bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of seawater temperature and seasonal irradiance on growth, reproduction, and survival of the endemic Antarctic brown alga Desmarestia menziesii (Phaeophyceae)
Authors: Matula Carolina Verónica , Quartino María Liliana , Nuñez Jesús Darío , Zacher Katharina , Bartsch Inka 
Published: February 2022

AbstractEndemic Antarctic macroalgae are especially adapted to live in extreme Antarctic conditions. Their potential biogeographic distribution niche is primarily controlled by the photoperiodic regime and seawater temperatures, since these parameters regulate growth, reproduction, and survival during the entire life cycle. Here we analyzed the upper survival temperature (UST) of juvenile sporophytes and the temperature range for sporophyte formation from gametophytes of Desmarestia menziesii, one of the dominant endemic Antarctic brown algal species. This process is a missing link to better evaluate the full biogeographical niche of this species. Two laboratory experiments were conducted. First, growth and maximum quantum yield of juvenile sporophytes were analyzed under a temperature gradient (0, 5, 10, 12, 13, 14, 15, and 16 °C) in a 16:8 h light:dark (LD) regime (Antarctic spring condition) for 2 weeks. Second, the formation of sporophytes from gametophytes (as a proxy of gametophyte reproduction) was evaluated during a 7 weeks period under a temperature gradient (0, 4, 8, 12, and 16 °C), and two different photoperiods: 6:18 h LD regime simulating winter conditions and a light regime simulating the Antarctic shift from winter to spring by gradually increasing the light period from 7.5:16.5 h LD (late winter) to 18.5:5.5 h LD (late spring). Sporophytes of D. menziesii were able to grow and survive up to 14 °C for 2 weeks without visible signs of morphological damage. Thus, this species shows the highest UST of all endemic Antarctic Desmarestiales species. In turn, gametophyte reproduction solely took place at 0 °C but not at 4–8 °C. The number of emerging sporophytes was six times higher under the light regime simulating the transition from winter to spring than under constant short day winter conditions. There was a negative relationship between the number of sporophytes formed and the gametophyte density at the beginning of the experiment, which provides evidence that gametophyte density exerts some control upon reproduction in D. menziesii. Results strongly indicate that although sporophytes and gametophytes may survive in warmer temperatures, the northernmost distribution limit of D. menziesii in South Georgia Islands is set by the low temperature requirements for gametophyte reproduction. Hence, global warming could have an impact on the distribution of this and other Antarctic species, by influencing their growth and reproduction.
The changing trends of image-guided biopsy of small renal masses before intervention—an analysis of European multinational prospective EuRECA registry
Authors: Chan Vinson Wai-Shun , Keeley Francis Xavier , Lagerveld Brunolf , Breen David J. , King Alexander , Nielsen Tommy Kjærgaard , van Strijen Marco , Garnon Julien , Alcorn Des , Graumann Ole , de Kerviler Eric , Zondervan Patricia , Walkden Miles , Lughezzani Giovanni , Wah Tze Min 
Published: February 2022

Abstract
Objectives
To evaluate the use of pre-cryoablation biopsy for small renal masses (SRMs) and the effects of increasing uptake on histological results of treated SRMs.

Methods
From 2015 to 2019, patients with sporadic T1N0M0 SRMs undergoing percutaneous, laparoscopic, or open cryoablation from 14 European institutions within the European Registry for Renal Cryoablation (EuRECA) were included for the retrospective analysis. Univariate and multivariate logistic models were used to evaluate the trends, histological results, and the factors influencing use of pre-cryoablation biopsy.

Results
In total, 871 patients (median (IQR) age, 69 (14), 298 women) undergoing cryoablation were evaluated. The use of pre-cryoablation biopsy has significantly increased from 42% (65/156) in 2015 to 72% (88/122) in 2019 (p < 0.001). Patients treated for a benign histology are significantly more likely to have presented later in the trend, where pre-cryoablation biopsy is more prevalent (OR: 0.64, 95% CI 0.51–0.81, p < 0.001). Patients treated for undiagnosed histology are also significantly less likely to have presented in 2018 compared to 2016 (OR 0.31, 95% CI 0.10–0.97, p = 0.044). Patients aged 70+ are less likely to be biopsies pre-cryoablation (p < 0.05). R.E.N.A.L. nephrometry score of 10+ and a Charlson Comorbidity Index > 1 are factors associated with lower likelihood to not have received a pre-cryoablation biopsy (p < 0.05).

