bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the solidification of the manifold of the t-distributed stochastic neighbour embedding for condition classification of machine tools
Authors: Wang Jing , Cheng Xiaobin , Wang Xun , Gao Yan , Liu Bin , Han Mingmei , Yang Jun 
Published: November 2021

Abstract
t-distributed stochastic neighbour embedding (t-SNE) is of considerable interest in machining condition monitoring for feature selection. In this paper, the neural networks are introduced to solidify the manifold of the t-SNE prior to classification. This leads to the improved feature selection method, namely the Net-SNE. Conventional statistical features are first extracted from vibration signals to form a high dimensional feature vector. The redundancies in the feature vector are subsequently removed by the t-SNE. Then the neural networks build a mapping model between the high dimensional feature vector and the selected features. The new data is calculated directly using the mapping model. The experiments were conducted on a lathe and a milling machine to collect vibration signals under common working conditions. The K-nearest neighbour classifier is applied to a small sample case and a class-imbalance case to compare the classification performance with and without the Net-SNE. The results demonstrate that the Net-SNE has the advantage over the t-SNE, since it can mine the discriminative features and solidifiy the manifold in the calculation of the new data. Moreover, the proposed method significantly improves the classification accuracy by Net-SNE, along with better classification performance in data-limited situations.
High-Resolution Ultrasound-Assisted Assessment of Preliminary Short-term Safety Outcomes of an Implant-Based Augmentation Mammaplasty Using a Bioengineered, Cell-Friendly, Smooth-Surface Device in Korean Females
Authors: Lee Sangdal , Jeong Jeong Pil , Sung Jung Youp , Choi Woo Sik , Moon Dong Seung , Kim Ho Chan , Kim Jae Hong 
Published: November 2021

AbstractBackgroundThe Motiva Ergonomix Round SilkSurface (Establishment Labs Holdings Inc., Alajuela, Costa Rica) is one of the representative brands of the fifth generation of a silicone gel-filled breast implant with a microtextured surface.ObjectivesIn this study, the authors describe preliminary short-term safety outcomes of an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface in Korean females.MethodsThe authors performed a retrospective analysis of medical records in a total of 69 females (n = 69) receiving an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface between September 26, 2017, and December 31, 2020. The authors analyzed incidences of postoperative complications.ResultsA total of 6 cases (8.7%) of postoperative complications occurred; these include 2 cases (2.9%) of early seroma, 1 case (1.4%) of capsular contracture, 2 cases (2.9%) of alterations in the shape, and 1 case (1.4%) of foreign body sensation. Time-to-events were estimated at 266.81 ± 273.17 days.ConclusionsThe authors describe our preliminary short-term safety outcomes of an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface in Korean females. But this deserves further large-scale studies with long periods of follow-up.Level of Evidence: 4
A deep learning model to identify gene expression level using cobinding transcription factor signals
Authors: Zhang Lirong , Yang Yanchao , Chai Lu , Li Qianzhong , Liu Junjie , Lin Hao , Liu Li 
Published: November 2021

Abstract
Gene expression is directly controlled by transcription factors (TFs) in a complex combination manner. It remains a challenging task to systematically infer how the cooperative binding of TFs drives gene activity. Here, we quantitatively analyzed the correlation between TFs and surveyed the TF interaction networks associated with gene expression in GM12878 and K562 cell lines. We identified six TF modules associated with gene expression in each cell line. Furthermore, according to the enrichment characteristics of TFs in these TF modules around a target gene, a convolutional neural network model, called TFCNN, was constructed to identify gene expression level. Results showed that the TFCNN model achieved a good prediction performance for gene expression. The average of the area under receiver operating characteristics curve (AUC) can reach up to 0.975 and 0.976, respectively in GM12878 and K562 cell lines. By comparison, we found that the TFCNN model outperformed the prediction models based on SVM and LDA. This is due to the TFCNN model could better extract the combinatorial interaction among TFs. Further analysis indicated that the abundant binding of regulatory TFs dominates expression of target genes, while the cooperative interaction between TFs has a subtle regulatory effects. And gene expression could be regulated by different TF combinations in a nonlinear way. These results are helpful for deciphering the mechanism of TF combination regulating gene expression.
Magnetic resonance reveals mitochondrial dysfunction and muscle remodelling in spinal muscular atrophy
Authors: Habets Laura E , Bartels Bart , Asselman Fay-Lynn , Hooijmans Melissa T , van den Berg Sandra , Nederveen Aart J , van der Pol W Ludo , Jeneson Jeroen A L 
Published: November 2021

