bluuebunny/crossref_metadata_2025_split huggingface dataset:
EDGE: the mass–metallicity relation as a critical test of galaxy formation physics
Authors: Agertz Oscar , Pontzen Andrew , Read Justin I , Rey Martin P , Orkney Matthew , Rosdahl Joakim , Teyssier Romain , Verbeke Robbert , Kretschmer Michael , Nickerson Sarah 
Published: October 2019

ABSTRACT
We introduce the ‘Engineering Dwarfs at Galaxy Formation’s Edge’ (EDGE) project to study the cosmological formation and evolution of the smallest galaxies in the Universe. In this first paper, we explore the effects of resolution and sub-grid physics on a single low-mass halo ($M_{\rm halo}=10^{9}{\, \rm M}_\odot$), simulated to redshift z = 0 at a mass and spatial resolution of $\sim 20{\, \rm M}_\odot$ and ∼3 pc. We consider different star formation prescriptions, supernova feedback strengths, and on-the-fly radiative transfer (RT). We show that RT changes the mode of galactic self-regulation at this halo mass, suppressing star formation by causing the interstellar and circumgalactic gas to remain predominantly warm (∼104 K) even before cosmic reionization. By contrast, without RT, star formation regulation occurs only through starbursts and their associated vigorous galactic outflows. In spite of this difference, the entire simulation suite (with the exception of models without any feedback) matches observed dwarf galaxy sizes, velocity dispersions, V-band magnitudes, and dynamical mass-to-light-ratios. This is because such structural scaling relations are predominantly set by the host dark matter halo, with the remaining model-to-model variation being smaller than the observational scatter. We find that only the stellar mass–metallicity relation differentiates the galaxy formation models. Explosive feedback ejects more metals from the dwarf, leading to a lower metallicity at a fixed stellar mass. We conclude that the stellar mass–metallicity relation of the very smallest galaxies provides a unique constraint on galaxy formation physics.
How Is Love of the Neighbour Possible? A Løgstrupian Response to a Lutheran Critique of Levinas—and Vice Versa
Authors: Stern Robert 
Published: October 2019

AbstractThis paper considers how both Levinas and Løgstrup seek to explain how love of the neighbour is possible. It focuses on a criticism of Levinas made by Merold Westphal, which follows Kierkegaard in arguing on Lutheran grounds that such love first requires a relation to God as a “middle term,” but that Levinas cannot appeal to this relation to account for neighbour love, as for him the God relation itself arises through love of the neighbour. In response, the paper explores how Løgstrup, while working in a Lutheran tradition, like Levinas also sees neighbour love as arising without any prior God relation, showing how the accounts that each offer of how this is possible serve to complement each other.
Capacities, capabilities, and the societal impact of the humanities
Authors: Sigurðarson Eiríkur Smári 
Published: October 2019

Abstract
This article explores new theoretical directions for understanding societal impact of the humanities and in a wider context. Arguing from the position that current evaluation policies and practises are in many cases ill-suited to research in the humanities, with risk of goal displacement, it takes up the debate about what the proper goals of research in the humanities are. Asking: If we risk goal displacement, what are the proper goals researchers are being led away from? Using Miranda Fricker’s theory of epistemic justice and Amartya Sen’s capability approach, it argues for the need for a ‘capability theory’ for social capacities to understand societal impact. On the basis of this, a better understanding of the societal impact of research in the humanities can be developed, as well as new ways of assessing (ex ante and ex post) the societal impact of research projects and programmes in the humanities.
Distinct cerebellar regions for body motion discrimination
Authors: Ferrari Chiara , Ciricugno Andrea , Battelli Lorella , Grossman Emily D , Cattaneo Zaira 
Published: October 2019

