Haviland David R
Published: January 2023

Gill’s mealybug, Ferrisia gilli (Gullan) (Hemiptera: Pseudococcidae), is a major pest of pistachio in California. Insecticide treatment is the primary control method and acetamiprid is widely used to control this pest. However, there have been numerous reports of control failures for F. gilli after field applications of recommended insecticides in recent years. The purpose of this study was to develop a method for routine monitoring of F. gilli susceptibility and quantify current levels of F. gilli susceptibility to acetamiprid. A leaf-dip bioassay method using lima bean leaves was established and baseline susceptibility responses of 5 field populations were determined. Lethal concentrations to kill 50% of population (LC50) for second instar nymphs at 48 h ranged from 0.367 to 2.398 µg(AI)ml−1 of acetamiprid. Similarly, lethal concentrations to kill 90% of population (LC90) for second instar nymphs at 48 h ranged from 2.887 to 10.752 µg(AI)ml−1 of acetamiprid. The F. gilli population collected from Hanford area showed up to 6.5-fold significantly decreased mortality to acetamiprid compared to other populations. The resistance identified in this study, although relatively low, indicates that there has been repeated pressure to select for acetamiprid resistance and resistance levels can further magnify if effective management steps are not taken. The baseline susceptibility established in this study can be used to investigate potential cause of recent acetamiprid failures against F. gilli. In the long-term, results of this study will support the development of resistance management strategies by monitoring shifts in the susceptibility of F. gilli populations.
Detection ofBartonella quintana(Hyphomicrobiales: Bartonellaceae) Among Day Laborers in Osaka, Japan, 2009–2010
Authors: Sasaki Toshinori , Matsuoka Mayumi , Sawabe Kyoko , Isawa Haruhiko , Shibayama Keigo , Kobayashi Mutsuo
Published: January 2023

Bartonella quintana is a gram-negative bacterium causing trench fever, an illness historically acquired by soldiers during World War I. More recently, outbreaks of trench fever have been reported in those experiencing homelessness in the United States, France, Russia, and Tokyo, as well as in children in Nepal and persons in Ethiopia. Reports of B. quintana infection outside of Tokyo are rare in Japan. The aim of this study was to examine body lice and blood obtained from people staying in shelters in Osaka (2009–2010) for B. quintana via polymerase chain reaction and enzyme-linked immunosorbent assays. Day laborers were defined as homeless individuals and shelter residents in this study. We detected genes of B. quintana in body lice by PCR and antibodies against B. quintana. The positive rate of B. quintana genes was 6/10 (60%) in body lice and the seroprevalence (IgG) of B. quintana was 4/10 (40%). This demonstrates that trench fever was endemic in people staying in shelters in Osaka in 2009–2010.
Measuring economic mobility in India using noisy data: a partial identification approach
Authors: Li Hao , Millimet Daniel L , Roychowdhury Punarjit
Published: January 2023

We examine economic mobility in India while accounting for misclassification to better understand the welfare effects of the rise in inequality. To proceed, we extend recently developed methods on the partial identification of transition matrices. Allowing for modest misclassification, we find overall mobility has been remarkably low: at least 65% of poor households remained poor or at-risk of being poor between 2005 and 2012. We also find Muslims, lower caste groups, and rural households are in a more disadvantageous position compared to Hindus, upper caste groups, and urban households. These findings cast doubt on the conventional wisdom that marginalized households in India are catching up.
Network self-exciting point processes to measure health impacts of COVID-19
Authors: Giudici Paolo , Pagnottoni Paolo , Spelta Alessandro
Published: January 2023

The assessment of the health impacts of the COVID-19 pandemic requires the consideration of mobility networks. To this aim, we propose to augment spatio-temporal point process models with mobility network covariates. We show how the resulting model can be employed to predict contagion patterns and to help in important decisions such as the distribution of vaccines. The application of the proposed methodology to 27 European countries shows that human mobility, along with vaccine doses and government policies, are significant predictors of the number of new COVID-19 reported infections and are therefore key variables for decision-making.
Covariate adjustment in multiarmed, possibly factorial experiments
Authors: Zhao Anqi , Ding Peng
Published: January 2023

