bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces
Authors: Kuhn Thierry , Buffi Matteo , Bindschedler Saskia , Chain Patrick S. , Gonzalez Diego , Stanley Claire E. , Wick Lukas Y. , Junier Pilar , Richter Xiang-Yi Li 
Published: September 2022

AbstractBackgroundTo disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements.ResultsWe designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells.ConclusionsThe 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.
Point-of-care viscoelastic coagulation assessment in healthy dogs during the perianesthetic period
Authors: Wang Wen H. , Lynch Alex M. , Balko Julie A. , Duffy Daniel J. , Robertson James B. , Posner Lysa P. 
Published: September 2022

AbstractBackgroundThe viscoelastic coagulation monitor (VCM Vet) is a novel, portable device that provides a global assessment of hemostasis. The study aims were to evaluate serial viscoelastic analysis during the perianesthetic period in healthy dogs and to compare the agreement between two VCM Vet devices. Twenty healthy dogs undergoing orthopedic surgery were enrolled. Whole blood samples were collected from an intravenous catheter at four time points: baseline, 15 min after premedication, 60 min after inhalant initiation, and 60 min after inhalant termination. Viscoelastic tests were performed in duplicate on different devices, providing: clot time (CT; seconds), clot formation time (CFT; seconds), alpha angle (α; degrees), amplitude (units) at 10 (A10) and 20 (A20) minutes post clot time, maximum clot firmness (MCF; units), and lysis index (%) at 30 (Li30) and 45 (Li45) minutes post maximum clot formation.ResultsOne hundred sixty samples were analyzed. The speed of CT and CFT significantly decreased an average of 25.5 s (95% confidence interval [CI]15.9–35.0) and 6.9 s (95% CI 3.1–10.7) per time point, respectively. There were no significant changes in clot strength or lysis variables. The Bland–Altman style plot shows an acceptable rate of agreement for all variables with intra-class correlation ranging from 0.64–0.94.ConclusionThe rate of clot formation (CT and CFT) decreased over the perianesthetic period in healthy dogs undergoing surgery. These changes were small and occurred without changes in clot strength or fibrinolysis rate, thus were not clinically relevant. There was clinically acceptable consistency between devices.
Measurement of distal intramural spread and the optimal distal resection by naked eyes after neoadjuvant radiation for rectal cancers
Authors: Sun Ge , Ye Xiaolong , Zheng Kuo , Zhang Hang , Broens Paul , Trzpis Monika , Lou Zheng , Gao Xianhua , Liu Lianjie , Hao Liqiang , Furnee Edgar , Bai Chenguang , Zhang Wei 
Published: September 2022

Abstract
Background
The safe distance between the intraoperative resection line and the visible margin of the distal rectal tumor after preoperative radiotherapy is unclear. We aimed to investigate the furthest tumor intramural spread distance in fresh tissue to determine a safe distal intraoperative resection margin length.

Methods
Twenty rectal cancer specimens were collected after preoperative radiotherapy. Tumor intramural spread distances were defined as the distance between the tumor’s visible and microscopic margins. Visible tumor margins in fresh specimens were identified during the operation and were labeled with 5 - 0 sutures under the naked eye at the distal 5, 6, and 7 o’clock directions of visible margins immediately after removal of the tumor. After fixation with formalin, the sutures were injected with nanocarbon particles. Longitudinal tissues were collected along three labels and stained with hematoxylin and eosin. The spread distance after formalin fixation was measured between the furthest intramural spread of tumor cells and the nanocarbon under a microscope. A positive intramural spread distance indicated that the furthest tumor cell was distal to the nanocarbon, and a negative value indicated that the tumor cell was proximal to the nanocarbon. The tumor intramural spread distance in fresh tissue during the operation was 1.75 times the tumor intramural spread distance after formalin fixation according to the literature.

Results
At the distal 5, 6, and 7 o’clock direction, seven (35%), five (25%), and six (30%) patients, respectively, had distal tumor cell intramural spread distance > 0 mm. The mean and 95% confidence interval of tumor cell intramural spread distance in fresh tissue during operation was − 0.3 (95%CI − 4.0 ~ 3.4) mm, − 0.9 (95%CI − 3.4 ~ 1.7) mm, and − 0.4 (95%CI − 3.5 ~ 2.8) mm, respectively. The maximal intraoperative intramural spread distances in fresh tissue were 8.8, 7, and 7 mm, respectively.

