bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycoscience data content in the NCBI Glycans and PubChem
Authors: Kim Sunghwan , Zhang Jian , Cheng Tiejun , Li Qingliang , Bolton Evan E. 
Published: August 2024

Abstract
Studying﻿ glycans and their functions in the body aids in the understanding of disease mechanisms and developing new treatments. This necessitates resources that provide comprehensive glycan data integrated with relevant information from other scientific fields such as genomics, genetics, proteomics, metabolomics, and chemistry. The present paper describes two resources at the U.S. National Center for Biotechnology Information (NCBI), the NCBI Glycans and PubChem, which provide glycan-related information useful for the glycoscience research community. The NCBI Glycans (https://www.ncbi.nlm.nih.gov/glycans/) is a dedicated website for glycobiology data content at NCBI and provides quick access to glycan-related information scattered across multiple NCBI databases as well as other information resources external to NCBI. Importantly, the NCBI Glycans hosts the official web page for the symbol nomenclature for glycans (SNFG), which is the standard graphical representation of glycan structures recommended for scientific publication. On the other hand, PubChem (https://pubchem.ncbi.nlm.nih.gov) is a research-focused, large-scale public chemical database, containing a substantial number of glycan-containing records and is integrated with important glycoscience resources like GlyTouCan, GlyCosmos, and GlyGen. PubChem organizes glycan-related information within multiple data collections (i.e., Substance, Compound, Protein, Gene, Pathway, and Taxonomy) and provides various tools and services that allow users to access them both interactively through a web browser and programmatically through a REST-ful interface, including PUG-View. The NCBI Glycans and PubChem highlight glycan-related data and improve their accessibility, helping scientists exploit these data in their research.

Graphical Abstract
Fabrication of acoustically and physically validated artificial stones to natural kidney stones under shock waves and laser lithotripsy
Authors: Park Hyeji , So Sang Won , Castillo Christine Joy G. , Alharthi Majed M. , Zogan Mohammad Mesadef A. , Cho Sung Yong 
Published: August 2024

AbstractTo present an efficient method for fabricating artificial kidney stones with acoustic and physical properties to assess their fragmentation efficiency under shock waves and laser lithotripsy for very hard stones. The mixture ratio of super-hard plaster and water was adjusted to produce artificial kidney stones for comparison with > 95% human genuine calcium oxalate monohydrate (COM) and uric acid (UA) stones. Acoustic and physical properties, such as wave speed, stone hardness, density, compressive strength, and stone-free rates under shock-wave and laser lithotripsy, were assessed. The longitudinal wave speed of artificial stones prepared at a plaster-to-water ratio of 15:3 closely matched that of COM stones. Similarly, the transverse wave speed of artificial stones prepared at a plaster-to-water ratio of 15:3 to 15:5 aligned with that of COM stones. Stone fragmentation using shock-wave of artificial stones with mixed ratios ranging from 15:3 to 15:5 resembled that of COM stones. The Vickers hardness was similar to that of artificial stones produced with a mixing ratio of 15:3, similar to that of COM stones, while that of artificial stones produced with a mixing ratio of 15:5 was similar to that of UA stones. Density-wise, artificial stones with mixing ratios of 15:4 and 15:5 resembled COM stones. Compressive strength test results did not confirm the similarity between natural and artificial stones. The stone fragmentation using laser showed that stones produced with higher moisture content at a mixing ratio of 15:6 were similar to COM stones. This novel method for fabricating artificial kidney stones could be used to provide reliable materials for lithotripsy research.
Varying concentrations of tyrosine kinase inhibitors in chronic myeloid leukemia patients following bariatric surgery: a case series
Authors: Lau Cedric , van Kesteren Charlotte , Cao Yong Xin , Smeenk Robert M. , Daenen Laura G.M. , Janssen Jeroen J.W.M. , Westerweel Peter E. 
Published: August 2024

