bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures
Authors: Matsubara Masaaki , Bolton Evan E. , Aoki-Kinoshita Kiyoko F. , Yamada Issaku 
Published: August 2024

Abstract
Integration of glycan-related databases between different research fields is essential in glycoscience. It requires knowledge across the breadth of science because most glycans exist as glycoconjugates. On the other hand, especially between chemistry and biology, glycan data has not been easy to integrate due to the huge variety of glycan structure representations. We have developed WURCS (Web 3.0 Unique Representation of Carbohydrate Structures) as a notation for representing all glycan structures uniquely for the purpose of integrating data across scientific data resources. While the integration of glycan data in the field of biology has been greatly advanced, in the field of chemistry, progress has been hampered due to the lack of appropriate rules to extract sugars from chemical structures. Thus, we developed a unique algorithm to determine the range of structures allowed to be considered as sugars from the structural formulae of compounds, and we developed software to extract sugars in WURCS format according to this algorithm. In this manuscript, we show that our algorithm can extract sugars from glycoconjugate molecules represented at the molecular level and can distinguish them from other biomolecules, such as amino acids, nucleic acids, and lipids. Available as software, MolWURCS is freely available and downloadable (https://gitlab.com/glycoinfo/molwurcs).

Graphical Abstract
Growth rates of five coral species across a strong environmental gradient in the Colombian Caribbean
Authors: Bravo Matteo , Schoepf Verena 
Published: August 2024

AbstractCoral calcification is critical for reef growth and highly dependent on environmental conditions. Yet, little is known about how corals calcify under sub-optimal conditions (e.g., turbid waters, high nutrients, sedimentation) or coral growth in understudied regions such as the Colombian Caribbean. We therefore assessed the calcification and linear extension rates of five coral species across an inshore-to-offshore gradient in the Colombian Caribbean. A suite of environmental variables (temperature, light intensity, visibility, pH, nutrients) measured during the rainy season (May – November 2022) demonstrated more sub-optimal conditions inshore compared to offshore. Across all species, calcification rates were 59% and 37% lower inshore compared to the offshore and midshore sites, respectively. Across all sites, massive corals calcified up to 92% more than branching species but were more susceptible to heat stress and sub-optimal inshore conditions. However, branching species had reduced survival due to extreme climatic events (i.e., bleaching, hurricanes). A comparison with published rates for the wider Caribbean revealed that massive species in the Colombian Caribbean grow up to 11 times more than those in the wider Caribbean while branching species generally have similar growth rates, but this finding may have been influenced by fragment size and/or heat stress. Our findings indicate that present-day environmental conditions, coupled with more frequent extreme climatic events, will favor massive over branching species in midshore areas of the Colombian Caribbean. This suggests a possible shift towards faster calcifying massive species in future coral communities, possibly exacerbating the ongoing regional decline in branching species over the last decades.
A behavioral syndrome of competitiveness in a non-social rodent
Authors: Erixon Filippa , Eccard Jana A. , Huneke Rika , Dammhahn Melanie 
Published: August 2024

AbstractAnimals compete for limited resources such as food, mating partners, and territory. The outcome of this intraspecific competition should be determined by individual variation in behavioral traits, such as aggressiveness and dominance status. Consistent among-individual differences in behavior likely contribute to competitiveness and predispose individuals to acquire specific dominance ranks during parts of their adult life. Nevertheless, how dominance rank is correlated with animal personality traits remains largely unclear. In a first step towards better understanding these functional links, we studied trait integration into behavioral syndromes, using 26 captive male bank voles (Myodes glareolus). We repeatedly assessed boldness in an emergence test, exploration in an open-field test, aggressiveness in staged dyadic encounters, and the among-individual correlations between these behaviors. We further related these personality traits to dominance rank, from quantifying urine marking value (UMV), as marking in bank voles is related to dominance rank. We found repeatable variations in boldness, exploration, aggressiveness, and UMV, which were correlated at the among-individual level. Aggressiveness tended to be negatively correlated with body condition, a proxy for fitness. Thus, key personality traits and social rank are functionally integrated into a behavioral syndrome of intraspecific competitiveness. By joining social and non-social aspects of personality, our findings contribute to the ecological validation of personality traits and suggest how they contribute to higher-order component traits, such as dominance which directly affect fitness components.
Sea ice as habitat for microalgae, bacteria, virus, fungi, meio- and macrofauna: A review of an extreme environment
Authors: Lund-Hansen Lars Chresten , Gradinger Rolf , Hassett Brandon , Jayasinghe Sahan , Kennedy Fraser , Martin Andrew , McMinn Andrew , Søgaard Dorte H. , Sorrell Brian K. 
Published: August 2024