Conclusions
The intraoperative distance between the distal resection line and the visible margin of the rectal tumor after radiotherapy should not be less than 1 cm to ensure oncological safety.
An effective method to reduce lymphatic drainage post-lateral cervical lymph node dissection of differentiated thyroid cancer: a retrospective analysis
Authors: Zhang Ming-Liang , Guo Lou-Ming , Li Peng-Cheng , Zhang Jing-Kang , Guo Chen-Xu 
Published: September 2022

Abstract
Background
Lymph or chyle leak (LL/CL) is severe complications after lateral cervical lymph node dissection (LLND), mainly due to iatrogenic injury of the lymphatic duct. Efficient and well-operated methods to reduce postoperative drainage are still lacking. This was a feasibility study to evaluate a new method of preventing LL/CL compared to conventional treatment.

Method
We retrospectively analyzed 20 consecutive patients who used the “pedicled omohyoid flap covering (POFC)” method during LLND from January 2019 to December 2021 in our center as an observation group. Another 20 consecutive patients used the conventional method during LLND in this period as a control group. The clinical and pathological features of the two groups were compared, and the related factors that affected postoperative lymphatic drainage were analyzed with Cox proportional hazards models.

Results
The drainage volume per 24 h and the incidence of LL/CL in the control group were both higher than that in the observation group (all P < 0.05), and the number of lymph nodes dissected in the IV region > 10 and the use of the POFC method were the independent risk factors that significantly affected the incidence of LL/CL post LLND (all P < 0.05).

Conclusions
POFC is a safe and useful method for reducing drainage and preventing LL/CL post-LLND, especially for patients with heavy metastasis of the lymph nodes in the IV region.
H19 may regulate the immune cell infiltration in carcinogenesis of gastric cancer through miR-378a-5p/SERPINH1 signaling
Authors: Li Jianxin , Han Ting , Wang Xin , Wang Yinchun , Chen Xuan , Chen Wangsheng , Yang Qingqiang 
Published: September 2022

Abstract
Background
Increasing studies have indicated that noncoding RNA (ncRNA)-mediated competing endogenous RNA (ceRNA) network serves as a significant role in cancer progression, but the underlying regulatory mechanisms of which in gastric cancer (GC) remain largely unclear.

Methods
Based on Gene Expression Omnibus and The Cancer Genome Atlas datasets, potential biomarkers for GC were screened and validated by machine learning. Then, upstream regulatory ncRNA of potential biomarkers was identified to construct a novel ceRNA network in GC through means of stepwise reverse prediction and validation. Ultimately, tumor immune cell infiltration analysis was performed based on the EPIC algorithm.

Results
A total of 188 differentially expressed genes (DEGs) were screened, and three candidate diagnostic biomarkers (FAP, PSAPL1, and SERPINH1) for GC were identified and validated. Subsequently, H19 and miR-378a-5p were identified as upstream regulatory ncRNAs that could potentially bind SERPINH1 in GC. Moreover, Immune infiltration analysis revealed that each component in the ceRNA network (H19/miR-378a-5p/SERPINH1) was significantly correlated with the infiltration abundances of diverse tumor-infiltrating immune cells.

Conclusions
H19 may regulate the immune cell infiltration in carcinogenesis of GC through miR-378a-5p/SERPINH1 signaling.
Probing spatiotemporal PKA activity at the ryanodine receptor and SERCA2a nanodomains in cardomyocytes
Authors: Xu Bing , Wang Ying , Bahriz Sherif M. F. M. , Zhao Meimi , Zhu Chaoqun , Xiang Yang K. 
Published: September 2022

AbstractSpatiotemporal regulation of subcellular protein kinase A (PKA) activity for precise substrate phosphorylation is essential for cellular responses to hormonal stimulation. Ryanodine receptor 2 (RyR2) and (sarco)endoplasmic reticulum calcium ATPase 2a (SERCA2a) represent two critical targets of β adrenoceptor (βAR) signaling on the sarcoplasmic reticulum membrane for cardiac excitation and contraction coupling. Using novel biosensors, we show that cardiac β1AR signals to both RyR2 and SERCA2a nanodomains in cardiomyocytes from mice, rats, and rabbits, whereas the β2AR signaling is restricted from these nanodomains. Phosphodiesterase 4 (PDE4) and PDE3 control the baseline PKA activity and prevent β2AR signaling from reaching the RyR2 and SERCA2a nanodomains. Moreover, blocking inhibitory G protein allows β2AR signaling to the RyR2 but not the SERCA2a nanodomains. This study provides evidence for the differential roles of inhibitory G protein and PDEs in controlling the adrenergic subtype signaling at the RyR2 and SERCA2a nanodomains in cardiomyocytes.
Amine-modified nanoplastics promote the procoagulant activation of isolated human red blood cells and thrombus formation in rats
Authors: Kim Eun-Hye , Choi Sungbin , Kim Donghyun , Park Han Jin , Bian Yiying , Choi Sang Ho , Chung Han Young , Bae Ok-Nam 
Published: September 2022

Abstract
Background
Microplastics (MPs) and nanoplastics (NPs) formed from decomposed plastic are increasing environmental threats. Although MPs and NPs exposed through various routes enter the systemic circulation, the potential toxicity of those is largely unknown. We investigated whether polystyrene NPs (PS-NPs) promote the coagulation activity of red blood cells (RBCs).