Randomized experiments are the gold standard for causal inference and enable unbiased estimation of treatment effects. Regression adjustment provides a convenient way to incorporate covariate information for additional efficiency. This article provides a unified account of its utility for improving estimation efficiency in multiarmed experiments. We start with the commonly used additive and fully interacted models for regression adjustment in estimating average treatment effects (ATE), and clarify the trade-offs between the resulting ordinary least squares (OLS) estimators in terms of finite sample performance and asymptotic efficiency. We then move on to regression adjustment based on restricted least squares (RLS), and establish for the first time its properties for inferring ATE from the design-based perspective. The resulting inference has multiple guarantees. First, it is asymptotically efficient when the restriction is correctly specified. Second, it remains consistent as long as the restriction on the coefficients of the treatment indicators, if any, is correctly specified and separate from that on the coefficients of the treatment-covariate interactions. Third, it can have better finite sample performance than the unrestricted counterpart even when the restriction is moderately misspecified. It is thus our recommendation when the OLS fit of the fully interacted regression risks large finite sample variability in case of many covariates, many treatments, yet a moderate sample size. In addition, the newly established theory of RLS also provides a unified way of studying OLS-based inference from general regression specifications. As an illustration, we demonstrate its value for studying OLS-based regression adjustment in factorial experiments. Importantly, although we analyse inferential procedures that are motivated by OLS, we do not invoke any assumptions required by the underlying linear models.
Conformalized survival analysis
Authors: Candès Emmanuel , Lei Lihua , Ren Zhimei
Published: January 2023

In this paper, we develop an inferential method based on conformal prediction, which can wrap around any survival prediction algorithm to produce calibrated, covariate-dependent lower predictive bounds on survival times. In the Type I right-censoring setting, when the censoring times are completely exogenous, the lower predictive bounds have guaranteed coverage in finite samples without any assumptions other than that of operating on independent and identically distributed data points. Under a more general conditionally independent censoring assumption, the bounds satisfy a doubly robust property which states the following: marginal coverage is approximately guaranteed if either the censoring mechanism or the conditional survival function is estimated well. The validity and efficiency of our procedure are demonstrated on synthetic data and real COVID-19 data from the UK Biobank.
Infections in travellers returning to the UK: a retrospective analysis (2015–2020)
Authors: Warner Jennifer C , Hatziioanou Diane , Osborne Jane C , Bailey Daniel J , Brooks Timothy J G , Semper Amanda E
Published: January 2023

Background

Every year, many thousands of travellers return to the United Kingdom (UK) from visits to other countries and some will become unwell due to infections acquired abroad. Many imported infections have similar clinical presentations, such as fever and myalgia, so diagnostic testing is an important tool to improve patient management and outcomes. The aim of this study was to examine the demographics, travel history, presenting symptoms and diagnostic outcomes of referrals to the UK’s specialist diagnostic Rare & Imported Pathogens Laboratory (RIPL) for the period 2015–2020.

Methods

Anonymised clinical and laboratory data were extracted from RIPL’s Laboratory Information Management System and cleaned prior to descriptive analysis of the data. Travel history data were mapped to one of eight world regions, whereas symptom data were categorised into presenting syndromes. Diagnostic data were categorised as either positive, equivocal or negative.

Results

During the period 2015–2020, RIPL received 73 951 samples from 53 432 patients suspected of having infections that are rare in the UK. The most common age group for unwell returning travellers was 30–39 years and the most commonly reported travel destination was Southern and SE Asia. Dengue virus was the most diagnosed infection overall, followed by chikungunya, Zika, leptospirosis and spotted fever group Rickettsia. Dengue virus was among the top three most frequent diagnoses for all world regions except Europe and represented 62.5% of all confirmed/probable diagnoses.

