bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS
Authors: Agosti Donat , Penev Lyubomir , Ruch Patrick , Benichou Laurence , Ioannidis-Pantopikos Alexandros 
Published: August 2023

A goal of natural history institutions is to contribute to the understanding of biodiversity and disseminate this knowledge through scholarly publications and other public activities. In today’s world, it is expected that this knowledge, imprisoned in separated silos of millions of publications scattered through ca. 500 million published pages, is readily available for exploring and reusing by humans and artificial intelligence tools. The goal of the BiCIKL project and its key product, the Biodiversity Knowledge Hub (BKH), is to put together novel tools and services to publish and extract data from publications to create findable, accessible, interoperable and reusable (FAIR) corpus of digital data, and establish explicit links between the data in publications and cited data types (taxonomic names, gene sequences, occurrences, images). This corpus of data is made available to the researchers and practitioners through the Biodiversity Literature Repository (BLR), the “Biodiversity PMC” digital library, Synospecies, and the OpenBiodiv knowledge graph through analytic tools, including artificial intelligence, and to a large extend through the re-use by the Global Biodiversity Information Facility (GBIF) and ChecklistBank (CLB).
This presentation will focus on the entire ecosystem of interlinked services created by Plazi, Pensoft, the Muséum national d'Histoire naturelle, Paris (Science Press), the Consortium of European Taxonomic Facilities (CETAF) e-publishing working group, the Zenodo repository at the European Center for Nuclear Research (CERN) and the Literature Services of the Swiss Insitute of Bioinformatics (SIBiLS) to enforce both novel methods for prospective semantic publishing and text and data mining of legacy literature. In the end, all knowledge, published in various journals by many publishers in different parts of the world, comes together into a standardized and re-usable open and linked FAIR data pool for the benefit of the researchers and society.
Improving Collection-Based Biodiversity Research in Chile: Digitisation and Implementation of Web Portals
Authors: Segovia Ricardo , Guerrero Pablo , Squeo Francisco , Saez Juan 
Published: August 2023

Biodiversity portals are emerging as some of the most powerful tools for scientific research and management based on scientific collections. We discuss the importance of web portals in biodiversity research and highlight the commendable progress made by two digitisation projects in Chile: herbariodigital.cl and the Atlas of Chilean Biodiversity. The aim of herbariodigital.cl and ALA-Chile is to take advantage of technological advances to improve the digitisation of biodiversity data. Using cutting-edge methods, herbariodigital.cl has successfully digitised an extensive collection of plant specimens and associated data from Chilean herbaria (&gt;25,000 specimens), promoting a more accessible and inclusive platform for researchers, educators and decision-makers.
Recognising that the complex nature of biodiversity information requires a careful approach to data storage and organisation to ensure efficient exchange across different platforms, we discuss our experience of using the Darwin Core standard (Darwin Core Task Group 2009), a widely accepted data standard in the field of biodiversity informatics. In turn, we discuss the incongruence that arises from adopting different global taxonomic checklists, such as the GBIF taxonomic backbone (GBIF Secretariat 2022) and World Flora Online (WFO 2023), in addition to a localised community catalogue. Using these different taxonomic frameworks is a significant challenge, as discrepancies and inconsistencies can arise, leading to potential under- or over-estimation of biodiversity indicators. By addressing these challenges, we believe that both herbariodigital.cl and ALA-Chile will prove to be invaluable assets for scientific research, educational initiatives, and environmental monitoring and assessment.
The comprehensive digitisation of biodiversity information will make it easier for researchers to conduct interdisciplinary studies and formulate evidence-based conservation strategies. In addition, educators will be able to use these web portals to develop interactive teaching materials, fostering a deeper connection between students and the natural world. Stakeholders in both the public and private sectors can also make informed decisions about biodiversity offsetting.
In conclusion, we highlight the transformative impact of web portals in the field of biodiversity research. The remarkable progress made by herbariodigital.cl and ALA-Chile in digitising Chile's biodiversity information is opening up unprecedented opportunities for scientific research, education and environmental management. By overcoming the challenges of data standardisation and taxonomic harmonisation, these projects are paving the way for a more comprehensive and collaborative approach to understanding and conserving Chile's biodiversity.
α-d-Glucose-1,6-Biphosphate Induces Dendritic Cell Homing to Enhance the Antitumor Effect of Neoantigen Vaccines
Authors: Zhang Rui , Tang Lin , Wang Yusi , Li Qing , Yang Li 
Published: August 2023

