bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin accessibility and epigenetic deoxyribose nucleic acid (DNA) modifications in chronic kidney disease (CKD) osteoblasts: a study of bone and osteoblasts from pediatric patients with CKD
Authors: Martin Aline , Kawaguchi Riki , Wang Qing , Salusky Isidro B , Pereira Renata C , Wesseling-Perry Katherine 
Published: January 2024

Abstract
Maturation defects are intrinsic features of osteoblast lineage cells in CKD patients. These defects persist ex vivo, suggesting that CKD induces epigenetic changes in bone cells. To gain insights into which signaling pathways contribute to CKD-mediated, epigenetically driven, impairments in osteoblast maturation, we characterized RNA expression and DNA methylation patterns by RNA-Seq and MethylationEpic in primary osteoblasts from nine adolescent and young adult dialysis patients with end-stage kidney disease and three healthy references. ATAC-Seq was also performed on a subset of osteoblasts. Bone matrix protein expression was extracted from the iliac crest and evaluated by proteomics. Gene set enrichment analysis was used to establish signaling pathways consistently altered in chromatin accessibility, DNA methylation, and RNA expression patterns. Single genes were suppressed in primary osteoblasts using shRNA and mineralization characterized in vitro. The effect of nuclear factor of activated T cells (NFAT) signaling suppression was also assessed using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) incorporation. We found that signaling pathways critical for osteoblast differentiation were strongly downregulated in CKD osteoblasts. Gene set enrichment analysis identified highly significant methylation changes, differential chromatin accessibility, and altered RNA expression in NFAT signaling targets. NFAT inhibition reduced osteoblast proliferation. Combined analysis of osteoblast RNA expression and whole bone matrix composition identified 13 potential ligand-receptor pairs. In summary, epigenetic changes in CKD osteoblasts associate with altered expression of multiple osteoblast genes and signaling pathways. An increase in NFAT signaling may play a role in impaired CKD osteoblast maturation. Epigenetic changes also associate with an altered bone matrix, which may contribute to bone fragility. Further studies are necessary to elucidate the pathways affected by these genetic alterations since elucidating these pathways will be vital to correcting the underlying biology of bone disease in the CKD population.
Pten knockout in mouse preosteoblasts leads to changes in bone turnover and strength
Authors: Lorenz Judith , Richter Sandy , Kirstein Anna S , Kolbig Florentien , Nebe Michèle , Schulze Marco , Kiess Wieland , Spitzbarth Ingo , Klöting Nora , Le Duc Diana , Baschant Ulrike , Garten Antje 
Published: January 2024

Abstract
Bone development and remodeling are controlled by the phosphoinositide-3-kinase (Pi3k) signaling pathway. We investigated the effects of downregulation of phosphatase and tensin homolog (Pten), a negative regulator of Pi3k signaling, in a mouse model of Pten deficiency in preosteoblasts. We aimed to identify mechanisms that are involved in the regulation of bone turnover and are linked to bone disorders.
Femora, tibiae, and bone marrow stromal cells (BMSCs) isolated from mice with a conditional deletion of Pten (Pten cKO) in Osterix/Sp7-expressing osteoprogenitor cells were compared to Cre-negative controls. Bone phenotyping was performed by μCT measurements, bone histomorphometry, quantification of bone turnover markers CTX and procollagen type 1 N propeptide (P1NP), and three-point bending test. Proliferation of BMSCs was measured by counting nuclei and Ki-67–stained cells. In vitro, osteogenic differentiation capacity was determined by ALP staining, as well as by detecting gene expression of osteogenic markers.
BMSCs from Pten cKO mice were functionally different from control BMSCs. Osteogenic markers were increased in BMSCs derived from Pten cKO mice, while Pten protein expression was lower and Akt phosphorylation was increased. We detected a higher trabecular bone volume and an altered cortical bone morphology in Pten cKO bones with a progressive decrease in bone and tissue mineral density. Pten cKO bones displayed fewer osteoclasts and more osteoblasts (P = .00095) per trabecular bone surface and a higher trabecular bone formation rate. Biomechanical analysis revealed a significantly higher bone strength (P = .00012 for males) and elasticity of Pten cKO femora. On the cellular level, both proliferation and osteogenic differentiation capacity of Pten cKO BMSCs were significantly increased compared to controls.
Our findings suggest that Pten knockout in osteoprogenitor cells increases bone stability and elasticity by increasing trabecular bone mass and leads to increased proliferation and osteogenic differentiation of BMSCs.
Advanced glycation end products are not associated with bone mineral density, trabecular bone score, and bone turnover markers in adults with and without type 1 diabetes: a cross-sectional study
Authors: Coll Julie-Catherine , Turcotte Anne-Frédérique , Leslie William D , Michou Laëtitia , Weisnagel Stanley John , Mac-Way Fabrice , Albert Caroline , Berger Claudie , Morin Suzanne N , Rabasa-Lhoret Rémi , Gagnon Claudia 
Published: January 2024