AbstractBariatric surgery is increasingly performed to treat severe obesity. As a result of anatomical and physiological changes in the gastrointestinal tract, the pharmacokinetics (PK) of oral drugs can be altered, affecting their efficacy and safety. This includes the class of tyrosine kinase inhibitors (TKIs) which are used to treat chronic myeloid leukemia (CML). This case series describes the clinical course of four CML cases with a history of bariatric surgery. The patients used various TKIs (nilotinib, dasatinib, bosutinib, ponatinib, and imatinib) for which 15 drug levels were measured. The measured TKI concentrations were in part subtherapeutic, and highly variable when compared to mean levels measured in the general population. Multiple drug levels were measured in these patients, as the clinicians were aware of the possible impact of bariatric surgery. The drug levels were used as additional input for clinical decision-making. All four patients required TKI switches and/or dose modifications to achieve an effective and tolerable treatment. Eventually, adequate clinical and molecular remissions were achieved in all cases. In summary, TKI concentrations of patients undergoing bariatric surgery may be subtherapeutic. Moreover, there is substantial interindividual and intraindividual variation, which may be explained by the complex interference of bariatric surgery and associated weight loss. For clinical practice, therapeutic drug monitoring is advised in patients with a history of bariatric surgery in case of suboptimal response or loss of response.
From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae)
Authors: Nocella Elisa , Fassio Giulia , Zuccon Dario , Puillandre Nicolas , Modica Maria Vittoria , Oliverio Marco 
Published: August 2024

AbstractIn this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily’s ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.
Biobank for craniosynostosis and faciocraniosynostosis, rare pediatric congenital craniofacial disorders: a study protocol
Authors: De Martino Lucia , Mirabelli Peppino , Quaglietta Lucia , Ferrara Ursula Pia , Picariello Stefania , De Gennaro Domenico Vincenzo , Aiello Marco , Smaldone Giovanni , Aliberti Ferdinando , Spennato Pietro , De Brasi Daniele , Covelli Eugenio , Cinalli Giuseppe 
Published: August 2024

Abstract
Purpose
Craniosynostosis (CRS) is a rare congenital cranial malformation in which 1 or more cranial or facial sutures are fused in utero or rapidly fused in early infancy. The cranial sutures separate the skull bone plates and enable rapid growth of the skull in the first 2 years of life, in which growth is largely dictated by growth of the brain. CRS is a rare disease that occurs in 1 in 2100 to 1 in 2500 births and may be either nonsyndromic (also referred to as isolated) or syndromic. In syndromic CRS, other birth defects are present next to the CRS. The distinction between nonsyndromic and syndromic manifestations is made on the basis of dysmorphologic evaluation and genetic evaluation. Owing to advances in genetic diagnostics, nonsyndromic patients are increasingly recognized as syndromic patients. CRS treatment is almost entirely surgical and is sometimes paired with postoperative helmet therapy for maintenance. Corrective procedures are complex, long, and associated with the risk of numerous complications, including heavy blood loss and its sequelae. Although surgery may restore a normal appearance, even in nonsyndromic patients, patients may experience persistent deficits in intellectual ability and cognitive function. The European Commission (EC) has prioritized rare diseases in recent horizon European research programs; indeed, collections or even individual samples may be extremely valuable for research.

Methods and results
Here, we present a study protocol in which the combined expertise of clinicians and researchers will be exploited to generate a biobank dedicated to CRS. The generation of the CRS biobank presented in this study will include the collection of different types of biological materials as well as advanced radiological images available to the scientific community.