AbstractThe novel concept of the review is a focus on the organisms living in the sea ice and what mechanisms they have developed for their existence. The review describes the physical environment of the sea ice and the microorganisms living there as microalgae, bacteria, virus, fungi, meio- and macrofauna where they inhabit the brine channels and exposed to low temperatures as down to −25 °C and high salinities—up to 300. Nutrients, O2, CO2, pH, light, and UV are also identified as stressors regarding the metabolism of the microorganisms. It is argued that sea ice must be recognized as an extreme environment as based on records of very high or very low concentrations or intensities of the stressors that living organisms in the ice are exposed to and able to endure. Each taxonomic group of organisms in the sea ice are dealt with in detail in terms of the explicit stressors the group is exposed to, and specifically what known mechanisms that the organisms have amended to secure existence and life. These mechanisms are known for some group of organisms as autotrophs, bacteria, meio- and macrofauna but less so for virus and fungi. The review concludes that sea ice is an extreme environment where the stressors vary significantly in both space and time, both in consort and solitary, classifying organisms living there as polyextremophiles and extremophiles. The review relates further to extraterrestrial moons covered with sea ice and these habitats and points toward sea ice on Earth for prospective studies until further technological advances.
External validation of the MAGNIFI-CD index in patients with complex perianal fistulising Crohn’s disease
Authors: Beek Kim J. , Mulders Lieven G. M. , van Rijn Kyra L. , Horsthuis Karin , Tielbeek Jeroen A. W. , Buskens Christianne J. , D’Haens Geert R. , Gecse Krisztina B. , Stoker Jaap 
Published: August 2024

Abstract

Background
There is an increasing need for objective treatment monitoring in perianal fistulising Crohn’s disease (pfCD). Therefore, the magnetic resonance novel index for fistula imaging in CD (MAGNIFI-CD) index has been designed and internally validated on the ADMIRE-CD trial cohort. The aim of this study was to externally validate the MAGNIFI-CD index to monitor response to medical and surgical treatment regimens in pfCD.

Methods
A retrospective longitudinal cohort was established of consecutive patients with complex pfCD treated with surgical and/or medical therapy and a baseline and follow-up MRI between January 2007 and May 2021. The MAGNIFI-CD index was scored by two independent, abdominal radiologists blinded for time points and clinical outcomes. Responsiveness, reliability, and test accuracy regarding clinically important improvement were assessed. Cut-offs for response and remission were selected classified on fistula drainage assessment and physician global assessment.

Results
A total of 65 patients (51% female, median age 32 years) were included. A clinically relevant responsiveness of the MAGNIFI-CD was shown, with a significant decrease in clinical remitters and responders with a median MAGNIFI-CD of 18.0 [7.5–20.0] to 9.0 [0.8–16.0] (p < 0.001) and non-significant change in non-responders with a median MAGNIFI-CD of 20.0 [12.0–23.0] to 18.0 [13.0–21.0] (p = 0.22). There was an ‘almost perfect’ interobserver agreement (ICC = 0.87; 95% CI 0.80–0.92) for the MAGNIFI-CD index. An optimal cut-off value was defined as a decrease of 2 points for clinical response, and a MAGNIFI-CD ≤ 6 for remission at follow-up MRI.

Conclusion
The MAGNIFI-CD index is a responsive and reliable MRI scoring instrument for treatment monitoring in perianal fistulising Crohn’s disease.