Abstract
Neoantigen vaccines have achieved good therapeutic effects in animal experiments and early clinical trials on certain malignant tumors. However, their overall objective effectiveness in clinical trials still needs to be improved. Low-efficiency dendritic cell (DC) migration (&lt;5%) to lymph nodes is one of the factors that limits vaccine effectiveness. For neoantigen vaccines, improving the homing efficiency of DCs is expected to further improve the immunotherapeutic effect. In this study, we used α-d-glucose-1,6-biphosphate (α-d-Glu), a metabolite that successfully enhanced C57BL/6J mouse bone marrow–derived DC homing induced by neoantigen peptide, mRNA, and DC vaccines during the administration process and improved the antitumor effects in the mouse C57BL/6J model with a neoantigen vaccine. We clarified that α-d-Glu activated MAPK8IP1 by inhibiting the expression of microRNA-10a-5p, thereby activating the MAPK signaling pathway to promote DC homing. Excitingly, the efficiency of α-d-Glu in promoting DC migration is not weaker than that of PGE2, which is the gold standard used to promote DC migration in clinical trials of DC vaccines. Thus, this study lays the foundation for further enhancing the objective clinical response rate of neoantigen vaccines and overcoming the limitation of an insufficient clinical response rate for neoantigen vaccines caused by low DC homing efficiency.
Intestinal IL-1β Plays a Role in Protecting against SARS-CoV-2 Infection
Authors: Lücke Jöran , Heinrich Fabian , Malsy Jakob , Meins Nicholas , Schnell Josa , Böttcher Marius , Nawrocki Mikolaj , Zhang Tao , Bertram Franziska , Sabihi Morsal , Kempski Jan , Blankenburg Tom , Duprée Anna , Reeh Matthias , Wolter Stefan , Mann Oliver , Izbicki Jakob R , Lohse Ansgar W , Gagliani Nicola , Lütgehetmann Marc , Bunders Madeleine J , Altfeld Marcus , Sauter Guido , Giannou Anastasios D , Krasemann Susanne , Ondruschka Benjamin , Huber Samuel 
Published: August 2023

Abstract
The intestine is constantly balancing the maintenance of a homeostatic microbiome and the protection of the host against pathogens such as viruses. Many cytokines mediate protective inflammatory responses in the intestine, among them IL-1β. IL-1β is a proinflammatory cytokine typically activated upon specific danger signals sensed by the inflammasome. SARS-CoV-2 is capable of infecting multiple organs, including the intestinal tract. Severe cases of COVID-19 were shown to be associated with a dysregulated immune response, and blocking of proinflammatory pathways was demonstrated to improve patient survival. Indeed, anakinra, an Ab against the receptor of IL-1β, has recently been approved to treat patients with severe COVID-19. However, the role of IL-1β during intestinal SARS-CoV-2 infection has not yet been investigated. Here, we analyzed postmortem intestinal and blood samples from patients who died of COVID-19. We demonstrated that high levels of intestinal IL-1β were associated with longer survival time and lower intestinal SARS-CoV-2 RNA loads. Concurrently, type I IFN expression positively correlated with IL-1β levels in the intestine. Using human intestinal organoids, we showed that autocrine IL-1β sustains RNA expression of IFN type I by the intestinal epithelial layer. These results outline a previously unrecognized key role of intestinal IL-1β during SARS-CoV-2 infection.
Characterization of Markers of Chloroquine Resistance in Plasmodium Falciparum among Pregnant Women in Oyo State
Authors: Azeez Mufutau Mosunmade , Akinbo Frederick Olusegun 
Published: August 2023

Background:
Chloroquine (CQ) which is one of the 4-aminoquinolines was once the mainstay of malaria treatment before it was officially withdrawn due to widespread resistance to it by Plasmodium species. It is one of the cheapest, safest, easily produced antimalarial compounds and has one of the longest half-lives among the antimalarial drugs which are also safe for use in pregnancy. Reversal of CQ resistance back to sensitivity has been documented after a period of withdrawal, and this may be a great relief in achievement of effective antimalarial chemotherapy at a relatively cheaper cost in Nigeria. This study investigated the characterization of markers of CQ resistance in Plasmodium falciparum infection among pregnant women in Oyo State following several years of official CQ withdrawal for treatment in Nigeria.