Conclusion
An increased use of pre-cryoablation biopsy was observed and cryoablation patients treated with a benign histology are more likely to have presented in periods where pre-cryoablation biopsy is not as prevalent. Comparative studies are needed to draw definitive conclusions on the effect of pre-cryoablation biopsy on SRM treatments.

Key Points
• The use of biopsy pre-ablation session has increased significantly from 42% of all patients in 2015 to 74% in 2019.
• Patients are less likely to be treated for a benign tumour if they presented later in the trend, where pre-cryoablation biopsy is more prevalent, compared to later in the trend (OR 0.64, 95% CI 0.51–0.81, p < 0.001).
• Patients with comorbidities or a complex tumour (R.E.N.A.L. nephrometry score > 10) are less likely to not undergo biopsy as a separate session to cryoablation.
Mouse genomic and cellular annotations
Authors: Long Helen , Reeves Richard , Simon Michelle M. 
Published: February 2022

AbstractMice have emerged as one of the most popular and valuable model organisms in the research of human biology. This is due to their genetic and physiological similarity to humans, short generation times, availability of genetically homologous inbred strains, and relatively easy laboratory maintenance. Therefore, following the release of the initial human reference genome, the generation of the mouse reference genome was prioritised and represented an important scientific resource for the mouse genetics community. In 2002, the Mouse Genome Sequencing Consortium published an initial draft of the mouse reference genome which contained ~ 96% of the euchromatic genome of female C57BL/6 J mice. Almost two decades on from the publication of the initial draft, sequencing efforts have continued to increase the completeness and accuracy of the C57BL/6 J reference genome alongside advances in genome annotation. Additionally new sequencing technologies have provided a wealth of data that has added to the repertoire of annotations associated with traditional genomic annotations. Including but not limited to advances in regulatory elements, the 3D genome and individual cellular states. In this review we focus on the reference genome C57BL/6 J and summarise the different aspects of genomic and cellular annotations, as well as their relevance to mouse genetic research. We denote a genomic annotation as a functional unit of the genome. Cellular annotations are annotations of cell type or state, defined by the transcriptomic expression profile of a cell. Due to the wide-ranging number and diversity of annotations describing the mouse genome, we focus on gene, repeat and regulatory element annotation as well as two relatively new technologies; 3D genome architecture and single-cell sequencing outlining their utility in genetic research and their current challenges.
Cross-calibration of a combined electrostatic and time-of-flight analyzer for energy- and charge-state-resolved spectrometry of tin laser-produced plasma
Authors: Poirier L. , Bayerle A. , Lassise A. , Torretti F. , Schupp R. , Behnke L. , Mostafa Y. , Ubachs W. , Versolato O. O. , Hoekstra R. 
Published: February 2022

AbstractWe present the results of the calibration of a channeltron-based electrostatic analyzer operating in time-of-flight mode (ESA-ToF) using tin ions resulting from laser-produced plasma, over a wide range of charge states and energies. Specifically, the channeltron electron multiplier detection efficiency and the spectrometer resolution are calibrated, and count rate effects are characterized. With the obtained overall response function, the ESA-ToF is shown to accurately reproduce charge-integrated measurements separately and simultaneously obtained from a Faraday cup (FC), up to a constant factor the finding of which enables absolute cross-calibration of the ESA-ToF using the FC as an absolute benchmark. Absolute charge-state-resolved ion energy distributions are obtained from ns-pulse Nd:YAG-laser-produced microdroplet tin plasmas in a setting relevant for state-of-the-art extreme ultraviolet nanolithography.
Comparison of endoscopic and microscopic tympanoplasty in patients with chronic otitis media
Authors: Yang Qimei , Wang Bing , Zhang Jin , Liu Hui , Xu Min , Zhang Wen 
Published: February 2022

Abstract
Background
To compare the results between type I tympanoplasty performed with transcanal endoscopic ear surgery (TEES) and microscopic ear surgery (MES) for treatment of chronic otitis media in a homogenous group of patients.

