bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration
Authors: Grissa Dhouha , Junge Alexander , Oprea Tudor I , Jensen Lars Juhl 
Published: March 2022

Abstract
The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease–gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the text-mined associations, which have increased by at least 9-fold at all confidence cutoffs. We show that this dramatic increase is primarily due to adding full-text articles to the text corpus, secondarily due to improvements to both the disease and gene dictionaries used for named entity recognition, and only to a very small extent due to the growth in number of PubMed abstracts. DISEASES now also makes use of a new GWAS database, Target Illumination by GWAS Analytics, which considerably increased the number of GWAS-derived disease–gene associations. DISEASES itself is also integrated into several other databases and resources, including GeneCards/MalaCards, Pharos/Target Central Resource Database and the Cytoscape stringApp. All data in DISEASES are updated on a weekly basis and is available via a web interface at https://diseases.jensenlab.org, from where it can also be downloaded under open licenses.
Database URL: https://diseases.jensenlab.org
High-sensitivity cardiac troponin serving as a useful marker for the early recognition of relapse of isolated cardiac sarcoidosis: a case report
Authors: Tashiro Akira , Tanaka Yasuaki , Hikita Hiroyuki , Takahashi Atsushi 
Published: March 2022

Abstract

Background
Isolated cardiac sarcoidosis is a relatively rare disease that is difficult to manage because of challenges in determining the progression and flare-up of cardiac lesions. Routine reduction of glucocorticoid doses may lead to treatment failure and disease relapse, which are associated with increased mortality.

Case summary
Herein, we present the case of a 49-year-old woman with isolated cardiac sarcoidosis in whom high-sensitivity cardiac troponin served as a biomarker for tailoring immunosuppressive therapy. She presented with progressive dyspnoea on exertion for 2 months and had elevated levels of high-sensitivity cardiac troponin I (hs-cTnI) at presentation. A diagnosis of isolated cardiac sarcoidosis was made based on the finding of electrocardiography, echocardiography, cardiac magnetic resonance imaging, and 18F-fluorodeoxyglucose (FDG) positron emission tomography. After the introduction of glucocorticoids, the hs-cTnI concentration immediately decreased, followed by the disappearance of FDG uptake in the heart. However, 2 months after oral prednisolone was reduced to the maintenance dose, the hs-cTnI concentration began to increase gradually, and 2 months later, worsening heart failure, progression of impaired left ventricular function, and de novo accumulation of FDG in the heart were observed, confirming the relapse of cardiac sarcoidosis. Intensified glucocorticoid therapy resulted in another immediate decrease in hs-cTnI concentration and improved heart failure management.

Discussion
This case highlights the potential of hs-cTnI to serve as a serum biomarker for monitoring disease activity and response to immunosuppressive therapy in patients with cardiac sarcoidosis. The hs-cTnI could be a highly sensitive and cost-effective biomarker reflecting the inflammatory status of cardiac sarcoidosis.
Functional variability in adhesion and flocculation of yeast megasatellite genes
Authors: Saguez Cyril , Viterbo David , Descorps-Declère Stéphane , Cormack Brendan P , Dujon Bernard , Richard Guy-Franck 
Published: March 2022

Abstract
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell–cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several Candida glabrata megasatellite-containing genes and found that 2 of them were positively involved in adhesion to epithelial cells, whereas 3 genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling Candida glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230-kbp segmental duplication.
No increased risk of mature B-cell non-Hodgkin lymphoma after Q fever detected: results from a 16-year ecological analysis of the Dutch population incorporating the 2007–2010 Q fever outbreak
Authors: Weehuizen Jesper M , van Roeden Sonja E , Hogewoning Sander J , van der Hoek Wim , Bonten Marc J M , Hoepelman Andy I M , Bleeker-Rovers Chantal P , Wever Peter C , Oosterheert Jan Jelrik 
Published: March 2022

Abstract

Background
A causative role of Coxiella burnetii (the causative agent of Q fever) in the pathogenesis of B-cell non-Hodgkin lymphoma (NHL) has been suggested, although supporting studies show conflicting evidence. We assessed whether this association is present by performing a detailed analysis on the risk of mature B-cell NHL after Q fever during and after the largest Q fever outbreak reported worldwide in the entire Dutch population over a 16-year period.

Methods
We performed an ecological analysis. The incidence of mature B-cell NHL in the entire Dutch population from 2002 until 2017 was studied and modelled with reported acute Q fever cases as the determinant. The adjusted relative risk of NHL after acute Q fever as the primary outcome measure was calculated using a Poisson regression.