Clinical relevance statement
The MAGNIFI-CD index is a well-structured, responsive scoring instrument to assess fistula severity and activity that allows quantitative detection of changes in therapy response in patients with perianal fistulising Crohn’s disease, thereby facilitating endpoints in clinical trials.

Key Points

Well-defined cut-offs for response and remission are needed for objective treatment monitoring of perianal fistulising Crohn’s disease (pfCD).

Cut-off values for remission and for response at 6 months follow-up were defined. Interobserver agreement was good.

The MAGNIFI-CD index is responsive and reliable for treatment monitoring and is suitable for use in clinical trials.

Graphical Abstract
Assessing GPT-4 multimodal performance in radiological image analysis
Authors: Brin Dana , Sorin Vera , Barash Yiftach , Konen Eli , Glicksberg Benjamin S. , Nadkarni Girish N. , Klang Eyal 
Published: August 2024

Abstract
Objectives
This study aims to assess the performance of a multimodal artificial intelligence (AI) model capable of analyzing both images and textual data (GPT-4V), in interpreting radiological images. It focuses on a range of modalities, anatomical regions, and pathologies to explore the potential of zero-shot generative AI in enhancing diagnostic processes in radiology.

Methods
We analyzed 230 anonymized emergency room diagnostic images, consecutively collected over 1 week, using GPT-4V. Modalities included ultrasound (US), computerized tomography (CT), and X-ray images. The interpretations provided by GPT-4V were then compared with those of senior radiologists. This comparison aimed to evaluate the accuracy of GPT-4V in recognizing the imaging modality, anatomical region, and pathology present in the images.

Results
GPT-4V identified the imaging modality correctly in 100% of cases (221/221), the anatomical region in 87.1% (189/217), and the pathology in 35.2% (76/216).
However, the model’s performance varied significantly across different modalities, with anatomical region identification accuracy ranging from 60.9% (39/64) in US images to 97% (98/101) and 100% (52/52) in CT and X-ray images (p < 0.001).
Similarly, pathology identification ranged from 9.1% (6/66) in US images to 36.4% (36/99) in CT and 66.7% (34/51) in X-ray images (p < 0.001).
These variations indicate inconsistencies in GPT-4V’s ability to interpret radiological images accurately.

Conclusion
While the integration of AI in radiology, exemplified by multimodal GPT-4, offers promising avenues for diagnostic enhancement, the current capabilities of GPT-4V are not yet reliable for interpreting radiological images. This study underscores the necessity for ongoing development to achieve dependable performance in radiology diagnostics.

Clinical relevance statement
Although GPT-4V shows promise in radiological image interpretation, its high diagnostic hallucination rate (> 40%) indicates it cannot be trusted for clinical use as a standalone tool. Improvements are necessary to enhance its reliability and ensure patient safety.

Key Points

GPT-4V’s capability in analyzing images offers new clinical possibilities in radiology.

GPT-4V excels in identifying imaging modalities but demonstrates inconsistent anatomy and pathology detection.

Ongoing AI advancements are necessary to enhance diagnostic reliability in radiological applications.
Sex estimation from skull measurements of a contemporary Japanese population using three-dimensional computed tomography images
Authors: Hoshioka Yumi , Torimitsu Suguru , Makino Yohsuke , Yajima Daisuke , Chiba Fumiko , Yamaguchi Rutsuko , Inokuchi Go , Motomura Ayumi , Tsuneya Shigeki , Iwase Hirotaro 
Published: August 2024

Abstract
In this study, we assessed the sexual dimorphism of the contemporary Japanese skull and established sex discriminant function equations based on cranial measurements using three-dimensional (3D) computed tomography (CT) images. The CT images of 263 corpses (142 males, 121 females) that underwent postmortem CT scanning and subsequent forensic autopsy were evaluated. Twenty-one cranial measurements were obtained from 3D CT reconstructed images, which extracted only bone data. We performed descriptive statistics and discriminant function analyses for the measurements. Nineteen measurements were significantly larger in males, suggesting sexual dimorphism of the Japanese skulls. Univariate discriminant function analyses using these measurements showed a sex classification accuracy of 57.8–88.2%, and bizygomatic breadth provided the highest correct prediction rate. Multivariate discriminant function analyses offered the most accurate model using seven variables with an estimation rate of 93.9%. Our results suggest that cranial measurements based on 3D CT images may help in the sex estimation of unidentified bodies in a contemporary Japanese population.
Analysis of Patients’ Dietary Status/Restrictions Following Instrumental Swallow Evaluations in Skilled Nursing Facilities
Authors: Hopkins-Rossabi Theresa , Lenze Amy , Lindler Sarah Carter , Hardy Catherine , Temple Sarah Labruce 
Published: August 2024

