Miracle-dz/UniFAR-FTUs huggingface dataset:
A Twisted Filament and Its Helix Structure Formation

The relation is investigated between the wave number k 0 of a twisted polypropylene filament and the wave number k 1 of the double helix composed of the filaments. The sum of the wave numbers is zero, illustrating the rule of wave number conservation unless the product t = ka of the wave number k and radius a of the filament is large. The deviation from the rule Δt is proportional to t 0 3 ≡ k 0 3 a 3, and the proportionality constant y is equal to the elasticity/rigidity ratio E/G.
Complex posttraumatic stress disorder: The need to consolidate a distinct clinical syndrome or to reevaluate features of psychiatric disorders following interpersonal trauma?

Complex posttraumatic stress disorder (Complex PTSD) has been recently proposed as a distinct clinical entity in the WHO International Classification of Diseases, 11th version, due to be published, two decades after its first initiation. It is described as an enhanced version of the current definition of PTSD, with clinical features of PTSD plus three additional clusters of symptoms namely emotional dysregulation, negative self-cognitions and interpersonal hardship, thus resembling the clinical features commonly encountered in borderline personality disorder (BPD). Complex PTSD is related to complex trauma which is defined by its threatening and entrapping context, generally interpersonal in nature. In this manuscript, we review the current findings related to traumatic events predisposing the above-mentioned disorders as well as the biological correlates surrounding them, along with their clinical features. Furthermore, we suggest that besides the present distinct clinical diagnoses (PTSD; Complex PTSD; BPD), there is a cluster of these comorbid disorders, that follow a continuum of trauma and biological severity on a spectrum of common or similar clinical features and should be treated as such. More studies are needed to confirm or reject this hypothesis, particularly in clinical terms and how they correlate to clinical entities’ biological background, endorsing a shift from the phenomenologically only classification of psychiatric disorders towards a more biologically validated classification.
Proposed Diagnostic Criteria for Smartphone Addiction

Background Global smartphone penetration has led to unprecedented addictive behaviors. The aims of this study are to develop diagnostic criteria of smartphone addiction and to examine the discriminative ability and the validity of the diagnostic criteria. Methods We developed twelve candidate criteria for characteristic symptoms of smartphone addiction and four criteria for functional impairment caused by excessive smartphone use. The participants consisted of 281 college students. Each participant was systematically assessed for smartphone-using behaviors by psychiatrist’s structured diagnostic interview. The sensitivity, specificity, and diagnostic accuracy of the candidate symptom criteria were analyzed with reference to the psychiatrists’ clinical global impression. The optimal model selection with its cutoff point of the diagnostic criteria differentiating the smartphone addicted subjects from non-addicted subjects was then determined by the best diagnostic accuracy. Results Six symptom criteria model with optimal cutoff point were determined based on the maximal diagnostic accuracy. The proposed smartphone addiction diagnostic criteria consisted of (1) six symptom criteria, (2) four functional impairment criteria and (3) exclusion criteria. Setting three symptom criteria as the cutoff point resulted in the highest diagnostic accuracy (84.3%), while the sensitivity and specificity were 79.4% and 87.5%, respectively. We suggested determining the functional impairment by two or more of the four domains considering the high accessibility and penetration of smartphone use. Conclusion The diagnostic criteria of smartphone addiction demonstrated the core symptoms “impaired control” paralleled with substance related and addictive disorders. The functional impairment involved multiple domains provide a strict standard for clinical assessment.
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Significance Wood decay fungi have historically been characterized as either white rot, which degrade all components of plant cell walls, including lignin, or brown rot, which leave lignin largely intact. Genomic analyses have shown that white-rot species possess multiple lignin-degrading peroxidases (PODs) and expanded suites of enzymes attacking crystalline cellulose. To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. Moreover, they appear to degrade lignin, based on decay analyses on wood wafers. Our results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms. Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
Breaking the Link between Environmental Degradation and Oil Palm Expansion: A Method for Enabling Sustainable Oil Palm Expansion