Abstract
It is unclear if AGEs are involved in the bone fragility of type 1 diabetes (T1D). We evaluated whether skin AGEs by skin autofluorescence and serum AGEs (pentosidine, carboxymethyl-lysine [CML]) are independently associated with BMD by DXA (lumbar spine, hip, distal radius), trabecular bone score (TBS), serum bone turnover markers (BTMs: CTX; P1NP; osteocalcin), and sclerostin in participants with and without T1D. Linear regression models were used, with interaction terms to test effect modification by T1D status. In participants with T1D, correlations between skin and serum AGEs as well as between AGEs and 3-year HbA1C were evaluated using Spearman’s correlations. Data are mean ± SD or median (interquartile range). We included individuals who participated in a cross-sectional study and had BMD and TBS assessment (106 T1D/65 controls, 53.2% women, age 43 ± 15 yr, BMI 26.6 ± 5.5 kg/m2). Participants with T1D had diabetes for 27.6 ± 12.3 yr, a mean 3-yr HbA1C of 7.5 ± 0.9% and skin AGEs of 2.15 ± 0.54 arbitrary units. A subgroup of 65 T1D/57 controls had BTMs and sclerostin measurements, and those with T1D also had serum pentosidine (16.8[8.2–32.0] ng/mL) and CML [48.0 ± 16.8] ng/mL) measured. Femoral neck BMD, TBS, and BTMs were lower, while sclerostin levels were similar in participants with T1D vs controls. T1D status did not modify the associations between AGEs and bone outcomes. Skin AGEs were significantly associated with total hip and femoral neck BMD, TBS, BTMs, and sclerostin before, but not after, adjustment for confounders. Serum AGEs were not associated with any bone outcome. There were no significant correlations between skin and serum AGEs or between AGEs and 3-yr HbA1C. In conclusion, skin and serum AGEs are not independently associated with BMD, TBS, BTMs, and sclerostin in participants with relatively well-controlled T1D and participants without diabetes.
A study on ship hull form transformation using convolutional autoencoder
Authors: Seo Jeongbeom , Kim Dayeon , Lee Inwon 
Published: January 2024

Abstract
The optimal ship hull form in contemporary design practice primarily consists of three parts: hull form modification, performance prediction, and optimization. Hull form modification is a crucial step to affect optimization efficiency because the baseline hull form is varied to search for performance improvements. The conventional hull form modification methods mainly rely on human decisions and intervention. As a direct expression of the three-dimensional hull form, the lines are not appropriate for machine learning techniques. This is because they do not explicitly express a meaningful performance metric despite their relatively large data dimension. To solve this problem and develop a novel machine-based hull form design technique, an autoencoder, which is a dimensional reduction technique based on an artificial neural network, was created in this study. Specifically, a convolutional autoencoder was designed; firstly, a convolutional neural network (CNN) preprocessor was used to effectively train the offsets, which are the half-width coordinate values on the hull surface, to extract feature maps. Secondly, the stacked encoder compressed the feature maps into an optimal lower dimensional-latent vector. Finally, a transposed convolution layer restored the dimension of the lines. In this study, 21 250 hull forms belonging to three different ship types of containership, LNG carrier, and tanker, were used as training data. To describe the hull form in more detail, each was divided into several zones, which were then input into the CNN preprocessor separately. After the training, a low-dimensional manifold consisting of the components of the latent vector was derived to represent the distinctive hull form features of the three ship types considered. The autoencoder technique was then combined with another novel approach of the surrogate model to form an objective function neural network. Further combination with the deterministic particle swarm optimization method led to a successful hull form optimization example. In summary, the present convolutional autoencoder has demonstrated its significance within the machine learning-based design process for ship hull forms.
Exploring Racial Disparities in the 1918 Influenza Pandemic: A Case Study of Durham, North Carolina
Authors: Bryant Mallory , Baker Jeffrey 
Published: January 2024