Abstract
Visual processing of human movements is critical for adaptive social behavior. Cerebellar activations have been observed during biological motion discrimination in prior neuroimaging studies, and cerebellar lesions may be detrimental for this task. However, whether the cerebellum plays a causal role in biological motion discrimination has never been tested. Here, we addressed this issue in three different experiments by interfering with the posterior cerebellar lobe using transcranial magnetic stimulation (TMS) during a biological discrimination task. In Experiments 1 and 2, we found that TMS delivered at onset of the visual stimuli over the vermis (vermal lobule VI), but not over the left cerebellar hemisphere (left lobule VI/Crus I), interfered with participants’ ability to distinguish biological from scrambled motion compared to stimulation of a control site (vertex). Interestingly, when stimulation was delivered at a later time point (300 ms after stimulus onset), participants performed worse when TMS was delivered over the left cerebellar hemisphere compared to the vermis and the vertex (Experiment 3). Our data show that the posterior cerebellum is causally involved in biological motion discrimination and suggest that different sectors of the posterior cerebellar lobe may contribute to the task at different time points.
Insights into hookworm prevalence in Asia: a systematic review and meta-analysis
Authors: Zibaei Mohammad , Nosrati Mohammad Reza Chaechi , Shadnoosh Farnosh , Houshmand Elham , Karami Maryam Fasihi , Rafsanjani Mandana Khorsandi , Majidiani Hamidreza , Ghaffarifar Fatemeh , Cortes Hélder Carola Espiguinha , Dalvand Sahar , Badri Milad 
Published: October 2019

Abstract

Introduction
Hookworm infections are neglected tropical diseases of humans and animals worldwide. A meta-analysis and systematic review was designed to evaluate the prevalence of hookworm infection in animal and human hosts in Asia until July 2018.

Methods
The available online articles of five English databases (PubMed, Scopus, Science Direct, Web of Science and Google Scholar) were explored.

Results
The most parasitized carnivores were jackal (48%, CI: 4 to 91%), followed by dog (41%, CI: 29 to 53%), cat (26%, CI: 14 to 38%) and the red fox (19%, CI: 13 to 24%). The weighted prevalence of Ancylostoma braziliensis, A. caninum, A. ceylanicum, A. tubaeforme and Uncinaria stenocephala isolated from different canids were found to be 27% (CI: 21 to 33%), 23% (CI: 7.0 to 53%), 24% (CI: 12 to 35%), 44% (CI: 37 to 51%) and 37% (CI: 18 to 55%), respectively. In total, 98 records were obtained for human hookworms from 3209 760 examined individuals and the calculated weighted prevalence in this population was 19% (CI: 17 to 20%).

Conclusions
These findings highlight a desirable ecological milieu for parasite survival and transmission in such territories, which implicates revisiting control programs and public health infrastructures in those areas.
The Integrated Voxel Analysis Method (IVAM) to Diagnose Onset of Alzheimer’s Disease and Identify Brain Regions through Structural MRI Images
Authors: Hur Matthew , Aghajanyan Armen 
Published: October 2019

AbstractMagnetic Resonance Imaging (MRI) provides three-dimensional anatomical and physiological details of the human brain. We describe the Integrated Voxel Analysis Method (IVAM) which, through machine learning, classifies MRI images of brains afflicted with early Alzheimer’s Disease (AD). This fully automatic method uses an extra trees regressor model in which the feature vector input contains the intensities of voxels, whereby the effect of AD on a single voxel can be predicted. The resulting tree predicts based on the following two steps: a K-nearest neighbor (KNN) algorithm based on Euclidean distance with the feature vector to classify whole images based on their distribution of affected voxels and a voxel-by-voxel classification by the tree of every voxel in the image. An Ising model filter follows voxel-by-voxel tree-classification to remove artifacts and to facilitate clustering of classification results which identify significant voxel clusters affected by AD. We apply this method to T1-weighted MRI images obtained from the Open Access Series of Imaging Studies (OASIS) using images belonging to normal and early AD-afflicted individuals associated with a Client Dementia Rating (CDR) which we use as the target in the supervised learning. Furthermore, statistical analysis using a pre-labeled brain atlas automatically identifies significantly affected brain regions. While achieving 90% AD classification accuracy on 198 images in the OASIS dataset, the method reveals morphological differences caused by the onset of AD.
From frail to fit after allogeneic hematopoietic cell transplantation: Scope of the problem and a strength-based solution
Authors: Sweetnam Jason , Twohey Eric , Skendzel Sasha , Stingle John , Arora Mukta , Baraki Austin , Cao Qing , Grillo Sonya , Holtan Shernan G. 
Published: October 2019

