bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical shear flow regulates the malignancy of colorectal cancer cells
Authors: Tseng Yu‐Ting , Tsai Ching‐Chung , Chen Ping‐Chen , Lin Bo‐Yan , Hsu Sodio C. N. , Huang Shu‐Ping , Huang Bin 
Published: May 2024

AbstractColorectal cancer (CRC) is notable for its high mortality and high metastatic characteristics. The shear force generated by bloodstream provides mechanical signals regulating multiple responses of cells, including metastatic cancer cells, dispersing in blood vessels. We, therefore, studied the effect of shear flow on circulating CRC cells in the present study. The CRC cell line SW620 was subjected to shear flow of 12.5 dynes/cm2 for 1 and 2 h separately. Resulting elevated caspase‐9 and ‐3 indicated that shear flow initiated the apoptosis of SW620. Enlarged cell size associated with a higher level of cyclin D1 was coincident with the flow cytometric results indicating that the cell cycle was arrested at the G1 phase. An elevated phosphor‐eNOSS1177 increased the production of nitric oxide and led to reactive oxygen species‐mediated oxidative stress. Shear flow also regulated epithelial–mesenchymal transition (EMT) by increasing E‐cadherin and ZO‐1 while decreasing Snail and Twist1. The migration and invasion of sheared SW620 were also substantially decreased. Further investigations showed that mitochondrial membrane potential was significantly decreased, whereas mitochondrial mass and ATP production were not changed. In addition to the shear flow of 12.5 dynes/cm2, the expressions of EMT were compared at lower (6.25 dynes/cm2) and at higher (25 dynes/cm2) shear flow. The results showed that lower shear flow increased mesenchymal characteristics and higher shear flow increased epithelial characteristics. Shear flow reduces the malignancy of CRC in their metastatic dispersal that opens up new ways to improve cancer therapies by applying a mechanical shear flow device.
The road to sustainability: Examining key drivers in open access diamond journal publishing
Authors: Yoon JungWon , Ku Halin , Chung EunKyung 
Published: May 2024

AbstractDespite the rising interest in open access (OA) diamond journals as a scholarly journal publishing model, their sustainability remains a pressing concern. Using the Open Access Diamond Journals Study (OADJS) Dataset, we examined the characteristics and factors of OA diamond journal publishing that are associated with high sustainability. From 1335 journals, 476 journals with low sustainability and 438 journals with high sustainability were selected and compared. Our analysis revealed that factors such as the region and official language of the publishing country and the discipline, ownership, and financial status of the journal were significantly associated with sustainability. Journals owned by government or national agencies, those with financial stability, and those promoting open practices like unrestricted text and data mining are more likely to be sustainable. This study also discusses the implications of these findings for the future of scholarly publishing and the open science movement. Ultimately, we emphasize the need for national and international support to enhance the sustainability of OA diamond journals and propose that a collective approach involving policymakers, funding agencies, and journal administrators is crucial for fostering a sustainable open access ecosystem.
Defining model complexity: An ecological perspective
Authors: Malmborg Charlotte A. , Willson Alyssa M. , Bradley L. M. , Beatty Meghan A. , Klinges David H. , Koren Gerbrand , Lewis Abigail S. L. , Oshinubi Kayode , Woelmer Whitney M. 
Published: May 2024

AbstractModels have become a key component of scientific hypothesis testing and climate and sustainability planning, as enabled by increased data availability and computing power. As a result, understanding how the perceived ‘complexity’ of a model corresponds to its accuracy and predictive power has become a prevalent research topic. However, a wide variety of definitions of model complexity have been proposed and used, leading to an imprecise understanding of what model complexity is and its consequences across research studies, study systems, and disciplines. Here, we propose a more explicit definition of model complexity, incorporating four facets—model class, model inputs, model parameters, and computational complexity—which are modulated by the complexity of the real‐world process being modelled. We illustrate these facets with several examples drawn from ecological literature. Overall, we argue that precise terminology and metrics of model complexity (e.g., number of parameters, number of inputs) may be necessary to characterize the emergent outcomes of complexity, including model comparison, model performance, model transferability and decision support.
In situ temperature determination using magnetic resonance spectroscopy thermometry for noninvasive postmortem examinations
Authors: Zoelch Niklaus , Heimer Jakob , Richter Henning , Luechinger Roger , Archibald Jessica , Thali Michael J. , Gascho Dominic 
Published: May 2024