AbstractGenetic therapy has changed the prognosis of hereditary proximal spinal muscular atrophy, although treatment efficacy has been variable. There is a clear need for deeper understanding of underlying causes of muscle weakness and exercise intolerance in patients with this disease to further optimize treatment strategies. Animal models suggest that in addition to motor neuron and associated musculature degeneration, intrinsic abnormalities of muscle itself including mitochondrial dysfunction contribute to the disease aetiology.To test this hypothesis in patients, we conducted the first in vivo clinical investigation of muscle bioenergetics. We recruited 15 patients and 15 healthy age and gender-matched control subjects in this cross-sectional clinico-radiological study. MRI and 31P magnetic resonance spectroscopy, the modality of choice to interrogate muscle energetics and phenotypic fibre-type makeup, was performed of the proximal arm musculature in combination with fatiguing arm-cycling exercise and blood lactate testing. We derived bioenergetic parameter estimates including: blood lactate, intramuscular pH and inorganic phosphate accumulation during exercise, and muscle dynamic recovery constants. A linear correlation was used to test for associations between muscle morphological and bioenergetic parameters and clinico-functional measures of muscle weakness.MRI showed significant atrophy of triceps but not biceps muscles in patients. Maximal voluntary contraction force normalized to muscle cross-sectional area for both arm muscles was 1.4-fold lower in patients than in controls, indicating altered intrinsic muscle properties other than atrophy contributed to muscle weakness in this cohort. In vivo31P magnetic resonance spectroscopy identified white-to-red remodelling of residual proximal arm musculature in patients on the basis of altered intramuscular inorganic phosphate accumulation during arm-cycling in red versus white and intermediate myofibres. Blood lactate rise during arm-cycling was blunted in patients and correlated with muscle weakness and phenotypic muscle makeup. Post-exercise metabolic recovery was slower in residual intramuscular white myofibres in patients demonstrating mitochondrial ATP synthetic dysfunction in this particular fibre type.This study provides the first in vivo evidence in patients that degeneration of motor neurons and associated musculature causing atrophy and muscle weakness in 5q spinal muscular atrophy type 3 and 4 is aggravated by disproportionate depletion of myofibres that contract fastest and strongest. Our finding of decreased mitochondrial ATP synthetic function selectively in residual white myofibres provides both a possible clue to understanding the apparent vulnerability of this particular fibre type in 5q spinal muscular atrophy types 3 and 4 as well as a new biomarker and target for therapy.
Neuroanatomical anomalies associated with rareAP4E1mutations in people who stutter
Authors: Chow Ho Ming , Li Hua , Liu Siyuan , Frigerio-Domingues Carlos , Drayna Dennis 
Published: November 2021

AbstractDevelopmental stuttering is a common speech disorder with strong genetic underpinnings. Recently, stuttering has been associated with mutations in genes involved in lysosomal enzyme trafficking. However, how these mutations affect the brains of people who stutter remains largely unknown. In this study, we compared grey matter volume and white matter fractional anisotropy between a unique group of seven subjects who stutter and carry the same rare heterozygous AP4E1 coding mutations and seven unrelated controls without such variants. The carriers of the AP4E1 mutations are members of a large Cameroonian family in which the association between AP4E1 and persistent stuttering was previously identified. Compared to controls, mutation carriers showed reduced grey matter volume in the thalamus, visual areas and the posterior cingulate cortex. Moreover, reduced fractional anisotropy was observed in the corpus callosum, consistent with the results of previous neuroimaging studies of people who stutter with unknown genetic backgrounds. Analysis of gene expression data showed that these structural differences appeared at the locations in which expression of AP4E1 is relatively high. Moreover, the pattern of grey matter volume differences was significantly associated with AP4E1 expression across the left supratentorial regions. This spatial congruency further supports the connection between AP4E1 mutations and the observed structural differences.
Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration
Authors: Siddiq Mustafa M , Hannila Sari S , Zorina Yana , Nikulina Elena , Rabinovich Vera , Hou Jianwei , Huq Rumana , Richman Erica L , Tolentino Rosa E , Hansen Jens , Velenosi Adam , Kwon Brian K , Tsirka Stella E , Maze Ian , Sebra Robert , Beaumont Kristin G , Toro Carlos A , Cardozo Christopher P , Iyengar Ravi , Filbin Marie T 
Published: November 2021