AbstractBackgroundFrailty is a common but underdiagnosed syndrome among long-term survivors of allogeneic hematopoietic cell transplantation (HCT). Conditions such as malnutrition, fatigue, and weakness may suggest frailty despite patients not receiving a formal diagnosis. Furthermore, the optimal interventions to overcome frailty in long-term survivors of allogeneic HCT is not yet established.Patients and MethodsThis study consists of a retrospective and prospective component. First, we completed a retrospective review using diagnosis data from the electronic medical record to estimate the prevalence of components of frailty in 1077 recipients of allogeneic HCT through 5 years post-transplant. Second, we developed a community-based pilot study of strength training for long-term survivors of allogeneic HCT that addressed several common barriers exercise engagement and adherence. Four allogeneic HCT recipients (2 males, 2 females) and 4 controls (2 males, 2 females) completed the strength training pilot study, consisting of a baseline assessment, 10 weeks of personalized and supervised strength programming at least once weekly as a group, and an end-of-study assessment to measure progress in strength, body composition, and a standardized measure of self-efficacy.ResultsDespite a lack of a formal diagnosis, approximately 80% of HCT recipients in this series received a diagnosis of a component of frailty (weakness, fatigue, or malnutrition), and over 1/3 of HCT recipients had symptoms extending beyond 1 year. Over the course of the strength training pilot study, both pre-frail/frail allogeneic HCT recipients and healthy controls doubled their total strength, lost body fat, and gained muscle mass. Self-efficacy improved from baseline in allogeneic HCT recipients after the strength training pilot program.DiscussionBased upon the prevalence of frailty-related diagnoses among long-term survivors of HCT, a comprehensive mitigation strategy needs to be developed for this population. A community-based strength training program that includes a personalized component, a group setting, and caregiver/partner involvement appears feasible and overcomes several established barriers to exercise engagement and adherence.
Lower limb muscle activity underlying temporal gait asymmetry post-stroke
Authors: Rozanski Gabriela M. , Huntley Andrew H. , Crosby Lucas D. , Schinkel-Ivy Alison , Mansfield Avril , Patterson Kara K. 
Published: October 2019

AbstractObjectiveAsymmetric walking after stroke is common, detrimental, and difficult to treat, but current knowledge of underlying physiological mechanisms is limited. This study investigated electromyographic (EMG) features of temporal gait asymmetry (TGA).MethodsParticipants post-stroke with or without TGA and control adults (n=27, 8, and 9, respectively) performed self-paced overground gait trials. EMG, force plate, and motion capture data were collected. Lower limb muscle activity was compared across groups and sides (more/less affected). Correlation between burst timing variables and asymmetry ratios was examined.ResultsSignificant group by side interaction effects were found: fewer TGA group dorsiflexor bursts during swing (p=.0009), more affected plantarflexor stance activity ended early (p=.0006) and less affected dorsiflexor on/off time was delayed (p<.01) in persons with asymmetry compared to symmetric and normative controls. Less affected side EMG timing correlated most with swing time ratio (r=0.68-0.90, p<.001).ConclusionsTemporal patterns of muscular activation, particularly about the ankle around the stance-to-swing transition period, are associated with TGA. The results may reflect specific impairments or compensations that affect locomotor coordination.SignificanceNeuromuscular underpinnings of spatiotemporal asymmetry have not been previously characterized. These novel findings may inform targeted therapeutic strategies to improve gait quality after stroke.
DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility
Authors: Liu Qiao , Hua Kui , Zhang Xuegong , Wong Wing Hung , Jiang Rui 
Published: October 2019

