Miracle-dz/UniFAR-FTUs huggingface dataset:
3D Amide Proton Transfer Weighted Brain Tumor Imaging With Compressed SENSE: Effects of Different Acceleration Factors

Objectives The aim of the current study was to evaluate the performance of compressed SENSE (CS) for 3D amide proton transfer weighted (APTw) brain tumor imaging with different acceleration factors (AFs), and the results were compared with those of conventional SENSE. Methods Approximately 51 patients with brain tumor (22 males, 49.95 ± 10.52 years) with meningiomas (n = 16), metastases (n = 12), or gliomas (n = 23) were enrolled. All the patients received 3D APTw imaging scans on a 3.0 T scanner with acceleration by CS (AFs: CS2, CS3, CS4, and CS5) and SENSE (AF: S1.6). Two readers independently and subjectively evaluated the APTw images relative to image quality and measured confidence concerning image blur, distortion, motion, and ghosting artifacts, lesion recognition, and contour delineation with a 5-point Likert scale. Mean amide proton transfer (APT) values of brain tumors (APTtumor), the contralateral normal-appearing white matter (APTCNAWM), and the peritumoral edema area (if present, APTedema) and the tumor volume (VAPT) were measured for objective evaluation and determination of the optimal AF. The Ki67 labeling index was also measured by using standard immunohistochemical staining procedures in samples from patients with gliomas, and the correlation between tumor APT values and the Ki67 index was analyzed. Results The image quality of AF = CS5 was significantly lower than that of other groups. VAPT showed significant differences among the six sequences in meningiomas (p = 0.048) and gliomas (p = 0.023). The pairwise comparison showed that the VAPT values of meningiomas measured from images by CS5 were significantly lower, and gliomas were significantly larger than those by SENSE1.6 and other CS accelerations, (p < 0.05). APTtumor (p = 0.191) showed no significant difference among the three types of tumors. The APTtumor values of gliomas measured by APTw images with the SENSE factor of 1.6 and the CS factor of 2, 3, and 4 (except for CS5) were all positively correlated with Ki67. Conclusion Compressed SENSE could be successfully extended to accelerated 3D APTw imaging of brain tumors without compromising image quality using the AF of 4.
Large Margin and Local Structure Preservation Sparse Representation Classifier for Alzheimer’s Magnetic Resonance Imaging Classification

Alzheimer’s disease (AD) is a progressive dementia in which the brain shrinks as the disease progresses. The use of machine learning and brain magnetic resonance imaging (MRI) for the early diagnosis of AD has a high probability of clinical value and social significance. Sparse representation classifier (SRC) is widely used in MRI image classification. However, the traditional SRC only considers the reconstruction error and classification error of the dictionary, and does not consider the global and local structural information between images, which results in unsatisfactory classification performance. Therefore, a large margin and local structure preservation sparse representation classifier (LMLS-SRC) is developed in this manuscript. The LMLS-SRC algorithm uses the classification large margin term based on the representation coefficient, which results in compactness between representation coefficients of the same class and a large margin between representation coefficients of different classes. The LMLS-SRC algorithm uses local structure preservation term to inherit the manifold structure of the original data. In addition, the LMLS-SRC algorithm imposes the ℓ2,1-norm on the representation coefficients to enhance the sparsity and robustness of the model. Experiments on the KAGGLE Alzheimer’s dataset show that the LMLS-SRC algorithm can effectively diagnose non AD, moderate AD, mild AD, and very mild AD.
Rhythm May Be Key to Linking Language and Cognition in Young Infants: Evidence From Machine Learning