AbstractMagnetic resonance spectroscopy (MRS) thermometry offers a noninvasive, localized method for estimating temperature by leveraging the temperature‐dependent chemical shift of water relative to a temperature‐stable reference metabolite under suitable calibration. Consequentially, this technique has significant potential as a tool for postmortem MR examinations in forensic medicine and pathology. In these examinations, the deceased are examined at a wide range of body temperatures, and MRS thermometry may be used for the temperature adjustment of magnetic resonance imaging (MRI) protocols or for corrections in the analysis of MRI or MRS data. However, it is not yet clear to what extent postmortem changes may influence temperature estimation with MRS thermometry. In addition, N‐acetylaspartate, which is commonly used as an in vivo reference metabolite, is known to decrease with increasing postmortem interval (PMI). This study shows that lactate, which is not only present in significant amounts postmortem but also has a temperature‐stable chemical shift, can serve as a suitable reference metabolite for postmortem MRS thermometry. Using lactate, temperature estimation in postmortem brain tissue of severed sheep heads was accurate up to 60 h after death, with a mean absolute error of less than 0.5°C. For this purpose, published calibrations intended for in vivo measurements were used. Although postmortem decomposition resulted in severe metabolic changes, no consistent deviations were observed between measurements with an MR‐compatible temperature probe and MRS thermometry with lactate as a reference metabolite. In addition, MRS thermometry was applied to 84 deceased who underwent a MR examination as part of the legal examination. MRS thermometry provided plausible results of brain temperature in comparison with rectal temperature. Even for deceased with a PMI well above 60 h, MRS thermometry still provided reliable readings. The results show a good suitability of MRS thermometry for postmortem examinations in forensic medicine.
Enhancing T1 signal of normal‐appearing white matter with divided subtracted inversion recovery: A pilot study in mild traumatic brain injury
Authors: Losa Letizia , Peruzzo Denis , Galbiati Sara , Locatelli Federica , Agarwal Nivedita 
Published: May 2024

AbstractMagnetic resonance imaging (MRI) and cognitive profiles in patients with mild traumatic brain injury (mTBI) are often discordant. Conventional MRI seldom captures the full extent of pathological changes in the normal‐appearing white matter (NAWM). The divided subtracted inversion recovery (dSIR) technique may enhance T1 differences in NAWM, making them easily visible. We aimed to implement dSIR on a clinical scanner and tested results in mTBI patients. To produce dSIR images, Inversion Recovery‐Turbo Spin Echo sequences were modified using six different inversion times (TI) on a 3‐T scanner in healthy participants and patients with mTBI. The multiple TIs determined normal white (TIshort) and gray matter (TIlong) nulling points in healthy subjects, which were used to create dSIR images. In one patient, the protocol was repeated at 3 months to identify changes after rehabilitation. Diffusion tensor imaging (DTI)‐derived mean diffusivity (MD) and fractional anisotropy (FA) maps were aligned to dSIR images to ensure that signal was not artefactual. Ten healthy participants (five females; age 24 ± 3 [95% CI: 21, 26] years) were included. TIshort and TIlong were set at 450 and 750 ms, respectively. In both patients (one male, age 17 years; one female, age 14 years), dSIR images revealed areas with increased T1 in the NAWM not visible on conventional MRI. dSIR‐based hyperintensities corresponded to elevated MD and reduced FA. Substantial changes were found at follow‐up with improvement in DTI‐based parameters. dSIR images enhance subtle changes in the NAWM of patients with mTBI by amplifying their intrinsic T1 signal.
Management of paediatric monomorphic post‐transplant lymphoproliferative disorders with low‐intensity treatment: A multicentre international experience
Authors: Guerra‐García Pilar , Bomken Simon , Ling Rebecca , Lazareva Arina , Gupte Girish , Amrolia Persis , Andrés Mara , Diez‐Sebastián Jesús , Taj Mary M. 
Published: May 2024

