bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomarkers That Predict Crohn’s Disease Outcomes
Authors: Olivera Pablo A , Silverberg Mark S 
Published: September 2023

Abstract
Crohn’s disease (CD), a chronic inflammatory condition of the digestive tract, poses significant challenges in terms of disease prognosis and treatment selection. Biomarkers have the potential to predict CD outcomes and guide clinical decision-making. This review aims to summarize the current literature on promising biomarkers associated with CD outcomes and their potential clinical implications. The identification of reliable biomarkers for CD outcomes is of paramount importance in tailoring treatment strategies, monitoring disease activity, and predicting the risk of complications. Clinical prognostic factors traditionally used to assess disease severity, and the likelihood of complications have limitations in accuracy and predictive value. Thus, there is a need for more precise biomarkers, particularly in newly diagnosed and treatment-naive patients. Pharmacogenomic markers, such as TPMT and NUDT15 polymorphisms, have been utilized to identify patients at risk of adverse events with thiopurine therapy. Several biomarkers, including HLA haplotypes, oncostatin M expression, and transcriptomic profiles, have shown associations with response to anti-TNF therapy. Confocal laser endomicroscopy and single-cell analyses hold promise in predicting treatment response to specific therapies. The identification of biomarkers associated with post-operative recurrence in CD is crucial, as it could lead to changes in management algorithms. Several promising microbiome signatures and proteomic profiles have been identified. In conclusion, biomarkers have the potential to revolutionize the management of CD by providing valuable prognostic information and guiding treatment decisions. However, further research and validation are necessary to establish their clinical utility and integration into routine practice.
Uncertainty, Investment and Productivity with Relational Contracts
Authors: Malcomson James M 
Published: September 2023

Abstract
With relational contracts, increased uncertainty with no change in factor prices is shown to reduce investment in the long run even if the parties are risk-neutral. This contrasts with models based on the impact of financial risk on the cost of capital and on the option value arising from irreversible investment. For the latter, Bloom et al. (Econometrica, 2018) find that a negative first-moment shock, in addition to increased uncertainty, best matches the data. This paper develops a relational contract model to demonstrate the impact of uncertainty on investment, depending on whether investment is general or specific. It then uses a specification calibrated with parameters from Bloom et al. (Econometrica, 2018) to show that this model can generate effects on productivity and investment of the magnitude of the negative aggregate shock in that paper purely with an increase in uncertainty.
Transgenic approaches in medical entomology: 2022 highlights
Authors: Simões Maria L 
Published: September 2023

Abstract
Transgenesis has emerged as a powerful tool to control arthropod vectors and the diseases they transmit. Here, we highlight the latest developments on transgenic approaches in ticks, Anopheles and Aedes mosquitoes, based on recent findings and significant papers from 2022. We survey topics ranging from population replacement, population suppression, gene drive, sex ratio distortion, public engagement and capacity building, and gene editing in ticks. While presenting these advancements, we discuss the current challenges surrounding the application of arthropod transgenesis for the development of novel vector control strategies.
The female and pupa of Uranotaenia (Pseudoficalbia) bhutanensis (Diptera: Culicidae)
Authors: Somboon Pradya , Namgay Rinzin , Harbach Ralph E 
Published: September 2023

Abstract
Uranotaenia bhutanensis Somboon, Namgay & Harbach was recently described as a new species of the Bimaculata Series of the subgenus Pseudoficalbia Theobald based on larvae collected from a log hole at high altitude in Bhutan. The adult female and pupa are described in this article based on the subsequent discovery of 2 paratype females with associated pupal exuviae.
Invasive Haemaphysalis longicornis (Acari: Ixodidae) investigation in South Carolina: new records of establishment, pathogen prevalence, and blood meal analyses
Authors: Dye-Braumuller Kyndall C , Gual-Gonzalez Lídia , Abiodun Titi , Rustin Lauren P , Evans Chris L , Meyer Madeleine M , Zellars Kia , Neault Mike J , Nolan Melissa S 
Published: September 2023

Abstract
The first established population of the Asian longhorned tick Haemaphysalis longicornis (Neumann, Acari: Ixodidae) was discovered in a northern South Carolina county in June 2022. A coordinated investigation was launched to investigate the invasive tick’s pathogen infection prevalence and blood meal preferences. Almost 2,000 Ha. longicornis ticks were collected from one cattle field. A majority of collected ticks had evidence of cattle and dog blood meals, and multiple samples were tested positive for Borrelia burgdorferi s.l. and Theileria orientalis—first reports for these pathogens in this tick species in South Carolina. This investigation was the direct result of a collaborative education campaign and tick surveillance program launched earlier in the year with multiple state partners.
Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote
Authors: Sands Elizabeth , Davies Sian , Puxty Richard John , Vergé Valerie , Bouget François-Yves , Scanlan David John , Carré Isabelle Alice 
Published: September 2023