AbstractMany residents in Skilled Nursing Facilities (SNFs) present with dysphagia and receive altered diets or liquids to minimize the risk of complications. Limited access to timely instrumental evaluations of swallow may impede the best management of these dysphagic residents. De-identified FEES reports completed by a mobile FEES company during a single month, January 2019, were reviewed. Descriptive statistics were used to summarize the pre-study diet/liquid levels and the post-study diet/liquid recommendations. FEES reports (n = 952) were reviewed. Before the FEES evaluation, 209 residents were receiving only non-oral nutrition. After the FEES evaluation, 76% of these residents were recommended to receive oral nutrition. Before the FEES evaluation, 442 (46%) residents were receiving thickened liquids, after the FEES evaluation, 244 (26%) were recommended to have a less restrictive liquid level. Before the FEES evaluation, 576 (60%) residents were receiving altered food texture, after the FEES evaluation, 413 (43%) were recommended to have a less restrictive food texture. The percentage of residents recommended to receive thin liquids increased from 32 to 68% and those recommended to receive a regular diet increased from 18 to 34%. These data indicate that access to instrumental swallow evaluations in the SNF setting generally resulted in lifting liquid and diet restrictions for many residents in the cohort reviewed and potentially improved their quality of life.
Isolated C1 arch fractures: C1-2 fusion vs. C1 osteosynthesis – surgical strategies for potentially unstable injuries
Authors: Denton Hazel , McDonnell Jake M. , Curran Jack , Wilson Kielan , Temperley Hugo , Cunniffe Gráinne , Morris Seamus , Darwish Stacey , Butler Joseph S. 
Published: August 2024

Abstract
Study Design
Narrative Review.

Objectives
The premise of this review is to provide a review of the literature pertaining to studies describing outcomes of surgical cohorts when implementing C1 osteosynthesis for arch fractures with or without transverse atlantal ligamentous (TAL) injury.

Methods
A comprehensive search strategy was implemented across several search engines to identify studies which evaluate the outcomes of C1 osteosynthesis for patients with C1 arch fractures with and without TAL injury.

Results
Ten studies were identified. Parameters reported included osteosynthesis fusion rates, deformity correction, preservation of motion segments, patient reported outcome measures and overall complications. Overall, C1 osteosynthesis showed excellent fusion rates with complications comparable to traditional techniques denoted in literature. Furthermore, the osteosynthesis technique depicted good overall deformity correction and preservation of motion segments, in addition to good patient reported outcomes.

Conclusion
It appears C1 osteosynthesis offers a safe and efficacious alternative option for the surgical treatment of C1 fractures with TAL rupture. It has the potential to reduce deformity, increase ROM, improve PROMs and has complication rates comparable with those of fusion techniques. However more robust prospective evidence is required.
Exploring the Use of Alternative Promoters for Enhanced Transgene and sgRNA Expression in Atlantic Salmon Cells
Authors: Reza Mohammad Ali Noman , Harvey Thomas Nelson , Regmi Axmee , Torgersen Jacob Seilø , Sandvik Guro Katrine 
Published: August 2024