Abstract
Axonal regeneration in the mature CNS is limited by extracellular inhibitory factors. Triple knockout mice lacking the major myelin-associated inhibitors do not display spontaneous regeneration after injury, indicating the presence of other inhibitors. Searching for such inhibitors, we have detected elevated levels of histone H3 in human CSF 24 h after spinal cord injury. Following dorsal column lesions in mice and optic nerve crushes in rats, elevated levels of extracellular histone H3 were detected at the injury site. Similar to myelin-associated inhibitors, these extracellular histones induced growth cone collapse and inhibited neurite outgrowth. Histones mediate inhibition through the transcription factor Y-box-binding protein 1 and Toll-like receptor 2, and these effects are independent of the Nogo receptor. Histone-mediated inhibition can be reversed by the addition of activated protein C in vitro, and activated protein C treatment promotes axonal regeneration in the crushed optic nerve in vivo. These findings identify extracellular histones as a new class of nerve regeneration-inhibiting molecules within the injured CNS.
Passive localization of the central sulcus during sleep based on intracranial EEG
Authors: Alkawadri Rafeed , Zaveri Hitten P , Sheth Kevin N , Spencer Dennis D 
Published: November 2021

Abstract
We test the performance of a novel operator-independent EEG-based method for passive identification of the central sulcus (CS) and sensorimotor (SM) cortex. We studied seven patients with intractable epilepsy undergoing intracranial EEG (icEEG) monitoring, in whom CS localization was accomplished by standard methods. Our innovative approach takes advantage of intrinsic properties of the primary motor cortex (MC), which exhibits enhanced icEEG band-power and coherence across the CS. For each contact, we computed a composite power, coherence, and entropy values for activity in the high gamma band (80–115) Hz of 6–10 min of NREM sleep. Statistically transformed EEG data values that did not reach a threshold (th) were set to 0. We computed a metric M based on the transformed values and the mean Euclidian distance of each contact from contacts with Z-scores higher than 0. The last step was implemented to accentuate local network activity. The SM cortex exhibited higher EEG-band-power than non-SM cortex (P &lt; 0.0002). There was no significant difference between the motor/premotor and sensory cortices (P &lt; 0.47). CS was localized in all patients with 0.4 &lt; th &lt; 0.6. The primary hand and leg motor areas showed the highest metric values followed by the tongue motor area. Higher threshold values were specific (94%) for the anterior bank of the CS but not sensitive (42%). Intermediate threshold values achieved an acceptable trade-off (0.4: 89% specific and 70% sensitive).
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure
Authors: Wu Jing , Zhao Min , Li Tao , Sun Jinxiu , Chen Qi , Yin Chengliang , Jia Zhilong , Zhao Chenghui , Lin Gui , Ni Yuan , Xie Guotong , Shi Jinlong , He Kunlun 
Published: November 2021

Abstract
As the terminal clinical phenotype of almost all types of cardiovascular diseases, heart failure (HF) is a complex and heterogeneous syndrome leading to considerable morbidity and mortality. Existing HF-related omics studies mainly focus on case/control comparisons, small cohorts of special subtypes, etc., and a large amount of multi-omics data and knowledge have been generated. However, it is difficult for researchers to obtain biological and clinical insights from these scattered data and knowledge. In this paper, we built the Heart Failure Integrated Platform (HFIP) for data exploration, fusion analysis and visualization by collecting and curating existing multi-omics data and knowledge from various public sources and also provided an auto-updating mechanism for future integration. The developed HFIP contained 253 datasets (7842 samples), multiple analysis flow, and 14 independent tools. In addition, based on the integration of existing databases and literature, a knowledge base for HF was constructed with a scoring system for evaluating the relationship between molecular signals and HF. The knowledge base includes 1956 genes and annotation information. The literature mining module was developed to assist the researcher to overview the hotspots and contexts in basic and clinical research. HFIP can be used as a data-driven and knowledge-guided platform for the basic and clinical research of HF.
Database URL: http://heartfailure.medical-bigdata.com
Death, sex, and fertility: female infanticide in rural Spain, 1750–1950
Authors: Beltrán Tapia Francisco J , Marco-Gracia Francisco J 
Published: November 2021