Conclusions

None of the top five infections diagnosed by RIPL in travellers are vaccine-preventable, therefore understanding traveller demographics, destination-specific risk factors and encouraging preventative behaviours is the best available strategy to reduce the number of returning travellers who become infected. Prompt referral of acute samples with a detailed travel history, including purpose of travel and activities undertaken as well as dates and destinations can be a valuable tool in designing public health interventions and diagnostic algorithms.
Getting to the roots of N, P, and K uptake
Authors: Lyzenga Wendy J , Liu Zhigang , Olukayode Toluwase , Zhao Yang , Kochian Leon V , Ham Byung-Kook
Published: January 2023

The soil contributes to the main pool of essential mineral nutrients for plants. These mineral nutrients are critical elements for the building blocks of plant biomolecules, play fundamental roles in cell processes, and act in various enzymatic reactions. The roots are the main entry point for mineral nutrients used within the plant to grow, develop, and produce seeds. In this regard, a suite of plant nutrient transport systems, sensors, and signaling proteins function in acquiring mineral nutrients through the roots. Mineral nutrients from chemical fertilizers, composed mainly of nitrogen, phosphorus, and potassium (NPK), are added to agricultural land to maximize crop yields, worldwide. However, improving nutrient uptake and use within crops is critical for economically and environmentally sustainable agriculture. Therefore, we review the molecular basis for N, P, and K nutrient uptake into the roots. Remarkably, plants are responsive to heterogeneous nutrient distribution and align root growth and nutrient uptake with nutrient-rich patches. We highlight the relationship between nutrient distribution in the growth environment and root system architecture. We discuss the exchange of information between the root and shoot systems through the xylem and phloem, which coordinates nutrient uptake with photosynthesis. The size and structure of the root system, along with the abundance and activity of nutrient transporters, largely determine the nutrient acquisition rate. Lastly, we discuss connections between N, P, and K uptake and signaling.
Teaching 19th-Century Literature Beyond the Secularisation Thesis: Introduction to the Special Forum
Authors: McQueen Joseph
Published: January 2023

The widescale revision of the secularisation thesis continues apace across the humanities and more specifically in 19th-century studies—a field that until recently often assumed the ‘subtraction’ story of secularisation in which, as Charles Taylor explains, modernity leads to the inevitable demise of religion. But how does this revised outlook inform the teaching of 19th-century literature? In other words, if we now question the notion that the 19th century sees the inexorable decline of faith, how does that questioning change the way we teach Romantic and/or Victorian literature? The following special forum addresses such questions.
Dropping the Albatross: Teaching Religion and Literature in a Postsecular Age
Authors: Barbeau Jeffrey W
Published: January 2023

Teaching literature after the ‘secularisation thesis’ requires both a critical recognition of the distinctly religious origins of the British Romantic movement and the intentional recovery of a wider range of authors and religious beliefs during the age. In this essay, I offer a brief consideration of disciplinary integration within higher education, with particular attention to the work of John Henry Newman, S.T. Coleridge, and Daniel Hardy. Next, I offer a case study that presents an ecofeminist reading of S.T. Coleridge’s ‘Rime of the Ancient Mariner’ with an assist from the religious scholarship of Sallie McFague. Finally, I conclude with some brief recommendations on how faculty might teach religion and literature in the classroom and, in the process, contribute to the current effort within higher education to diversify the curriculum.
Religion, Reading, and Metacognition in the Victorian Literature Classroom
Authors: Plourde Aubrey
Published: January 2023

The Victorian literature course, ‘Victorians Reading Religion’, relocates the religious friction of the 19th century, focusing less on scientific threats, crises of faith, and schisms within Victorian churches, and more on how the shifting religious landscape of 19th-century British culture prompted Victorian thinkers to renegotiate their approaches to reading. Using Olive Schriener’s Story of an African Farm (1883) as a prime example, attending to these overlapping iterations of religious experience offers us three correlated opportunities: firstly, it helps students loosen the identity categories they might otherwise consistently apply too tidily. Secondly, it reintroduces literature as a space in which they can evaluate morality. Finally, centring religion in literary studies prompts students to recognise the ways in which the work we do in a literature classroom is itself religious. Together, these pedagogical opportunities produce occasions for metacognition that help students articulate the value of humanistic study in the increasingly instrumentalised landscape of higher education.
Making Strange: Teaching 19th-Century Gothic and Fantastic Literature
Authors: Milbank Alison
Published: January 2023