AbstractThis study facilitates design of expression vectors and lentivirus tools for gene editing of Atlantic salmon. We have characterized widely used heterologous promoters and novel endogenous promoters in Atlantic salmon cells. We used qPCR to evaluate the activity of several U6 promoters for sgRNA expression, including human U6 (hU6), tilapia U6 (tU6), mouse U6 (mU6), zebrafish U6 (zU6), Atlantic salmon U6 (sU6), medaka U6 (medU6), and fugu U6 (fU6) promoters. We also evaluated several polymerase type II (pol II) promoters by luciferase assay. Our results showed that hU6 and tU6 promoters were the most active among all the tested U6 promoters, and heterologous promoters (CMV, hEF1α core) had higher activity compared to endogenous Atlantic salmon promoters sHSP8, sNUC3L, sEF1α. Among endogenous pol II promoters, sEF1α and sHSP8 displayed higher activity than sNUC3L, sHSP703, sHSP7C, sXRCC1L, and sETF. We observed that extending the promoter sequence to include the region up to the start codon (ATG) resulted in a significant increase in expression efficiency for sNUC3L and sEF1α. We also show that mutating the PRDM1 motif will significantly decrease the activity of the sEF1α promoter. The presence of the PRDM1 motif in sHSP8 promoter was also associated with relatively high expression compared to the promoters that naturally lacked this motif, such as sNUC3L. We speculate that this short sequence might be included in other promoters to further enhance the promoter activity, but further experiments are needed to confirm this. Our findings provide valuable insights into the activity of different promoters in Atlantic salmon cells and can be used to facilitate further transgenic studies and improve the efficiency of transgene expression in Atlantic salmon.
Newsvendor problem with discrete demand and constrained first moment under ambiguity
Authors: Cinfrignini Andrea , Petturiti Davide , Stabile Gabriele 
Published: August 2024

AbstractWe study a single period newsvendor problem under ambiguity in the presence of a discrete random demand. Ambiguity is introduced in the model by $$\epsilon $$
ϵ
-contaminating the newsvendor’s prior probability measure with respect to two suitable classes of probability measures, assuring that the lower expected demand and the upper expected demand are both equal to the prior expected demand. Assuming that the newsvendor has a pessimistic attitude towards ambiguity, we characterize the order quantity that either maximizes the lower expected profit or minimizes the upper expected loss. Since the two contamination classes are cores of two distinct belief functions, we show that the maximin and minimax problems translate in the maximization and minimization of two distinct Choquet integrals.
From mixed to hybrid facies volcanic debris avalanche at Colima Volcano: sedimentology and numerical modeling as evidence of transport and emplacement mechanisms
Authors: Roverato Matteo , Capra Lucia 
Published: August 2024

AbstractNumerous partial collapses of Colima Volcano have occurred in its history, accompanied by the emplacement of volcanic debris avalanche deposits (VDADs). The collapse that generated the Tonila VDAD (T-VDAD; ~ 1 km3; ~ 15Ka cal. BP) occurred during “wet” paleoclimatic conditions in a high humidity environment, and water within the volcanic edifice, which played a significant role in the volcano’s instability and avalanche transport. This study aims to provide new data on the processes involved in the transport and emplacement mechanisms of debris avalanches based on a detailed granulometric and microtextural characterization and numerical modeling. In general, T-VDAD exhibited massive dynamic behavior during its transport, without segregation process, although some variation of the grains-size occurs from proximal to distal reaches from the source. At microscopic level, evidence suggests particle–particle interactions of rapid, high-energy, high velocity collisional nature, promoting comminution, which increases the fines content with distance. The general high content of fine material into the T-VDAD, combined with a significant water content within the mass before the collapse, due to partial edifice saturation, may have contributed to enhance its mobility. The T-VDAD mobility is here tested with the Titan2d numerical model; results show important paleo-topography implications and that the Coulomb frictional model with basal friction angles similar to previously tested cases best fits the areal propagation of the T-VDAD, confirming that, despite the fluid content that enhanced downslope transformation, the flow still behaved as a homogeneous and incompressible continuum with energy dissipation concentrated within its base.
A Direct Approach to the Polar Representation of Plane Tensors
Authors: Picchi Scardaoni Marco 
Published: August 2024

AbstractWe show we can derive the so called polar representation of 2D symmetric second and fourth order real tensors essentially just relying on the spectral theorem for unitary tensors in the complex field. The use of a coordinate-free approach allows us to clearly and methodically detect rotation-invariant quantities and to readily (and directly) deduce the representation theorems.