bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical report and genetic analysis of rare premature infant nephronophthisis caused by biallelic TTC21B variants
Authors: Li Yingying , Dai Liying , Xu Hong , Huang Jin , Zhang Jinqiu , Mei Zhenzhu , Zhang Rui 
Published: March 2024

AbstractBackgroundNephronophthisis (NPHP) is a genetically heterogeneous disease that can lead to end‐stage renal disease (ESRD) in children. The TTC21B variant is associated with NPHP12 and mainly characterized by cystic kidney disease, skeletal malformation, liver fibrosis, and retinopathy. Affected patients range from children to adults. Some patients experience ESRD in infancy or early childhood, but clinical reports on neonatal patients are rare. We report a case of NPHP12 in a premature infant and analyze its genetic etiology.MethodsTrio‐whole exome sequencing analysis was performed on the patient and her parents; bioinformatics software was used to predict and analyze the hazards of the variants. Sanger sequencing was performed to verify variants. We calculated the free energy between mutant IFT139 and the IFT121‐IFT122‐IFT43 complex structure using molecular dynamics (MD). Finally, the clinical and genetic characteristics of patients with hotspot variant Cys518Arg were reviewed.ResultsGenetic analysis revealed compound‐heterozyous TTC21B variants in the patient, c.497delA (p.Lys166fs*36) and c.1552T>C (p.Cys518Arg). Her father and mother had heterozygous c.497delA (p.Lys166fs*36) and heterozygous c.1552T>C (p.Cys518Arg), respectively. Cys518Arg represents a hotspot variant, and the MD calculation results show that this can reduce the structural stability of the IFT121‐IFT122‐IFT139‐IFT43 complex structure. A literature review showed that Cys518Arg might lead to the early occurrence of ESRD.ConclusionsCompound‐heterozygous TTC21B variants underlie the phenotype in this patient. Thus, Cys518Arg may be a hotspot variant in the Chinese population. Genetic testing should be recommended for NPHP in neonates and early infants.
A theoretical framework to investigate the effect of high permittivity materials in MRI using anatomy‐mimicking cylinders
Authors: Miranda Vincenzo , Ruello Giuseppe , Lattanzi Riccardo 
Published: March 2024

AbstractPurposeRecent numerical and empirical results proved that high permittivity materials (HPM) used in pads placed near the subject or directly integrated with coils can increase the SNR and reduce the specific absorption rate (SAR) in MRI. In this paper, we propose an analytical investigation of the effect on the magnetic field distribution of a layer of HPM surrounding an anatomy‐mimicking cylindrical sample.MethodsThe study is based on a reformulation of the Mie scattering for cylindrical geometry, following an approach recently introduced for spherical samples. The total field in each medium is decomposed in terms of inward and outward electromagnetic waves, and the fields are expressed as series of cylindrical harmonics, whose coefficients can be interpreted as classical reflection and transmission coefficients.ResultsOur new formulation allows a quantitative evaluation of the effect of the HPM layer for varying permittivity and thickness, and it provides an intuitive understanding of such effect in terms of propagation and scattering of the RF field.ConclusionWe show how HPM can filter out the modes that only contribute to the noise or RF power deposition, resulting in higher SNR or lower SAR, respectively. Our proposed framework provides physical insight on how to properly design HPM for MRI applications.
Submillimeter balanced SSFP BOLD–functional MRI accelerated with 3D stack‐of‐spirals at 9.4 T
Authors: Iyyappan Valsala Praveen , Veldmann Marten , Bosch Dario , Scheffler Klaus , Ehses Philipp 
Published: March 2024