Materials and Methods:
Thick and thin blood films were made from venous blood collected from 316 consenting pregnant women and dispensed into ethylenediaminetetraacetic acid bottles after initial screening with SD Bioline RDT kit. The blood films were processed for malaria microscopy using 10% Giemsa stain. Dry blood spots on Whatman no. 1 filter paper were used for parasite DNA extraction and subsequent detection of CQ resistance markers using restriction fragment length polymorphism.

Results:
Eighty-two out of the 316 samples were positive for P. falciparum and subjected to molecular analysis for the detection of Pfcrt and Pfmdr1 mutant genes. Out of the 82 positive cases, 75 and 80 expressed mutant Pfcrt and Pfmdr1 genes, respectively, while 73 expressed both Pfcrt and Pfmdr1 genes.

Conclusion:
The high prevalence of the two major molecular markers of CQ resistance in this study, portends a concern in achieving resurgence of sensitivity after years of official withdrawal, thus official malaria management protocols should be strictly adhered to by ensuring testing before drug use while also avoiding self-medication.
Phytochemical and Biological Studies of Salvia Chorasanica
Authors: Mollaei Saeed , Asgharian Parina 
Published: August 2023

Background:

Salvia chorasanica is a perennial herb endemic to Iran, which grows wild. Due to the lack of data on S. chorasanica, the present work focused on chemical composition, as well as antioxidant and antibacterial properties of essential oil and five extracts from aerial parts of S. chorasanica.

Methods:
The analysis of chemical composition was done using gas chromatography (GC), GC–mass spectrometry, and high-performance liquid chromatography–photodiode array. Total phenolic and flavonoid contents and antioxidant activities were determined spectrophotometrically. Furthermore, antibacterial activities were investigated using the disk-diffusion method.

Results:
The essential oil analysis indicated that (-)-spathulenol, (-)-caryophyllene oxide, and (E)-caryophyllene were the major compounds. The extracts analysis indicated that ethyl acetate and methanol extracts had high phenolic compounds, and rosmarinic acid, caffeic acid, and luteolin-7-O-glucoside were identified as main phenolic compounds. The biological results showed that the highest antioxidant activity was obtained in the ethyl acetate extract. n-hexane and dichloromethane extracts were highly active against Staphylococcus aureus and Bacillus pumilus bacteria.

Conclusions:
It can be concluded that the phytochemical compositions and biological activities of S. chorasanica could be changed using different extraction solvents.
Robot-assisted repair of hiatal hernia: Advantages and disadvantages in comparison to conventional laparoscopic repair: A literature review
Authors: Pelzner Kim , Mueller Dolores T , Fuchs Claudia , Maus Martin , Bruns Christiane J , Fuchs Hans F , Leers Jessica M 
Published: August 2023

Abstract
The laparoscopic fundoplication has proven to be the standard technique of antireflux surgery and hiatal hernia (HH) repair over the last decade. However, robot-assisted surgery is more and more implemented in daily practice. Several studies have proven the feasibility and safety of robot-assisted HH repair and antireflux surgery. Both approaches seem to be similar regarding perioperative and postoperative complications, length of hospital stay, postoperative symptoms, and quality of life, as well as objective assessment of gastric acid exposure. Nevertheless, high total costs as well as a considerably longer total operating time of robot-assisted surgery need to be considered. The role of robot-assisted surgery in complex cases is promising but needs to be evaluated. Eventually, the decision regarding the technique used should be based on the surgeon’s discretion and experience.
Small-bowel obstruction complicating TransREctus sheath PrePeritoneal (TREPP) mesh repair of an inguinal hernia: A case report
Authors: Andriessen Marcel J G , Bloemendaal Alexander L A 
Published: August 2023