AbstractAlthough computational approaches have been complementing high-throughput biological experiments for the identification of functional regions in the human genome, it remains a great challenge to systematically decipher interactions between transcription factors and regulatory elements to achieve interpretable annotations of chromatin accessibility across diverse cellular contexts. Towards this problem, we propose DeepCAGE, a deep learning framework that integrates sequence information and binding status of transcription factors, for the accurate prediction of chromatin accessible regions at a genome-wide scale in a variety of cell types. DeepCAGE takes advantage of a densely connected deep convolutional neural network architecture to automatically learn sequence signatures of known chromatin accessible regions, and then incorporates such features with expression levels and binding activities of human core transcription factors to predict novel chromatin accessible regions. In a series of systematic comparisons with existing methods, DeepCAGE exhibits superior performance in not only the classification but also the regression of chromatin accessibility signals. In detailed analysis of transcription factor activities, DeepCAGE successfully extracts novel binding motifs and measures the contribution of a transcription factor to the regulation with respect to a specific locus in a certain cell type. When applied to whole-genome sequencing data analysis, our method successfully prioritizes putative deleterious variants underlying a human complex trait, and thus provides insights into the understanding of disease-associated genetic variants. DeepCAGE can be downloaded from https://github.com/kimmo1019/DeepCAGE.
Host gill attachment enables blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome
Authors: Heggland Erna Irene , Dondrup Michael , Nilsen Frank , Eichner Christiane 
Published: October 2019

ABSTRACTBlood-feeding is a common strategy among parasitizing arthropods, including the ectoparasitic salmon louse (Lepeophtheirus salmonis), feeding off its salmon host’s skin and blood. Blood is rich in nutrients, among these iron and heme. These are essential molecules for the louse, yet their oxidative properties render them toxic to cells if not handled properly. Blood-feeding might therefore alter parasite gene expression. We infected Atlantic salmon with salmon louse copepodids and sampled the lice in two different experiments at day 10 and 18 post infestation. Parasite development and presence of host blood in their intestines were determined. We find that lice start feeding on blood when becoming mobile preadults if sitting on the fish body, however they may initiate in blood-feeding at the chalimus I stage if attached to gills. Lice attached to gills develop at a slower rate. Lice of similar instar age from gills versus lice from skin epidermis were analyzed for gene expression by RNA-sequencing in samples taken at day 10 for both experiments and at day 18 for one of the experiments. By differential expression analysis, we found 355 transcripts elevated in lice sampled from gills and 202 transcripts elevated in lice sampled from skin consistent in all experiments. Genes annotated with “peptidase activity” are among the ones elevated in lice sampled from gills, while in the other group genes annotated with “phosphorylation” and “phosphatase” is pervasive. Transcripts elevated in lice sampled from gills are often genes relatively highly expressed in the louse intestine compared with other tissues, while this was not the case for transcripts found elevated in lice sampled from skin. In both groups, more than half the transcripts are from genes higher expressed after attachment. In conclusion, blood-feeding results in an alteration in gene expression, and a premature onset of blood-feeding likely causes the parasite to develop at a slower pace.
Predicting MMSE Score from Finger-Tapping Measurement
Authors: Jian Ma 
Published: October 2019

AbstractDementia is a leading cause of diseases for the elderly. Early diagnosis is very important for the elderly living with dementias. In this paper, we propose a method for dementia diagnosis by predicting MMSE score from finger-tapping measurement with machine learning pipeline. Based on measurement of finger tapping movement, the pipeline is first to select finger-tapping attributes with copula entropy and then to predict MMSE score from the selected attributes with predictive models. Experiments on real world data show that the predictive models such developed present good prediction performance. As a byproduct, the associations between certain finger-tapping attributes (‘Number of taps’ and ‘SD of inter-tapping interval’) and MMSE score are discovered with copula entropy, which may be interpreted as the biological relationship between cognitive ability and motor ability and therefore makes the predictive models explainable. The selected finger-tapping attributes can be considered as dementia biomarkers.
Novel mediation analysis of human plasma proteome and metabolome reveals mediators of improved glycemia after gastric bypass surgery
Authors: Dreyfuss Jonathan M , Yuchi Yixing , Pan Hui , Dong Xuehong , Simonson Donald C. , Vernon Ashley , Aryal Pratik , Konkar Anish , Sebastian Yinong , Higgs Brandon W , Grimsby Joseph , Rondinone Cristina M. , Kasif Simon , Kahn Barbara B. , Foster Kathleen , Goldfine Allison , Patti Mary-Elizabeth 
Published: October 2019