Results
Between January 2002 and December 2017, 266 050 745 person-years were observed, with 61 424 diagnosed with mature B-cell NHL. In total, 4310 persons were diagnosed with acute Q fever, with the highest incidence in 2009. The adjusted relative risk of NHL after acute Q fever was 1.02 (95% CI 0.97–1.06, P = 0.49) and 0.98 (95% CI 0.89–1.07, P = 0.60), 0.99 (95% CI 0.87–1.12, P = 0.85) and 0.98 (95% 0.88–1.08, P = 0.67) for subgroups of diffuse large B-cell lymphoma, follicular lymphoma or B-cell chronic lymphocytic leukaemia, respectively. Modelling with lag times (1–4 years) did not change interpretation.

Conclusion
We found no evidence for an association between C. burnetii and NHL after studying the risk of mature B-cell NHL after a large Q fever outbreak in Netherlands.
Mitigation of benznidazole toxicity and oxidative stress following ascorbic acid supplementation in an adult traveller with chronic indeterminate Chagas’ disease
Authors: Van Den Broucke Steven , Van Herreweghe Maxim , Breynaert Annelies , Van Esbroeck Marjan , Truyens Carine , De Bruyne Tess , Hermans Nina , Huits Ralph 
Published: March 2022

Abstract

Background
Benznidazole is an effective drug in the trypanocidal treatment of acute and chronic indeterminate Chagas’ disease (CD). However, adverse drug reactions (ADR) are common and frequently cause patients to discontinue treatment.

Objectives
We hypothesized that antioxidant supplementation could mitigate benznidazole-induced toxicity.

Methods
We co-supplemented an adult traveller with chronic indeterminate CD who experienced benznidazole ADR with ascorbic acid (AA), 1000 mg/day. We measured selected serum biomarkers of oxidative stress [total antioxidant status (TAS), total oxidative status (TOS), nuclear factor erythroid 2-related factor 2 (Nrf2), malondialdehyde (MDA), extracellular glutathione peroxidase (GPX3), catalase (CAT) and total superoxide dismutase (T-SOD)] at timepoints before and throughout benznidazole treatment and after AA co-supplementation.

Results
AA co-supplementation effectively mitigated benznidazole-induced ADR during the aetiological treatment of chronic indeterminate CD. The kinetics of serum biomarkers of oxidative stress suggested significantly decreased oxidative insult in our patient.

Conclusions
We hypothesize that the key pathophysiological mechanism of benznidazole-associated toxicity is oxidative stress, rather than hypersensitivity. AA co-supplementation may improve adherence to benznidazole treatment of chronic indeterminate (or acute) CD. Oxidative stress biomarkers have the potential to guide the clinical management of CD. Prospective studies are needed to establish the benefit of antioxidant co-supplementation to benznidazole treatment of CD in reducing benznidazole toxicity, parasite clearance and the prevention of end-organ damage.
Benefits and Risks of Intercropping for Crop Resilience and Pest Management
Authors: Huss C P , Holmes K D , Blubaugh C K 
Published: March 2022

Abstract
To combat climate change, farmers must innovate through ecological intensification to boost food production, increase resilience to weather extremes, and shrink the carbon footprint of agriculture. Intercropping (where alternative crops or noncrop plants are integrated with cash crops) can strengthen and stabilize agroecosystems under climate change by improving resource use efficiency, enhancing soil water holding capacity, and increasing the diversity and quality of habitat for beneficial insects that provide pollination services and natural pest control. Despite these benefits, intercropping has yet to be widely adopted due to perceived risks and challenges including decreased crop yield, increased management complexity, a steep learning curve for successful management, and increased susceptibility to pests. Here, we explore the major benefits of intercropping in agricultural systems for pest control and climate resilience reported in 24 meta-analyses, while addressing risks and barriers to implementation. Most studies demonstrate clear benefits of intercropping for weed, pathogen, insect pest control, relative yield, and gross profitability. However, relatively few studies document ecosystem services conferred by intercrops alongside labor costs, which are key to economic sustainability for farmers. In addition to clearer demonstrations of the economic viability of intercropping, farmers also need strong technical and financial support during the adoption process to help them troubleshoot the site-specific complexities and challenges of managing polycultures. Ecological intensification of agriculture requires a more strategic approach than simplified production systems and is not without risks and challenges. Calibrating incentive programs to reduce financial burdens of risk for farmers could promote more widespread adoption of intercropping.
When time is not of the essence: constraints to the carbon balance of bryophytes
Authors: Perera-Castro Alicia V , González-Rodríguez Águeda M , Fernández-Marín Beatriz 
Published: March 2022

