bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three dimensional (bio)printing of blood vessels: from vascularized tissues to functional arteries
Authors: Makode Shubham , Maurya Satyajit , Niknam Seyed A , Mollocana-Lara Evelyn , Jaberi Kiana , Faramarzi Negar , Tamayol Ali , Mortazavi Mehdi 
Published: January 2024

Abstract
Tissue engineering has emerged as a strategy for producing functional tissues and organs to treat diseases and injuries. Many chronic conditions directly or indirectly affect normal blood vessel functioning, necessary for material exchange and transport through the body and within tissue-engineered constructs. The interest in vascular tissue engineering is due to two reasons: (1) functional grafts can be used to replace diseased blood vessels, and (2) engineering effective vasculature within other engineered tissues enables connection with the host’s circulatory system, supporting their survival. Among various practices, (bio)printing has emerged as a powerful tool to engineer biomimetic constructs. This has been made possible with precise control of cell deposition and matrix environment along with the advancements in biomaterials. (Bio)printing has been used for both engineering stand-alone vascular grafts as well as vasculature within engineered tissues for regenerative applications. In this review article, we discuss various conditions associated with blood vessels, the need for artificial blood vessels, the anatomy and physiology of different blood vessels, available 3D (bio)printing techniques to fabricate tissue-engineered vascular grafts and vasculature in scaffolds, and the comparison among the different techniques. We conclude our review with a brief discussion about future opportunities in the area of blood vessel tissue engineering.
Hydrodynamic shear stress’ impact on mammalian cell properties and its applications in 3D bioprinting
Authors: Zhang Yani , O’Mahony Aidan , He Yong , Barber Tracie 
Published: January 2024

Abstract
As an effective cell assembly method, three-dimensional bioprinting has been widely used in building organ models and tissue repair over the past decade. However, different shear stresses induced throughout the entire printing process can cause complex impacts on cell integrity, including reducing cell viability, provoking morphological changes and altering cellular functionalities. The potential effects that may occur and the conditions under which these effects manifest are not clearly understood. Here, we review systematically how different mammalian cells respond under shear stress. We enumerate available experimental apparatus, and we categorise properties that can be affected under disparate stress patterns. We also summarise cell damaging mathematical models as a predicting reference for the design of bioprinting systems. We concluded that it is essential to quantify specific cell resistance to shear stress for the optimisation of bioprinting systems. Besides, as substantial positive impacts, including inducing cell alignment and promoting cell motility, can be generated by shear stress, we suggest that we find the proper range of shear stress and actively utilise its positive influences in the development of future systems.
A microscale 3D organ on a chip for recapitulating reciprocal neuroendocrine crosstalk between the hypothalamus and the pituitary gland
Authors: Park Se-Ra , Kook Myung Geun , Kim Soo-Rim , Lee Jin Woo , Yu Young Soo , Park Chan Hum , Lim Soyi , Oh Byung-Chul , Jung YunJae , Hong In-Sun 
Published: January 2024

Abstract
Conventional 2D or even recently developed 3D in vitro culture models for hypothalamus and pituitary gland cannot successfully recapitulate reciprocal neuroendocrine communications between these two pivotal neuroendocrine tissues known to play an essential role in controlling the body’s endocrine system, survival, and reproduction. In addition, most current vitro culture models for neuroendocrine tissues fail to properly reflect their complex multicellular structure. In this context, we developed a novel microscale chip platform, termed the ‘hypothalamic–pituitary (HP) axis-on-a-chip,’ which integrates various cellular components of the hypothalamus and pituitary gland with biomaterials such as collagen and hyaluronic acid. We used non-toxic blood coagulation factors (fibrinogen and thrombin) as natural cross-linking agents to increase the mechanical strength of biomaterials without showing residual toxicity to overcome drawbacks of conventional chemical cross-linking agents. Furthermore, we identified and verified SERPINB2 as a reliable neuroendocrine toxic marker, with its expression significantly increased in both hypothalamus and pituitary gland cells following exposure to various types of toxins. Next, we introduced SERPINB2-fluorescence reporter system into loaded hypothalamic cells and pituitary gland cells within each chamber of the HP axis on a chip, respectively. By incorporating this SERPINB2 detection system into the loaded hypothalamic and pituitary gland cells within our chip platform, Our HP axis-on-chip platform can better mimic reciprocal neuroendocrine crosstalk between the hypothalamus and the pituitary gland in the brain microenvironments with improved efficiency in evaluating neuroendocrine toxicities of certain drug candidates.
Evaluation of zirconia surfaces and shear bond strength after acid–etching with ultrasonic vibration
Authors: Zhang Xiaozhen , Nie Hepeng , Lv Jiaxin , Yuan Shanshan , Wang Juan , Cai Kunzhan , Wu Jin , Zhang Qingqing , Tang Chunbo 
Published: January 2024