Methods
A retrospective study was performed in our department between January 2011 and January 2016 to review primary type I tympanoplasty cases with a subtotal perforation, an intact ossicular chain, a dry ear for at least 1 month, normal middle ear mucosa, and a follow-up period of at least 6 months post surgery. The adoption of TEES or MES was divided temporally (before and since 2013). TEES was undertaken in 224 patients (224 ears) and MES in 121 patients (121 ears).

Results
The successful graft take rate was 94.64% (212/224) in the TEES group and 90.91% (110/121) in the MES group (P = 0.239). The improvements in the air conduction levels between the 2 groups were not statistically different at 1, 3, or 6 (> 6) months (P > 0.05) after surgery. The improvements in the air–bone gaps were not significantly different between the 2 groups (P > 0.05). The average hearing gains in the TEES group 6 (and > 6) months post surgery were 11.85 ± 5.47 dB, which was better than 10.48 ± 5.18 dB in the MES group (P = 0.031). The use of medical resources was lower in the TEES group than in the MES group regarding the average operating time (49.22 ± 8.24 min vs 81.22 ± 14.73 min, respectively; P < 0.0001). Patients receiving MES had a significant higher incidence of the wound problems (ear pain, numbness around the ears, and wet ear; P < 0.05).

Conclusion
TEES for type I tympanoplasty seems to achieve a shorter operative time and ideal tympanic membrane healing rate and hearing results in patients with chronic otitis media.
Evaluating an automated machine learning model that predicts visual acuity outcomes in patients with neovascular age-related macular degeneration
Authors: Abbas Abdallah , O’Byrne Ciara , Fu Dun Jack , Moraes Gabriella , Balaskas Konstantinos , Struyven Robbert , Beqiri Sara , Wagner Siegfried K. , Korot Edward , Keane Pearse A. 
Published: February 2022

Abstract
Purpose
Neovascular age-related macular degeneration (nAMD) is a major global cause of blindness. Whilst anti-vascular endothelial growth factor (anti-VEGF) treatment is effective, response varies considerably between individuals. Thus, patients face substantial uncertainty regarding their future ability to perform daily tasks. In this study, we evaluate the performance of an automated machine learning (AutoML) model which predicts visual acuity (VA) outcomes in patients receiving treatment for nAMD, in comparison to a manually coded model built using the same dataset. Furthermore, we evaluate model performance across ethnic groups and analyse how the models reach their predictions.

Methods
Binary classification models were trained to predict whether patients’ VA would be ‘Above’ or ‘Below’ a score of 70 one year after initiating treatment, measured using the Early Treatment Diabetic Retinopathy Study (ETDRS) chart. The AutoML model was built using the Google Cloud Platform, whilst the bespoke model was trained using an XGBoost framework. Models were compared and analysed using the What-if Tool (WIT), a novel model-agnostic interpretability tool.

Results
Our study included 1631 eyes from patients attending Moorfields Eye Hospital. The AutoML model (area under the curve [AUC], 0.849) achieved a highly similar performance to the XGBoost model (AUC, 0.847). Using the WIT, we found that the models over-predicted negative outcomes in Asian patients and performed worse in those with an ethnic category of Other. Baseline VA, age and ethnicity were the most important determinants of model predictions. Partial dependence plot analysis revealed a sigmoidal relationship between baseline VA and the probability of an outcome of ‘Above’.

Conclusion
We have described and validated an AutoML-WIT pipeline which enables clinicians with minimal coding skills to match the performance of a state-of-the-art algorithm and obtain explainable predictions.
Anatomical and functional outcomes of pneumatic vitreolysis for treatment of vitreomacular traction with and without macular holes
Authors: Baumann Carmen , Sabatino Francesco , Zheng Yalin , Johannigmann-Malek Navid , Maier Mathias , Kaye Stephen B. , Patton Niall 
Published: February 2022

Abstract
Purpose
To evaluate the outcome of pneumatic vitreolysis (PVL) for vitreomacular traction (VMT) with or without full thickness macular hole (MH) < 400 µm.

Methods
Forty-seven eyes of 47 patients were included who had undergone PVL for VMT with or without MH. Main outcome measures were release of VMT, MH closure, best-corrected visual acuity (BCVA) and adverse events.