Abstract
Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content, and photophysiology after acclimation to monochromatic red, green, or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light-absorbing pigments. It responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originated from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate light-quality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.
A comparative study on outcomes of fasting vs postprandial thyroid function tests among pregnant mothers in a tertiary care setting in Sri Lanka
Authors: Mohideen Shifaniya Banu , Herath Thamara , Manathunga Supun 
Published: September 2023

Abstract

Objective
Accurate estimation of serum thyrotropin (TSH) is crucial in the diagnosis of subclinical hypothyroidism (SCH) in pregnancy. We aimed to investigate whether there are significant differences between fasting and nonfasting thyroid function tests (TFTs) among pregnant mothers.

Methods
We studied 100 pregnant mothers with previously unknown thyroid dysfunction. An equal number of participants were included in each trimester. All pregnant mothers underwent fasting and 2-hour postprandial TFTs (TSH, free T4).

Results
Postprandial TSH (mean 1.01 mIU/L, SD 0.80) was significantly lower than the fasting TSH (mean 1.47 mIU/L, SD 1.18) in pregnancy (P &lt; .01). Postprandial free T4 (mean 10.30 pmol/L, SD 2.01) was also lowered compared with fasting free T4 (mean 10.70 pmol/L, SD 1.99) in pregnancy (P &lt; .01). The prevalence of SCH in pregnancy estimated using fasting TSH was 9.4% (SD 3%). In contrast, the prevalence was only 3.5% (SD 2%) when postprandial TSH was used.

Conclusion
Compared with the fasting state, postprandial TSH demonstrates a statistically significant reduction that greatly influences the diagnosis of SCH in pregnant mothers. Therefore, we conclude that the timing of sampling for TFTs should be standardized, especially in the pregnant population.
Survivals in Cheap Print, 1750–1800: Some Preliminary Estimates
Authors: Atkinson David 
Published: September 2023

Abstract
This paper seeks to establish some preliminary numbers for the survival rates of some different kinds of cheap print, especially ballads and chapbooks, from the second half of the eighteenth century. The basic method is to compare contemporary booksellers’ lists with modern records of surviving copies, especially ESTC. An important question is whether survival rates can be correlated with price and/or type of content, and whether the publications of certain booksellers have survived better than others. Methodological problems of such a study include variation in sample size, and especially the unreliability of results based on very small samples, and the critical role of collectors in ensuring that publications of this kind survived at all.
Compositors’ Spelling Preferences and the Integrity of 2 Henry VI
Authors: Vickers Brian 
Published: September 2023

Abstract
The recent New Oxford Shakespeare Authorship Companion states that 2 Henry VI was co-authored by Shakespeare and Marlowe, citing an essay by Paul Vincent arguing that a change in the spelling of the interjection O/Oh showed a change in authorship. Vincent affirmed that ‘playwrights usually favoured one alternative far more than the other, and that the compositors of the First Folio regularly followed their copy text.’ He compiled a list of the variant spellings, arranged by Act and scene, identifying which compositors had set each section. Vincent argued that a passage corresponding to Act 3 in modern editions (the Folio is undivided) containing few instances of either O or Oh signalled an authorial change. When the evidence is arranged according to the sequence in which the two compositors set the pages, no consistent preference can be seen, thus disproving the case for Marlowe’s co-authorship.
Multiclustering needlet ILC for CMB B-mode component separation
Authors: Carones Alessandro , Migliaccio Marina , Puglisi Giuseppe , Baccigalupi Carlo , Marinucci Domenico , Vittorio Nicola , Poletti Davide ,   for the LiteBIRD collaboration
Published: September 2023

ABSTRACT
The Cosmic Microwave Background (CMB) primordial B-mode signal is predicted to be much lower than the polarized Galactic emission (foregrounds) in any region of the sky pointing to the need for sophisticated component separation methods. Among them, the blind Needlet Internal Linear Combination (NILC) has great relevance given our current poor knowledge of the B-mode foregrounds. However, the expected level of spatial variability of the foreground spectral properties complicates the NILC subtraction of the Galactic contamination. We therefore propose a novel extension of the NILC approach, the Multiclustering NILC (MC-NILC), which performs NILC variance minimization on separate regions of the sky (clusters) properly chosen to have similar spectral properties of the B-mode Galactic emission within them. Clusters are identified thresholding either the ratio of simulated foregrounds-only B modes (ideal case) or the one of cleaned templates of Galactic emission obtained from realistic simulations. In this work we present an application of MC-NILC to the future LiteBIRD satellite, which targets the observation of both reionization and recombination peaks of the primordial B-mode angular power spectrum with a total error on the tensor-to-scalar ratio δr &lt; 0.001. We show that MC-NILC provides a CMB solution with residual foreground and noise contamination that is significantly lower than the NILC one and the primordial signal targeted by LiteBIRD at all angular scales for the ideal case and at the reionization peak for a realistic ratio. Thus, MC-NILC will represent a powerful method to mitigate B-mode foregrounds for future CMB polarization experiments.
The signature of refreshed shocks in the afterglow of GRB 030329
Authors: Moss Michael J , Mochkovitch Robert , Daigne Frédéric , Beniamini Paz , Guiriec Sylvain 
Published: September 2023