Land degradation is a global concern. In tropical areas it primarily concerns the conversion of forest into non-forest lands and the associated losses of environmental services. Defining such degradation is not straightforward hampering effective reduction in degradation and use of already degraded lands for more productive purposes. To facilitate the processes of avoided degradation and land rehabilitation, we have developed a methodology in which we have used international environmental and social sustainability standards to determine the suitability of lands for sustainable agricultural expansion. The method was developed and tested in one of the frontiers of agricultural expansion, West Kalimantan province in Indonesia. The focus was on oil palm expansion, which is considered as a major driver for deforestation in tropical regions globally. The results suggest that substantial changes in current land-use planning are necessary for most new plantations to comply with international sustainability standards. Through visualizing options for sustainable expansion with our methodology, we demonstrate that the link between oil palm expansion and degradation can be broken. Application of the methodology with criteria and thresholds similar to ours could help the Indonesian government and the industry to achieve its pro-growth, pro-job, pro-poor and pro-environment development goals. For sustainable agricultural production, context specific guidance has to be developed in areas suitable for expansion. Our methodology can serve as a template for designing such commodity and country specific tools and deliver such guidance.
Electronic tracking tag programming is critical to data collection for behavioral time‐series analysis

Electronic tracking tags are major tools of ecological research and management, but programming sophisticated tags can be challenging. We discovered that a common programming scheme can negatively affect the quality of tracks collected by Argos tags. Here we describe the problem and how it occurred. We then simulated a series of tracks with different data collection schemes to investigate how spatial precision and temporal frequency affect the overall quality of tracking data. Tracks were simulated using a two-state composite correlated random walk (CCRW). Tracks were simulated with two spatial scales, using parameters estimated from northern elephant seal (large scale) and California sea lion (small scale) tracking data. Onto each simulated track, observations of varying precision, frequency, and censoring were imposed. We then fit the CCRW in a state-space model (SSM) to the simulated observations in order to assess how data quality and frequency affected recovery of known behavioral state and location. We show that when movement scales are small, regular observations were critical to recover behavior and location. In addition, tracks with frequent regular locations (increasing N) overcame low spatial accuracy (e.g., Argos) to detect small-scale movement patterns, suggesting frequently collected Argos locations may be as good as infrequently collected GPS in some circumstances. From these results and our experience tracking animals generally, we produce a set of guidelines for those manufacturing, programming, and deploying electronic tracking tags to maximize the utility of the data they produce.
Probabilistic Analysis of the Material and Shape Properties for Human Liver

Realistic assessments of liver injury risk for the entire occupant population require incorporating inter-subject variations into numerical human models. The main objective of this study was to quantify the variations in shape and material properties of the human liver. Statistical shape analysis was applied to analyze the geometrical variation using a surface set of 15 adult human livers recorded in an occupant posture. Principal component analysis was then utilized to obtain the modes of variation, the mean model, and a set of 95% statistical boundary shape models. Specimen-specific finite element (FE) models were employed to quantify material and failure properties of human liver parenchyma. The mean material model parameters were then determined, and a stochastic optimization approach was utilized to determine the standard deviations of the material model parameters. The distributions of the material parameters were used to develop probabilistic FE models of the liver implemented in THUMS human FE model to simulate oblique impact tests under three impact speeds. In addition, the influence of organ preservation on the biomechanical responses of animal livers was investigated using indentation and tensile tests. Results showed that the first five modes of the human liver shape models accounted for more than 70% of the overall anatomical variations. The Ogden material model with two parameters showed a good fit to experimental tensile data before failure. Significant changes of the biomechanical responses of liver parenchyma were found after cooling or freezing storage. The force-deflection responses of THUMS model with probabilistic liver material models were within the test corridors obtained from cadaveric tests. Significant differences were observed in the maximum and minimum principal Green-Lagrangian strain values recorded in the THUMS liver model with the default and updated average material properties. The results from this study could help in the development of more biofidelic human models, which may provide a better understanding of injury mechanisms of the liver during automobile collisions.
Data Augmentation Generative Adversarial Networks

Effective training of neural networks requires much data. In the low-data regime, parameters are underdetermined, and learnt networks generalise poorly. Data Augmentation alleviates this by using existing data more effectively. However standard data augmentation produces only limited plausible alternative data. Given there is potential to generate a much broader set of augmentations, we design and train a generative model to do data augmentation. The model, based on image conditional Generative Adversarial Networks, takes data from a source domain and learns to take any data item and generalise it to generate other within-class data items. As this generative process does not depend on the classes themselves, it can be applied to novel unseen classes of data. We show that a Data Augmentation Generative Adversarial Network (DAGAN) augments standard vanilla classifiers well. We also show a DAGAN can enhance few-shot learning systems such as Matching Networks. We demonstrate these approaches on Omniglot, on EMNIST having learnt the DAGAN on Omniglot, and VGG-Face data. In our experiments we can see over 13% increase in accuracy in the low-data regime experiments in Omniglot (from 69% to 82%), EMNIST (73.9% to 76%) and VGG-Face (4.5% to 12%); in Matching Networks for Omniglot we observe an increase of 0.5% (from 96.9% to 97.4%) and an increase of 1.8% in EMNIST (from 59.5% to 61.3%).
Differential patterns of functional connectivity in Progressive and Stable Mild Cognitive Impairment subjects