Results
Thirty-three patients had isolated VMT and 14 patients VMT with a MH. Four weeks after PVL, the overall VMT release rate was 35/47 (74.5%): 25/37 (67.6%) in phakic and 10/10 (100%) in pseudophakic eyes (p = 0.03). Four of 14 MH (28.6%) were closed. Twenty-two of 47 (46.8%) eyes required a subsequent PPV: 12/33 (36.4%) in the VMT only group and 10/14 (71.4%) in the VMT with MH group. Mean BCVA improved from 0.48 (± 0.24) to 0.34 (± 0.23) logMAR at 6 months in patients with VMT alone (p < 0.001), and from 0.57 (± 0.27) to 0.41 (± 0.28) logMAR in patients with VMT and MH (p = 0.008). Adverse events included new formation of a large MH in 4/33 (12.1%) eyes, failure of MH closure in 10/14 (71.4%) eyes, progression of mean minimum linear diameter (MLD) MH size from baseline 139 (± 67) to 396 (± 130) µm (p < 0.001) and development of a retinal detachment in 4/47 (8.5%) eyes.

Conclusion
While PVL leads to a high VMT release rate particularly in pseudophakic eyes, it is associated with a relatively high incidence of MH formation, MH size progression and retinal detachment.
The composite Triassic–Eocene Poshteh pluton, eastern Iran, an Eo-Cimmerian element south of the main Paleotethys suture
Authors: Mahmoudi Shahryar , Corfu Fernando 
Published: February 2022

AbstractThe composite Poshteh Pluton, at the northeastern margin of the Central Iranian Microplate near Taybad in eastern Iran, is positioned at a critical tectonic junction, south of the inferred main Paleotethys suture and along the major regional Doruneh Fault system. It consists of two distinct intrusions. Quartz monzonite is dated in this study by zircon U–Pb ID-TIMS to 215.8 ± 0.5 Ma, an age that coincides with the time of closure of the Paleotethys during the late collisional stages of the Eo-Cimmerian Orogeny. It is geochemically very similar to coeval plutons present along and north of the Paleotethys suture, where they intruded Carboniferous-Permian arc sequences, ophiolites and flysch. The Poshteh quartz monzonite is located south of the suture in a position similar to the Anarak and related complexes further west, which previously have been interpreted as reflecting Mesozoic and Cenozoic disruption of the Eo-Cimmerian Orogen by extensional and transtensional processes. The Triassic quartz monzonite was subsequently invaded by granite at 41.23 ± 0.31 Ma. The emplacement was in part structurally controlled by the Doruneh Fault system and associated to hydrothermal alteration and Fe mineralization. The granite is thus a coeval member of a widespread late Eocene to Oligocene plutonic suite in the region, and likely the result of delamination and melting of the subcontinental lithosphere.
A systematic literature review of empirical research on quality requirements
Authors: Olsson Thomas , Sentilles Séverine , Papatheocharous Efi 
Published: February 2022

AbstractQuality requirements deal with how well a product should perform the intended functionality, such as start-up time and learnability. Researchers argue they are important and at the same time studies indicate there are deficiencies in practice. Our goal is to review the state of evidence for quality requirements. We want to understand the empirical research on quality requirements topics as well as evaluations of quality requirements solutions. We used a hybrid method for our systematic literature review. We defined a start set based on two literature reviews combined with a keyword-based search from selected publication venues. We snowballed based on the start set. We screened 530 papers and included 84 papers in our review. Case study method is the most common (43), followed by surveys (15) and tests (13). We found no replication studies. The two most commonly studied themes are (1) differentiating characteristics of quality requirements compared to other types of requirements, (2) the importance and prevalence of quality requirements. Quality models, QUPER, and the NFR method are evaluated in several studies, with positive indications. Goal modeling is the only modeling approach evaluated. However, all studies are small scale and long-term costs and impact are not studied. We conclude that more research is needed as empirical research on quality requirements is not increasing at the same rate as software engineering research in general. We see a gap between research and practice. The solutions proposed are usually evaluated in an academic context and surveys on quality requirements in industry indicate unsystematic handling of quality requirements.
Periodontal infectogenomics: a systematic review update of associations between host genetic variants and subgingival microbial detection
Authors: Zoheir Noha , Kurushima Yuko , Lin Guo-Hao , Nibali Luigi 
Published: February 2022

Abstract
Objective
The aim of this study was to systematically update the evidence for associations between host genetic variants and subgingival microbial detection and counts.