Results
We tested several types of PS-NPs using human RBCs and found that amine-modified 100 nm PS-NPs were the most potent. We measured the uptake of PS-NPs using flow cytometry and confocal microscopy. Electron microscopy revealed morphological changes of RBCs by PS-NPs. PS-NPs induced the externalization of phosphatidylserine, generation of microvesicles in RBCs, and perturbations in the intracellular microenvironment. PS-NPs increased the activity of scramblases responsible for phospholipid translocation in RBCs. PS-NPs modulated the functional interaction to adjacent tissues and coagulation cascade, enhancing RBC adhesion and thrombin generation. Our observations in human RBCs were consistent with those in isolated rat RBCs, showing no inter-species differences. In rat venous thrombosis models, the intravenous administration of PS-NPs enhanced thrombus formation.

Conclusion
Amine-modified PS-NPs induce the prothrombotic activation of RBCs causing thrombus formation. We believe that our study will contribute to understanding the potential toxicity of amine-modified polystyrene particles in blood cells and cardiovascular systems.
Effect of dorsal nerve fascial island flap on repairing distal soft tissue defects at the proximal segment of the index, middle, ring, and little fingers
Authors: Wang Xun , Lv Jingdan , Liu Shujiao , Xu Shuangyue , Yan Guoliang 
Published: September 2022

Abstract
Background
To investigate the effect of the dorsal nerve fascial island (DNFI) flap on repairing finger soft tissue defects at the distal segments.

Methods
Fifty patients with distal soft tissue defects at the index, middle, ring, or little fingers were treated with a DNFI flap at the proximal phalanx between February 2008 and May 2018. The nutrient vascular chain around the dorsal branch of the proper palmar digital nerves served as the flap axis. The dorsal branch of the proper palmar digital arteries provided blood supply. The fascia pedicle served as the venous system. All patients were followed for 6 months.

Results
All 50 flaps survived. The appearance, color, and texture of the skin returned to normal. The sensory function was partially restored. The two-point discrimination of the finger flap was 7–10 mm.

Conclusions
The DNFI flap at the proximal phalanges of the index, middle, ring, and little fingers is an effective surgical option. The technique has a high flap survival rate and long pedicle, which can repair different parts of the finger. The flap also restores the sensory function of the finger without damaging the main nerves or blood vessels. The flap treatment is an optimal option for finger soft tissue defects at the distal segments.
Radiomics analysis using MR imaging of subchondral bone for identification of knee osteoarthritis
Authors: Xue Zhihao , Wang Liao , Sun Qi , Xu Jia , Liu Ying , Ai Songtao , Zhang Lichi , Liu Chenglei 
Published: September 2022

Abstract
Background
To develop a magnetic resonance imaging (MRI)-based radiomics predictive model for the identification of knee osteoarthritis (OA), based on the tibial and femoral subchondral bone, and compare with the trabecular structural parameter-based model.

Methods
Eighty-eight consecutive knees were scanned with 3T MRI and scored using MRI osteoarthritis Knee Scores (MOAKS), in which 56 knees were diagnosed to have OA. The modality of sagittal three-dimensional balanced fast-field echo sequence (3D BFFE) was used to image the subchondral bone. Four trabecular structural parameters (bone volume fraction [BV/TV], trabecular thickness [Tb.Th], trabecular separation [Tb.Sp], and trabecular number) and 93 radiomics features were extracted from four regions of the lateral and medial aspects of the femur condyle and tibial plateau. Least absolute shrinkage and selection operator (LASSO) was used for feature selection. Machine learning-based support vector machine models were constructed to identify knee OA. The performance of the models was assessed by area under the curve (AUC) of the receiver operator characteristic (ROC). The correlation between radiomics features and trabecular structural parameters was analyzed using Pearson’s correlation coefficient.

Results
Our radiomics-based classification model achieved the AUC score of 0.961 (95% confidence interval [CI], 0.912–1.000) when distinguishing between normal and knee OA, which was higher than that of the trabecular parameter-based model (AUC, 0.873; 95% CI, 0.788–0.957). The first-order, texture, and Laplacian of Gaussian-based radiomics features correlated positively with Tb.Th and BV/TV, but negatively with Tb.Sp (P < 0.05).