AbstractPurposeThis work aims to improve the speed of balanced SSFP (bSSFP) acquisition with segmented 3D stack‐of‐spirals for functional brain studies at ultrahigh field.MethodsFunctional experiments were performed with an accelerated 3D stack‐of‐spirals sequence with water excitation for fat suppression. The resulting data were reconstructed using an iterative algorithm with corrections for system imperfections such as trajectory deviations and B0 inhomogeneity. In the first set of experiments, we evaluated the signal change and stability with respect to echo and TR for a full‐field checkerboard stimulus. To demonstrate the high spatio‐temporal resolution of the developed method, the results of three optimized protocols at submillimeter resolution (0.6‐mm isotropic and 0.8‐mm isotropic) and at 1.2 mm isotropic resolution for whole‐brain coverage were shown.ResultsWater excitation and the model‐based iterative reconstruction improved image quality. The BOLD‐related signal changes increased with longer TE and longer TR. We observed an increase in thermal noise performance at lower TE and higher TR. However, signal stability deteriorates at higher TE and TR. Therefore, optimized protocols used shorter TE and moderately long TR to maximize the sensitivity and speed. Reproducible activations were detected along the gray‐matter gyri in the submillimeter protocols with a median signal change of approximately 4% across subjects.ConclusionsThree‐dimensional stack‐of‐spirals enables passband balanced SSFP functional imaging at a much higher spatial and temporal scale, compared with conventional spoiled gradient‐echo train sequences.
Prospectively accelerated dynamic speech magnetic resonance imaging at 3 T using a self‐navigated spiral‐based manifold regularized scheme
Authors: Rusho Rushdi Zahid , Ahmed Abdul Haseeb , Kruger Stanley , Alam Wahidul , Meyer David , Howard David , Story Brad , Jacob Mathews , Lingala Sajan Goud 
Published: March 2024

AbstractThis work develops and evaluates a self‐navigated variable density spiral (VDS)‐based manifold regularization scheme to prospectively improve dynamic speech magnetic resonance imaging (MRI) at 3 T. Short readout duration spirals (1.3‐ms long) were used to minimize sensitivity to off‐resonance. A custom 16‐channel speech coil was used for improved parallel imaging of vocal tract structures. The manifold model leveraged similarities between frames sharing similar vocal tract postures without explicit motion binning. The self‐navigating capability of VDS was leveraged to learn the Laplacian structure of the manifold. Reconstruction was posed as a sensitivity‐encoding–based nonlocal soft‐weighted temporal regularization scheme. Our approach was compared with view‐sharing, low‐rank, temporal finite difference, extra dimension‐based sparsity reconstruction constraints. Undersampling experiments were conducted on five volunteers performing repetitive and arbitrary speaking tasks at different speaking rates. Quantitative evaluation in terms of mean square error over moving edges was performed in a retrospective undersampling experiment on one volunteer. For prospective undersampling, blinded image quality evaluation in the categories of alias artifacts, spatial blurring, and temporal blurring was performed by three experts in voice research. Region of interest analysis at articulator boundaries was performed in both experiments to assess articulatory motion. Improved performance with manifold reconstruction constraints was observed over existing constraints. With prospective undersampling, a spatial resolution of 2.4 × 2.4 mm2/pixel and a temporal resolution of 17.4 ms/frame for single‐slice imaging, and 52.2 ms/frame for concurrent three‐slice imaging, were achieved. We demonstrated implicit motion binning by analyzing the mechanics of the Laplacian matrix. Manifold regularization demonstrated superior image quality scores in reducing spatial and temporal blurring compared with all other reconstruction constraints. While it exhibited faint (nonsignificant) alias artifacts that were similar to temporal finite difference, it provided statistically significant improvements compared with the other constraints. In conclusion, the self‐navigated manifold regularized scheme enabled robust high spatiotemporal resolution dynamic speech MRI at 3 T.
The publicness of private foundations: Online accountability and Internet presence
Authors: Park Gowun , Suárez David 
Published: March 2024