Abstract
We present a case of a small-bowel obstruction due to herniation through a peritoneal defect after TransREctus sheath PrePeritoneal (TREPP) mesh repair for an inguinal hernia.
Ergonomics in robot-assisted surgery in comparison to open or conventional laparoendoscopic surgery: A narrative review
Authors: Müller Dolores T , Ahn Juliane , Brunner Stefanie , Poggemeier Julia , Storms Christian , Reisewitz Alissa , Schmidt Thomas , Bruns Christiane J , Fuchs Hans F 
Published: August 2023

Abstract
Although often forgotten in everyday routine and underestimated, especially in a surgical work environment, ergonomics are essential for endurance, efficiency, and a long and healthy work life. According to current studies, the rate of musculoskeletal disorders among minimally invasive surgeons ranges between 23% and 80%, which is lower compared with open surgery (66%–94%), but nevertheless shows the everyday relevance of this topic. An efficient and ergonomic design of the operating room has been widely discussed and guidelines have been imposed to create the optimal workspace. Furthermore, with the implementation of technical advancements and the introduction of robotic operating techniques, ergonomics have become an essential differentiating factor between systems. Surgical ergonomics are not universal but differ between open, laparoscopic, and robotic surgery. With the introduction of new robotic systems, many ergonomic challenges faced in open and laparoscopic surgeries have been overcome, whereas new challenges have been created. Nevertheless, ergonomics in surgery will need to be addressed and taken seriously, as a healthy workspace has gained more importance than ever.
The first robotic STORRM: A case report
Authors: Hakmi Hazim , Pacheco Tulio B S , Halpern David K 
Published: August 2023

Abstract
Parastomal hernias present a continued challenge to the general surgeon. There are a myriad of techniques available, with hernia recurrence rates varying between 10 to greater than 50%. Mesh reinforcement and underlay or sublay placement are associated with lower hernia recurrence rates. Many patients with parastomal hernia have associated comorbidities which increase their risk for perioperative wound complications. Robotic and minimally invasive techniques offer decreased rate of wound complications, but can be challenging to perform if the stoma needs to be relocated. For patients with complex parastomal hernias requiring abdominal wall reconstruction with transversus abdominis release and retromuscular mesh placement, it can be difficult to align the layers of the abdominal wall and create an aperture in the mesh to allow for a straight passage of the conduit and prevent subsequent angulation of the bowel. Stapled Transabdominal Ostomy Reinforcement with retromuscular mesh, or STORRM technique, has been previously described elsewhere as a technique whereby a circular EEA (End-to-End Anastomoses) stapler is used to create a straight tunnel through the mesh and abdominal wall layers, standardize sizing, fixate the mesh, and substitute traditional cruciate incisions with a stapled reinforcement of the aperture in the mesh/tissues.
A Retrospective Study on Clinical Experience with Tofacitinib in the Treatment of Rheumatoid Arthritis at a Tertiary Care Center
Authors: Kumar Ashok , Rudrakar Rahul , Gupta Kushagra 
Published: August 2023

Abstract

Introduction:
Tofacitinib is the first oral Janus kinase (JAK) inhibitor approved for the treatment of rheumatoid arthritis (RA). Since the expiry of its patent, the drug has become affordable to patients in India. The present study describes our experience with tofacitinib in patients with RA.

Objective:
To retrospectively study the 6-month outcome of patients with RA treated with tofacitinib.

Methods:
We retrieved the records of all consecutive patients with RA who were commenced on tofacitinib in the rheumatology clinic of our tertiary care hospital from December 2020 to December 2021. The drug was prescribed as per recommended indications at a dose of 5 mg twice daily. Age, sex, duration of disease, and prior treatment received were noted. Baseline and 6-month data on the tender joint count, swollen joint count, patient global assessment, and physician global assessment were obtained from the records. Similarly, baseline and 6-month laboratory parameters (CBC, Erythrocyte sedimentation rate, C-reactive protein, LFT, and KFT) were also retrieved. Disease activity was assessed using SDAI at baseline and after 6 months. Adverse effects documented in the records were carefully noted.

Results:
Seventy-five patients had been commenced on tofacitinib between December 2020 and December 2021. Five patients were lost to follow-up. Twelve patients had stopped the drug after 2–3 months because of inefficacy while 7 had stopped the drug because of adverse effects. Thus, 51 patients (out of 75) had taken tofacitinib for 6 months or more. Of these, 39 achieved EULAR good response (low-disease activity-23, remission-16) and 12 achieved EULAR moderate response. Adverse effects occurred in 27 (36%) patients and included weight gain (8%), cytopenia (6.6%), folliculitis (4%), and alopecia (4%). Others included anxiety, dyspepsia, constipation, chest pain, dyslipidemia, herpes zoster, hypertension, oral thrush, sensory neuropathy, somnolence, and urinary tract infection.