Materials and methods
Following a previous systematic review (Nibali et al. J Clin Periodontol 43(11): 889-900, 15), an update of a systematic search of the literature was conducted in Ovid Medline, Embase, LILACS, and Cochrane Library for studies reporting data on host genetic variants and detection of microbes subgingivally published in the last 6 years.

Results
A total of 19 studies were included in the review, from an initial search of 2797 titles. Studies consisted mainly of candidate gene studies and of one genome-wide analysis. A total of 62 studies were considered for summary findings, including 43 identified in the previous systematic review of studies published up to 2015. Meta-analyses were done when appropriate including both papers in the original review and in the update. Meta-analyses revealed lack of associations between IL1 composite genotype and subgingival detection of Aggregatibacter acinomycetemcomitans, Poprhyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Prevotella intermedia. Promising evidence is emerging from other genetic variants and from sub-analyses of data from genome-association studies. Among other studies with candidate-gene, target SNPs were mainly within the IL10, IL6, IL4, IL8, IL17A, and VDR gene.

Conclusions
IL1 composite genotype does not seem to be associated with subgingival microbial detection. Promising associations should be pursued by future studies, including studies employing -OMICS technologies.

Clinical relevance
A better knowledge of which host genetic variant predispose to subgingival microbial colonization and to the development of progression of periodontal disease could potentially help to better understand periodontal disease pathogenesis and help with its management.
tRNA modification profiles in obligate and moderate thermophilic bacilli
Authors: Panosyan Hovik , Traube Franziska R. , Brandmayr Caterina , Wagner Mirko , Carell Thomas 
Published: February 2022

AbstractTransfer RNAs (tRNAs) are the most ancient RNA molecules in the cell, modification pattern of which is linked to phylogeny. The aim of this study was to determine the tRNA modification profiles of obligate (Anoxybacillus, Geobacillus, Paragebacillus) and moderate (Bacillus, Brevibacillus, Ureibacillus, Paenibacillus) thermophilic aerobic bacilli strains to find out its linkage to phylogenetic variations between species. LC-MS was applied for the quantification of modified nucleosides using both natural and isotopically labeled standards. The presence of m2A and m7G modifications at high levels was determined in all species. Relatively high level of i6A and m5C modification was observed for Paenibacillus and Ureibacillus, respectively. The lowest level of Cm modification was found in Bacillus. The modification ms2i6A and m1G were absent in Brevibacillus and Ureibacillus, respectively, while modifications Am and m22G were observed only for Ureibacillus. While both obligate and moderate thermophilic species contain Gm, m1G and ms2i6A modifications, large quantities of them (especially Gm and ms2i6A modification) were detected in obligate thermophilic ones (Geobacillus, Paragebacillus and Anoxybacillus). The collective set of modified tRNA bases is genus-specific and linked to the phylogeny of bacilli. In addition, the dataset could be applied to distinguish obligate thermophilic bacilli from moderate ones.
Interhemispheric asymmetry of climate change projections of boreal winter surface winds in CanESM5 large ensemble simulations
Authors: Yu Bin , Zhang Xuebin , Li Guilong , Yu Wei 
Published: February 2022

Abstract
A recent study of global wind power using an ensemble of ten CMIP5 climate simulations indicated an interhemispheric asymmetry of wind power changes over the twenty-first century, featured by power decreases across the Northern Hemisphere mid-latitudes and increases across the tropics and subtropics of the Southern Hemisphere. Here we analyze future projections of surface mean and extreme winds by means of a single-model initial-condition 50-member ensemble of climate simulations generated with CanESM5, the Canadian model participated in CMIP6. We analyze the ensemble mean and spread of boreal winter mean and extreme wind trends over the next half-century (2021–2070) and explore the contribution of internal climate variability to these trends. Surface wind speed is projected to mostly decrease in northern mid-low latitudes and southern mid-latitudes and increase in northern high latitudes and southern tropical and subtropical regions, with considerable regional variations. Large ensemble spreads are apparent, especially with remarkable differences over northern parts of South America and northern Russia. The interhemispheric asymmetry of wind projections is found in most ensemble members, and can be related to large-scale changes in surface temperature and atmospheric circulation. The extreme wind has similar structure of future projections, whereas its reductions tend to be more consistent over northern mid-latitudes. The projected mean and extreme wind changes are attributed to changes in both externally anthropogenic forced and internal climate variability generated components. The spread in wind projections is partially due to large-scale atmospheric circulation variability.