AbstractPrivate foundations face persistent charges of plutocracy and secrecy, undermining their legitimacy as philanthropic organizations that contribute to the public good, yet they can respond to the criticism proactively through online accountability and Internet presence. To what extent do foundations use web‐based tools to demonstrate public accountability, how are these tools used for this purpose, and what explains foundation participation in this form of self‐regulation? We argue that managerialism, organizational fields, and stakeholder relationships will matter for online accountability and Internet presence because they capture or reflect the “publicness” of private foundations. We test our conceptual framework on two online tools—websites and social media—using a dataset of private foundations located in Washington state. We find that few private foundations have a website or a social media account, and our analysis of those tools suggests that substantive accountability is not a high priority for those that do. Our empirical models nevertheless reveal that several components of our conceptual framework are associated with multiple forms of disclosure (operational, financial, and performance) and dialogic communication, a contribution to research on nonprofit accountability that also advances the literature on the organizational behavior of foundations.
Metabolic effects of an essential amino acid supplement in adolescents with PCOS and obesity
Authors: Fordham Talyia M. , Morelli Nazeen S. , Garcia‐Reyes Yesenia , Ware Meredith A. , Rahat Haseeb , Sundararajan Divya , Fuller Kelly N. Z. , Severn Cameron , Pyle Laura , Malloy Craig R. , Jin Eunsook S. , Parks Elizabeth J. , Wolfe Robert R. , Cree Melanie G. 
Published: March 2024

AbstractObjectivePolycystic ovary syndrome (PCOS) is characterized by hyperandrogenism, insulin resistance, and hepatic steatosis (HS). Because dietary essential amino acid (EAA) supplementation has been shown to decrease HS in various populations, this study's objective was to determine whether supplementation would decrease HS in PCOS.MethodsA randomized, double‐blind, crossover, placebo‐controlled trial was conducted in 21 adolescents with PCOS (BMI 37.3 ± 6.5 kg/m2, age 15.6 ± 1.3 years). Liver fat, very low‐density lipoprotein (VLDL) lipogenesis, and triacylglycerol (TG) metabolism were measured following each 28‐day phase of placebo or EAA.ResultsCompared to placebo, EAA was associated with no difference in body weight (p = 0.673). Two markers of liver health improved: HS was lower (−0.8% absolute, −7.5% relative reduction, p = 0.013), as was plasma aspartate aminotransferase (AST) (−8%, p = 0.004). Plasma TG (−9%, p = 0.015) and VLDL‐TG (−21%, p = 0.031) were reduced as well. VLDL‐TG palmitate derived from lipogenesis was not different between the phases, nor was insulin sensitivity (p > 0.400 for both). Surprisingly, during the EAA phase, participants reported consuming fewer carbohydrates (p = 0.038) and total sugars (p = 0.046).ConclusionsSimilar to studies in older adults, short‐term EAA supplementation in adolescents resulted in significantly lower liver fat, AST, and plasma lipids and thus may prove to be an effective treatment in this population. Additional research is needed to elucidate the mechanisms for these effects.
Plasma proteomic profile of abdominal obesity in older adults
Authors: Sathyan Sanish , Milman Sofiya , Ayers Emmeline , Gao Tina , Verghese Joe , Barzilai Nir 
Published: March 2024

AbstractObjectiveThis study examines the plasma proteomic profile of abdominal obesity in older adults.MethodsThe association of abdominal obesity (waist circumference [WC]) with 4265 plasma proteins identified using the SomaScan Assay was examined in 969 Ashkenazi Jewish participants (LonGenity cohort), aged 65 years and older (mean [SD] age 75.7 [6.7] years, 55.4% women), using regression models. Pathway analysis, as well as weighted correlation network analysis, was performed. WC was determined from the proteome using elastic net regression.ResultsA total of 480 out of 4265 proteins were associated with WC in the linear regression model. Leptin (β [SE] = 12.363 [0.490]), inhibin β C chain (INHBC; β [SE] = 24.324 [1.448]), insulin‐like growth factor‐binding protein 2 (IGFBP‐2; β [SE] = −12.782 [0.841]), heparan‐sulfate 6‐O‐sulfotransferase 3 (H6ST3; β [SE] = −39.995 [2.729]), and matrix‐remodeling‐associated protein 8 (MXRA8; β [SE] = −27.101 [1.850]) were the top proteins associated with WC. Cell adhesion, extracellular matrix remodeling, and IGF transport pathways were the top enriched pathways associated with WC. WC signature determined from plasma proteins was highly correlated with measured WC (r = 0.80) and was associated with various metabolic and physical traits.ConclusionsThe study unveiled a multifaceted plasma proteomic profile of abdominal obesity in older adults, offering insights into its wide‐ranging impact on the proteome. It also elucidated novel proteins, clusters of correlated proteins, and pathways that are intricately associated with abdominal obesity.
First‐Principles Studies on Transition Metal Doped Mo2B2 as Anode Material for Li‐Ion Batteries
Authors: Shi Jianjian , Yu Chaojie , Kang Wei , Xiao Xiuchan , Sun Xiaoli 
Published: March 2024

