bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Study of the Effectiveness of Vedolizumab Versus Ustekinumab After Anti-TNF Failure in Crohn’s Disease (Versus-CD): Data from the ENEIDA Registry
Authors: García María José , Rivero Montserrat , Fernández-Clotet Agnès , de Francisco Ruth , Sicilia Beatriz , Mesonero Francisco , de Castro María Luisa , Casanova María José , Bertoletti Federico , García-Alonso Francisco Javier , López-García Alicia , Vicente Raquel , Calvet Xavier , Barreiro-de Acosta Manuel , Ferrer Rosique Juan , Varela Trastoy Pilar , Nuñez Alejandro , Ricart Elena , Riestra Sabino , Arias García Lara , Rodríguez María , Arranz Laura , Pajares Ramón , Mena Raquel , Calafat Margalida , Camo Patricia , Bermejo Fernando , Ponferrada Ángel , Madrigal Rosa Eva , Llaó Jordina , Sesé Eva , Sánchez Eugenia , Pineda Mariño Juan Ramón , González Muñoza Carlos , Carbajo López Ana Yaiza , Julián Ana Belén , Villoria Ferrer Albert , Baston-Rey Iria , Jara Lorena , Almela Pedro , Codesido Laura , de la Maza Saioa , Leal Carles , Caballol Berta , Pérez-Martínez Isabel , Vinuesa Campo Raquel , Crespo Javier , Domènech Eugeni , Chaparro María , Gisbert Javier P 
Published: July 2023

Abstract

Background
Both vedolizumab and ustekinumab are approved for the management of Crohn’s disease [CD]. Data on which one would be the most beneficial option when anti-tumour necrosis factor [anti-TNF] agents fail are limited.

Aims
To compare the durability, effectiveness, and safety of vedolizumab and ustekinumab after anti-TNF failure or intolerance in CD.

Methods
CD patients from the ENEIDA registry who received vedolizumab or ustekinumab after anti-TNF failure or intolerance were included. Durability and effectiveness were evaluated in both the short and the long term. Effectiveness was defined according to the Harvey–Bradshaw index [HBI]. The safety profile was compared between the two treatments. The propensity score was calculated by the inverse probability weighting method to balance confounder factors.

Results
A total of 835 patients from 30 centres were included, 207 treated with vedolizumab and 628 with ustekinumab. Dose intensification was performed in 295 patients. Vedolizumab [vs ustekinumab] was associated with a higher risk of treatment discontinuation (hazard ratio [HR] 2.55, 95% confidence interval [CI]: 2.02–3.21), adjusted by corticosteroids at baseline [HR 1.27; 95% CI: 1.00–1.62], moderate–severe activity in HBI [HR 1.79; 95% CI: 1.20–2.48], and high levels of C-reactive protein at baseline [HR 1.06; 95% CI: 1.02–1.10]. The inverse probability weighting method confirmed these results. Clinical response, remission, and corticosteroid-free clinical remission were higher with ustekinumab than with vedolizumab. Both drugs had a low risk of adverse events with no differences between them.

Conclusion
In CD patients who have failed anti-TNF agents, ustekinumab seems to be superior to vedolizumab in terms of durability and effectiveness in clinical practice. The safety profile is good and similar for both treatments.
Identity and diversity of pollens collected by two managed bee species while in blueberry fields for pollination
Authors: Graham Kelsey K , Milbrath Meghan O , Killewald Michael , Soehnlen Annuet , Zhang Yajun , Isaacs Rufus 
Published: July 2023