Abstract
The paradox of excess mortality among White Americans during the 1918 influenza pandemic has long puzzled historians and scientists. Recent scholarship has suggested that this disparity was not true for the country as a whole, but rather regional variation was observed. The factors influencing these disparities remain speculative. A case study was conducted of Durham, North Carolina, a city known nationally for the achievements of its Black middle class, to further explore these themes relying on numerous sources including newspapers and death certificates. Though Durham’s overall mortality was lower than many places in North Carolina, the White mortality rate greatly exceeded that of the Black population. Previously described theories, including Alfred Crosby’s exposure hypothesis and segregation, were explored. The most notable difference between Durham’s pandemic narrative and other comparable towns was the robust healthcare response, which was made possible by the excellence of the Black nursing force from Lincoln Hospital. Nursing care was the best treatment available for the 1918 influenza, but most of the nation experienced severe nursing shortages due to the war effort. This study thus provides an example of how the Black health community has proven an active agent in countering the structural forces driving racial disparities.
Study on the fastening property of precision locknut under simulated dynamic impact loading with consideration of interference factors
Authors: Chang Huey-Ling , Chen Chih-Ming , Lee Chun-Ying , Huang Zi-Xuan 
Published: January 2024

Abstract
Screw thread fastening system is the category of mechanical connection utilizing both wedge and friction actions to transfer clamping force and torque. This fastening system shows the advantages of simple in structure and ease in application. However, its shortcomings include the performance limitation by dimension and precision, stress concentration induced by the notch geometry, loosening in dynamical service, susceptible to atmospheric condition, etc. Therefore, the possible interference on the anti-loosening property of the locknut by noise factors of the ambient temperature, operator characteristics, and type of torque wrench used was investigated using Taguchi method in this study beside the main control factors of type of locknut, fit clearance, and type of lubrication grease. The goal was to evaluate the anti-loosening property of the locknut, i.e. the anti-loosening ratio and axial force ratio, in a more realistic manner. The connection joint of the locknut was subjected to cyclic transverse impact and the anti-loosening property was measured after a specified number of cycles. The loading effect on the surface roughness of thread surface was examined and discussed after the test. It was found that the factor of locknut type dominated the influence over the lubrication grease and fit clearance factors. Through the analysis, the design with optimal combination of the control factors improved the axial force ratio and anti-loosening ratio by 7.8% and 47.9%, respectively.
Combined approach in the treatment of comminuted lateral Hoffa fracture: a case report
Authors: Nastov Nebojsha , Bekteshi Labinot , Nikolovski Andrej 
Published: January 2024

Abstract
Coronal-plane intra-articular fractures of the femoral condyle (Hoffa fractures) are rare, and difficult to diagnose and treat. They mostly result as a consequence of high-energy trauma and are combined with concomitant fractures (patellar, tibia shaft) and/or soft-tissue damage. A plain X-ray can miss the diagnosis initially and therefore computerized tomography scan is recommended, which can also help in the preoperative planning. The vast majority of these fractures are unicondylar (mostly lateral condyle fractured). The approach for their treatment can be anterior or posterior. In cases of fracture comminution, much more mutilant approaches with osteotomy have been described. A combined two-stage approach can be used to obtain anatomical reduction and fixation of all the fragments. We present a case of a 46-year-old male patient with comminuted lateral Hoffa fracture treated with a combined approach (extended posterior approach to the proximal tibia and lateral parapatellar) in a time interval of one month.
Severe right ventricular infarction due to iatrogenic aortocoronary dissection successfully treated by surgical repair and extracorporeal membrane oxygenation
Authors: Ono Shunya , Kawamoto Shuhei , Fukushima Toshiya , Shimozawa Motoharu , Tateishi Retsu , Haba Fumiya , Nakahara Yoshinori , Kanemura Takeyuki 
Published: January 2024