Conclusion
The activation of a CRS biobank will provide an opportunity to improve translational research on CRS and to share its benefits with the scientific community and patients and their families.
iRhom2 deficiency reduces sepsis-induced mortality associated with the attenuation of lung macrophages in mice
Authors: Kim Jihye , Kim Jee Hyun , Kim Younghoon , Lee Jooyoung , Lee Hyun Jung , Koh Seong-Joon , Im Jong Pil , Kim Joo Sung 
Published: August 2024

AbstractSepsis has a high mortality rate and leads to multi-organ failure, including lung injury. Inactive rhomboid protease family protein (iRhom2) has been identified as accountable for the release of TNF-α, a crucial mediator in the development of sepsis. This study aimed to evaluate the role of iRhom2 in sepsis and sepsis-induced acute lung injury (ALI). TNF-α and IL-6 secretion in vitro by peritoneal macrophages from wild-type (WT) and iRhom2 knoukout (KO) mice was assessed by enzyme-linked immunosorbent assay. Cecal ligation and puncture (CLP)-induced murine sepsis model was used for in vivo experiments. To evaluate the role of iRhom2 deficiency on survival during sepsis, both WT and iRhom2 KO mice were monitored for 8 consecutive days following the CLP. For histologic and biochemical examination, the mice were killed 18 h after CLP. iRhom2 deficiency improved the survival of mice after CLP. iRhom2 deficiency decreased CD68+ macrophage infiltration in lung tissues. Multiplex immunohistochemistry revealed that the proportion of Ki-67+ CD68+ macrophages was significantly lower in iRhom2 KO mice than that in WT mice after CLP. Moreover, CLP-induced release of TNF-α and IL-6 in the serum were significantly inhibited by iRhom2 deficiency. iRhom2 deficiency reduced NF-kB p65 and IκBα phosphorylation after CLP. iRhom2 deficiency reduces sepsis-related mortality associated with attenuated macrophage infiltration and proliferation in early lung injury. iRhom2 may play a pivotal role in the pathogenesis of sepsis and early stage of sepsis-induced ALI. Thus, iRhom2 may be a potential therapeutic target for the management of sepsis and sepsis-induced ALI.
The HUNT lung-SNP model: genetic variants plus clinical variables improve lung cancer risk assessment over clinical models
Authors: Nguyen Olav Toai Duc , Fotopoulos Ioannis , Nøst Therese Haugdahl , Markaki Maria , Lagani Vincenzo , Tsamardinos Ioannis , Røe Oluf Dimitri 
Published: August 2024

Abstract
Purpose
The HUNT Lung Cancer Model (HUNT LCM) predicts individualized 6-year lung cancer (LC) risk among individuals who ever smoked cigarettes with high precision based on eight clinical variables. Can the performance be improved by adding genetic information?

Methods
A polygenic model was developed in the prospective Norwegian HUNT2 study with clinical and genotype data of individuals who ever smoked cigarettes (n = 30749, median follow up 15.26 years) where 160 LC were diagnosed within six years. It included the variables of the original HUNT LCM plus 22 single nucleotide polymorphisms (SNPs) highly associated with LC. External validation was performed in the prospective Norwegian Tromsø Study (n = 2663).

Results
The novel HUNT Lung-SNP model significantly improved risk ranking of individuals over the HUNT LCM in both HUNT2 (p < 0.001) and Tromsø (p < 0.05) cohorts. Furthermore, detection rate (number of participants selected to detect one LC case) was significantly better for the HUNT Lung-SNP vs. HUNT LCM in both cohorts (42 vs. 48, p = 0.003 and 11 vs. 14, p = 0.025, respectively) as well as versus the NLST, NELSON and 2021 USPSTF criteria. The area under the receiver operating characteristic curve (AUC) was higher for the HUNT Lung-SNP in both cohorts, but significant only in HUNT2 (AUC 0.875 vs. 0.844, p < 0.001). However, the integrated discrimination improvement index (IDI) indicates a significant improvement of LC risk stratification by the HUNT Lung-SNP in both cohorts (IDI 0.019, p < 0.001 (HUNT2) and 0.013, p < 0.001 (Tromsø)).