Rhythm is key to language acquisition. Across languages, rhythmic features highlight fundamental linguistic elements of the sound stream and structural relations among them. A sensitivity to rhythmic features, which begins in utero, is evident at birth. What is less clear is whether rhythm supports infants' earliest links between language and cognition. Prior evidence has documented that for infants as young as 3 and 4 months, listening to their native language (English) supports the core cognitive capacity of object categorization. This precocious link is initially part of a broader template: listening to a non-native language from the same rhythmic class as (e.g., German, but not Cantonese) and to vocalizations of non-human primates (e.g., lemur, Eulemur macaco flavifrons, but not birds e.g., zebra-finches, Taeniopygia guttata) provide English-acquiring infants the same cognitive advantage as does listening to their native language. Here, we implement a machine-learning (ML) approach to ask whether there are acoustic properties, available on the surface of these vocalizations, that permit infants' to identify which vocalizations are candidate links to cognition. We provided the model with a robust sample of vocalizations that, from the vantage point of English-acquiring 4-month-olds, either support object categorization (English, German, lemur vocalizations) or fail to do so (Cantonese, zebra-finch vocalizations). We assess (a) whether supervised ML classification models can distinguish those vocalizations that support cognition from those that do not, and (b) which class(es) of acoustic features (including rhythmic, spectral envelope, and pitch features) best support that classification. Our analysis reveals that principal components derived from rhythm-relevant acoustic features were among the most robust in supporting the classification. Classifications performed using temporal envelope components were also robust. These new findings provide in principle evidence that infants' earliest links between vocalizations and cognition may be subserved by their perceptual sensitivity to rhythmic and spectral elements available on the surface of these vocalizations, and that these may guide infants' identification of candidate links to cognition.
Alcohol Septal Ablation or Septal Myectomy? An Updated Systematic Review and Meta-Analysis of Septal Reduction Therapy for Hypertrophic Obstructive Cardiomyopathy

Objective To evaluate the safety and effectiveness of alcohol septal ablation (ASA) and septal myectomy (SM) for the treatment of hypertrophic obstructive cardiomyopathy. Methods We searched the PubMed, MEDLINE, EMBASE, and CBM databases for observational research articles related to ASA and SM published from the establishment of the databases to November 2021. All ultimate selected articles were highly related to our target. The Newcastle-Ottawa Scale was used to evaluate the literature quality. A fixed or random effect model was performed in the meta-analysis depending on the heterogeneity of the included studies. The Mantel-Haenszelt test with relative risk ratio (RR) and 95% confidence interval (CI) was used to measure the effect indicator of binary data, while the inverse variance method with weighted mean difference (WMD) and 95% CI was used to measure the effect indicator of continuous data. Results A totally of 3,647 cases (1,555 cases treated with ASA and 2,092 cases treated with SM) were included. The results of the systematic review indicated no statistically significant difference in postoperative all-cause mortality (RR = 0.82; 95% CI: 0.65–1.04; P = 0.10) between patients treated with ASA and SM, but both the reduction in the postoperative left ventricular outflow tract pressure gradient (WMD = 9.35 mmHg, 95% CI: 5.38–13.31, P < 0.00001) and the post-operative improvement on cardiac function, assessed by the grade of New York Heart Association (NYHA), compared to pre-operative measurements (WMD = 0.13; 95% CI: 0.00–0.26; P < 0.04) in the ASA group were slightly inferior to those in the SM group. In addition, both the risk of pacemaker implantation (RR = 2.83, 95% CI: 2.06–3.88; P < 0.00001) and the risk of reoperation (RR = 11.23, 95% CI: 6.21–20.31; P < 0.00001) are recorded at a higher level after ASA procedure. Conclusion Both ASA and SM have a high degree of safety, but the reduction in the postoperative left ventricular outflow tract pressure gradient and the improvement on cardiac function are slightly inferior to SM. In addition, both the risk of pacemaker implantation and the risk of reoperation are recorded at a higher level after ASA procedure. The operative plan should be chosen through multidisciplinary discussions in combination with the wishes of the patients and the actual clinical situation.
Applying Theory to Explain the Influence of Factors External to an Organization on the Implementation of an Evidence-Based Intervention

Despite its widely acknowledged influence on implementation, limited research has been done on how the external environment (i.e., outer setting) determines when organizations adopt and implement new interventions. Determinant frameworks identify several outer setting-level factors such as funding streams, inter-organizational relationships, and peer pressure. However, these frameworks do not explain how or why outer-setting factors influence implementation. To advance research in this area, we argue for the importance of deriving theory-based propositions from organization theory to explain how outer setting factors influence organizations. Drawing on the work of the Organization Theory in Implementation Science (OTIS) project, we identified 20 propositions from five classic organization theories—Complexity Theory, Contingency Theory, Institutional Theory, Resource Dependence Theory, and Transaction Cost Economics. We then applied those propositions to hypothesize relationships among outer setting factors, implementation strategies, and implementation outcomes in five case studies of evidenced-based tobacco control interventions. The five case studies address the implementation of smoke-free policies, community health worker-led tobacco education and cessation programs, 5 A's (Ask, Advise, Assess, Assist, and Arrange), point-of-sale tobacco marketing policy interventions, and quitlines. The case studies illustrate how propositions may be used to guide the selection and testing of implementation strategies. Organization theories provide a menu of propositions that offer guidance for selecting and optimizing high-leverage implementation strategies that target factors at the level of outer setting. Furthermore, these propositions suggest testable hypotheses regarding the mechanisms underlying the influence of outer-setting factors on how and why organizations adopt and implement interventions.
Intersectional Invisibility in Women’s Diversity Interventions

