julilili42/papers huggingface dataset:
Differing Connectivity of Exner’s Area for Numbers and Letters
2016-06-16

There is a growing body of evidence indicating a crucial role of Exner’s area in (hand-) writing symbolic codes such as letters and words. However, a recent study reported a patient with a lesion affecting Broca’s and Exner’s area, who suffered from severe peripheral agraphia for letters but not for Arabic digits. The authors suggested a speculative account postulating differential connectivity of Exner’s area for numbers and letters in order to explain this dissociation. In the present study, we evaluated this account, employing atlas-based tractography for the patient’s anatomy, deterministic fiber-tracking as well as an automated toolkit to investigate the connectivity of Exner’s area in healthy adults. In particular, fiber pathways connecting Exner’s area with areas associated with language processing (e.g., the arcuate fascicle, ventral pathways encompassing the external/extreme capsule system) reached the inferior part of Exner’s area, while fronto-parietal fibers (e.g., the superior longitudinal fascicle) connected the upper part of Exner’s area with the intraparietal sulcus typically involved in number processing. Our results substantiated the differential connectivity account for Exner’s area by identifying the neural connections between fiber tracts and cortex areas of interest. Our data strongly suggest that white matter connectivity should be taken into account when investigating the neural underpinnings of impaired and intact human cognition.
The genetic structure of the world’s first farmers
2016-06-16

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
Colonization with third-generation cephalosporin-resistant Enterobacteriaceae on hospital admission: prevalence and risk factors
2016-06-17

To our knowledge, this is the largest admission prevalence study of 3GCREB in Europe. The observed prevalence of 9.5% 3GCREB carriage was higher than previously reported and differed significantly among centres. In addition to previously identified risk factors, the treatment of GERD proved to be an independent risk factor for 3GCREB colonization.
Association between Thigh Muscle Volume and Leg Muscle Power in Older Women
2016-06-17

The construct of sarcopenia is still discussed with regard to best appropriate measures of muscle volume and muscle function. The aim of this post-hoc analysis of a cross-sectional experimental study was to investigate and describe the hierarchy of the association between thigh muscle volume and measurements of functional performance in older women. Thigh muscle volume of 68 independently living older women (mean age 77.6 years) was measured via magnetic resonance imaging. Isometric strength was assessed for leg extension in a movement laboratory in sitting position with the knee flexed at 90° and for hand grip. Maximum and habitual gait speed was measured on an electronic walk way. Leg muscle power was measured during single leg push and during sit-to-stand performance. Thigh muscle volume was associated with sit-to-stand performance power (r = 0.628), leg push power (r = 0.550), isometric quadriceps strength (r = 0.442), hand grip strength (r = 0.367), fast gait speed (r = 0.291), habitual gait speed (r = 0.256), body mass index (r = 0.411) and age (r = -0.392). Muscle power showed the highest association with thigh muscle volume in healthy older women. Sit-to-stand performance power showed an even higher association with thigh muscle volume compared to single leg push power.
Highly potent intracellular membrane-associated Aβ seeds
2016-06-17

Abstract An early event in Alzheimer’s disease (AD) pathogenesis is the formation of extracellular aggregates of amyloid-β peptide (Aβ), thought to be initiated by a prion-like seeding mechanism. However, the molecular nature and location of the Aβ seeds remain rather elusive. Active Aβ seeds are found in crude homogenates of amyloid-laden brains and in the soluble fraction thereof. To analyze the seeding activity of the pellet fraction, we have either separated or directly immunoisolated membranes from such homogenates. Here, we found considerable Aβ seeding activity associated with membranes in the absence of detectable amyloid fibrils. We also found that Aβ seeds on mitochondrial or associated membranes efficiently induced Aβ aggregation in vitro and seed β-amyloidosis in vivo . Aβ seeds at intracellular membranes may contribute to the spreading of Aβ aggregation along neuronal pathways and to the induction of intracellular pathologies downstream of Aβ.
Infant oral mutilation in East Africa – therapeutic and ritual grounds
2016-06-17

Summary This paper reviews the practice and ritual traditions of infant oral mutilation, drawing on a literature search in PubMed and Google Scholar, historical reports, relevant textbooks, NGO materials and personal observations of the authors.
Attention Cueing and Activity Equally Reduce False Alarm Rate in Visual-Auditory Associative Learning through Improving Memory
2016-06-17