AbstractBackgroundMonomorphic post‐transplant lymphoproliferative disorder (mPTLD) is a major cause of morbidity/mortality following solid organ transplant (SOT), with infection, mPTLD progression and organ rejection presenting equal risks. Balancing these risks is challenging, and the intensity of therapy required by individual patients is not defined. Although an increasing body of evidence supports the use of a stepwise escalation of therapy through reduction in immunosuppression (RIS) to rituximab monotherapy and low‐dose chemo‐immunotherapy, many centres still use B‐cell non‐Hodgkin lymphoma (B‐NHL) protocols, especially when managing Burkitt/Burkitt‐like (BL) PTLD. This study sought to define outcomes for children managed in the UK or Spanish centres using low‐intensity first‐line treatments.ProcedureRetrospective data were anonymously collected on patients younger than 18 years of age, with post‐SOT mPTLD diagnosed between 2000 and 2020. Only patients given low‐intensity treatment at initial diagnosis were included.ResultsFifty‐six patients were identified. Age range was 0.9–18 years (median 10.7). Most (62.5%) had early‐onset PTLD. Haematopathological analysis showed 75% were diffuse large B‐cell like, 14.3% were BL and nine of 33 (27%) harboured a MYC‐rearrangement. Stage III–IV disease was present in 78.6%. All but one had RIS, 26 received rituximab monotherapy and 24 low‐dose chemo‐immunotherapy, mostly R‐COP. Intensified B‐NHL chemotherapy was required in 10/56 (17.9%). There were a total of 13 deaths in this cohort, three related to PTLD progression. The 1‐year overall survival (OS), event‐free survival (EFS) and progression‐free survival (PFS) were 92.8%, 78.6% and 80.2%, respectively.ConclusionsR‐COP provides an effective low‐dose chemotherapy option. Escalation to more intensive therapies in the minority of inadequately controlled patients is an effective strategy.
Insight into the relationship between interfacial structure and thermal conductivity in epoxy resin/Al2O3 composite
Authors: Qiao Jian , Lv Yang , Chen Yun , Yang Wei , Zhang Chong , Chen Xin , Wong Chunyu , Liu Qing , Lu Jibao , Zhang Tao , Zeng Xiaoliang , Sun Rong 
Published: May 2024

AbstractThe relationship between interfacial structure and thermal conductivity in epoxy resin/Al2O3 composite is important but is still elusive. Here, we illuminate this issue by investigating the role of four silane coupling agents in thermal conductivity for epoxy resin/Al2O3 composites. The results show that 3‐glycidoxypropyltrimethoxysilane (KH560) is the best silane coupling agent to modify Al2O3, resulting in the lowest viscosity and the highest thermal conductivity of the epoxy resin/Al2O3‐KH560 composite compared with alternative systems. This is attributed to the strong interfacial interaction between Al2O3‐KH560 and epoxy resin, as confirmed by the Fowkes model and broadband dielectric spectroscopy. The interfacial thermal resistance between the epoxy resin and Al2O3 is also quantitatively measured via a photothermal radiometry technique. The epoxy resin/Al2O3‐KH560 also has the lowest interfacial thermal resistance (1.50 ± 0.02 × 10−6 m2 K W−1), compared with the other three systems. This study advances the understanding of the relationship between interfacial structure and thermal conductivity in polymer composites.Highlights
The relationship between interfacial structure and thermal conductivity in epoxy resin/Al2O3 composite is understood.
The interfacial structure is characterized by broadband dielectric spectroscopy.
The interfacial thermal resistance is quantitatively measured via a photothermal radiometry technique.
Investigation on the blooming behavior of additives in nitrile butadiene rubber at elevated temperature
Authors: Wang Chuanfang , Xia Zhidong , Fu Peng 
Published: May 2024