Abstract
The data available so far indicate that the photosynthetic and relative growth rates of bryophytes are 10% of those reported for tracheophytes. By examining the existing literature and reanalysing data published in over 100 studies, this review examines the ecophysiological, biochemical, and structural reasons behind this phenomenon. The limiting Rubisco content and surface for gas exchange are the internal factors that can explain the low photosynthetic and growth rates of bryophytes. The role of the thicker cell walls of bryophytes in limiting CO2 diffusion is unclear, due to the current uncertainties regarding their porosity and permeability to CO2. From this review, it is also evident that, despite bryophytes having low photosynthetic rates, their positive carbon balance is tightly related to their capacity to deal with extreme conditions. Contributing factors include their capacity to deal with large daily temperature oscillations, and their capacity to delay the cessation of photosynthesis under water deficit (or to tolerate desiccation in extreme situations). Although further studies on bryophytes are needed before more solid conclusions can be drawn, it seems that their success relies on their remarkable tolerance to a highly variable environment, possibly at the expense of their maximum photosynthetic rate.
Transient Pseudothrombocytopenia Detected 8 Months After COVID-19 Vaccination
Authors: Higuchi Takakazu , Hoshi Takao , Nakajima Astuko , Haruki Kosuke 
Published: March 2022

Abstract
Pseudothrombocytopenia is an in vitro phenomenon of platelet aggregation due to conformational changes and exposure of cryptic antigens on the platelet surface caused by anticoagulants, leading to the aggregation of platelets and falsely lower automated platelet counts. Although it has no clinical relevance, it can lead to unnecessary fear, diagnostic errors, or unnecessary tests and interventions when unrecognized.
Pseudothrombocytopenia was detected in a 25-year-old woman 8 months after the second dose of mRNA COVID-19 vaccine, BNT162b2. The pseudothrombocytopenia was transient and the duration was shorter than 3 months. As pseudothromobocytopenia is not detected unless blood is drawn for other objectives, it is difficult to determine its true occurrence among recipients of vaccines. This case shows that pseudothrombocytopenia may develop transiently even months after COVID-19 vaccination and should be considered when thrombocytopenia is found in recipients of the vaccine to avoid unnecessary fear, diagnostic errors, or unnecessary tests and interventions.
Across the green valley withHSTgrisms: colour evolution, crossing time-scales, and the growth of the red sequence atz = 1.0–1.8
Authors: Noirot Gaël , Sawicki Marcin , Abraham Roberto , Bradač Maruša , Iyer Kartheik , Moutard Thibaud , Pacifici Camilla , Ravindranath Swara , Willott Chris J 
Published: March 2022

ABSTRACTWe measure the colour evolution and quenching time-scales of z = 1.0–1.8 galaxies across the green valley. We derive rest-frame NUVrK colours and select blue-cloud, green-valley, and red-sequence galaxies from the spectral energy distribution modelling of CANDELS GOODS-South and UDS multiband photometry. Separately, we constrain the star-formation history (SFH) parameters (ages, τ) of these galaxies by fitting their deep archival HST grism spectroscopy. We derive the galaxy colour–age relation and show that only rapidly evolving galaxies with characteristic delayed-τ SFH time-scales of &lt;0.5 Gyr reach the red sequence at these redshifts, after a period of accelerated colour evolution across the green valley. These results indicate that the stellar mass build-up of these galaxies stays minimal after leaving the blue cloud and entering the green valley (i.e. it may represent $\lesssim 5{{\ \rm per\ cent}}$ of the galaxies’ final, quiescent masses). Visual inspection of age-sensitive features in the stacked spectra also supports the view that these galaxies follow a quenching sequence along the blue-cloud → green-valley → red-sequence track. For this rapidly evolving population, we measure a green-valley crossing time-scale of $0.99^{+0.42}_{-0.25}$ Gyr and a crossing rate at the bottom of the green valley of $0.82^{+0.27}_{-0.25}$ mag Gyr−1. Based on these time-scales, we estimate that the number density of massive (M⋆ &gt; 1010M⊙) red-sequence galaxies doubles every Gyr at these redshifts, in remarkable agreement with the evolution of the quiescent galaxy stellar mass function. These results offer a new approach to measuring galaxy quenching over time and represent a pathfinder study for future JWST, Euclid, and Roman Space Telescope programs.
Tensile strength and surface energy of CO2 ice in the context of planet formation
Authors: Fritscher M , Teiser J 
Published: March 2022

ABSTRACT
Planetesimals grow from agglomerates of small particles, either by pebble accretion or by direct growth. In both cases, the stability of macroscopic agglomerates of fine grains plays a crucial role for the growth, the evolution, and the fate of planetesimals regarding sticking, fragmentation or erosion. While in the inner protoplanetary disc silicates dominate the system, different ice species are the dominant solids in the outer parts. CO2 ice is one of the most abundant species in the outer parts of protoplanetary discs. Here, we present experiments on the stability of highly porous CO2 agglomerates. The CO2 grains are generated by adiabatic expansion of CO2 gas within a cryogenic environment. The agglomerates are compressed to cylinders and the tensile strength is measured using the Brazilian test. The dependence of the tensile strength of porous CO2 agglomerates on the volume filling is well described by a power law. With the well defined geometry, we calculate a surface energy of $\gamma = 0.060\pm 0.022\, \rm J\, m^{-2}$.
Self-consistent dynamical models with a finite extent – I. The uniform density sphere
Authors: Baes Maarten 
Published: March 2022