Abstract
The nutritional needs and foraging behavior of managed bees often lead to pollen collection from flowers other than the focal crop during crop pollination. To understand the pollen needs and preferences of managed bees during blueberry pollination, we identified pollen collected by Apis mellifera Linnaeus, 1758 (Hymenoptera: Apidae) and Bombus impatiens Cresson, 1863 (Hymenoptera: Apidae) colonies across two years. Bumble bees collected a wider diversity of pollens compared to honey bees, whereas honey bees were more focused on abundant resources. Despite blueberries being the most abundant resource in the landscape, it was not the most collected pollen by either bee species in 2018. However, it was the most collected pollen by bumble bees in 2019 and they collected substantially more blueberry pollen than honey bees in both years. In 2018, buckthorn, Rhamnus L. (Rosales: Rhamnaceae) or Frangula Mill. (Rosales: Rhamnaceae), and willow, Salix L. (Malpighiales: Salicaceae), pollens were abundantly collected by both bee species. In 2019, cherry, Prunus L. (Rosales: Rosaceae), and willow (Salix) pollens were collected at high proportions by both species. Brambles, Rubus L. (Rosales: Rosaceae), and white clover, Trifolium repens L. (Fabales: Fabaceae), were also common pollen sources for honey bees, whereas oak, Quercus L. (Fagales: Fagaceae), was collected by bumble bees. Landscape analyses also revealed that certain land cover types were positively correlated with the collection of preferred pollen types. Herbaceous wetlands were associated with collection of buckthorn (Rhamnus/Frangula), willow (Salix), and cherry (Prunus) pollen, which were primary pollen resources for both bee species. There was no correlation between landscape diversity and pollen diversity, suggesting that colonies forage based on nutritional requirements rather than resource availability.
Arnaud du Sarrat and the international music trade in Halle and Leipzig c.1700
Authors: Górny Tomasz 
Published: July 2023

Abstract
Arnaud du Sarrat is known primarily as a bookseller and publisher based in Berlin, where he worked as Estienne Roger’s official agent from 1706 at the latest. This article, however, focuses on his activity in Halle between 1694/5 and 1702, when he was bookseller and bookbinder to the university. An analysis of four catalogues presents insights into the printed music available in his stores in Halle and Leipzig at the turn of the 18th century. A study is made of du Sarrat’s relationship with the Dutch book market, especially with booksellers from Amsterdam; and du Sarrat’s correspondence with Theophilus Dorrington suggests how Pietist networks also allowed for the transmission of books.
Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis onColtricia
Authors: Zhao Heng , Dai Yu-Cheng , Wu Fang , Liu Xiao-Yong , Maurice Sundy , Krutovsky Konstantin V , Pavlov Igor N , Lindner Daniel L , Martin Francis M , Yuan Yuan 
Published: July 2023

AbstractTo elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
SODAR: managing multiomics study data and metadata
Authors: Nieminen Mikko , Stolpe Oliver , Kuhring Mathias , Weiner January , Pett Patrick , Beule Dieter , Holtgrewe Manuel 
Published: July 2023

Abstract
Scientists employing omics in life science studies face challenges such as the modeling of multiassay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are the results of the assays or subsequent computation. Users with diverse backgrounds, ranging from computational scientists to wet-lab scientists, have dissimilar needs when it comes to data access, with programmatic interfaces being favored by the former and graphical ones by the latter.
We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses these challenges by providing a web-based graphical user interface for managing multiassay studies and describing them using the ISA (Investigation, Study, Assay) data model and the ISA-Tab file format. Data storage is handled using the iRODS data management system, which handles large quantities of files and substantial amounts of data. SODAR also offers programmable APIs and command-line access for metadata and file storage.
SODAR supports complex omics integration studies and can be easily installed. The software is written in Python 3 and freely available at https://github.com/bihealth/sodar-server under the MIT license.
Despite Increased Disease Activity, Women who Attended a Dedicated Inflammatory Bowel Disease and Pregnancy Clinic Had Infants With Higher Apgar Scores: A Population-Based Study
Authors: Lee Sangmin , Seow Cynthia H , Nerenberg Kara , Bertazzon Stefania , Leung Yvette , Huang Vivian , Whitten Tara , Coward Stephanie , Panaccione Remo , Kaplan Gilaad G , Metcalfe Amy 
Published: July 2023

Abstract

Background
Attendance at a subspecialty pregnancy clinic for women with inflammatory bowel disease (IBD) improves disease-specific pregnancy knowledge. We examined the impact of attendance at a dedicated IBD-pregnancy clinic on IBD and perinatal outcomes.

Methods
Using linked administrative databases in Alberta, Canada (2012-2019), we identified 1061 pregnant women with IBD who delivered singleton liveborn infants in-hospital who did (n = 314) and did not attend (n = 747) the clinic. Propensity score weighted multivariable log-binomial and multinomial logistic regression models were used to determine the risk of IBD and perinatal outcomes.