Conclusion
The HUNT Lung-SNP model could have a clinical impact on LC screening and has the potential to replace the HUNT LCM as well as the NLST, NELSON and 2021 USPSTF criteria in a screening setting. However, the model should be further validated in other populations and evaluated in a prospective trial setting.
Improving light availability and creating high-frequency light–dark cycles in raceway ponds through vortex-induced vibrations for microalgae cultivation: a fluid dynamic study
Authors: Akca Mehmet Sadik , Kinaci Omer Kemal , Inanc Bulent 
Published: August 2024

AbstractLimited light availability due to insufficient vertical mixing strongly reduces the applicability of raceway ponds (RWPs). To overcome this and create light–dark (L/D) cycles for enhanced biomass production through improved vertical mixing, vortex-induced vibration (VIV) system was implemented by the authors in a previous study to an existing pilot-scale RWP. In this study, experimental characterization of fluid dynamics for VIV-implemented RWP is carried out. Particle image velocimetry (PIV) technique is applied to visualize the flow. The extents of the vertical mixing due to VIV and the characteristics of L/D cycles were examined by tracking selected particles. Pond depth was hypothetically divided into three zones, namely dark, light Iimited and light saturated for detailed analysis of cell trajectories. It has been observed that VIV cylinder oscillation can efficiently facilitate the transfer of cells from light-limited to light-saturated zones. Among the cells that were tracked, 44% initially at dark zone entered the light-limited zone and 100% of initially at light-limited zone entered the light-saturated zone. 33% of all tracked cells experienced high-frequency L/D cycles with an average frequency of 35.69 s−1 and 0.49 light fraction. The impact of VIV was not discernible in the deeper sections of the pond, due to constrained oscillation amplitudes. Our findings suggest that the approximately 20% increase in biomass production reported in our previous study can be attributed to the synergistic effects of enhanced L/D cycle frequencies and improved light availability resulting from the transfer of cells from dark to light-limited zones. To further enhance the effectiveness of VIV, design improvements were developed. It was concluded that light availability could be significantly improved with the presented method for more effective use of RWPs.
The association of hyponatremia and early postoperative complications in aseptic revision total shoulder arthroplasty
Authors: Liu Steven H. , Bramian Allen , Loyst Rachel A. , Kashanchi Kevin , Wang Edward D. 
Published: August 2024

Abstract
Purpose
This study investigates the association between preoperative serum sodium levels and 30-day postoperative complications following aseptic revision total shoulder arthroplasty (TSA).

Methods
The American College of Surgeons National Surgical Quality Improvement Program database was queried for all patients who underwent aseptic revision TSA from 2015 to 2022. The study population was divided into two groups based on preoperative serum sodium levels: eunatremia (135–144 mEq/L) and hyponatremia (< 135 mEq/L). Logistic regression analysis was performed to investigate the relationship between hyponatremia and early postoperative complications.

Results
Compared to eunatremia, hyponatremia was independently associated with a significantly greater likelihood of experiencing any complication (odds ratio [OR] 1.65, 95% confidence interval [CI] 1.14–2.40; P = .008), blood transfusions (OR 2.45, 95% CI 1.24–4.83; P = .010), unplanned reoperation (OR 2.27, 95% CI 1.07–4.79; P = .032), and length of stay > 2 days (OR 1.63, 95% CI 1.09–2.45; P = .017).

Conclusion
Hyponatremia was associated with a greater rate of early postoperative complications following noninfectious revision TSA. This study sheds light on the role of preoperative hyponatremia as a risk factor for postoperative complications and may help surgeons better select surgical candidates and improve surgical outcomes in the setting of revision TSA.
Humangenetische Diagnostik bei onkologischen Erkrankungen
Authors: Elbracht Miriam , Auber Bernd , Kurth Ingo , Stenzinger Albrecht , Schaaf Christian P. , Schroeder Christopher ,   die DNPM AG Diagnostik
Published: August 2024