Abstract
To evaluate the effect of surface reaction process after hydrofluoric (HF) acid etching using ultrasound and the shear bond strength (SBS) of resin cement to zirconia polycrystal (Y-TZP) ceramic. Y-TZP ceramic sheets were divided into rinsing group (Group P), ultrasonic cleaning group (Group C), and ultrasonic reaction + rinsing group (Group CP), and all the groups were treated for 5, 10, 20, 30, 40, 50, and 60 min, respectively. The surface morphology, elements distribution, roughness, and wettability of the ceramic sheets in each group were observed. The SBS of ceramic-resin bonding specimens was tested after immersion and after cooling-heating cycles, respectively. Octahedral and spiculate products were observed on the surface of Y-TZP that was etched with HF acid in Group P. The amount of these products increased over time. In contrast, only a few octahedral products remained on the surface of Y-TZP in Groups C and CP. Within the same reaction time, the surface reaction of the CP group was stronger than that of the other two groups, accompanied by a more uniform morphology. The shear force in Group C was the lowest, and the shear force reduction in Group CP was the least after cooling-heating cycling, with statistically significant differences (P< 0.05). After the reaction time exceeded 30 min, the shear force in each group decreased instead of increasing. Octahedral and spiculate acid etching products on the surface of HF acid-etched Y-TZP can enhance the bonding force of zirconia. Ultrasonic cleaning would drive the exfoliation of acid etching products from the sample surface, leading to the decrease of the bonding force. The acid etching with ultrasonic vibration can accelerate the HF acid etching process of Y-TZP ceramics, which is conducive to improving the bond strength to resin and durability.
Do changing circulation types raise the frequency of summertime thunderstorms and large hail in Europe?
Authors: Ghasemifard Homa , Groenemeijer Pieter , Battaglioli Francesco , Púčik Tomáš 
Published: January 2024

Abstract
We study the role of changes in circulation type frequency on the evolution of summertime thunderstorm and large hail frequency across Europe since 1950 until 2020 to find out if they are responsible for the changes that an additive regression convective hazard models model (AR-CHaMo) predicts to have happened. To define circulation types, the 500 hPa geopotential height anomaly field on each day was clustered into 14 distinct patterns using principal component analysis and k-means clustering. We show that lightning and hail occurrence, both observed and modeled by AR-CHaMo, strongly depend on the circulation type, with a higher frequency observed in poleward flow downstream of a trough and on the lee side of mountains. AR-CHaMo predicts strong increases in hail frequency across central parts of Europe to have occurred in the 1950–2020 period. During this period, changes in circulation type frequency are small and only significant for 2 of the 14 clusters. The trends in both lightning and hail frequency to be expected if they were solely determined by circulation patterns, are small, with typical values of 1%–3% per decade relative to the mean, whereas the trends expected by AR-CHaMo are on the order of 4%–10% in most areas. Across many regions, the sign of the changes does not agree in sign, in particular across European Russia where circulation types have become more favorable for lightning and hail, but a decreasing probability was modeled by AR-CHaMo. We conclude that changing circulation types are, in general, not responsible for changes in thunderstorm and hail frequency, which included the strong increase of conditions favorable for large hail in central Europe.
Products of hyperelliptic Jacobians with maximal Galois image
Authors: Garnek Jędrzej 
Published: January 2024

In this note we study the associated adelic representation of a product of hyperelliptic Jacobians. We give a simple criterion that ensures that this representation has maximal Galois image in a certain sense. As an application, we provide a method of constructing products of Jacobians with division fields as disjoint as they can be.
Long-term impact of the COVID-19 pandemic on the quality of life of people with dementia and their family carers
Authors: Read Sanna , Hicks Ben , Budden Emily , Douglass Jacob , Grahamslaw Amanda , Herrero Elena , Joseph Gregory , Kirkup Christine , Pusey Martha , Russell Alice , Sondh Harsharon , Sondh Sharon , Storey Bryony , Towson Georgia , Baxter Kate , Birks Yvonne , Brayne Carol , Colclough Carmen , Dangoor Margaret , Dixon Josie , Donaghy Paul , Gridley Kate , Harris Peter R , Hu Bo , King Derek , Knapp Martin , Miles Eleanor , Mueller Christoph , Perach Rotem , Robinson Louise , Rusted Jennifer , Thomas Alan J , Wittenberg Raphael , Banerjee Sube 
Published: January 2024

Abstract

Introduction
Few studies have longitudinally mapped quality of life (QoL) trajectories of newly diagnosed people with dementia and their carers, particularly during coronavirus disease-2019 (COVID-19).