ABSTRACT
GRB 030329 displays one clear and, possibly, multiple less intense fast-rising (Δt/t ∼ 0.3) jumps in its optical afterglow light curve. The decay rate of the optical light curve remains the same before and after the flux jumps. This may be the signature of energy injection into the shocked material at the front of the jet. In this study, we model the Gamma-ray Burst (GRB) ejecta as a series of shells. We follow the dynamical evolution of the ejecta as it interacts with itself (i.e. internal shocks) and with the circumburst medium (i.e. external forward and reverse shocks), and calculate the emission from each shock event assuming synchrotron emission. We confirm the viability of the proposed model in which the jumps in the optical afterglow light curve of GRB 030329 are produced via refreshed shocks. The refreshed shocks may be the signatures of collisions between earlier ejected material with an average Lorentz factor $\bar{\Gamma }\gtrsim 100$ and later ejected material with $\bar{\Gamma } \sim 10$ once the early material has decelerated due to interaction with the circumburst medium. We show that even if the late material is ejected with a spread of Lorentz factors, internal shocks naturally produce a narrow distribution of Lorentz factors (ΔΓ/Γ ≲ 0.1), which is a necessary condition to produce the observed quick rise times of the jumps. These results imply a phase of internal shocks at some point in the dynamical evolution of the ejecta, which requires a low magnetization in the outflow.
Determining the dark matter distribution in simulated galaxies with deep learning
Authors: de los Rios Martín , Petač Mihael , Zaldivar Bryan , Bonaventura Nina R , Calore Francesca , Iocco Fabio 
Published: September 2023

ABSTRACTWe present a novel method of inferring the dark matter (DM) content and spatial distribution within galaxies, using convolutional neural networks (CNNs) trained within state-of-the-art hydrodynamical simulations (Illustris–TNG100). Within the controlled environment of the simulation, the framework we have developed is capable of inferring the DM mass distribution within galaxies of mass ∼1011–$10^{13} \, M_\odot$ from the gravitationally baryon-dominated internal regions to the DM-rich, baryon-depleted outskirts of the galaxies, with a mean absolute error always below ≈0.25 when using photometrical and spectroscopic information. With respect to traditional methods, the one presented here also possesses the advantages of not relying on a pre-assigned shape for the DM distribution, to be applicable to galaxies not necessarily in isolation, and to perform very well even in the absence of spectroscopic observations.
Evolution of fallback discs around millisecond magnetars: effect of supercritical accretion on GRB afterglows
Authors: Çıkıntoğlu Sercan , Şaşmaz Sinem , Erkut M Hakan , Ekşi K Yavuz 
Published: September 2023

ABSTRACT
Some models of gamma-ray bursts (GRBs) invoke nascent millisecond magnetars as the central engine and address the X-ray afterglows with the interaction of magnetar magnetospheres with fallback discs. We study the evolution of fallback discs interacting with the millisecond magnetars. Initially, the accretion rate in the fallback disc is very high, well above the rate required for the Eddington limit. The inner parts of such a disc, even if it is cooling by the neutrino emission, get spherical due to the radiation pressure, which regulates the mass-accretion rate within the spherization radius. Such a disc can not penetrate the light cylinder radius for the typical magnetic fields, and the initial spin frequencies invoked for the magnetars. As a result of the autoregulation of the accretion flow, the fallback disc can not interact directly with the magnetar’s magnetosphere within the first few days. This has implications for the fallback disc models of GRB afterglows since the accretion and propeller luminosities, in the presence of radiation pressure, are too low to address the typical luminosities of X-ray afterglows.
Magnetic fields catalyse massive black hole formation and growth
Authors: Begelman Mitchell C , Silk Joseph 
Published: September 2023