Abstract
Iatrogenic aortocoronary dissection (IACD) is a rare but potentially fatal complication of percutaneous coronary intervention or coronary angiography (CAG). In particular, if the condition of the patient is complicated by cardiogenic shock and right ventricular (RV) dysfunction, the mortality rate is high. Herein, we report the case of an 85-year-old woman with IACD who underwent elective CAG of the right coronary artery complicated with cardiogenic shock due to RV infarction. After prompt surgical repair and postoperative extracorporeal membrane oxygenation, the postoperative course was uneventful and the patient was discharged to a rehabilitation facility.
Berry shrivel in grapevine: a review considering multiple approaches
Authors: Griesser Michaela , Savoi Stefania , Bondada Bhaskar , Forneck Astrid , Keller Markus 
Published: January 2024

Abstract
Grapevine berry shrivel, a ripening disorder, causes significant economic losses in the worldwide wine and table grape industries. An early interruption in ripening leads to this disorder, resulting in shriveling and reduced sugar accumulation affecting yield and fruit quality. Loss of sink strength associated with berry mesocarp cell death is an early symptom of this disorder; however, potential internal or external triggers are yet to be explored. No pathogens have been identified that might cause the ripening syndrome. Understanding the underlying causes and mechanisms contributing to berry shrivel is crucial for developing effective mitigation strategies and finding solutions for other ripening disorders associated with climacteric and non-climacteric fruits. This review discusses alterations in the fruit ripening mechanism induced by berry shrivel disorder, focusing primarily on sugar transport and metabolism, cell wall modification and cell death, and changes in the phytohormone profile. The essential open questions are highlighted and analyzed, thus identifying the critical knowledge gaps and key challenges for future research.
Multiple power-law tails in the density and column-density distribution in contracting star-forming clumps
Authors: Veltchev Todor V , Girichidis Philipp , Marinkova Lyubov , Donkov Sava , Stanchev Orlin , Klessen Ralf S 
Published: January 2024

ABSTRACT
We present a numerical study of the evolution of power-law tails (PLTs) in the (column-)density distributions (N-PDF, ρ-PDF) in contracting star-forming clumps in primordial gas, without and with some initial rotational and/or turbulent support. In all considered runs multiple PLTs emerge shortly after the formation of the first protostar. The first PLT (PLT 1) in the ρ-PDF is a stable feature with slope q1 ≃ −1.3 which corresponds – under the condition of preserved spherical symmetry – to the outer envelope of the protostellar object with density profile ρ ∝ l−2 in the classical Larson–Penston collapse model, where l is the radius. The second PLT (PLT 2) in the ρ-PDF is stable in the pure-infall runs but fluctuates significantly in the runs with initial support against gravity as dozens of protostars form and their mutual tidal forces change the density structure. Its mean slope, 〈q2〉 ≃ −2, corresponds to a density profile of ρ ∝ l−3/2 which describes a core in free fall in the classical Larson–Penston collapse model or an attractor solution at scales with dominating protostellar gravity. PLT 1 and PLT 2 in the N-PDFs are generally consistent with the observational data of Galactic low-mass star-forming regions from Herschel data. In the runs with initial support against gravity a third PLT (PLT 3) in the ρ-PDFs appears simultaneously with or after the emergence of PLT 2. It is very shallow, with mean slope of 〈q3〉 ≃ −1, and is associated with the formation of thin protostellar accretion discs.
Disrupted dwarf binary merger as the possible origin of NGC 2419 and Sagittarius stream substructure
Authors: Davies Elliot Y , Belokurov Vasily , Monty Stephanie , Evans N Wyn 
Published: January 2024

ABSTRACT
Using N-body simulations, we demonstrate that satellite dwarf galaxy pairs which undergo significant mixing (∼6 Gyr) can have their respective most bound particles separated great distances upon subsequently merging with a more massive host. This may provide an explanation as to the origin of the complex globular cluster NGC 2419, which is found within the tail of the Sagittarius dwarf spheroidal galaxy, yet separated from its central remnant by over 100 kpc. Dynamical investigations could support the chemical evidence which already points to the NGC 2419 being a nuclear star cluster. Motivated by the distinct nature of NGC 2419, we run a suite of simulations whereby an initial pre-infall merger of two satellites is followed by a post-infall merger of the remnant into a Milky Way-like host potential. We present a striking example from our suite in this work, in which this separation is reproduced by the most bound particles of the two pre-infall satellites. Additionally, this double merger scenario can induce unusual on-sky features in the tidal debris of the post-infall merger, such as clouds, overdensities, and potentially new arms that could resemble the bifurcation observed in Sagittarius.
Meningococcal Disease in Persons With HIV Reported Through Active Surveillance in the United States, 2009–2019
Authors: Rudmann Keegan C , Cooper Gabrielle , Marjuki Henju , Reingold Arthur , Barnes Meghan , Petit Susan , Moore Ashley , Harrison Lee H , Lynfield Ruth , Khanlian Sarah A , Anderson Bridget J , Martin Tasha , Schaffner William , McNamara Lucy A , Rubis Amy B 
Published: January 2024

