bluuebunny/crossref_metadata_2025_split huggingface dataset:
Name IDs and Name Matching for Catalogue of Life: Existing Services and Prospects
Authors: Bánki Olaf , Döring Markus , Jeppesen Thomas 
Published: August 2023

ChecklistBank, developed by Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF), is a publishing platform and open data repository focused on taxonomic and nomenclatural data sets (checklists). It contains close to 50K datasets, mostly originating from digitised peer reviewed scientific articles mediated by Plazi, amongst others. The COL Checklist (Bánki et al. 2023) is assembled out of a selection of the data sources in ChecklistBank. The Catalogue of Life Checklist is issued with name usage identifiers, as well as a digital object identifier for the Checklist version (with an associated dataset key). The more than 160 data sources that make up the COL Checklist are also issued with digital object identifiers as well as a data set key. The combination of a name usage identifier and the data set key allows for the tracking of names between the various COL Checklist versions. ChecklistBank is built in an open API. It supports data sharing through various exchange formats of the Darwin Core (Darwin Core Task Group 2009) data standard (e.g., Darwin Core-Archives (GBIF 2021) and ColDP), and provides several download and name matching options.
The Transforming European Taxonomy through Training, Research, and Innovations (TETTRIs) European Union funded project will contribute to a couple of improvements to ChecklistBank. In the context of the TETTRIs project, a new name usage (i.e., taxon or synonym) matching service against any dataset in ChecklistBank, not just the COL Checklist, was developed. A single name matching service takes query parameters for a single name and optionally its classification. The service allows for bulk matching of names against the ChecklistBank API. This contains the option of matching a classification in a CSV file. The bulk matching allows all names of an entire or a subtree of an existing ChecklistBank dataset to act as the source for names instead of the input matching a CSV file. The bulk matching services are asynchronous and notify a user by email when the results are ready to be downloaded in a CSV file.
Building on the Functionalities of GBIF-COL ChecklistBank
Authors: Bánki Olaf , Hobern Donald , Döring Markus 
Published: August 2023

ChecklistBank, co-developed by Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF), provides a suite of functionalities for building taxonomic data solutions. In addition to serving as a publishing platform and open data repository for taxonomic and nomenclatural data, ChecklistBank includes tools for managing the assembly of new species lists from other datasets published to the platform. The ChecklistBank API provides access to all data sources, including the COL Checklist, all mediated through ChecklistBank. It also allows for (bulk) matching of names, and provides an overview of the name usage identifiers used by COL and the identifiers for the same taxon originating from other data sources.
The ChecklistBank infrastructure is still in development, but is starting to allow for various kinds of usages and services, including quality assurance and quality control. Examples will be presented of possible functionalities and services that could be added to ChecklistBank in future, including:

An option to push a ChecklistBank dataset to Github and then automate reimport from the same source (with appropriate validation). A Github representation, based upon the Catalogue of Life Data Package (ColDP) data model, could serve as a general resource against which developers can build new lightweight editing or batch update tools, including merge tools to bring in new names from ChecklistBank datasets, with Github providing versioning support and triggers for synchronisation with Github

An option to establish similar bidirectional editing models with other environments such as TaxonWorks or Aphia,

Notifications for checklist curators when previously unseen names and combinations for their group appear in new or updated ChecklistBank datasets

Enhancements to the data model and user interface to support better quality/completeness indicators (traffic lights).

An option to push a ChecklistBank dataset to Github and then automate reimport from the same source (with appropriate validation). A Github representation, based upon the Catalogue of Life Data Package (ColDP) data model, could serve as a general resource against which developers can build new lightweight editing or batch update tools, including merge tools to bring in new names from ChecklistBank datasets, with Github providing versioning support and triggers for synchronisation with Github
An option to establish similar bidirectional editing models with other environments such as TaxonWorks or Aphia,
Notifications for checklist curators when previously unseen names and combinations for their group appear in new or updated ChecklistBank datasets
Enhancements to the data model and user interface to support better quality/completeness indicators (traffic lights).
Towards a More Comprehensive Catalogue of Life Checklist
Authors: Hernández-Robles Diana , Plata Camila , Döring Markus , Bánki Olaf 
Published: August 2023