Results
The median number of clinic visits was 3 (Q1-Q3, 3-5), with 34.7% completing a preconception consultation. A greater proportion of women who attended lived near the clinic, were nulliparous, had a disease flare prior to pregnancy, and were on maintenance IBD medication (P &lt; .05). Women who attended had increased risks of a disease flare during pregnancy (adjusted risk ratio [aRR], 2.02; 95% CI, 1.45-2.82), an IBD-related emergency department visit during pregnancy (aRR, 2.66; 95% CI, 1.92-3.68), and cesarean delivery (aRR, 1.78; 95% CI, 1.23-2.57). Despite this, clinic attendees had a decreased risk of delivering an infant with a low Apgar score at 1 minute (risk ratio [RR], 0.49; 95% CI, 0.32-0.76) and 5 minutes (RR, 0.32; 95% CI, 0.12-0.87).

Conclusions
Women who attended a dedicated IBD-pregnancy clinic were more likely to have a disease flare prior to pregnancy, reflecting a more severe disease phenotype, but had similar perinatal outcomes and infants with better Apgar scores at birth. Our study suggests the value of these subspecialty clinics in providing enhanced IBD-specific prenatal care.
Antiviral activity of copper contact surfaces against MS2 coliphage and hepatitis A virus
Authors: Camacho Juan C , Shieh Y Carol , Redan Benjamin W , Koontz John L 
Published: July 2023

Abstract

Aims
Viral diseases can be indirectly transmitted by contaminated non-food contact surfaces to final food products by cross-contamination. The interaction of metal surfaces and viruses, MS2 coliphage and hepatitis A virus (HAV), was investigated for strategy development in decreasing this transmission risk.

Methods and results
MS2 deposited onto stainless-steel surface was stable but inactivated at 0.95 log10 PFU min−1 on 99.9% copper surfaces. Greater copper-inactivation of MS2 was observed in (a) simple media (phosphate buffered saline, PBS) than protein-rich media (beef extract buffer), and (b) acidic than pH ≥ 6.8 environments. Among food matrices (strawberry juices and beef broth), the greatest MS2 inactivation by copper occurred in filtered strawberry juice at pH 3.5. At a reduction of 0.17 log10 PFU min−1, HAV survived longer than MS2 on copper by FRhK-4 cell infectivity assay.

Conclusions
The inactivation of virus on copper surfaces was greater in acidic viral surrounding environments and in simple PBS medium. In the same 99% PBS medium, MS2 may not be an appropriate surrogate for HAV when assessing viral inactivation on copper surfaces.
Testing for clomiphene in keratinous matrices (hair and nail)
Authors: Kintz Pascal , Gheddar Laurie , Blanchot Adeline , Ameline Alice , Raul Jean-Sébastien 
Published: July 2023

Abstract
Clomiphene or clomifene is a selective estrogen receptor modulator used to treat female fertility in case of ovulatory dysfunction. In sport, clomiphene is prohibited at all times for use by athletes and is listed in the section S4.2 (hormone and metabolic modulators) by the World Anti-Doping Agency. Indeed, clomiphene can indirectly increase testosterone levels in the body and can mitigate some side effects of synthetic steroid abuse. Despite its prescription to millions of subjects, its detection in human hair or nail clippings has never been reported. The aim of this study was to develop a specific method to identify clomiphene in hair and nail clippings by liquid chromatography–quadrupole tandem mass spectrometry. The procedure was then applied in a case of challenged doping results. The method involves sonication/incubation for 1 h of 30 mg of pulverized material in 1 mL of methanol in the presence of 2 ng diazepam-d5 used as internal standard. The chromatographic separation was performed using a HSS C18 column with a 15 min gradient elution. After spiking blank hair and nail with the corresponding amounts of clomiphene, linearity was verified from 1 to 500 pg/mg (r2 = 0.9994 and 0.9995 for hair and nail, respectively). The limit of detection was estimated at 0.3 pg/mg for both matrices. No interference was noted from endogenous compounds, particularly steroids. Clomiphene was identified at 85 and 20 pg/mg in the pubic hair and the fingernail clippings, respectively, of a male athlete challenging an adverse analytical finding.
Prosecuting the Crime against Humanity of Apartheid
Authors: Kemp Gerhard , Nortje Windell 
Published: July 2023