Conclusions
Our results suggested that our MRI-based radiomics models can be used as biomarkers for the classification of OA and are superior to the conventional structural parameter-based model.
Rare clinical phenotype of filaminopathy presenting as restrictive cardiomyopathy and myopathy in childhood
Authors: Muravyev A. , Vershinina T. , Tesner P. , Sjoberg G. , Fomicheva Yu. , Čajbiková N. Novák , Kozyreva A. , Zhuk S. , Mamaeva E. , Tarnovskaya S. , Jornholt J. , Sokolnikova P. , Pervunina T. , Vasichkina E. , Sejersen T. , Kostareva A. 
Published: September 2022

Abstract
Background
FLNC is one of the few genes associated with all types of cardiomyopathies, but it also underlies neuromuscular phenotype. The combination of concomitant neuromuscular and cardiac involvement is not often observed in filaminopathies and the impact of this on the disease prognosis has hitherto not been analyzed.

Results
Here we provide a detailed clinical, genetic, and structural prediction analysis of distinct FLNC-associated phenotypes based on twelve pediatric cases. They include early-onset restrictive cardiomyopathy (RCM) in association with congenital myopathy. In all patients the initial diagnosis was established during the first year of life and in five out of twelve (41.7%) patients the first symptoms were observed at birth. RCM was present in all patients, often in combination with septal defects. No ventricular arrhythmias were noted in any of the patients presented here. Myopathy was confirmed by neurological examination, electromyography, and morphological studies. Arthrogryposes was diagnosed in six patients and remained clinically meaningful with increasing age in three of them. One patient underwent successful heart transplantation at the age of 18 years and two patients are currently included in the waiting list for heart transplantation. Two died due to congestive heart failure. One patient had ICD instally as primary prevention of SCD. In ten out of twelve patients the disease was associated with missense variants and only in two cases loss of function variants were detected. In half of the described cases, an amino acid substitution A1186V, altering the structure of IgFLNc10, was found.

Conclusions
The present description of twelve cases of early-onset restrictive cardiomyopathy with congenital myopathy and FLNC mutation, underlines a distinct unique phenotype that can be suggested as a separate clinical form of filaminopathies. Amino acid substitution A1186V, which was observed in half of the cases, defines a mutational hotspot for the reported combination of myopathy and cardiomyopathy. Several independent molecular mechanisms of FLNC mutations linked to filamin structure and function can explain the broad spectrum of FLNC-associated phenotypes. Early disease presentation and unfavorable prognosis of heart failure demanding heart transplantation make awareness of this clinical form of filaminopathy of great clinical importance.
Identifying project topics and requirements in a citizen science project in rare diseases: a participative study
Authors: Neff Michaela , Storf Holger , Vasseur Jessica , Scheidt Jörg , Zerr Thomas , Khouri Andreas , Schaaf Jannik 
Published: September 2022

Abstract
Background
Due to their low prevalence (< 5 in 10,000), rare diseases are an important area of research, with the active participation of those affected being a key factor. In the Citizen Science project “SelEe” (Researching rare diseases in a citizen science approach), citizens collaborate with researchers using a digital application, developed as part of the project together with those affected, to answer research questions on rare diseases. The aim of this study was to define the rare diseases to be considered, the project topics and the initial requirements for the implementation in a digital application.

Methods
To address our research questions, we took several steps to engage citizens, especially those affected by rare diseases. This approach included the following methods: pre- and post-survey (questionnaire), two workshops with focus group discussion and a requirements analysis workshop (with user stories).

Results
In the pre-survey, citizens suggested 45 different rare diseases and many different disease groups to be considered in the project. Two main project topics (A) “Patient-guided documentation and data collection” (20 votes) and (B) “Exchange of experience and networking” (13 votes) were identified as priorities in the workshops and ranked in the post-survey. The requirements workshop resulted in ten user stories and six initial requirements to be implemented in the digital application.

Conclusion
Qualitative, citizen science research can be used to collectively identify stakeholder needs, project topics and requirements for a digital application in specific areas, such as rare diseases.
Comprehensive and scalable quantification of splicing differences with MntJULiP
Authors: Yang Guangyu , Sabunciyan Sarven , Florea Liliana 
Published: September 2022

AbstractTools for differential splicing detection have failed to provide a comprehensive and consistent view of splicing variation. We present MntJULiP, a novel method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP detects both changes in intron splicing ratios and changes in absolute splicing levels with high accuracy, and can find classes of variation overlooked by other tools. MntJULiP identifies over 29,000 differentially spliced introns in 1398 GTEx brain samples, including 11,242 novel introns discovered in this dataset. Highly scalable, MntJULiP can process thousands of samples within hours to reveal splicing constituents of phenotypic differentiation.