The Catalogue of Life (COL) Checklist 2023 (Bánki et al. 2023) includes over 2.1 million accepted species underpinned by a large international community of more than 500 expert taxonomists. The 164 supporting sources are available through ChecklistBank, a publishing platform and open data respository with a focus on taxonomic and nomenclatural data sources. It also includes all the tools and processes that are needed to assemble the COL Checklist. ChecklistBank is jointly developed by Catalogue of Life and the Global Biodiversity Information Facility (GBIF). The results presented here build on efforts carried out in the European Union-funded project Biodiversity Community Integrated Knowledge Library (BiCKL).
Despite all the global efforts over the past 27 years, there still remain significant gaps in the COL Checklist: incompleteness, outdated data in several taxonomic groups, lack of synonyms and a considerable time lag in being up-to-date with continuously published literature. However, there are not enough experts to check and update it as fast as new information is published e.g., descriptions of new species, covering lesser-known taxonomic groups, clarifying synonym relations, interpreting new classifications. For that reason, there is an intrinsic need to rely on a new process that combines:

the expertise of taxonomists contributing to well curated databases with global coverage;

recent knowledge compiled in checklists and catalogues published at regional and national scales in different formats and through different platforms;

new and improved informatics tools that can harvest those data with text mining schemas and integrate them into ChecklistBank and the COL Checklist based on revised and supported criteria and a careful quality control that will avoid the inclusion of errors or doubtful information.

the expertise of taxonomists contributing to well curated databases with global coverage;
recent knowledge compiled in checklists and catalogues published at regional and national scales in different formats and through different platforms;
new and improved informatics tools that can harvest those data with text mining schemas and integrate them into ChecklistBank and the COL Checklist based on revised and supported criteria and a careful quality control that will avoid the inclusion of errors or doubtful information.
Combining these elements would result in an extended release of the COL Checklist that is an enriched version, integrating a wider variety of taxonomic sources and informatic developments not considered previously. This process will feature sequential releases that will address different needs and will be useful for delivering taxonomic services for GBIF and ultimately replacing its backbone taxonomy (GBIF Secretariat 2022). The extended release of the COL Checklist will be more comprehensive, including names that will fill significant gaps, synonyms and fossil taxa, and a single consensus classification that avoids conflicts.
Sec22b and Stx4 Depletion Has No Major Effect on Cross-Presentation of PLGA Microsphere–Encapsulated Antigen and a Synthetic Long Peptide In Vitro
Authors: Tondeur Emma G M , Voerman Jane S A , Geleijnse Mitchell A A , van Hofwegen Laure S , van Krimpen Anneloes , Koerner Julia , Mishra Gunja , Song Ziye , Schliehe Christopher 
Published: August 2023

Abstract
The induction of CTL responses by vaccines is important to combat infectious diseases and cancer. Biodegradable poly(lactic-co-glycolic acid) (PLGA) microspheres and synthetic long peptides are efficiently internalized by professional APCs and prime CTL responses after cross-presentation of Ags on MHC class I molecules. Specifically, they mainly use the cytosolic pathway of cross-presentation that requires endosomal escape, proteasomal processing, and subsequent MHC class I loading of Ags in the endoplasmic reticulum (ER) and/or the endosome. The vesicle SNARE protein Sec22b has been described as important for this pathway by mediating vesical trafficking for the delivery of ER-derived proteins to the endosome. As this function has also been challenged, we investigated the role of Sec22b in cross-presentation of the PLGA microsphere–encapsulated model Ag OVA and a related synthetic long peptide. Using CRISPR/Cas9-mediated genome editing, we generated Sec22b knockouts in two murine C57BL/6-derived APC lines and found no evidence for an essential role of Sec22b. Although pending experimental evidence, the target SNARE protein syntaxin 4 (Stx4) has been suggested to promote cross-presentation by interacting with Sec22b for the fusion of ER-derived vesicles with the endosome. In the current study, we show that, similar to Sec22b, Stx4 knockout in murine APCs had very limited effects on cross-presentation under the conditions tested. This study contributes to characterizing cross-presentation of two promising Ag delivery systems and adds to the discussion about the role of Sec22b/Stx4 in related pathways. Our data point toward SNARE protein redundancy in the cytosolic pathway of cross-presentation.
Comparison of marginal and internal adaptation of provisional polymethyl methacrylate restorations fabricated by two three-dimensional printers: An in vitro study
Authors: Hasanzade Mahya , Zabandan Dariush , Mosaddad Seyed Ali , Habibzadeh Sareh 
Published: August 2023

Background:
Chairside fabrication of provisional restorations using three-dimensional (3D) printers is rising in digital dentistry. The purpose of this research was to compare the marginal and internal adaptation of provisional polymethyl methacrylate (PMMA) restorations fabricated by two different 3D printers.