How can the teacher open what Charles Taylor describes as the ‘immanent frame’ of a secular self-sufficient view of reality? This article describes two modules studying non-realist literary modes—Gothic and fantasy writing—which seek to do this. God and the Gothic reverses the psychological turn in 19th-century Gothic to examine the way Tzvetan Todorov’s idea of the fantastic hesitation can be used to enable an opening to the transcendent and offers a new way of narrating Victorian Gothic through Gaskell, Oliphant, and Machen. Religion and Fantasy invokes the defamiliarising technique of Victor Shklovsky and the magic idealism of Novalis to connect German and British imaginative writing from Coleridge, through John Ruskin, Charles Kingsley, and Christina Rossetti.
A burst storm from the repeating FRB 20200120E in an M81 globular cluster
Authors: Nimmo K , Hessels J W T , Snelders M P , Karuppusamy R , Hewitt D M , Kirsten F , Marcote B , Bach U , Bansod A , Barr E D , Behrend J , Bezrukovs V , Buttaccio S , Feiler R , Gawroński M P , Lindqvist M , Orbidans A , Puchalska W , Wang N , Winchen T , Wolak P , Wu J , Yuan J
Published: January 2023

The repeating fast radio burst (FRB) source FRB 20200120E is exceptional because of its proximity and association with a globular cluster. Here we report 60 bursts detected with the Effelsberg telescope at 1.4 GHz. We observe large variations in the burst rate, and report the first FRB 20200120E ‘burst storm’, where the source suddenly became active and 53 bursts (fluence ≥0.04 Jy ms) occurred within only 40 min. We find no strict periodicity in the burst arrival times, nor any evidence for periodicity in the source’s activity between observations. The burst storm shows a steep energy distribution (power-law index α = 2.39 ± 0.12) and a bimodal wait-time distribution, with log-normal means of 0.94$^{+0.07}_{-0.06}$ s and 23.61$^{+3.06}_{-2.71}$ s. We attribute these wait-time distribution peaks to a characteristic event time-scale and pseudo-Poisson burst rate, respectively. The secondary wait-time peak at ∼1 s is ∼50 × longer than the ∼24 ms time-scale seen for both FRB 20121102A and FRB 20201124A – potentially indicating a larger emission region, or slower burst propagation. FRB 20200120E shows order-of-magnitude lower burst durations and luminosities compared with FRB 20121102A and FRB 20201124A. Lastly, in contrast to FRB 20121102A, which has observed dispersion measure (DM) variations of ΔDM > 1 pc cm−3 on month-to-year time-scales, we determine that FRB 20200120E’s DM has remained stable (ΔDM < 0.15 pc cm−3) over >10 months. Overall, the observational characteristics of FRB 20200120E deviate quantitatively from other active repeaters, but it is unclear whether it is qualitatively a different type of source.
PICSARR: high-precision polarimetry using CMOS image sensors
Authors: Bailey Jeremy , Cotton Daniel V , De Horta Ain , Kedziora-Chudczer Lucyna , Shastri Om
Published: January 2023

We have built and tested a compact, low-cost, but very high performance astronomical polarimeter based on a continuously rotating half-wave plate and a high-speed imaging detector. The polarimeter is suitable for small telescopes up to ∼1 m in aperture. The optical system provides very high transmission over a wide wavelength range from the atmospheric ultraviolet cut-off to ∼1000 nm. The high quantum efficiency, low noise, and high speed of the detectors enable bright stars to be observed with high precision as well as polarization imaging of extended sources. We have measured the performance of the instrument on 20 and 60 cm aperture telescopes. We show some examples of the type of science possible with this instrument. The polarimeter is particularly suited to studies of the wavelength dependence and time variability of the polarization of stars and planets.