AbstractThe degradation of rubber performance in service environments is closely associated with the blooming behavior of additives in the rubber. This study investigates surface precipitates and changes in tensile properties of nitrile butadiene rubber (NBR) after storage at 85°C in air. The morphology, elemental composition, phase composition, and functional groups of the precipitates were analyzed by scanning electron microscopy, energy dispersion spectroscopy, X‐ray diffraction, and fourier transform infrared spectroscopy. Based on the morphology of internal rubber particles and precipitates and variations in the Zn/C mass ratio (ERZn), the reaction between zinc oxide and stearic acid in rubber under long‐term thermal environment was determined. Four stages of blooming for the mixture of zinc oxide and zinc stearate were inferred, and the impact of the blooming on the degradation of tensile properties of NBR was established. A dramatic decrease in the elongation at break (δk) of NBR was correlated with the blooming of zinc stearate and its correspondingly weakened plasticizing effect.Highlights
The core‐shell structured mixture of ZnO and Zn(St)2 bloomed onto the surface of nitrile butadiene rubber.
The ratio of mass percentages of Zn to C evaluated the blooming process of additives.
The migration and blooming process of precipitates were divided into four stages.
The decrease in elongation of the rubber was attributed to the blooming of Zn(St)2.
Feasibility study on thin‐film PV laminates for road integration
Authors: Colberts Fallon , Kingma Aldo , Gómez Nicolás Héctor Carreño , Roosen Dorrit , Ahmad Serdar , Vroon Zeger 
Published: May 2024

AbstractIntegration of photovoltaics (PV) into the built environment (BIPV) and infrastructure (IIPV) is required to increase the installed capacity of PV worldwide, while still leaving sufficient area for other land uses. Although BIPV applications have proven to play a significant role in the energy transition, road integrated IIPV concepts are less developed and bring challenges in mechanical and electrical stability and safety that still need to be addressed. In this work, the feasibility of integrating thin‐film CIGS (Copper Indium Gallium Selenide) modules into road tiles is investigated. PV road stacks were produced by gluing CIGS laminates onto concrete tiles and covering them with epoxy and glass granulates to form impact‐ and anti‐skid layers. IV (current–voltage) characteristics show that, respectively, a thin and thick epoxy layer results in 2% and 6.6% relative loss in power conversion efficiency. Although a thin protective layer would be beneficial to the power conversion efficiency of road modules, raveling tests show increased risk for electrical failure when a thin top layer is used. Pull‐off tests showed that the weakest adhesive strength (0.8 N/mm2) is between the thin‐film laminate and concrete, offering sufficient adhesive strength to at least withstand light traffic loading. Raveling and wheel tracking tests show no mass loss and only minor deformation of the stack, respectively, indicating no real risk of raveling or rutting. Thermal cycling and damp heat exposure of the PV road tiles show that yellowing of the top layers can significantly reduce performance over longer periods of outdoor operation. Damp heat exposure after mechanical loading shows no indication of moisture ingress on any of the tested configurations, suggesting the proposed CIGS laminate stack is able to withstand light traffic loading. From the measurement results, it can be concluded that thin‐film CIGS modules are mechanically and electrically suitable for road integration. Power conversion efficiencies over 12% can be attained with this technology, indicating its potential for renewable energy generation in road infrastructure. Performance stability can especially benefit from alternative top layer materials that maintain high transparency over long lifetimes. Additionally, pilot tests are required to demonstrate the potential of the technology in a controlled outdoor environment.
Insights on the G protein‐coupled receptor helix 8 solution structure and orientation using a neurotensin receptor 1 peptide
Authors: Bower James B. , Robson Scott A. , Ziarek Joshua J. 
Published: May 2024