ABSTRACT
The standard method to generate dynamical models with a finite extent is to apply a truncation in binding energy to the distribution function (DF). This approach has the disadvantages that one cannot choose the density to start with, that the important dynamical quantities cannot be calculated analytically, and that a fraction of the possible bound orbits are excluded a priori. We explore another route and start from a truncation in radius rather than a truncation in binding energy. We focus on the simplest truncated density profile, the uniform density sphere. We explore the most common inversion techniques to generate DFs for the uniform density sphere, corresponding to a large range of possible anisotropy profiles. We find that the uniform density sphere cannot be supported by the standard isotropic, constant anisotropy or Osipkov–Merritt models, as all these models are characterized by negative DFs. We generalize the Cuddeford inversion method to models with a tangential anisotropy and present a one-parameter family of dynamical models for the uniform density sphere. Each member of this family is characterized by an anisotropy profile that smoothly decreases from an arbitrary value β0 ≤ 0 at the centre to completely tangential at the outer radius. All models have a positive DF over the entire phase space, and a non-zero occupancy of all possible bound orbits. This shows that one can generate non-trivial self-consistent dynamical models based on preset density profile with a finite extent.
The evolution of protoplanetary discs in star formation and feedback simulations
Authors: Qiao Lin , Haworth Thomas J , Sellek Andrew D , Ali Ahmad A 
Published: March 2022

ABSTRACT
We couple star cluster formation and feedback simulations of a Carina-like star-forming region with 1D disc evolutionary models to study the impact of external photoevaporation on disc populations in massive star-forming regions. To investigate the effect of shielding of young stellar objects by star-forming material, we track the far-ultraviolet (FUV) field history at each star in the cluster with two methods: (i) Monte Carlo radiative transfer accounting for the shielding of stars from the FUV by the star-forming cloud and (ii) geometric dilution of the radiation from other stars, which ignores shielding effects. We found that significant shielding only occurs for a small fraction of discs and offers protection from external photoevaporation for &lt;0.5 Myr. However, this initial protection can prevent significant early gas/dust mass-loss and disc radius reduction due to external photoevaporation. Particularly, shielding for 0.5 Myr is sufficient for much of the solid reservoir to evolve to larger sizes where it will not be entrained in an external wind. Shielding is therefore potentially significant for terrestrial planet formation in retaining the solid mass budget, but the continued stripping of gas when shielding ends could still impact migration and the gas reservoir for giant planet atmospheres. Our models highlight issues with treating all discs in a cluster with a single characteristic age, since shielded objects are typically only the youngest. Our model predicts that the majority of discs in a 2 Myr Carina-like environment are subject to strong external photoevaporation.
From giant clumps to clouds – II. The emergence of thick disc kinematics from the conditions of star formation in high redshift gas rich galaxies
Authors: van Donkelaar Floor , Agertz Oscar , Renaud Florent 
Published: March 2022

ABSTRACT
High-redshift disc galaxies are more gas rich, clumpier, and more turbulent than local Universe galaxies. This early era of galaxy formation imprints the distribution and kinematics of the stars that we observe today, but it is not yet well established how. In this work, we use simulations of isolated Milky Way-mass disc galaxies to study how kinematic properties of stars change when varying the gas fraction. This allows us to quantify the roles played by internal processes, e.g. gas turbulence and gravitational scattering off massive gas clumps, in establishing the observed stellar velocity dispersions and orbital eccentricities. We find that models with gas fractions &gt;20 per cent feature a turbulent and clumpy interstellar medium (ISM), leading to zero-age stellar velocity dispersions $\sim 20\!-\!30\, {\rm km\, s}^{-1}$ and high-mean orbital eccentricities. Low eccentricities cannot arise from these physical conditions. For gas fractions below 20 per cent, the ISM becomes less turbulent, with stellar velocity dispersions $\lt 10\, {\rm km\, s}^{-1}$, and nearly circular orbits for young stars. The turbulence present in gas-rich high redshift galaxies hence acts as a ‘barrier’ against the formation of thin discs. We compare our findings to the Milky Way’s age–velocity dispersion relation and argue that velocity dispersions imprinted already at star formation by the ISM contribute significantly at all times. Finally, we show that observed orbital eccentricities in the Milky Way’s thick and thin discs can be explained entirely as imprints by the star-forming ISM, rather than by mergers or secular processes.