bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel machine learning enabled hybrid optimization framework for efficient and transferable coarse-graining of a model polymer
Authors: Hajizadeh Ellie , Shireen Zakiya , Weeratunge Hansani , Menzel Adrian , Phillips Andrew W , Larson Ronald , Smith-Miles Kate 
Published: June 2022

Abstract
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained
(CG) model of a polyether material. The proposed framework combines the two fundamentally different classical optimization approaches for the development of coarse-grained model parameters; namely bottom-up and top-down approaches. This is achieved through combining machine learning models (ML) with optimization algorithms, trained using molecular dynamics (MD) simulation data. In the bottom-up approach, bonded interactions of the CG model are optimized using deep neural networks (DNN), where atomistic bonded distributions are matched. The atomistic
distributions emulate the local chain structure. In the top-down approach, optimization of nonbonded potentials is accomplished by reproducing the temperature-dependent experimental density. We demonstrate that CG model parameters achieved through our machine-learning enabled hybrid optimization framework fulfills the thermodynamic consistency and transferability issues associated with the classical approaches to coarse-graining model polymers. We demonstrate the efficiency, accuracy, and transferability of the developed CG model, using our novel framework through accurate predictions of chain size as well as chain dynamics, including the limiting behavior of the glass transition temperature, diffusion, and stress relaxation spectrum, where none were included in the potential parameterization process. The accuracy of the predicted properties are evaluated in the context of molecular theories and available experimental data.
Amyloidogenesis via interfacial shear in a containerless biochemical reactor aboard the International Space Station
Authors: Hirsa Amir , McMackin Patrick , Adam Joe , Griffin Shannon 
Published: June 2022

Abstract
Fluid interfaces significantly influence the dynamics of protein solutions, effects that can be isolated by performing experiments in microgravity, greatly reducing the amount of solid boundaries present, allowing air-liquid interfaces to become dominant. This investigation examined the effects of protein concentration on interfacial shear-induced fibrillization of insulin in microgravity within a containerless biochemical reactor, the ring-sheared drop (RSD), aboard the international space station (ISS). Human insulin was used as a model amyloidogenic protein for studying protein kinetics with applications to in situ pharmaceutical production, tissue engineering, and diseases such as Alzheimer’s, Parkinson’s, infectious prions, and type 2 diabetes. Experiments investigated three main stages of amyloidogenesis: nucleation studied by seeding monomeric solutions with fibril aggregates, fibrillization quantified using intrinsic fibrillization rate after fitting measured solution intensity to a sigmoidal function, and gelation observed by detection of solidification fronts. Results demonstrated that in surface-dominated amyloidogenic protein solutions: seeding with fibrils induces fibrillization of monomeric protein, intrinsic fibrillization rate is independent of concentration, and that there is a minimum fibril concentration for gelation with gelation rate and rapidity of onset increasing monotonically with increasing protein concentration. These findings matched well with results of previous studies within ground-based analogs.
Inferring the diurnal variability of OH radical concentrations over the Amazon from BVOC measurements
Authors: Ringsdorf Akima , Edtbauer Achim , de Arellano Jordi Vila-Guerau , Pfannerstill Eva , gromov Sergey , Kumar Vinod , Pozzer Andrea , Wolff Stefan , Tsokankunku Anywhere , Soergel Matthias , Sá Marta , de Araujo Alessandro , Ditas Florian , Pöhlker Christopher , Lelieveld Jos , Williams Jonathan 
Published: June 2022

Abstract
The atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed harmful and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged transport times between 80 m to 325 m decrease from 105 to 15 minutes over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (13:00–14:00LT) reaching 1x106 ± 1.1x106 molecules cm− 3 controlled by the coupling between BVOC emission fluxes, convective turbulence, air chemistry and photolysis rates. The results were evaluated against a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model.
Evaluation of CBP, CEBPA and DNMT3A genes in Diagnosis and Prognosis of Acute Myeloid Leukemia.
Authors: Assem Magda , Leithy Asmaa A. El , Hassan Naglaa M , Abozaid Mohamed , Allam Rasha Mahmoud , Kamal Mohamed A. M , Ibrahim Noha H 
Published: June 2022