AbstractMolecular mechanisms by which Roux-en-Y gastric bypass (RYGB) improves glycemic control and metabolism in type 2 diabetes (T2D) remain incompletely understood. In the SLIMM-T2D trial, participants with T2D were randomized to RYGB or nonsurgical management and their fasting plasma proteome and metabolome were analyzed for up to 3 years. To identify analytes that mediate improvement in outcomes, we developed a high-throughput mediation analysis method (Hitman), which is significantly more powerful than existing methods. Top-ranking analyte mediators of glycemia improvement were growth hormone receptor and prolylhydroxyproline, which were more significant than any clinical mediator, including BMI. Beta-alanine and Histidine Metabolism (both including CNDP1) were top differentially regulated pathways, and Valine, Leucine and Isoleucine Degradation was also a top differentially-regulated pathway and a top mediator of improvement in insulin resistance. The identified analytes may serve as novel targets for T2D therapy. More broadly, Hitman can identify analyte mediators of outcomes in randomized trials for which high-throughput data are available.
CCSeq: Clusters of Colocalized Sequences
Authors: Golas Stefan 
Published: October 2019

Abstract0.1MotivationPotential transcription factor (TF) complexes may be identified by testing whether the binding sequences of individual TF proteins form clusters with each other. These clusters may also indicate TF inhibition due to competitive occupancy of enhancer regions. Genome annotation data containing the coordinates of enhancer sequences is highly accessible via position-weight matrix tools.0.2ResultsAn algorithm called CCSeq (Clusters of Colocalized Sequences) was developed for identifying clusters of sequences along a one-dimensional line, such as a chromosome, given genome annotation files and a cut-off distance as inputs. The algorithm was applied to the binding sequences of the constituent proteins of two known transcription factor complexes, the HSF1 homotrimer and one form of the NF-κB complex, a dimer of NFKB2 and RELB. 28 clusters of HSF1 trimer binding sequences were identified on chromosome Y, and 16 clusters of the NFKB2 and RELB dimer were identified on chromosome 17, compared to 0 clusters identified in any of the five simulated random distributions for each of the two sets of TF proteins. Additionally, structural patterns of these binding sequence clusters are described.0.3Availability and ImplementationThis algorithm is freely available as an R package on the open source R repository CRAN at the following link:https://cran.r-project.org/package=colocalized. Genome annotation files were obtained from the PWMScan tool athttps://ccg.epfl.ch/pwmtools/pwmscan.phphosted by the Swiss Insitute of Bioinformatics (2) (3).
Brain networks processing temporal information in dynamic facial expressions
Authors: Skiba Rafal M. , Vuilleumier Patrik 
Published: October 2019

AbstractPerception of emotional expressions in faces relies on the integration of distinct facial features. We used fMRI to examine the role of local and global motion information in facial movements during exposure to novel dynamic face stimuli. We found that synchronous expressions distinctively engaged medial prefrontal areas in the ventral anterior cingulate cortex (vACC), supplementary premotor areas, and bilateral superior frontal gyrus (global temporal-spatial processing). Asynchronous expressions in which one part of the face (e.g., eyes) unfolded before the other (e.g., mouth) activated more the right superior temporal sulcus (STS) and inferior frontal gyrus (local temporal-spatial processing). DCM analysis further showed that processing of asynchronous expression features was associated with a differential information flow, centered on STS, which received direct input from occipital cortex and projected to the amygdala. Moreover, STS and amygdala displayed selective interactions with vACC where the integration of both local and global motion cues (present in synchronous expressions) could take place. These results provide new evidence for a role of both local and global temporal dynamics in emotional expressions, extracted in partly separate brain pathways. Importantly, we show that dynamic expressions with synchronous movement cues may distinctively engage brain areas responsible for motor execution of expressions.