Materials and Methods:
In this in vitro investigation, an intact maxillary 1st molar acrylic model was first digitalized by a laboratory scanner. It was then prepared for an all-ceramic restoration and scanned again by the same scanner. The final restoration was designed in Exocad according to the scan files with a 50 μm cement gap. PMMA restorations were printed by two 3D printers; Group 1: Asiga (n = 10) and Group 2: Digident (n = 10). The replica technique was used to assess the marginal and internal fit of the restorations, and one-way ANOVA was used to analyze the data. P <0.05 was regarded as statistically significant.

Results:
The mean marginal gap of crowns in Group 1 was significantly lower than that of Group 2 (75 vs. 195 μ, P = 0.001). Regarding internal adaptation, no significant difference was found between the axial gap values in both groups (P > 0.05). The mean occluso-axial gap (90 vs. 140 μ, P = 0.026) and the mean occlusal gap (116 vs. 300 μ, P = 0.001) of crowns in Group 1 were significantly smaller compared to the equivalent values in Group 2.

Conclusion:
Provisional PMMA crowns fabricated by the Asiga printer showed significantly higher marginal and internal adaptation than those manufactured by Digident at all points except for the axial surface.
Comparison of the apical seal obtained by Adseal, Proseal, and AH26 sealers in root canal obturation with lateral compaction technique
Authors: Saeidi Akam , Hajipour Romina , Mahmoudi Elham , Feizi Farideh , Khafri Soraya 
Published: August 2023

Background:
Root canal obturation is an important step in endodontic treatment, which is performed aiming to three-dimensionally seal the canal and prevent microleakage, reentry, and proliferation of microorganisms in the root canal system. On the other hand, microleakage eventually leads to root canal treatment failure. Sealing ability is an important property of endodontic sealers. This in vitro study aimed to compare the quality of apical seals obtained by three endodontic sealers.

Materials and Methods:
This in vitro experimental study evaluated 48 extracted single-canal maxillary incisors. Hard- and soft-tissue residues were removed and the teeth were immersed in 5.25% of sodium hypochlorite for disinfection. The teeth were decoronated at the cementoenamel junction with a diamond disc such that 10 mm of root length remained. Canal patency was ensured using a #10 K-file. The canals were then instrumented with ProTaper rotary system. The canals were randomly divided into three experimental groups for the application of Adseal, Proseal, and AH26 sealers, and positive and negative control groups. Sealers were applied in the canals using lateral compaction technique. The external root surfaces were then coated with two layers of nail varnish except for the apical 3 mm. The amount of microleakage was quantified using the dye-penetration technique. The Tukey's test was used to compare the microleakage between the experimental and control groups. The Kruskal–Wallis test was applied to compare the microleakage of experimental groups (P < 0.05).

Results:
The amount of microleakage in canals filled with Adseal, Proseal, and AH26 sealers with lateral compaction technique was 2.33 ± 0.64, 2.2 ± 0.81, and 2.22 ± 0.71 μm, respectively. No significant difference was noted among the three sealers regarding microleakage (P = 0.84). However, the amount of microleakage in the sealer groups was significantly lower than that in the control group (P < 0.001).

Conclusion:
The application of Adseal, Proseal, and AH26 had equal efficacy for the provision of optimal apical seal in filling of root canals with lateral compaction technique. The application of sealers yielded a significantly superior apical seal compared with the control group.
Prevalence and Predictors of Prediabetes in Adolescents and Young Adults with Turner Syndrome: A Cross-Sectional Study from Eastern India
Authors: Mondal Sunetra , Gargari Piyas , Bose Chiranjit , Chowdhury Subhankar , Mukhopadhyay Satinath 
Published: August 2023

Background:
Individuals with Turner syndrome (TS) have a high risk for prediabetes/type 2 Diabetes Mellitus (T2DM). There is scarce data regarding risk factors for prediabetes in TS, specially from South Asia.