Abstract
Background: CBP, CEBPA and DNMT3A are tumor suppressor genes whose dysfunction has been reported in hematologic malignancies. Acute myeloid leukemia is the most common type of white cell neoplasm among adults. Our aim is to assess the expression level of CBP, CEBPA and DNMT3A genes in an Egyptian cohort with AML. We investigated the correlation between the selected genes’ mRNA levels and their association with the clinical characteristics and survival. MethodsA total of 53 adult participants diagnosed with AML were enrolled in the study. Quantitative RT-PCR was used to assess CBP, CEPBA and DNMT3A expression. Results: There was no significant difference between males and females in the relative expression level of CBP, CEBPA, and DNMT3A. Similarly, none of the three genes showed statistically significant correlation with age at the time of diagnosis or FAB subtypes of AML. The correlation matrix of the three genes detected a significant correlation only between CBP and CEBPA expression (rS= .518, P=0.000). Survival analysis of our cohort showed no association of any of the studied genes with neither overall nor disease free survival. Conclusion: Our finding may indicate a complementary role of CBP and CEBPA in AML pathogenesis; however, further investigation on larger samples is still warranted to study the relationship of these genes with AML survival.
Association between lignan intake from different types of plant-based foods and obesity indicators in the Netherlands
Authors: Zaki Umi Kalsum Hussain , Trijsburg Laura , Feskens Edith J.M. 
Published: June 2022

Abstract
This study aimed to assess whether lignan intake is associated with lower body mass index (BMI) and waist circumference in a Dutch population. Data on lignan content of foods was extracted from a lignan database of Dutch plant-based foods and complemented with three other references to estimate lignan intake in 1012 Dutch men and women participating in the NQ-plus prospective cohort study. The association between lignan intake and BMI and waist circumference was assessed using linear regression analysis. Three multivariate models were used to investigate the association of BMI and waist circumference with total lignan intake. Model 1 included adjustments for lifestyle variables, in model 2 adjustments were made for energy intake and nutrients, and in model 3 these adjustment were combined. The median lignan intake was 3226 µg/day (mean 4763 µg/day, SD 5386 µg/day). Lignan intake was strongly skewed towards higher values, ranging from 40-50500 µg/day. The major sources of lignans were bread, which contributed 52%, nuts, seeds, and snacks (21%), and vegetables (12%) to the lignan intake. After adjustments lignan intake was associated with a lower waist circumference (-0.93 cm, 95 % CI: -0.88; -1.00). No association between BMI and lignan intake was observed. A higher lignan intake is significantly associated with a smaller waist circumference in Dutch adults. To what extent a high lignan intake can reduce waist circumference in obese patients or can prevent onset of abdominal obesity remains to be tested in future intervention studies.
Tβ4 and PDTC displayed recovery on the glial and neuronal alterations in an early Alzheimer’s disease model
Authors: Wang Meng , Li Zi-Long , Feng Li-Rong , Chang Ke-Wei , Yang Wei-Na , Liu Qi , Sindhwani Shria , Qian Yi-Hua 
Published: June 2022

Abstract
Alzheimer’s disease (AD) is the leading cause of dementia, with no effective therapies to reduce this progressive form of nerve cell death. Peptide thymosin β4 (Tβ4) controls actin polymerization and showed reduced neuroinflammation in middle stage AD model mice. To report the effect and mechanism of Tβ4 in early stage of AD model mice, Tβ4 overexpression or knockdown in 4 months APP/PS1 mice brain was achieved by genetic engineering methods. Two months later, behavioral test, electroencephalogram (EEG) test, immunofluorescence, immunohistochemistry, immunoblotting, dot blot, RT-PCR and transmission electron microscopy (TEM) were applied. The findings showed that the overexpression of Tβ4 displayed reduced microglia and astrocytes activation, arrested neuronal degeneration, repaired myelin sheath degeneration, decreased NF-κBp65 protein level, and restored EEG abnormality. Conversely, knockdown of Tβ4 led to lysosomal dysfunction, neuronal function weakening, myelin sheath loss, increased NF-κBp65 protein level, and further impaired image discrimination or spatial (working) memory in the APP/PS1 mice. The combination of TLR4 antagonist or NF-κBp65 inhibitor further reduced the inflammatory protein level. gv971 significantly reduced the glial reactivity and improved the neuronal survival, but not the learning and memory impairment of APP/PS1 mice. Combining Tβ4 with other therapies may be an effective strategy to combat the complex changes in AD.
A Noval Approach towards Neuro Acoustic Loops &amp; their intervention in various Neuro Psychiatric Disorders
Authors: Aasim Shahzad , Ahmad Suhail , Butt Muheet , Wani Hilal , Fatima Rifat , Ganie Abdul , Dar Nizam Ud Din 
Published: June 2022