Methods
In a UK cohort study, 261 newly diagnosed people with dementia and 206 family carers were assessed prior to the pandemic (July 2019–March 2020), followed up after the first lockdown (July–October 2020) and then again a year and 2 years later. Latent growth curve modelling examined the level and change of QoL over the four time-points using dementia-specific QoL measures (DEMQOL and C-DEMQOL).

Results
Despite variations in individual change scores, our results suggest that generally people with dementia maintained their QoL during the pandemic and experienced some increase towards the end of the period. This contrasted with carers who reported a general deterioration in their QoL over the same period. ‘Confidence in future’ and ‘Feeling supported’ were the only carer QoL subscales to show some recovery post-pandemic.

Discussion
It is positive that even during a period of global disruption, decline in QoL is not inevitable following the onset of dementia. However, it is of concern that carer QoL declined during this same period even after COVID-19 restrictions had been lifted. Carers play an invaluable role in the lives of people with dementia and wider society, and our findings suggest that, post-pandemic, they may require greater support to maintain their QoL.
Care pathways in older patients seen in a multidisciplinary same day emergency care (SDEC) unit
Authors: Elias Tania C N , Jacklin Chloe , Bowen Jordan , Lasserson Daniel S , Pendlebury Sarah T 
Published: January 2024

Abstract

Background
Same day emergency care (SDEC) services are being advocated in the UK for frail, older patients in whom hospitalisation may be associated with harm but there are few data on the ‘ambulatory pathway’. We therefore determined the patient pathways pre- and post-first assessment in a SDEC unit focussed on older people.

Methods
In consecutive patients, we prospectively recorded follow-up SDEC service reviews (face-to-face, telephone, Hospital-at-Home domiciliary visits), outpatient referrals (e.g. to specialist clinics, imaging, and community/voluntary/social services), and hospital admissions &lt;30 days. In the first 67 patients, we also recorded healthcare interactions (except GP attendances) in the 180 days pre- and post-first assessment.

Results
Among 533 patients (mean/SD age = 75.0/17.5 years, 246, 46% deemed frail) assessed in an SDEC unit, 210 were admitted within 30 days (152 immediately). In the 381(71%) remaining initially ambulatory, there were 587 SDEC follow-up reviews and 747 other outpatient referrals (mean = 3.5 per patient) with only 34 (9%) patients being discharged with no further follow-up. In the subset (n = 67), the number of ‘healthcare days’ was greater in the 180 days post- versus pre-SDEC assessment (mean/SD = 26/27 versus 13/22 days, P = 0.003) even after excluding hospital admission days, with greater healthcare days in frail versus non-frail patients.

Discussion and Conclusion
SDEC assessment in older, frail patients was associated with a 2-fold increase in frequency of healthcare interactions with complex care pathways involving multiple services. Our findings have implications for the development of admission-avoidance models including cost-effectiveness and optimal delivery of the multi-dimensional aspects of acute geriatric care in the ambulatory setting.
Minimal Detectable Change for the ImPACT Subtests at Baseline
Authors: Quigley Kristen G , Fenner Madison , Pavilionis Philip , Constantino Nora L , Moran Ryan N , Murray Nicholas G 
Published: January 2024

Abstract

Objective
To establish the minimal detectable change (MDC) of the subtests that comprise the composite scores from remotely administered Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) baselines.

Method
Remote ImPACT baseline data from 172 (male = 45, female = 127) National Collegiate Athletic Association Division I student-athletes from the 2020 and 2021 athletic preseasons were used to calculate the MDC at the 95%, 90%, and 80% confidence intervals (CIs) for all subtest scores used to generate the four core composite scores and the impulse control composite.

Results
The MDCs for the verbal memory subtests at the 95% CI were 10.31 for word memory percent correct, 4.68 for symbol match total correct hidden, and 18.25 for three letters percentage correct. Visual memory subtest MDCs were 19.03 for design memory total percent correct and 4.90 for XO total correct memory. Visual motor speed subtest MDCs were 18.89 for XO total correct interference and 5.40 for three letters average counted correctly. Reaction time (RT) MDCs were 0.12 for XO average correct, 0.95 for symbol match average correct RT, and 0.28 for color match average correct. Impulse control MDCs were 5.97 for XO total incorrect and 1.15 for color match total commissions. One-way repeated measures MANOVA, repeated measures ANOVAs, and Wilcoxon signed-ranks test all suggested no significant difference between any subtests across two remote ImPACT baselines.