In our daily life, we continually exploit already learned multisensory associations and form new ones when facing novel situations. Improving our associative learning results in higher cognitive capabilities. We experimentally and computationally studied the learning performance of healthy subjects in a visual-auditory sensory associative learning task across active learning, attention cueing learning, and passive learning modes. According to our results, the learning mode had no significant effect on learning association of congruent pairs. In addition, subjects' performance in learning congruent samples was not correlated with their vigilance score. Nevertheless, vigilance score was significantly correlated with the learning performance of the non-congruent pairs. Moreover, in the last block of the passive learning mode, subjects significantly made more mistakes in taking non-congruent pairs as associated and consciously reported lower confidence. These results indicate that attention and activity equally enhanced visual-auditory associative learning for non-congruent pairs, while false alarm rate in the passive learning mode did not decrease after the second block. We investigated the cause of higher false alarm rate in the passive learning mode by using a computational model, composed of a reinforcement learning module and a memory-decay module. The results suggest that the higher rate of memory decay is the source of making more mistakes and reporting lower confidence in non-congruent pairs in the passive learning mode.
Fluctuations of the Intraocular Pressure in One Eye Influence the Intraocular Pressure in the Fellow Eye
2016-06-17

Our results showed some evidence for the existence of the OCR in healthy individuals. Significant IOP elevation in one eye resulted in IOP reduction in the fellow eye. Interestingly, this phenomenon did not exist vice versa.
Compendium Of Data, Source Code And Text Associated With The Publication "The Need For A Taphonomic Perspective In Spatial Analysis: Formation Processes At The Early Pleistocene Site Of Pirro Nord (P13), Apricena, Italy"
2016-06-17

Compendium of data, source code and text associated with the publication "The need for a taphonomic perspective in spatial analysis: Formation processes at the Early Pleistocene site of Pirro Nord (P13), Apricena, Italy" authored by D. Giusti and M. Arzarello (DOI:10.1016/j.jasrep.2016.06.014)
Recording, analysis, and interpretation of spreading depolarizations in neurointensive care: Review and recommendations of the COSBID research group
2016-06-18

Spreading depolarizations (SD) are waves of abrupt, near-complete breakdown of neuronal transmembrane ion gradients, are the largest possible pathophysiologic disruption of viable cerebral gray matter, and are a crucial mechanism of lesion development. Spreading depolarizations are increasingly recorded during multimodal neuromonitoring in neurocritical care as a causal biomarker providing a diagnostic summary measure of metabolic failure and excitotoxic injury. Focal ischemia causes spreading depolarization within minutes. Further spreading depolarizations arise for hours to days due to energy supply-demand mismatch in viable tissue. Spreading depolarizations exacerbate neuronal injury through prolonged ionic breakdown and spreading depolarization-related hypoperfusion (spreading ischemia). Local duration of the depolarization indicates local tissue energy status and risk of injury. Regional electrocorticographic monitoring affords even remote detection of injury because spreading depolarizations propagate widely from ischemic or metabolically stressed zones; characteristic patterns, including temporal clusters of spreading depolarizations and persistent depression of spontaneous cortical activity, can be recognized and quantified. Here, we describe the experimental basis for interpreting these patterns and illustrate their translation to human disease. We further provide consensus recommendations for electrocorticographic methods to record, classify, and score spreading depolarizations and associated spreading depressions. These methods offer distinct advantages over other neuromonitoring modalities and allow for future refinement through less invasive and more automated approaches.
The F, Cl, Br and I Contents of Reference Glasses BHVO‐2G, BIR‐1G, BCR‐2G, GSD‐1G, GSE‐1G, NIST SRM 610 and NIST SRM 612
2016-06-18

Halogen contents for the widely distributed reference glasses BHVO ‐2G, BIR ‐1G, BCR ‐2G, GSD ‐1G, GSE ‐1G, NIST SRM 610 and NIST SRM 612 were investigated by pyrohydrolysis combined with ion chromatography, total reflection X‐ray fluorescence analysis, instrumental neutron activation analysis, the noble gas method, electron probe microanalysis and laser ablation‐inductively coupled plasma‐mass spectrometry. Glasses BHVO ‐2G, GSD ‐1G and GSE ‐1G have halogen contents that can be reproduced at the 15% level by all bulk techniques and cover a significant range in halogen mass fractions for F (~ 20–300 μg g −1 ), Cl (~ 70–1220 μg g −1 ) and Br (~ 0.2–285 μg g −1 ) and I (~ 9–3560 ng g −1 ). The BIR ‐1G glass has low F (&lt; 15 μg g −1 ), Cl (~ 20 μg g −1 ), Br (15 ng g −1 ) and I (3 ng g −1 ). The halogen contents for the silica‐rich NIST SRM 610 and 612 glasses were poorly reproduced by the different techniques. The relatively high Cl, Br and I abundances in glasses GSD ‐1G and GSE ‐1G mean that these glasses are well suited for calibrating spatially resolved micro‐analytical studies on silicate glasses, melt and fluid inclusions. Combined EPMA and laser ablation‐inductively coupled plasma‐mass spectrometry data for glass GSE ‐1G demonstrate homogeneity at the 10% level for Cl and Br.
Uniparental disomy of chromosome 16 unmasks recessive mutations of FA2H /SPG35 in 4 families
2016-06-18