Abstract
The interface of sound in general and music in particular has known and unknown dimensions in human physiology, human psychology and larger well-being of human health. Acoustic therapies and stimulation have been scientifically proven to have a powerful effect on the brain. Recent researches have shown that music can help in many aspects of the brain including pain reduction, stress relief, Seizure, Stroke, memory, and brain injuries. The intervention of sound or music as a type of treatment can be medicine less and mostly concentrates on selective sound frequencies or acoustic loops. In this paper an attempt is made to study the intervention of these sound frequencies in general and their effects on neuro-psychiatric mechanisms and allied phenomenon. The quantification of specific frequencies (Acoustic loops) which will ameliorate the various disorders after their identification can also be correlated with various biochemical parameters that will be analysed with regards to the changes effected by these interventions. The proposed research work might provide a novel approach of treatment for neuro psychiatric disorders using the above stated therapy. The work intends to provide the effect of this therapy on 50 patients/subjects which are taken in isolation wherein the results on selected subjects has been quite demanding. These patients have been already diagnosed with psychiatric disorders at SKIMS and are being re-accessed at NARC using Acoustic Loop Therapy. The proposed work will also provide a scaling or quantitative approach in the intervention of Neuro Acoustic disorders.
In vivo multiscale measurements of solid stresses in tumors reveal scale-dependent stress transmission
Authors: Zhang Sue , Passaro Rachel , Regan Kathryn , Hadzipasic Muhamed , Grifno Gabrielle , Zheng Siyi , O'Connor Logan , Chu Vinson , Kim Sung Yeon , Yang Jiarui , Banerji Rohin , Karrobi Kavon , Roblyer Darren , Grinstaff Mark , Nia Hadi 
Published: June 2022

Abstract
Solid stress, one of the physical hallmarks of cancer, affects trafficking and infiltration of immune cells, promotes metastasis and tumorigenic pathways, and impedes therapeutic delivery. Despite these clinical ramifications, questions remain regarding the origins and consequences of solid stresses and the differential response of tumor versus normal cells to solid stresses. Answering these fundamental questions requires probing solid stresses at the cellular scale, where biological and immunological responses manifest, as well as in vivo, where the complexities of the tumor microenvironment are present. Here, we report the first in vivo and multi-scale measurements of solid stress in mouse models of breast cancer using multi-modal intravital microscopy of deformable hydrogels complemented with mathematical modeling. Utilizing the capabilities of these methods, such as the high-resolution, longitudinal, and 3-D measurements of local solid stress, we measure and compare solid stresses (i) at the single cell vs tissue scale, (ii) primary vs metastatic tumors, (iii) in vivo vs in vitro settings, and (iv) in vivo vs post-mortem. Surprisingly, we find solid stress transmission is scale-dependent, as tumor cells experience a factor of 6 reduction in stress in comparison to stress measured at the tissue scale. This finding implicates the presence of potential biophysical mechanisms that tumor cells utilize to protect themselves against lethally high solid stresses. This insight into the scale-dependence of solid stress genesis will further inform the discovery of new therapeutic strategies that sensitize cancer cells to solid stresses to induce cell death.
Augmented reality elastography ultrasound via generate adversarial network for breast cancer diagnosis
Authors: Yu Jinhua , Yao Zhao , Luo Ting , Dong YiJie , Jia XiaoHong , Deng YinHui , Zhu Ying , Zhang JingWen , Liu Juan , Yang LiChun , Luo XiaoMao , Li ZhiYao , Xu YanJun , Hu Bin , Huang YunXia , Chang Cai , Xu JinFeng , Luo Hui , Dong Fajin , Xia XiaoNa , Wu ChengRong , Hu WenJia , Wu Gang , Li QiaoYing , Chen Qin , Deng WanYue , Jiang QiongChao , Mou YongLin , Yan HuanNan , Xu XiaoJing , Yan HongJu , Zhou Ping , Shao Yang , Cui LiGang , He Ping , Qian LinXue , Liu JinPing , Shi LiYing , Zhao YaNan , Xu YongYuan , Zhan WeiWei , Wang YuanYuan , Zhou Jianqiao , Wu GuoQing 
Published: June 2022