Abstract
Apartheid is a crime against humanity, yet no person has ever been prosecuted for this crime. In 2021 two individuals were indicted in South Africa for the crime of apartheid. This is an historic first in the country which gave the policy of apartheid its name and material content. The indictment is, however, also a reminder that the non-prosecution of apartheid is a legal and moral issue to be understood in the context of South Africa’s transition from apartheid to democracy. Furthermore, the indictment, while historic and of international significance, concerns constitutional, procedural and prosecutorial issues that illustrate the complexities of the application of international criminal law in domestic criminal justice systems. This contribution argues that all these factors should be acknowledged and analysed. Ultimately, and despite the many obstacles and complexities, it is submitted that it is right to indict individuals who, through their crimes, made the apartheid system possible even if they were not in positions of leadership.
Individualized risk assessment of distant metastases in oral cavity carcinoma: a validated predictive-score model
Authors: Id Said Badr , Alfaraj Fatimah A , Marta Gustavo N , Kowalski Luiz P , Kohler Hugo F , Huang Shao H , Su Jie , Xu Wei , Eng Lawson , de Moraes Fabio Y , Hahn Ezra , Kim John J , O’Sullivan Brian , Ringash Jolie , Waldron John , Matos Leandro L , Prisman Eitan , Irish Jonathan C , Yao Christopher M K L , de Almeida John R , Goldstein David P , Hope Andrew , Hosni Ali 
Published: July 2023

Abstract

Background
We aimed to develop and validate a risk-scoring system for distant metastases (DMs) in oral cavity carcinoma (OCC).

Methods
Patients with OCC who were treated at 4 tertiary cancer institutions with curative surgery with or without postoperative radiation/chemoradiation therapy were randomly assigned to discovery or validation cohorts (3:2 ratio). Cases were staged on the basis of tumor, node, and metastasis staging according to the eighth edition of the American Joint Committee on Cancer/Union for International Cancer Control guidelines. Predictors of DMs on multivariable analysis in the discovery cohort were used to develop a risk-score model and classify patients into risk groups. The utility of the risk classification was evaluated in the validation cohort.

Results
Overall, 2749 patients were analyzed. Predictors (risk score coefficient) of DMs in the discovery cohort were the following: pathological stage (p)T3-4 (0.4), pN+ (N1: 0.8; N2: 1.0; N3: 1.5), histologic grade (G) 3 (G3, 0.7), and lymphovascular invasion (0.4). The DM risk groups were defined by the sum of the following risk score coefficients: high (&gt;1.7), intermediate (0.7-1.7), and standard risk (&lt;0.7). The 5-year DM rates (high/intermediate/standard risk groups) were 30%/15%/4% in the discovery cohort (C-index = 0.79) and 35%/16%/5% in the validation cohort, respectively (C-index = 0.77; both P &lt; .001). In the whole cohort, this predictive model showed excellent discriminative ability in predicting DMs without locoregional failure (29%/11%/1%), later (&gt;2 year) DMs (11%/4%/2%), and DMs in patients treated with surgery (20%/12%/5%), postoperative radiation therapy (34%/17%/4%), and postoperative chemoradiation therapy (39%/18%/7%) (all P &lt; .001). The 5-year overall survival rates in the overall cohort were 25%/51%/67% (P &lt; .001).

Conclusions
Patients at higher risk for DMs were identified by use of a predictive-score model for DMs that included pT3-4, pN1/2/3, G3, and lymphovascular invasion. Identified patients may be evaluated for individualized risk-adaptive treatment escalation and/or surveillance strategies.
Ex vivo repair and autotransplantation for a complex renal artery aneurysm
Authors: Chui Juanita N , Wang Kejia , Puttaswamy Vikram 
Published: July 2023