ZusammenfassungBei etwa 10 % der Krebserkrankungen kann eine angeborene pathogene Veränderung in einem Gen identifiziert werden, welches mit einem Tumorrisikosyndrom (TRS) assoziiert ist. Personen, die eine solche Veränderung tragen, haben je nach betroffenem Gen und Art der Veränderung ein erhöhtes Lebenszeitrisiko für das Auftreten von Tumorerkrankungen und möglicherweise weiteren assoziierten Symptomen. Die Identifikation von TRS ist somit hinsichtlich Früherkennung, Vorsorge und zunehmend auch für die onkologische Therapie von entscheidender Bedeutung. Hierbei ist aufgrund der Erblichkeit der TRS nicht nur die erkrankte Person zu berücksichtigen, sondern auch weitere Risikopersonen aus der Familie, denen eine Anlageträgerdiagnostik und ein zunehmend spezialisiertes klinisches Management angeboten wird. Humangenetische Ambulanzen sind hierbei die zentrale Anlaufstelle für Patientinnen und Patienten und deren Angehörige, wenn es um die Frage der Erblichkeit geht. Durch die vermehrt molekulare Ausrichtung onkologischer Diagnostik und Therapie wird der Verdacht auf ein TRS immer häufiger auch im Rahmen einer molekulargenetischen und molekularpathologischen Befundung gestellt. Die interdisziplinäre Festlegung des weiteren klinischen Managements gemeinsam durch alle beteiligten Fachgruppen, z. B. im Rahmen von spezialisierten Boards, ist hierbei entscheidend, um die Herausforderungen der Präzisionsonkologie mit Bewertung genetischer Varianten, deren Konsequenzen und deren Nutzbarkeit für die Akut- und präemptive Therapie erfolgreich umzusetzen. Die humangenetische Expertise ist hierbei Baustein für die Befundung und Bewertung konstitutioneller genetischer Varianten und trägt somit zum interdisziplinären Management bei.
A TCP-based covert channel with integrity check and retransmission
Authors: Bistarelli Stefano , Imparato Andrea , Santini Francesco 
Published: August 2024

AbstractWe propose a covert channel and its implementation in Windows OS. This storage channel uses the Initial Sequence Number of TCP to hide four characters of text and the identification field to “sign” the message and thus understand if it has been altered during the transmission. The secret is sent in the first SYN segment to open a connection, and an ACK-RST response acknowledges the receipt. Designed error-correction codes make the protocol more robust and able to handle (IP) packet drops and transmission errors. In this paper, we provide a detailed discussion of the implementation and an evaluation of the stealthiness of the proposed channel: we inspect the generated traffic with two IDSs and RITA, a tool performing statistical analysis to detect malware beaconing.
Respiratory motion-corrected T1 mapping of the abdomen
Authors: Zhang Jana Huiyue , Neumann Tom , Schaeffter Tobias , Kolbitsch Christoph , Kerkering Kirsten Miriam 
Published: August 2024

Abstract
Objective
The purpose of this study was to investigate an approach for motion-corrected T1 mapping of the abdomen that allows for free breathing data acquisition with 100% scan efficiency.

Materials and methods
Data were acquired using a continuous golden radial trajectory and multiple inversion pulses. For the correction of respiratory motion, motion estimation based on a surrogate was performed from the same data used for T1 mapping. Image-based self-navigation allowed for binning and reconstruction of respiratory-resolved images, which were used for the estimation of respiratory motion fields. Finally, motion-corrected T1 maps were calculated from the data applying the estimated motion fields. The method was evaluated in five healthy volunteers. For the assessment of the image-based navigator, we compared it to a simultaneously acquired ultrawide band radar signal. Motion-corrected T1 maps were evaluated qualitatively and quantitatively for different scan times.

Results
For all volunteers, the motion-corrected T1 maps showed fewer motion artifacts in the liver as well as sharper kidney structures and blood vessels compared to uncorrected T1 maps. Moreover, the relative error to the reference breathhold T1 maps could be reduced from up to 25% for the uncorrected T1 maps to below 10% for the motion-corrected maps for the average value of a region of interest, while the scan time could be reduced to 6-8 s.

Discussion
The proposed approach allows for respiratory motion-corrected T1 mapping in the abdomen and ensures accurate T1 maps without the need for any breathholds.