Abstract
Elastography ultrasound (EUS) imaging is a vital ultrasound imaging modality. The current use of EUS faces many challenges, such as vulnerability to subjective manipulation, echo signal attenuation, and unknown risks of elastic pressure in certain delicate tissues. The hardware requirement of EUS also hinders the trend of miniaturization of ultrasound equipment. We therefore present a cost-efficient solution by designing a deep neural network to synthesize augmented reality EUS (AR-EUS) from conventional B-mode images. By using 4580 cases from 15 medical centers, we evaluate the performance of AR-EUS on breast cancer diagnosis. The quantitative metric and blind evaluation results show no significant difference between AR-EUS and real EUS in image authenticity and in clinical diagnosis. The performance of pocket-sized ultrasound in breast tumor diagnosis is also significantly improved after AR-EUS is equipped. These results highlight the potential of AR-EUS in clinical application.
A cost-effectiveness analysis of toripalimab plus TP versus TP for the first-line treatment of advanced esophageal cancer
Authors: Zeng Fan-yuan , Ye Zhuo-miao , Wang Hao-lun , Xu Zhe , Zhou Qin , Li Huan 
Published: June 2022

Abstract
Objective: We evaluated the cost-effectiveness of Toripalimab plus TP in treating patients with esophageal cancer in this study.Perspective: the Chinese payers.Methods: A Markov model was developed from the Chinese payers’ perspectives.We conducted a cost-effectiveness analysis.One-way and probabilistic sensitivity analyses were conducted to explore the impact of uncertainties on the cost-effectiveness’s results. Scenario analysis was also performed.Results: The ICER for Toripalimab plus chemotherapy versus chemotherapy was $16834.30. An increase of 0.83 QALYs and 1.39 LYs. For Toripalimab plus TP, the ICER/QALY is $20302.54 compared to TP alone at the WTP of $37653.The ICERs were the most sensitive to the utility of PD. Conclusions: Toripalimab plus TP therapy for advanced oesophageal cancer would be cost-effective compared with TP.
Association of lung function and hyperglycemia: a 10-year study in China
Authors: Li Wei , Ning Yi , Ma Yuan , Lin Xinshan , Man Sailimai , Wang Bo , Wang Chen , Yang Ting 
Published: June 2022

Abstract
Background
Nowadays chronic respiratory diseases are a major burden in terms of morbidity and mortality and of increasing public health concern in China. Meanwhile, prevalence of diabetes has increased more than 10 times over forty years. A few studies investigating the association between chronic respiratory diseases and diabetes mellitus have been done these years. However, the association was not clear, and we aimed to answer this question with solid proof.
Methods
Our study is a single-center study performed in MJ Healthcare Center in Beijing. We enrolled subjects aged ≥ 20 years undergoing at least two regular health check-ups between 2009 and 2019 in MJ Healthcare Center in Beijing. Each health check-up included regular tests, biochemical tests, a pulmonary function test and a questionnaire. 11,107 adults were included and cross-sectional and longitudinal analysis were performed.
Results
We found that both pre-diabetic and diabetic adults had lower lung function compared to normal population at baseline, indicating that lung function decrement may start from prediabetic status. Quantitatively, with 1 mmol/L increase of FPG (fasting plasma glucose), FVC (forced vital capacity), FEV1 (forced expiratory volume), FVC% and FEV1% lowered 25ml, 13ml, 0.71%-1.03% and 0.46%-0.72% respectively. However, no statistical significance was found regarding the rates for the lung function decline between different baseline diabetes status.
Conclusion
People with higher blood glucose had more severe lung function decline and lung function decrement started from pre-diabetic status, but there was no difference in the rate of lung function decrease based on different baseline diabetic status.
Resonance algorithm: An intuitive algorithm to find all shortest paths between two nodes
Authors: Liu Yu , Lin Qiguang , Hong Binbin , Peng Yunru , Hjerpe Daniel , Liu Xiaofeng 
Published: June 2022