Many diversity interventions for women are ineffective. One reason for this may be that the field that diversity interventions are usually based on, the social sciences, often do not consider intra-group differences among women. Specifically, differences by racialization may be excluded from such diversity interventions. The present research examines whether racially marginalized women have different diversity interventions needs than White women, and whether organizations are less likely to represent those needs (i.e., intersectional invisibility). Across an open-ended coding (n = 293) and a ranking study (n = 489), Black women noted a need to incorporate intersectional differences, Asian women prioritized methods to address challenges to their authority, and White women indicated a need to address agency perceptions. Improving work-life balance and networks was a shared concern among participants, though we theorized different racially gendered reasons for why these intervention needs are relevant to each group. In Study 3 (n = 92 organizations), we analyzed organizations’ websites using word count and textual analysis. Organizations— including the Education, Science, and Research sector— most readily advocated for women through enhancing agency. They were also less likely to mention dealing with perceptions of excessive agency or addressing intersectional considerations. The organizations broadly mentioned other marginalized groups besides women, but rarely did they do so intersectionality. Taken together, our findings demonstrate different intervention priorities across differently racialized groups. We found evidence of intersectional invisibility where organizations were more likely to address agency-enhancing intervention needs while failing to include other intervention needs relevant for Black women and Asian women. We discuss the implications of these findings for organizations, in general, as well as potential implications for the field of academic social sciences.
Biomechanical Effects of 3D-Printed Bioceramic Scaffolds With Porous Gradient Structures on the Regeneration of Alveolar Bone Defect: A Comprehensive Study

In the repair of alveolar bone defect, the microstructure of bone graft scaffolds is pivotal for their biological and biomechanical properties. However, it is currently controversial whether gradient structures perform better in biology and biomechanics than homogeneous structures when considering microstructural design. In this research, bioactive ceramic scaffolds with different porous gradient structures were designed and fabricated by 3D printing technology. Compression test, finite element analysis (FEA) revealed statistically significant differences in the biomechanical properties of three types of scaffolds. The mechanical properties of scaffolds approached the natural cancellous bone, and scaffolds with pore size decreased from the center to the perimeter (GII) had superior mechanical properties among the three groups. While in the simulation of Computational Fluid Dynamics (CFD), scaffolds with pore size increased from the center to the perimeter (GI) possessed the best permeability and largest flow velocity. Scaffolds were cultured in vitro with rBMSC or implanted in vivo for 4 or 8 weeks. Porous ceramics showed excellent biocompatibility. Results of in vivo were analysed by using micro-CT, concentric rings and VG staining. The GI was superior to the other groups with respect to osteogenicity. The Un (uniformed pore size) was slightly inferior to the GII. The concentric rings analysis demonstrated that the new bone in the GI was distributed in the periphery of defect area, whereas the GII was distributed in the center region. This study offers basic strategies and concepts for future design and development of scaffolds for the clinical restoration of alveolar bone defect.
Catching a Walker in the Act—DNA Partitioning by ParA Family of Proteins

Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
Evidences of Bedrock Forcing on Glacier Morphodynamics: A Case Study in Italian Alps