AbstractNew two‐dimensional (2D) transition‐metal borides have attracted considerable interest in research on electrode materials for Li‐ion batteries (LIBs) owing to their promising properties. In this study, 2D molybdenum boride (Mo2B2) with and without transition metal (TM, TM=Mn, Fe, Co, Ni, Ru, and Pt) atom doping was investigated. Our results indicated that all TM‐doped Mo2B2 samples exhibited excellent electronic conductivity, similar to the intrinsic 2D Mo2B2 metal behavior, which is highly beneficial for application in LIBs. Moreover, we found that the diffusion energy barriers of Li along paths 1 and 2 for all TM‐doped Mo2B2 samples are smaller than 0.30 and 0.24 eV of the pristine Mo2B2. In particular, for 2D Co‐doped Mo2B2, the diffusion energy barriers of Li along paths 1 and 2 are reduced to 0.14 and 0.11 eV, respectively, making them the lowest Li diffusion barriers in both paths 1 and 2. This indicates that TM doping can improve the electrochemical performance of 2D Mo2B2 and that Co‐doped Mo2B2 is a promising electrode material for LIBs. Our work not only identifies electrode materials with promising electrochemical performance but also provides guidance for the design of high‐performance electrode materials for LIBs.
Superior heat‐resistant polylactide/poly(butylene succinate) blend fibers via in‐situ reactive compatibilization
Authors: Huang Wei , Zhang Guiju , Zhou Yuxiang , Joziasse Cornelis A. P. , Wang Ruyin , du Sart Gerrit Gobius , Chen Peng 
Published: March 2024

AbstractBlending poly(butylene succinate) (PBS) with polylactide (PLLA) has proven effective in improving heat resistance of PLLA fibers. Unfortunately, it remains challenging to maintain good spinnability for PLLA/PBS blends with high content of PBS with which further improved heat resistance could be anticipated. In this study, reactive melt‐extrusion was devised to in‐situ generate PLLA‐PBS copolymers by introducing zinc acetate as a transesterification catalyst into PLLA/PBS blends. The compatibility between the PLLA and PBS phases was greatly improved by the formation of PLLA‐PBS copolymers, resulting in excellent melt‐spinnability even for the PLLA/PBS blends with high PBS content up to 20 wt%. In addition, an increase in crystallinity of PLLA was achieved in PLLA/PBS blend fibers, thanks to the enhanced compatibility. More importantly, the presence of PBS nuclei retarded the molecular orientation of the amorphous PLLA phase, consistent with the effective results from the relaxation heat‐setting treatment. These led to an exceptionally improved heat resistance of the PLLA/PBS blend fibers. As an encouraging result, the boiling water shrinkage was significantly reduced from ca. 20% for neat PLLA fibers to 3.7% for the PLLA/PBS blend fibers with 20 wt% PBS content. These findings may open up a facile and effective route to develop PLLA/PBS blend fibers showing sound spinnability, greatly improved heat resistance and softness.
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry
Authors: Ross Dylan H. , Bhotika Harsh , Zheng Xueyun , Smith Richard D. , Burnum‐Johnson Kristin E. , Bilbao Aivett 
Published: March 2024

AbstractIon mobility spectrometry‐mass spectrometry (IMS‐MS or IM‐MS) is a powerful analytical technique that combines the gas‐phase separation capabilities of IM with the identification and quantification capabilities of MS. IM‐MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS‐based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM‐MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open‐source software tools specifically tailored for the analysis and interpretation of data derived from IM‐MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
Biodegradable zwitterionic polymers as PEG alternatives for drug delivery
Authors: Zhang Ziwen , Sun Haotian , Giannino Justin , Wu Yun , Cheng Chong 
Published: March 2024