Methods:
We conducted a cross-sectional study on girls with TS aged 12–30 years who had achieved pubertal stage B3 and above—spontaneously or with oestrogen. Anthropometric measurements and biochemical tests were conducted, and medical records were reviewed for details about pubertal onset and progression, growth hormone (GH) and oestrogen therapy.

Results:
Out of 129 patients with TS in our database, 99 met the criteria for inclusion, mean age 18.33+/-3.78 years and mean BMI 20.57+/- 3.71 kg/m2. Prevalence of prediabetes was 23.23%. Plasma-glucose measured after 75 g-oral-anhydrous-glucose-load (OGTT-PPG) identified five additional prediabetes cases, who had normal fasting plasma glucose (FPG) or HbA1c%. Compared to those without prediabetes, TS with prediabetes (n = 23) had higher mean body weight, BMI, waist circumference (WC) [42.02+/- 5.83 vs 36.22+/-8.07, 22.77+/-2.78 vs 19.91+/- 3.72, 85.26+/- 3.52 vs 81.08+/- 4.59, pall < 0.03 ], higher median WC-to-height ratio (WHtR) and WC-to-hip ratio (WHR)((0.64 [0.6–0.69] vs 0.59[0.56- 0.66], 0.9[0.84–1.12] vs 0.85[0.75–1.01], pboth < 0.02), and higher LDL-cholesterol, triglycerides, and greater prevalence of hepatosteatosis (47.1% vs 21.1%, P < 0.01). Among GH recipients (n = 36), those with prediabetes had delayed initiation and shorter duration of GH therapy. There were no differences in cardiometabolic parameters or the prevalence of diabetes between different karyotypic variants of TS. BMI, WC and WHR had significant positive correlation with FBG, OGTT-PPG and HbA1c% (pall < 0.004). Delay in oestrogen initiation had a significant correlation with OGTT-PPG (Spearman’s-rho = 0.69, P < 0.004). BMI, WHR and pubertal status were independent predictors for prediabetes (OR: 1.27 [1.03–1.57]), 1.18 [1.04–1.34]) and 0.09[0.02–0.38], respectively, pall < 0.02), but karyotype was not. BMI had the highest sensitivity [cut-off: 21.04 kg/m2 (sensitivity: 82.6%, specificity: 62.2%) and WHR had the highest specificity [cut-off: 0.89 (sensitivity: 73.9%, specificity 78.4%)] for predicting prediabetes.

Conclusion:
Indian girls with TS have a high risk for prediabetes, irrespective of underlying karyotype and should be screened with oral glucose challenge to identify prediabetes. Timely intervention against central obesity and early initiation of GH and oestrogen should be ensured in TS. Late presenting girls should be closely monitored for dysglycaemia before and during treatment with GH and/or oestrogen.
TSPYL5 inhibits the tumorigenesis of colorectal cancer cells in vivo by triggering DNA damage
Authors: Huang Chao , Ruan Peng , He Chunping , Zhou Rui 
Published: August 2023

ABSTRACT

Context:
Testis-specific protein Y-encoded-like 5 (TSPYL5) suppresses several cancers in vivo, including colorectal cancer (CRC); however, its mechanism and role in CRC cell tumorigenesis in vivo remain unknown.

Aims:
To elucidate the molecular mechanisms of colorectal cancer and find new therapeutic targets to improve CRC patient outcomes.

Settings and Design:
Male mice (4 weeks old, 16–22 g) were housed in sterile cages in a temperature-controlled room (20–25°C) with a 12 h light/dark cycle and ad libitum food and water.

Methods and Materials:
TSPYL5 overexpressing or non-overexpressing HCT116 cells were used to create a nude mouse tumor model. Tumor tissue was evaluated histologically after hematoxylin and eosin (H and E) staining. TUNEL staining assessed tumor cell apoptosis. Ki67 expression in excised tumor tissue was measured by immunohistochemistry. Western blotting examined double-stranded break (DBS)-associated protein expression in vivo.

Statistical Analysis Used:
IBM SPSS Statistics for Windows, Version 21.0 was used for all analyses (IBM Corp., Armonk, NY, USA). At least three independent experiments yield a mean value ± standard deviation. Unpaired Student’s t-tests compared groups. One-way analysis of variance and Dunnett’s test were used to compare groups with a P value < 0.5.