Abstract
Persons with HIV (PWH) are at increased risk for bacterial infections, and previous publications document an increased risk for invasive meningococcal disease (IMD) in particular. This analysis provides evidence that PWH face a 6-fold increase in risk for IMD based on Active Bacterial Core surveillance data collected during 2009–2019.
The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth
Authors: Hosokawa Chika , Yagi Hiroki , Segami Shoji , Nagano Atsushi J , Koumoto Yasuko , Tamura Kentaro , Oka Yoshito , Matsushita Tomonao , Shimada Tomoo 
Published: January 2024

Abstract
Young seedlings use nutrients stored in the seeds to grow and acquire photosynthetic potential. This process, called seedling establishment, involves a developmental phase transition from heterotrophic to autotrophic growth. Some membrane-trafficking mutants of Arabidopsis (Arabidopsis thaliana), such as the katamari2 (kam2) mutant, exhibit growth arrest during seedling development, with a portion of individuals failing to develop true leaves on sucrose-free solid medium. However, the reason for this seedling arrest is unclear. In this study, we show that seedling arrest is a temporal growth arrest response that occurs not only in kam2 but also in wild-type (WT) Arabidopsis; however, the threshold for this response is lower in kam2 than in the WT. A subset of the arrested kam2 seedlings resumed growth after transfer to fresh sucrose-free medium. Growth arrest in kam2 on sucrose-free medium was restored by increasing the gel concentration of the medium or covering the surface of the medium with a perforated plastic sheet. WT Arabidopsis seedlings were also arrested when the gel concentration of sucrose-free medium was reduced. RNA sequencing revealed that transcriptomic changes associated with the rate of seedling establishment were observed as early as 4 d after sowing. Our results suggest that the growth arrest of both kam2 and WT seedlings is an adaptive stress response and is not simply caused by the lack of a carbon source in the medium. This study provides a new perspective on an environmental stress response under unfavorable conditions during the phase transition from heterotrophic to autotrophic growth in Arabidopsis.
Broad Chain-Length Specificity of the Alkane-Forming Enzymes NoCER1A and NoCER3A/B in Nymphaea odorata
Authors: Kojima Hisae , Yamamoto Kanta , Suzuki Takamasa , Hayakawa Yuri , Niwa Tomoko , Tokuhiro Kenro , Katahira Satoshi , Higashiyama Tetsuya , Ishiguro Sumie 
Published: January 2024

Abstract
Many terrestrial plants produce large quantities of alkanes for use in epicuticular wax and the pollen coat. However, their carbon chains must be long to be useful as fuel or as a petrochemical feedstock. Here, we focus on Nymphaea odorata, which produces relatively short alkanes in its anthers. We identified orthologs of the Arabidopsis alkane biosynthesis genes AtCER1 and AtCER3 in N. odorata and designated them NoCER1A, NoCER3A and NoCER3B. Expression analysis of NoCER1A and NoCER3A/B in Arabidopsis cer mutants revealed that the N. odorata enzymes cooperated with the Arabidopsis enzymes and that the NoCER1A produced shorter alkanes than AtCER1, regardless of which CER3 protein it interacted with. These results indicate that AtCER1 frequently uses a C30 substrate, whereas NoCER1A, NoCER3A/B and AtCER3 react with a broad range of substrate chain lengths. The incorporation of shorter alkanes disturbed the formation of wax crystals required for water-repellent activity in stems, suggesting that chain-length specificity is important for surface cleaning. Moreover, cultured tobacco cells expressing NoCER1A and NoCER3A/B effectively produced C19–C23 alkanes, indicating that the introduction of the two enzymes is sufficient to produce alkanes. Taken together, our findings suggest that these N. odorata enzymes may be useful for the biological production of alkanes of specific lengths. 3D modeling revealed that CER1s and CER3s share a similar structure that consists of N- and C-terminal domains, in which their predicted active sites are respectively located. We predicted the complex structure of both enzymes and found a cavity that connects their active sites.