Abstract
The shortest path problem (SPP) is a classic problem and appears in a wide range of applications. Although a variety of algorithms already exist, new advances are still being made, mainly tuned for particular scenarios to have better performances. As a result, they become more and more technically complex and sophisticated. In this paper we developed an intuitive and nature-inspired algorithm to compute all possible shortest paths between two nodes in a graph: Resonance Algorithm (RA). It can handle any undirected, directed, or mixed graphs, irrespective of loops, unweighted or positively-weighted edges, and can be implemented in a fully decentralized manner. Although the original motivation for RA is not the speed per se, in certain scenarios (when sophisticated matrix operations can be employed, and when the map is very large and all possible shortest paths are demanded) it out-competes Dijkstra’s algorithm, which suggests that in those scenarios RA could also be practically useful.
Lymphatic dysfunction sustains memory impairment despite Aβ reduction by reactive astrocytes in an Alzheimer’s disease model
Authors: Lee Eun Ji , Choi Yoori , Park Eun-Joo , Lee Dong Soo 
Published: June 2022

Abstract
The central nervous system is not an immune-privileged system and is expected to communicate with the peripheral immune system. To understand the effects of the immune system in Alzheimer's disease (AD), anti-CD4 antibody treatment and deep cervical lymph node ligation were performed in the 5XFAD mouse model. These mice were also treated with an anti-amyloid antibody and focused ultrasound with microbubbles. Based on the analysis of pathology and behavior tests, CD4 T cells modulated microglial reactivity and amyloid pathology in the AD model, and dCLN ligation induced changes in the microglial response to stimulation and memory impairment by reactive astrocytes. These results demonstrated that lymphocytes and the lymphatic system regulate glial cell status, amyloid pathology, and memory function in AD. Therefore, peripheral immune cells and lymphatic dysfunction can be used as targets for AD treatment, and these dysfunctions should be considered in the development of AD therapeutics.
Identifying Metabolic Shifts in Crohn's Disease Using' Omics-Driven Contextualized Computational Metabolic Network Models
Authors: Fernandes Philip , Sharma Yash , McGrew Brooklyn , Zulqarnain Fatima , Shrivastava Aman , Ehsan Lubaina , Payne Dawson , Dillard Lillian , Powers Deborah , Aldridge Isabelle , Matthews Jason , Kugathasan Subra , Papin Jason A. , Fernández Facundo M. , Gaul David , Syed Sana 
Published: June 2022

Abstract
Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. A clear gap in our existing CD diagnostics and current disease management approaches is the lack of highly specific biomarkers that can be used to streamline or personalize disease management. Comprehensive profiling of metabolites holds promise; however, these high dimensional profiles need to be reduced to have relevance in the context of CD. Machine learning approaches are optimally suited to bridge this gap in knowledge by contextualizing the metabolic alterations in CD using genome-scale metabolic network reconstructions. Our work presents a framework for studying altered metabolic reactions between patients with CD and controls using publicly available transcriptomic data and existing gene-driven metabolic network reconstructions. Additionally, we apply the same methods to patient-derived ileal enteroids to explore the utility of using this experimental in vitro platform for studying CD. Furthermore, we have piloted an untargeted metabolomics approach as a proof-of-concept validation strategy in human ileal mucosal tissue. These findings suggest that in silico metabolic modeling can potentially identify pathways of clinical relevance in CD, paving the way for future discovery of novel diagnostic biomarkers and therapeutic targets.