Abstract
Relying on longitudinal micro data from rural Spain between 1750 and 1950, this article evidences that families mortally neglected a significant fraction of their female babies. Firstly, baptism records exhibited exceptionally high sex ratios at birth until the late nineteenth century. Secondly, having no previous male siblings increased the probability of male baptisms. Likewise, this same feature, together with the number of siblings alive, also increased female mortality during the first day of life. These findings are concentrated at higher parities and among landless and semi-landless families. Lastly, under-registration cannot explain these patterns affecting female mortality shortly after birth.
Miniseries 1—Part II: the comparative anatomy of the atrioventricular conduction axis
Authors: Macías Yolanda , de Almeida Marcos C , Tretter Justin T , Anderson Robert H , Spicer Diane E , Mohun Timothy J , Sánchez-Quintana Damián , Farré Jerónimo , Back Sternick Eduardo 
Published: November 2021

Abstract

Aims
The arrangement of the conduction axis is markedly different in various mammalian species. Knowledge of such variation may serve to question the validity of using animals as prospective models for design of systems for clinical use.

Methods and results
We compared the arrangement of the atrioventricular conduction axis in human, murine, canine, porcine, and bovine hearts, examining serially sectioned datasets from 20 human, 16 murine, 3 porcine, 5 canine, and 1 bovine hearts. We also analysed computed tomographic datasets obtained from bovines and one human heart. Unlike the situation in the human heart, there is no formation of an atrioventricular fibrous membranous septum in the murine, canine, porcine, nor bovine hearts. Canine, porcine, and bovine hearts also lack an infero-septal recess, when defined as a fibrous plate supporting the buttress of the atrial septum. In these species, half of the non-coronary leaflet is directly opposed to the ventricular septal surface.

Conclusion
There is a long right-sided non-branching component of the axis, which skirts the attachment of the non-coronary sinus of the aortic root. In the bovine heart, moreover, the left bundle branch usually extends intramyocardially as a solitary tape before surfacing and ramifying on the left ventricular septal surface. The difference in the atrioventricular conduction axis between species may influence the anatomical substrates for atrioventricular re-entry tachycardia, as well as providing inferences for assessing the risks of transcatheter implantation of the aortic valve. Further studies are now needed to assess these possibilities.
Miniseries 2—Septal and paraseptal accessory pathways—Part I: The anatomic basis for the understanding of para-Hisian accessory atrioventricular pathways
Authors: Anderson Robert H , Sanchez-Quintana Damian , Mori Shumpei , Spicer Diane E , Wellens Hein J J , Lokhwandala Yash , Cabrera Jose-Angel , Farre Jeronimo , Sternick Eduardo Back 
Published: November 2021

Abstract

Aims
Although the anatomy of the atrioventricular conduction axis was well described over a century ago, the precise arrangement in the regions surrounding its transition from the atrioventricular node to the so-called bundle of His remain uncertain. We aimed to clarify these relationships.

Methods and results
We have used our various datasets to examine the development and anatomical arrangement of the atrioventricular conduction axis, paying particular attention to the regions surrounding the point of penetration of the bundle of His. It is the areas directly adjacent to the transition of the atrioventricular conduction axis from the atrioventricular node to the non-branching atrioventricular bundle that constitute the para-Hisian areas. The atrioventricular conduction axis itself traverses the membranous part of the ventricular septum as it extends from the node to become the bundle, but the para-Hisian areas themselves are paraseptal. This is because they incorporate the fibrofatty tissues of the inferior pyramidal space and the superior atrioventricular groove. In this initial overarching review, we summarize the developmental and anatomical features of these areas along with the location and landmarks of the atrioventricular conduction axis. We emphasize the relationships between the inferior pyramidal space and the infero-septal recess of the subaortic outflow tract. The details are then explored in greater detail in the additional reviews provided within our miniseries.