Abstract
Renal artery aneurysms (RAA) are rare, occurring with an incidence of &lt;0.1%. Open repair remains the mainstay of treatment for anatomically complex aneurysms. Here, we present a case of a large hilar RAA managed with ex vivo reconstruction and heterotopic renal autotransplantation. In this case, the complex anatomy and location of the aneurysm precluded the use of an endovascular approach. In situ repair was deemed unfavorable because of the technical difficulty of the repair with the numerous arterial branches involved, risk of parenchymal injury from prolonged warm ischemic time, restricted surgical field and risk of aneurysm rupture. This case contributes to the literature on laparoscopic nephrectomy, ex vivo repair and autotransplantation as a safe and viable treatment strategy for patients with complex RAA.
Middleness: Provincial Fiction and the Aesthetics of Dull Life
Authors: Livesey Ruth 
Published: July 2023

Abstract
This article argues that the rise of the provincial novel in Britain during the 1860s set loose a radically democratizing aesthetic of everyday discriminations. The article suggests – through examples from the works of Elizabeth Gaskell and George Eliot – that provincial fiction embodies an aesthetics of what is termed ‘middleness’: a means of reading in which the social, cultural and geographical middle became an object of careful evaluative judgment. The article examines the aesthetic affordances of this form in relation to Sianne Ngai’s exploration of the category of the ‘interesting’. It places this practice of attention to the common and the dull in contrast to Matthew Arnold’s contemporaneous critique of provincialism as the chief weakness at the heart of English culture as it moved towards democracy. If Arnold’s mission in his critical essays was to establish a global standard of taste – collective agreement grounded in the judgement of what was ‘the best that has been thought and known in the world’ – then provincial fiction effected another sort of aesthetic community: one that valued the common and the dull.
An empirical approach to model selection: weak lensing and intrinsic alignments
Authors: Campos A , Samuroff S , Mandelbaum R 
Published: July 2023

ABSTRACT
In cosmology, we routinely choose between models to describe our data, and can incur biases due to insufficient models or lose constraining power with overly complex models. In this paper, we propose an empirical approach to model selection that explicitly balances parameter bias against model complexity. Our method uses synthetic data to calibrate the relation between bias and the χ2 difference between models. This allows us to interpret χ2 values obtained from real data (even if catalogues are blinded) and choose a model accordingly. We apply our method to the problem of intrinsic alignments – one of the most significant weak lensing systematics, and a major contributor to the error budget in modern lensing surveys. Specifically, we consider the example of the Dark Energy Survey Year 3 (DES Y3), and compare the commonly used non-linear alignment (NLA) and tidal alignment and tidal torque (TATT) models. The models are calibrated against bias in the Ωm–S8 plane. Once noise is accounted for, we find that it is possible to set a threshold Δχ2 that guarantees an analysis using NLA is unbiased at some specified level Nσ and confidence level. By contrast, we find that theoretically defined thresholds (based on, e.g. p-values for χ2) tend to be overly optimistic, and do not reliably rule out cosmological biases up to ∼1–2σ. Considering the real DES Y3 cosmic shear results, based on the reported difference in χ2 from NLA and TATT analyses, we find a roughly $30{{\ \rm per\ cent}}$ chance that were NLA to be the fiducial model, the results would be biased (in the Ωm–S8 plane) by more than 0.3σ. More broadly, the method we propose here is simple and general, and requires a relatively low level of resources. We foresee applications to future analyses as a model selection tool in many contexts.
Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells
Authors: Sung Sanghyun , Kim Eunkyeong , Niida Hiroyuki , Kim Chuna , Lee Junho 
Published: July 2023

Abstract
Telomere length must be maintained in actively dividing cells to avoid cellular arrest or death. In the absence of telomerase activity, activation of alternative lengthening of telomeres (ALT) allows the maintenance of telomeric length and prolongs the cellular lifespan. Our previous studies have established two types of ALT survivors from mouse embryonic stem cells. The key differences between these ALT survivors are telomere-constituting sequences: non-telomeric sequences and canonical telomeric repeats, with each type of ALT survivors being referred to as type I and type II, respectively. We explored how the characteristics of the two types of ALT lines reflect their fates using multi-omics approaches. The most notable gene expression signatures of type I and type II ALT cell lines were chromatin remodelling and DNA repair, respectively. Compared with type II cells, type I ALT cells accumulated more mutations and demonstrated persistent telomere instability. These findings indicate that cells of the same origin have separate routes for survival, thus providing insights into the plasticity of crisis-suffering cells and cancers.