It is now widely accepted that AD is characterized by a functional disconnection between brain regions. The disease appears to begin up to decades prior to clinical diagnosis. Therefore, in the present study we combined Magnetoencephalography, a memory task and functional connectivity analysis in Mild Cognitive Impairment (19) subjects in order to identify functional connectivity patterns that could characterize subjects who would eventually go on to develop the disease. We monitored 19 subjects and finally 5 of them develop d Alzheimer Disease. These progressive patients showed a differential profile of functiona l connectivity values compared to those patients that remained stable over time. Specifically there were higher synchronisation values over parietooccipital regions and over the anterior frontal reg ion in α and β frequency bands. The fact that we only include hit responses to analyze functional co uplings reinforces the idea that Progressive Mild Cognitive Impairment subjects over-synchronize brai n networks, in these two frequency bands (previously associated with working memory mechanis ms), to compensate and achieve a level of performance in the memory task that is similar to t he rest of the participants. The involvement of these brain regions in A β accumulation and its possible associations with hy per-synchronization are
Frailty and famine: Patterns of mortality and physiological stress among victims of famine in medieval London.

OBJECTIVES Famine can be defined as a shortage of foodstuffs that instigates widespread excess mortality due to starvation, infectious disease, and social disruption. Like other causes of catastrophic mortality, famine has the potential to be selective. This study examines how famines in medieval London were selective with respect to previous stress, age, and sex. METHODS This study compares famine burials to nonfamine (attritional) burials from the St Mary Spital cemetery, London (c. 1120-1540 AD). We evaluate the associations between age, sex, and skeletal stress indicators [cribra orbitalia, linear enamel hypoplasia (LEH), and periosteal lesions] using hierarchical log-linear analysis. Additionally, sex is modeled as a covariate affecting the Gompertz hazard of mortality. RESULTS Significant associations exist between famine burials and LEH and between attritional burials and periosteal lesions, independent of age or sex. Sex did not significantly affect risk of mortality in the 12th-13th centuries. However, males interred in attritional burials c. 1400-1539 AD faced a lower risk of mortality compared to females. DISCUSSION The LEH results suggest that early exposure to stressors increased frailty in the context of famine. The periosteal lesion results suggest that individuals were more likely to survive stressors and thus form these lesions under nonfamine conditions. Hazard analysis suggests that a cultural or biological transformation during this period affected sex differences in mortality. Possible causes include the selective mortality during the Black Death, which might have influenced risks of mortality among survivors, or unequal distribution of improvements in standards of living after the epidemic. Am J Phys Anthropol 160:272-283, 2016. © 2016 Wiley Periodicals, Inc.
Associations of RASSF1A, RARβ, and CDH1 promoter hypermethylation with oral cancer risk

Abstract Background: Oral tumor is a heterogeneous group of tumors, in which it has several different histopathological and molecular features. Recently, genetic and epigenetic alterations are often detected in the development of oral cancer. Gene promoter hypermethylation leads to the silencing of cancer related genes without changes of genes sequence. To clarify the effect of RAS association domain family protein 1a (RASSF1A), retinoic acid receptor beta (RARβ), and E-cadherin (CDH1) promoter hypermethylation on the risk of oral cancer, we performed this meta-analysis. Methods: PubMed, Web of Science, Embase, and Chinese National Knowledge Infrastructure (CNKI) databases were retrieved to identify eligible articles. Stata 12.0 software was used to analyze extracted data of the included articles. Odds ratios (ORs) with the corresponding 95% confidence interval (95% CI) were calculated to evaluate the associations of RASSF1A, RARβ, and CDH1 promoter hypermethylation with oral cancer risk. Results: Around 23 literatures with 29 studies were included in the final meta-analysis, in which 12 studies were about RASSF1A promoter methylation, 4 studies were about RARβ promoter methylation, and 13 studies were about CDH1 promoter methylation. Overall, the results of this meta-analysis showed that there were significant associations between RASSF1A, RARβ, and CDH1 promoter hypermethylation and oral cancer risk (RASSF1A, OR = 11.8, 95% CI = 6.14–22.66; RARβ, OR = 20.35, 95% CI = 5.64–73.39; CDH1, OR = 13.46, 95% CI = 5.31–34.17). In addition, we found that RASSF1A promoter hypermethylation exerted higher frequency in the tongue tumor than other site tumor in mouth (RASSF1A, tongue tumor vs other site tumor in mouth, unmethylation vs methylation, OR = 0.65, 95%CI = 0.44–0.98). Conclusion: RASSF1A, RARβ, and CDH1 promoter hypermethylation might significantly increase the risk of oral cancer.
Lessons from fMRI about Mapping Cortical Columns