AbstractPoly(ethylene glycol) (PEG) is a highly biocompatible and water‐soluble polymer that is widely utilized for biomedical applications. Unfortunately, the immunogenicity and antigenicity of PEG severely restrict the biomedical efficacy of pegylated therapeutics. As emerging PEG alternatives, biodegradable zwitterionic polymers (ZPs) have attracted significant interest in recent years. Biodegradable ZPs generally are not only water‐soluble and immunologically inert, but also possess a range of favorable biomedically relevant properties, without causing long‐term side effects for in vivo biomedical applications. This review presents a systematic overview of recent studies on biodegradable ZPs. Their structural designs and synthetic strategies by integrating biodegradable base polymers with zwitterions are addressed. Their applications in the delivery of small molecule drugs (as mono‐drugs or multi‐drugs) and proteins are highlighted.
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge
Authors: Yu Chenglei , Lin Xiangtian , Cheng Yuxuan , Xu Jiahong , Wang Hao , Yan Yuyao , Huang Yanting , Liu Lanxuan , Zhao Wei , Zhao Qin , Wang John , Zhang Lei 
Published: March 2024

AbstractAntibodies represent a crucial class of complex protein therapeutics and are essential in the treatment of a wide range of human diseases. Traditional antibody discovery methods, such as hybridoma and phage display technologies, suffer from limitations including inefficiency and a restricted exploration of the immense space of potential antibodies. To overcome these limitations, we propose a novel method for generating antibody sequences using deep learning algorithms called AbDPP (target‐oriented antibody design with pretraining and prior biological knowledge). AbDPP integrates a pretrained model for antibodies with biological region information, enabling the effective use of vast antibody sequence data and intricate biological system understanding to generate sequences. To target specific antigens, AbDPP incorporates an antibody property evaluation model, which is further optimized based on evaluation results to generate more focused sequences. The efficacy of AbDPP was assessed through multiple experiments, evaluating its ability to generate amino acids, improve neutralization and binding, maintain sequence consistency, and improve sequence diversity. Results demonstrated that AbDPP outperformed other methods in terms of the performance and quality of generated sequences, showcasing its potential to enhance antibody design and screening efficiency. In summary, this study contributes to the field by offering an innovative deep learning‐based method for antibody generation, addressing some limitations of traditional approaches, and underscoring the importance of integrating a specific antibody pretrained model and the biological properties of antibodies in generating novel sequences. The code and documentation underlying this article are freely available at https://github.com/zlfyj/AbDPP.
Pharmacokinetics and exposure–safety relationship of ciprofol for sedation in mechanically ventilated patients in the intensive care unit
Authors: Liu Lu , Wang Kun , Sun Zhongyi , Yan Pangke , Hu Mengyue , Liu Xiao , Chen Meixia , Wu Nan , Xiang Xiaoqiang 
Published: March 2024

AbstractCiprofol (HSK3486) is a newly developed, highly selective γ‐aminobutyric acid‐A (GABAA) receptor potentiator that is recently approved for a new indication of sedation for patients in the intensive care unit (ICU) in China. This analysis aimed to characterize the population pharmacokinetics (PopPKs) of ciprofol and evaluate the relationship of exposure with hypotension in mechanically ventilated patients in the ICU. A total of 462 subjects with 3918 concentration measurements from two clinical trials of mechanically ventilated patients in the ICU, four clinical trials of elective surgical patients, and six clinical trials of healthy subjects were used in the PopPK analysis. Exposure–safety relationship for hypotension was evaluated based on the data gathered from 112 subjects in two clinical trials of mechanically ventilated patients in the ICU. Ciprofol pharmacokinetics (PKs) was adequately described by a three‐compartment linear disposition model with first‐order elimination. Body weight, age, sex, blood sampling site (vein vs. arterial), study design (long‐term infusion vs. short‐term infusion), and patient population (ICU vs. non‐ICU) were identified as statistically significant covariates on the PKs of ciprofol. Within the exposure range of the mechanically ventilated ICU patient population, no meaningful association was observed between ciprofol exposure and the incidence of hypotension. These results support the dosing regimen currently used in mechanically ventilated patients in the ICU.