Conclusions
The ImPACT subtest scores did not significantly change between athletic seasons. Our study suggests the subtests be evaluated in conjunction with the composite scores to provide additional metrics for clinical interpretation.
RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes
Authors: Hackett William Edwin , Chang Deborah , Carvalho Luis , Zaia Joseph 
Published: January 2024

Abstract

Motivation
Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically synthesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. Glycoproteins, accounting for approximately half of all proteins, require specialized proteomics data analysis methods due to micro- and macro-heterogeneities as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, a specialized toolset is needed to determine if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations.

Results
We developed an R package, Relative Assessment of m/z Identifications by Similarity (RAMZIS), that uses similarity metrics to guide researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses a permutation test to generate contextual similarity, which assesses the quality of mass spectral data and outputs a graphical demonstration of the likelihood of finding biologically significant differences in glycosylation abundance datasets. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern change. RAMZIS is validated by theoretical cases and a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using this tool, researchers will be able to rigorously define the role of glycosylation and the changes that occur during biological processes.

Availability and implementation
https://github.com/WillHackett22/RAMZIS.
DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion
Authors: Hamano Momoko , Nakamura Toru , Ito Ryoku , Shimada Yuki , Iwata Michio , Takeshita Jun-ichi , Eguchi Ryohei , Yamanishi Yoshihiro 
Published: January 2024

Abstract

Motivation
Direct reprogramming (DR) is a process that directly converts somatic cells to target cells. Although DR via small molecules is safer than using transcription factors (TFs) in terms of avoidance of tumorigenic risk, the determination of DR-inducing small molecules is challenging.

Results
Here we present a novel in silico method, DIRECTEUR, to predict small molecules that replace TFs for DR. We extracted DR-characteristic genes using transcriptome profiles of cells in which DR was induced by TFs, and performed a variant of simulated annealing to explore small molecule combinations with similar gene expression patterns with DR-inducing TFs. We applied DIRECTEUR to predicting combinations of small molecules that convert fibroblasts into neurons or cardiomyocytes, and were able to reproduce experimentally verified and functionally related molecules inducing the corresponding conversions. The proposed method is expected to be useful for practical applications in regenerative medicine.

Availability and implementation
The code and data are available at the following link: https://github.com/HamanoLaboratory/DIRECTEUR.git.
vcfpp: a C++ API for rapid processing of the variant call format
Authors: Li Zilong 
Published: January 2024

Abstract

Motivation
Given the widespread use of the variant call format (VCF/BCF) coupled with continuous surge in big data, there remains a perpetual demand for fast and flexible methods to manipulate these comprehensive formats across various programming languages.

Results
This work presents vcfpp, a C++ API of HTSlib in a single file, providing an intuitive interface to manipulate VCF/BCF files rapidly and safely, in addition to being portable. Moreover, this work introduces the vcfppR package to demonstrate the development of a high-performance R package with vcfpp, allowing for rapid and straightforward variants analyses.

Availability and implementation
vcfpp is available from https://github.com/Zilong-Li/vcfpp under MIT license. vcfppR is available from https://cran.r-project.org/web/packages/vcfppR.
Interpreting protein abundance in Saccharomyces cerevisiae through relational learning
Authors: Brunnsåker Daniel , Kronström Filip , Tiukova Ievgeniia A , King Ross D 
Published: January 2024

Abstract

Motivation
Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies.

Results
By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances.

Availability and implementation
All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
Authors: Karaoğlanoğlu Fatih , Orabi Baraa , Flannigan Ryan , Chauve Cedric , Hach Faraz 
Published: January 2024

Abstract

Motivation
Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene fusion detection). However, the lack of abundant gold-standard datasets hinders the benchmarking of such tools. Therefore, the simulation of LR sequencing is an important and practical alternative. While the existing LR simulators aim to imitate the sequencing machine noise and to target specific library protocols, they lack some important library preparation steps (e.g. PCR) and are difficult to modify to new and changing library preparation techniques (e.g. single-cell LRs).

Results
We present TKSM, a modular and scalable LR simulator, designed so that each RNA modification step is targeted explicitly by a specific module. This allows the user to assemble a simulation pipeline as a combination of TKSM modules to emulate a specific sequencing design. Additionally, the input/output of all the core modules of TKSM follows the same simple format (Molecule Description Format) allowing the user to easily extend TKSM with new modules targeting new library preparation steps.

Availability and implementation
TKSM is available as an open source software at https://github.com/vpc-ccg/tksm.