Results:
TSPYL5 overexpression inhibited CRC cell tumorigenicity and damaged tumor cells in vivo. TSPYL5 overexpression also significantly increased Bax and p-H2AX (early double-stranded break indicators) and decreased Ki67, Bcl-2, and peroxisome proliferator-activated receptor expression.

Conclusions:
Collectively, TSPYL5 overexpression inhibited the tumorigenicity of CRC cells in vivo by inducing DNA damage.
Prognostic and pathological implications of contrast-enhanced ultrasound features in hepatocellular carcinoma
Authors: Wang Yuling , Chai Suwan , Cai Wenjia , Yu Jie , Liang Ping 
Published: August 2023

ABSTRACT

Background:
Contrast-enhanced ultrasound (CEUS) plays a vital role in diagnosing hepatocellular carcinoma (HCC) and, to some extent, reflects tumor prognosis. This suggests that some pathological features of HCC may be associated with CEUS features.

Aim:
This study aimed to verify the prognostic significance of four CEUS features and further explore their pathological significance.

Materials and Methods:
This study included 243 HCC patients who underwent a preoperative CEUS examination. All pathological diagnoses and immunohistochemical information were obtained from the pathological report. The prognostic significance of four CEUS features, including nodule-in-nodule architecture, mosaic architecture, intratumoral feeding arteries, and peritumoral arterial phase (AP) hyperenhancement, was analyzed. The correlation between prognostic-related features and immunohistochemical information was further analyzed.

Results:
The disease-free survival (DFS) of HCC was significantly affected by mosaic architecture or intratumoral feeding arteries (HR = 1.79; 95% confidence interval (95% CI), 1.09–2.95; P = 0.004; HR = 1.70; 95% CI, 1.07–2.71; P = 0.025, respectively). Intratumoral feeding arteries were positively correlated with the expression of serum alpha-fetoprotein (AFP), microvascular invasion (MVI), differentiation, size, and Ki-67, among which the correlation with size was the strongest, followed by Ki-67 and MVI. The mosaic architecture was positively correlated with serum AFP, MVI, differentiation, and size, among which the correlation with size was strongest, followed by MVI.

Conclusion:
The mosaic architecture and intratumoral feeding arteries of CEUS were closely related to the postoperative progression of HCC. Mosaic architecture had a good correlation with tumor size and MVI, whereas intratumoral feeding arteries were closely associated with tumor size and Ki-67 expression.
Microwave ablation for the treatment of peripheral ground–glass nodule-like lung cancer: Long-term results from a multi-center study
Authors: Yang Xia , Jin Yong , Lin Zhengyu , Li Xiaoguang , Huang Guanghui , Ni Yang , Li Wenhong , Han Xiaoying , Meng Min , Chen Jin , Lin Qingfeng , Bie Zhixin , Wang Chuntang , Li Yuliang , Ye Xin 
Published: August 2023

ABSTRACTIntroduction:Microwave ablation (MWA) is an effective and safe approach for the treatment of ground–glass nodule (GGN)-like lung cancer, but long-term follow-up is warranted. Therefore, this multi-center retrospective study aimed to evaluate the results of MWA for the treatment of peripheral GGN-like lung cancer with a long-term follow-up.Materials and Methods:From June 2013 to January 2018, a total of 87 patients (47 males and 40 females, mean age 64.6 ± 10.2 years) with 87 peripheral lung cancer lesions showing GGN (mean long axis diameter, 17 ± 5 mm) underwent computed tomography (CT)-guided percutaneous MWA. All GGN-like lung cancers were histologically verified. The primary endpoints were local progression-free survival (LPFS) and overall survival (OS). The secondary endpoints were cancer-specific survival (CSS) and complications.Results:During a median follow-up of 65 months, both the 3-year and 5-year LPFS rates were 96.6% and 96.6%. The OS rate was 94.3% at 3 years and 84.9% at 5 years, whereas the 3-year and 5-year CSS rates were 100% and 100%, respectively. No periprocedural deaths were observed. Complications were observed in 49 patients (51.6%). Grade 3 or higher complications included pneumothorax, pleural effusion, hemorrhage, and pulmonary infection, which were identified in ten (10.5%), two (2.1%), two (2.1%), and one (1.1%) patient, respectively.Conclusions:CT-guided percutaneous MWA is an effective, safe, and potentially curative treatment regimen for GGN-like lung cancer.