Recently developed fMRI can map small functional structures noninvasively and repeatedly without any depth limitation. However, there has been a persistent concern as to whether the high-resolution fMRI signals actually mark the sites of increased neural activity. To examine this outstanding issue, the authors used iso-orientation columns of isoflurane-anesthetized cats as a biological model and confirmed the neural correlation of fMRI iso-orientation maps by comparing them with intrinsic optical imaging maps. The results suggest that highest fMRI signals indeed indicate the sites of increased neuronal activity. Now fMRI can be used to determine plastic and/or developmental change of functional columnar structure possibly on a layer-to-layer basis. In this review, the authors focus mainly on what technical aspects should be considered when mapping functional cortical columns, including imaging techniques and experimental design. NEUROSCIENTIST 14(3):287–299, 2008. DOI: 10.1177/1073858407309541
Tensile Properties of Z-pins Reinforced Laminates

The delamination toughness of Z-pins reinforced laminates could be improved significantly and in-plane mechanical properties of the laminates were degraded with a few of Z-pins inserted in the through-thickness direction. The influence of Z-pin inserted parameters and moisture absorption condition on the tensile properties of the laminates was experimentally studied. The results showed that Z-pins can change microstructure and the original stress-strain state of the Z-pinned laminates, and the tensile strength and modulus of the laminates were obviously influenced. The tensile modulus of the Z-pinned laminates decreased with the increasing of Z-pins’ diameter and volume content, while it increased with that of Z-pins’ angle. The moisture absorption rate and balanced moisture content of Z-pinned laminates increased due to Z-pin inserted, which eventually resulted in accelerating degradation of performance of composites laminates.
Three-Dimensional Curing Stresses in Symmetric Cross-Ply Laminates with Temperature-Dependent Properties

A fully three-dimensional finite element analysis of curing stresses in cross-ply boron/epoxy composite laminates is presented. Comparisons are made between constant and temperature- dependent material properties and a constitutive model which includes the coupling between stress and temperature dependence of material properties. Also examined is the error introduced by the common assumption of equality of all shear moduli (G12, G13, G23) and certain Poisson's ratios (ν 12, ν13, ν23). Interlaminar stresses near the laminate midplane and 0/90 interface are presented, including effects which occur near the free corner of the laminate. Differences in the three thermal expansion models are found to be significant for the boron/epoxy system in some stress terms and negligible in others. The errors introduced by the coefficient equality assump tions are found to be small. Omission of the stress-thermal expansion interaction term is found to result in substantial underestimates of curing stresses. This is in agreement with the results of previous investigators which included the coupling term in a lamination theory model.
Stabilisation and consensus of linear systems with multiple input delays by truncated pseudo-predictor feedback

This paper provides a new approach referred to as pseudo-predictor feedback (PPF) for stabilisation of linear systems with multiple input delays. Differently from the traditional predictor feedback which is from the model reduction appoint of view, the proposed PPF utilises the idea of prediction by generalising the corresponding results for linear systems with a single input delay to the case of multiple input delays. Since the PPF will generally lead to distributed controllers, a truncated pseudo-predictor feedback (TPPF) approach is established instead, which gives finite dimensional controllers. It is shown that the TPPF can compensate arbitrarily large yet bounded delays as long as the open-loop system is only polynomially unstable. The proposed TPPF approach is then used to solve the consensus problems for multi-agent systems characterised by linear systems with multiple input delays. Numerical examples show the effectiveness of the proposed approach.
Adapting a Medical speech to speech translation system (MedSLT) to Arabic

We describe the adaptation for Arabic of the grammar-based MedSLT medical speech system. The system supports simple medical diagnosis questions about headaches using vocabulary of 322 words. We show that the MedSLT architecture based on motivated general grammars produces very good results, with a limited effort. Based on the grammars for other languages covered by the system, it is in fact very easy to develop an Arabic grammar and to specialize it efficiently for the different system tasks. In this paper, we focus on generation.