AbstractG‐protein coupled receptors (GPCRs) are the largest class of membrane proteins encoded in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C‐terminal tail (Ctail). Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the Ctail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and Ctail (H8–Ctail) to investigate its structural stability, conformational dynamics, and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2‐diheptanoyl‐sn‐glycero‐3‐phosphocholine is a potent stabilizer of H8 structure, whereas the commonly‐used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix – even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376–R392 from chemical shift perturbations, changes in resonance intensity, and chemical‐shift‐derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement NMR. Taken together, our studies reveal the H8–Ctail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.
Mutual annotation‐based prediction of protein domain functions with Domain2GO
Authors: Ulusoy Erva , Doğan Tunca 
Published: May 2024

AbstractIdentifying unknown functional properties of proteins is essential for understanding their roles in both health and disease states. The domain composition of a protein can reveal critical information in this context, as domains are structural and functional units that dictate how the protein should act at the molecular level. The expensive and time‐consuming nature of wet‐lab experimental approaches prompted researchers to develop computational strategies for predicting the functions of proteins. In this study, we proposed a new method called Domain2GO that infers associations between protein domains and function‐defining gene ontology (GO) terms, thus redefining the problem as domain function prediction. Domain2GO uses documented protein‐level GO annotations together with proteins' domain annotations. Co‐annotation patterns of domains and GO terms in the same proteins are examined using statistical resampling to obtain reliable associations. As a use‐case study, we evaluated the biological relevance of examples selected from the Domain2GO‐generated domain‐GO term mappings via literature review. Then, we applied Domain2GO to predict unknown protein functions by propagating domain‐associated GO terms to proteins annotated with these domains. For function prediction performance evaluation and comparison against other methods, we employed Critical Assessment of Function Annotation 3 (CAFA3) challenge datasets. The results demonstrated the high potential of Domain2GO, particularly for predicting molecular function and biological process terms, along with advantages such as producing interpretable results and having an exceptionally low computational cost. The approach presented here can be extended to other ontologies and biological entities to investigate unknown relationships in complex and large‐scale biological data. The source code, datasets, results, and user instructions for Domain2GO are available at https://github.com/HUBioDataLab/Domain2GO. Additionally, we offer a user‐friendly online tool at https://huggingface.co/spaces/HUBioDataLab/Domain2GO, which simplifies the prediction of functions of previously unannotated proteins solely using amino acid sequences.
Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate
Authors: Latifah Emi , Ivanesthi Indira Rizqita , Tseng Yi‐Kuan , Pan Hung‐Chuan , Wang Chien‐Chia 
Published: May 2024

AbstractProlyl‐tRNA synthetase (ProRS), belonging to the family of aminoacyl‐tRNA synthetases responsible for pairing specific amino acids with their respective tRNAs, is categorized into two distinct types: the eukaryote/archaeon‐like type (E‐type) and the prokaryote‐like type (P‐type). Notably, these types are specific to their corresponding cognate tRNAs. In an intriguing paradox, Thermus thermophilus ProRS (TtProRS) aligns with the E‐type ProRS but selectively charges the P‐type tRNAPro, featuring the bacterium‐specific acceptor‐stem elements G72 and A73. This investigation reveals TtProRS's notable resilience to the inhibitor halofuginone, a synthetic derivative of febrifugine emulating Pro‐A76, resembling the characteristics of the P‐type ProRS. Furthermore, akin to the P‐type ProRS, TtProRS identifies its cognate tRNA through recognition of the acceptor‐stem elements G72/A73, along with the anticodon elements G35/G36. However, in contrast to the P‐type ProRS, which relies on a strictly conserved R residue within the bacterium‐like motif 2 loop for recognizing G72/A73, TtProRS achieves this through a non‐conserved sequence, RTR, within the otherwise non‐interacting eukaryote‐like motif 2 loop. This investigation sheds light on the adaptive capacity of a typically conserved housekeeping enzyme to accommodate a novel substrate.