ABSTRACT
Large-scale magnetic fields in the nuclear regions of protogalaxies can promote the formation and early growth of supermassive black holes (SMBHs) by direct collapse and magnetically boosted accretion. Turbulence associated with gravitational infall and star formation can drive the rms field strength toward equipartition with the mean gas kinetic energy; this field has a generic tendency to self-organize into large coherent structures. If the poloidal component of the field (relative to the rotational axis of a star-forming disc) becomes organized on scales ≲r and attains an energy of order a few per cent of the turbulent energy in the disc, then dynamo effects are expected to generate magnetic torques capable of increasing the inflow speed and thickening the disc. The accretion flow can transport matter towards the centre of mass at a rate adequate to create and grow a massive direct-collapse black hole seed and fuel the subsequent AGN at a high rate, without becoming gravitationally unstable. Fragmentation and star formation are thus suppressed and do not necessarily deplete the mass supply for the accretion flow, in contrast to prevailing models for growing and fuelling SMBHs through disc accretion.
Stromule Geometry Allows Optimal Spatial Regulation of Organelle Interactions in the Quasi-2D Cytoplasm
Authors: Erickson Jessica Lee , Prautsch Jennifer , Reynvoet Frisine , Niemeyer Frederik , Hause Gerd , Johnston Iain G , Schattat Martin Harmut 
Published: September 2023

AbstractIn plant cells, plastids form elongated extensions called stromules, the regulation and purposes of which remain unclear. Here, we quantitatively explore how different stromule structures serve to enhance the ability of a plastid to interact with other organelles: increasing the effective space for interaction and biomolecular exchange between organelles. Interestingly, electron microscopy and confocal imaging showed that the cytoplasm in Arabidopsis thaliana and Nicotiana benthamiana epidermal cells is extremely thin (around 100 nm in regions without organelles), meaning that inter-organelle interactions effectively take place in 2D. We combine these imaging modalities with mathematical modeling and new in planta experiments to demonstrate how different stromule varieties (single or multiple, linear or branching) could be employed to optimize different aspects of inter-organelle interaction capacity in this 2D space. We found that stromule formation and branching provide a proportionally higher benefit to interaction capacity in 2D than in 3D. Additionally, this benefit depends on optimal plastid spacing. We hypothesize that cells can promote the formation of different stromule architectures in the quasi-2D cytoplasm to optimize their interaction interface to meet specific requirements. These results provide new insight into the mechanisms underlying the transition from low to high stromule numbers, the consequences for interaction with smaller organelles, how plastid access and plastid to nucleus signaling are balanced and the impact of plastid density on organelle interaction.
It’s a female’s world: sex ratio of polar pelagic ostracods tested across multiple spatiotemporal scales
Authors: Chen Emily Y-S , Trudnowska Emilia , Błachowiak-Samołyk Katarzyna 
Published: September 2023

Abstract
Biased sex ratios are commonly found in nature and were also observed in this study on pelagic ostracods in both the Arctic and Southern Oceans. Because changes in sex ratio may occur in response to environmental perturbations, studying this aspect in polar regions as they continue to warm is of ecological importance. Here, a robust spatiotemporal dataset of historical and contemporary sex data was compiled to explore variation in ostracod sex ratio with respect to species, depth, region, season and ontogeny. Global ostracod populations in both the Arctic and Antarctic demonstrated a stable female bias of ~ 60–70% over all tested factors. This female bias was even higher when only the premature A-1 stage was considered, regardless of the factor. The widespread stability in stage-specific sex ratio and its subtle changes, especially in the interannual context, show that marine Ostracoda has the potential to be a model organism for more comprehensive sex ratio research, but deeper investigation into their ecology and reproduction is necessary.
Extensive rewiring of the gene regulatory interactions between in vitro–produced conceptuses and endometrium during attachment
Authors: Biase Fernando H , Moorey Sarah E , Schnuelle Julie G , Rodning Soren , Ortega Marta Sofia , Spencer Thomas E 
Published: September 2023

AbstractPregnancy loss is a significant problem when embryos produced in vitro are transferred to a synchronized uterus. Currently, mechanisms that underlie losses of in vitro–produced embryos during implantation are largely unknown. We investigated this problem using cattle as a model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle. We identified that the transfer of an in vitro–produced embryo caused a significant alteration in transcript abundance of hundreds of genes in extraembryonic and endometrial tissues on gestation days 18 and 25, when compared to pregnancies initiated by artificial insemination. Many of the genes with altered transcript abundance are associated with biological processes that are relevant to the establishment of pregnancy. An integrative analysis of transcriptome data from the conceptus and endometrium identified hundreds of putative ligand–receptor pairs. There was a limited variation of ligand–receptor pairs in pregnancies initiated by in vitro–produced embryos on gestation day 18, and no alteration was observed on gestation day 25. In parallel, we identified that in vitro production of embryos caused an extensive alteration in the coexpression of genes expressed in the extraembryonic membranes and the corresponding endometrium on both gestation days. Both the transcriptional dysregulation that exists in the conceptus or endometrium independently and the rewiring of gene transcription between the conceptus and endometrium are a potential component of the mechanisms that contribute to pregnancy losses caused by in vitro production of embryos.