Conclusion:
Tofacitinib treatment resulted in remission in 16/75 (21%) and LDA in 23/75 (31%) in RA patients who were inadequate responders to conventional synthetic disease-modifying antirheumatic drugs/biological drugs. Adverse effects occurred in 36%.
Review Findings of Drug-induced Sleep Endoscopy (DISE) in Children with Obstructive Sleep Apnea (OSA)
Authors: Yeung Gerry Man-Fung , Leung Shuk-Yu , Kwok Ka-Li 
Published: August 2023

Background:
Drug-induced sleep endoscopy (DISE) is an objective assessment and diagnostic procedure of the upper airway obstruction (UAO) under sedation. Findings of DISE in Hong Kong pediatric group patients with obstructive sleep apnea (OSA) are limited.

Materials and Methods:
This is a single-center retrospective chart review study on DISE findings in pediatric patients with OSA documented by polysomnography (PSG). We used the DISE scoring system proposed by Chan 2014, Fishman 2013 together as our internal practice. A standard sedation protocol was conducted. Endoscopic findings were recorded and evaluated the level of obstruction, severity, and correlation with PSG parameters.

Results:
A total of 124 patients who underwent DISE were reviewed in our study. Multiple levels of obstruction had been observed in all patients. Forty-five (36.6%) patients suffered from severe obstruction in more than one level. Tongue base was the most common level being severely obstructed. DISE total score is positively correlated with obstructive apnea-hypopnea index (oAHI, r = 0.35, P = <0.001), negatively correlated with oxygen nadir (SpO2 nadir, r = –0.32, P = <0.001), and positively correlated with desaturation index (DI, r = 0.34, P < 0.001). In the subgroup analysis of the post-adenotonsillectomy (AT) group, scores in nostrils, tongue base, and supraglottic showed significantly increased. None of the subjects had complications from sedation or the endoscopy procedure.

Conclusion:
In our study, DISE was shown to be a safe, feasible, and informative assessment tool for pediatric OSA patients. In particular, multiple levels of obstruction were common in children and we observed a significant correlation between the severity of UAO measured by DISE in children with OSA and PSG parameters. Changes in UAO sites were observed when preoperative patients underwent surgical treatment.
Eficacia y seguridad del apremilast en pacientes con psoriasis moderada-severa
Authors: Giustozzi María Inés , Cura María Julia , Ko Ery Ayelén , Hernández Bárbara Agustina , Galimberti María Laura , Mazzuoccolo Luis Daniel 
Published: August 2023

Antecedentes: el apremilast es un inhibidor oral de la fosfodiesterasa 4, aprobado en nuestro país desde 2017 para el tratamiento de la psoriasis en placas moderada-severa y artritis psoriásica. Los datos sobre su eficacia y tolerabilidad en el mundo real son limitados.
Objetivos: evaluar la eficacia mediante la respuesta PASI 75 en la semana 16 y la seguridad en el mundo real del apremilast en un hospital de tercer nivel de argentina.
Diseño: prospectivamente se incluyeron todos los pacientes atendidos en la Sección de Psoriasis del Hospital Italiano de Buenos Aires, a los que se les indicó apremilast entre el 1 de junio de 2019 y el 30 de junio de 2022.
Materiales y métodos: los datos se obtuvieron de la historia clínica electrónica y se incorporaron en una base de-identificada diseñada a los fines de este trabajo, con acceso restringido a los investigadores.
Resultados: se incluyeron 19 pacientes con psoriasis en placas. Seis presentaban enfermedad leve y 12 moderada-severa. 5/18 pacientes alcanzaron el objetivo primario (respuesta PASI 75). Debieron suspender el tratamiento 11/19 debido a efectos adversos o fallas en el mismo.
Conclusiones: en nuestro estudio la eficacia de apremilast en contexto de vida real fue inferior a la comunicada en los estudios pivotales.