In mountain glaciers, the influence of bedrock geometry on glacier surface morphology is often assumed; quantitative evidence, however, is rare. In our research, we measured the ice thickness of the Planpincieux Glacier (North-west Italy) and detected the bedrock topography using ground-penetrating radar. Additionally, we investigated the glacier surface morphology using structure from motion and the glacier kinematics using digital image correlation of terrestrial images. A digital terrain analysis showed evidence of recurrent crevasses whose position corresponded to bedrock steps. On average, since 2014, their positions varied between 6 and 14 m and were 40 ± 8 m downstream of the bedrock steps. Bedrock and glacier topography presented out-of-phase correlated undulations that approximately fit a sinusoidal function of different amplitude. Moreover, we show the morphological evolution of an unstable sector whose thickness at the end of the ablation seasons has remained approximately constant since 2014. Contrarily, the ice melting during the 2020 ablation season caused a volume loss of >30%. Since, in general, the damages provoked by a potential ice avalanche depend primarily on the involved volume, this finding demonstrates that frequent morphology monitoring is essential for correct glacial hazard assessment.
Genetic Diversity, Habitat Relevance and Conservation Strategies of the Silver Carp in the Yangtze River by Simple Sequence Repeat

The spatial distribution of fish individuals is affected by habitat conditions and species ecological characteristics, and it also reflects the longtime adaptation to habitat at the phenotypic and genotypic level. As a typical river-lake migratory fish species, the silver carp habitat selection was determined by its migration preference and genetic features. In this study, 15 microsatellite fluorescent markers combined with capillary electrophoresis were used to analyze the genetic diversity, genetic differentiation, and structure of nature silver carp populations in the Sanzhou (SZ), Hukou (HK), Anqing (AQ), Zhenjiang (ZJ), and Rugao (RG) sections of the Yangtze River. The results showed that 15 microsatellite loci exhibited medium to high polymorphisms. The overall genetic diversity in the Yangtze River was high, with the average value of Shannon’s information index ranging from 1.559 to 1.668. The numbers of alleles (Ne) ranged from 1.630 to 10.100. The expected heterozygosity (He, 0.690–0.721) was higher than observed heterozygosity (Ho, 0.598–0.646), and the genetic variation mainly originated from within the population (94.69%). However, the entire population was in the state of heterozygous deletion, and HK, RG populations encountered the risk of inbreeding risk (F > 1). Interestingly, there was a distinct genetic structure for the population in the HK section, which indicated that local population has occurred to the silver carp in this river section, and they may also possess aggregation characteristics specific to the river-lake-connected (RLC) habitat. The results mostly support the conclusion that the RLC habitat is essential for geographic population formation. The potential impact of special habitats on natural populations should be considered, and continuous surveys on population dynamics should be performed.
High Diazotrophic Diversity but Low N2 Fixation Activity in the Northern Benguela Upwelling System Confirming the Enigma of Nitrogen Fixation in Oxygen Minimum Zone Waters

Oxygen minimum zones (OMZs) have been suggested as a suitable niche for the oxygen-sensitive process of biological fixation of dinitrogen (N2) gas. However, most N2 fixation rates reported from such waters are low. This low N2 fixation activity has been proposed to result from the unusual community of N2 fixers, in which cyanobacteria were typically underrepresented. The Northern Benguela Upwelling System (North BUS) is part of one of the most productive marine ecosystems and hosts a well-developed OMZ. Although previous observations indicated low to absent N2 fixation rates, the community composition of diazotrophs needed to understand the North BUS has not been described. Here, we present a first detailed analysis of the diazotrophic diversity in the North BUS OMZ and the Angola tropical zone (ATZ), based on genetic data and isotope speciation. Consistent with a previous study, we detected a slight N deficit in the OMZ, but isotope data did not indicate any active or past N2 fixation. The diazotroph community in the North BUS was dominated by non-cyanobacterial microbes clustering with members of gamma-proteobacteria, as is typical for other OMZ regions. However, we found a strikingly high diversity of Cluster III diazotrophs not yet described in other OMZs. In contrast to previous observations, we could also identify cyanobacteria of the clades Trichodesmium sp. , UCYN-A and Cyanothece sp. , in surface waters connected to or above the OMZ, which were potentially active as shown by the presence of genes and transcripts of the key functional marker gene for N2 fixation, nifH. While the detection of diazotrophs and the absence of active N2 fixation (based on isotopic speciation) are consistent with other OMZ observations, the detected regional variation in the diversity and presence of cyanobacteria indicate that we still are far from understanding the role of diazotrophs in OMZs, which, however, is relevant for understanding the N cycle in OMZ waters, as well for predicting the future development of OMZ biogeochemistry in a changing ocean.
Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis–antenna proteins, plant–pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.