Conclusion
Our anatomical findings, described here, provide the basis for our concomitant clinical review of the so-called para-Hisian arrhythmias. The findings also provide the basis for understanding the other variants of ventricular pre-excitation.
Light Intervention Effects on Circadian Activity Rhythm Parameters and Nighttime Sleep in Dementia Assessed by Wrist Actigraphy: A Systematic Review and Meta-Analysis
Authors: Canazei Markus , Papousek Ilona , Weiss Elisabeth M 
Published: November 2021

Abstract

Background and Objectives
Persons with dementia often show circadian rhythm disturbances and sleep problems. Timed light exposure seems to be a promising nonpharmacological treatment option. In this review, meta-analyses were run on light effects on circadian activity rhythm parameters in persons with dementia measured with wrist actimetry. Furthermore, we update a Cochrane review, published in 2014, on actigraphically measured light effects in nighttime sleep parameters in persons with dementia.

Research Design and Methods
Four electronic databases were searched for randomized controlled trials. Effects in meta-analyses were summarized by using mean differences and 95% confidence intervals. We followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to assess the risk of bias and registered the review protocol (PROSPERO: CRD42020149001).

Results
Thirteen trials met inclusion criteria, and either utilized light therapy devices, ambient room lighting systems, or dawn–dusk interventions. Eleven of these studies were subjected to meta-analyses. They did not reveal significant light effects on circadian activity parameters: amplitude (p = .62; n = 313), acrophase (p = .34; n = 313), intradaily variability (p = .51; n = 354), and interdaily stability (p = .38; n = 354). Furthermore, no light effects were found on sleep parameters: total sleep duration (p = .53; n = 594), sleep efficiency (p = .63; n = 333), wake after sleep onset (p = .95; n = 212), and sleep onset latency (p = .26; n = 156). Subgroup analyses, pooling data from 3 studies including persons with Alzheimer’s dementia, also did not show light effects on circadian activity and sleep parameters. The overall risk of bias of included studies was high.

Discussion and Implications
There is insufficient evidence for actigraphically measured circadian light effects in persons with dementia. More high-quality research is needed to recommend the application of adjunctive light.
Long-term outcomes after ascending aortic replacement and aortic root replacement for type A aortic dissection
Authors: Jormalainen Mikko , Kesävuori Risto , Raivio Peter , Vento Antti , Mustonen Caius , Honkanen Hannu-Pekka , Rosato Stefano , Simpanen Jarmo , Teittinen Kari , Biancari Fausto , Juvonen Tatu 
Published: November 2021

Abstract OBJECTIVESWe investigated whether the selective use of supracoronary ascending aorta replacement achieves late outcomes comparable to those of aortic root replacement for acute Stanford type A aortic dissection (TAAD).METHODSPatients who underwent surgery for acute type A aortic dissection from 2005 to 2018 at the Helsinki University Hospital, Finland, were included in this analysis. Late mortality was evaluated with the Kaplan–Meier method and proximal aortic reoperation, i.e. operation on the aortic root or aortic valve, with the competing risk method.RESULTSOut of 309 patients, 216 underwent supracoronary ascending aortic replacement and 93 had aortic root replacement. At 10 years, mortality was 33.8% after aortic root replacement and 35.2% after ascending aortic replacement (P = 0.806, adjusted hazard ratio 1.25, 95% confidence interval, 0.77–2.02), and the cumulative incidence of proximal aortic reoperation was 6.0% in the aortic root replacement group and 6.2% in the ascending aortic replacement group (P = 0.65; adjusted subdistributional hazard ratio 0.53, 95% confidence interval 0.15–1.89). Among 71 propensity score matched pairs, 10-year survival was 34.4% after aortic root replacement and 36.2% after ascending aortic replacement surgery (P = 0.70). Cumulative incidence of proximal aortic reoperation was 7.0% after aortic root replacement and 13.0% after ascending aortic replacement surgery (P = 0.22). Among 102 patients with complete imaging data [mean follow-up, 4.7 (3.2) years], the estimated growth rate of the aortic root diameter was 0.22 mm/year, that of its area 7.19 mm2/year and that of its perimeter 0.43 mm/year.CONCLUSIONSWhen stringent selection criteria were used to determine the extent of proximal aortic reconstruction, aortic root replacement and ascending aortic replacement for type A aortic dissection achieved comparable clinical outcomes.