UPD has rarely been described as causative mechanism in neurodegenerative diseases. Of note, we identified this mode of inheritance in 4 families with the rare diagnosis of spastic paraplegia type 35 (SPG35). Since UPD seems to be a relevant factor in SPG35 and probably additional autosomal recessive diseases, we recommend segregation analysis especially in nonconsanguineous homozygous index cases to unravel UPD as mutational mechanism. This finding may bear major repercussion for genetic counseling, given the markedly reduced risk of recurrence for affected families.
FORMATION OF MASSIVE PRIMORDIAL STARS: INTERMITTENT UV FEEDBACK WITH EPISODIC MASS ACCRETION
2016-06-20

ABSTRACT We present coupled stellar evolution (SE) and 3D radiation-hydrodynamic (RHD) simulations of the evolution of primordial protostars, their immediate environment, and the dynamic accretion history under the influence of stellar ionizing and dissociating UV feedback. Our coupled SE RHD calculations result in a wide diversity of final stellar masses covering 10 ≲ M * ≲ 10 3 . The formation of very massive (≳250 ) stars is possible under weak UV feedback, whereas ordinary massive (a few ×10 ) stars form when UV feedback can efficiently halt the accretion. This may explain the peculiar abundance pattern of a Galactic metal-poor star recently reported by Aoki et al., possibly the observational signature of very massive precursor primordial stars. Weak UV feedback occurs in cases of variable accretion, in particular when repeated short accretion bursts temporarily exceed 0.01 , causing the protostar to inflate. In the bloated state, the protostar has low surface temperature and UV feedback is suppressed until the star eventually contracts, on a thermal adjustment timescale, to create an H ii region. If the delay time between successive accretion bursts is sufficiently short, the protostar remains bloated for extended periods, initiating at most only short periods of UV feedback. Disk fragmentation does not necessarily reduce the final stellar mass. Quite the contrary, we find that disk fragmentation enhances episodic accretion as many fragments migrate inward and are accreted onto the star, thus allowing continued stellar mass growth under conditions of intermittent UV feedback. This trend becomes more prominent as we improve the resolution of our simulations. We argue that simulations with significantly higher resolution than reported previously are needed to derive accurate gas mass accretion rates onto primordial protostars.
Compensation or Restoration: Closed-Loop Feedback of Movement Quality for Assisted Reach-to-Grasp Exercises with a Multi-Joint Arm Exoskeleton
2016-06-20

Assistive technology allows for intensive practice and kinematic measurements during rehabilitation exercises. More recent approaches attach a gravity-compensating multi-joint exoskeleton to the upper extremity to facilitate task-oriented training in three-dimensional space with virtual reality feedback. The movement quality, however, is mostly captured through end-point measures that lack information on proximal inter-joint coordination. This limits the differentiation between compensation strategies and genuine restoration both during the exercise and in the course of rehabilitation. We extended in this proof-of-concept study a commercially available seven degree-of-freedom arm exoskeleton by using the real-time sensor data to display a three-dimensional multi-joint visualization of the user's arm. Ten healthy subjects and three severely affected chronic stroke patients performed reach-to-grasp exercises resembling activities of daily living assisted by the attached exoskeleton and received closed-loop online feedback of the three-dimensional movement in virtual reality. Patients in this pilot study differed significantly with regard to motor performance (accuracy, temporal efficiency, range of motion) and movement quality (proximal inter-joint coordination) from the healthy control group. In the course of 20 training and feedback sessions over 4 weeks, these pathological measures improved significantly toward the reference parameters of healthy participants. It was moreover feasible to capture the evolution of movement pattern kinematics of the shoulder and elbow and to quantify the individual degree of natural movement restoration for each patient. The virtual reality visualization and closed-loop feedback of joint-specific movement kinematics makes it possible to detect compensation strategies and may provide a tool to achieve the rehabilitation goals in accordance with the individual capacity for genuine functional restoration; a proposal that warrants further investigation in controlled studies with a larger cohort of stroke patients.
Hyperon forward spin polarizability gamma0 in baryon chiral perturbation theory
2016-06-20

We predict the values for baryon forward spin polarizabilities in fully covariant ChPT and including the virtual contributions of the spin-3/2 states.As the nucleon results are in good agreement with the experimental data and they do not depend on renormalization schemes, we extend the calculations to the hyperon sector.
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
2016-06-21

There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.
The Multiple Functions of Common Microbial Carbon Polymers, Glycogen and PHB, during Stress Responses in the Non-Diazotrophic Cyanobacterium Synechocystis sp. PCC 6803
2016-06-21

Classical microbial carbon polymers such as glycogen and polyhydroxybutyrate (PHB) have a crucial impact as both a sink and a reserve under macronutrient stress conditions. Most microbial species exclusively synthesize and degrade either glycogen or PHB. A few bacteria such as the phototrophic model organism Synechocystis sp. PCC 6803 surprisingly produce both physico-chemically different polymers under conditions of high C to N ratios. For the first time, the function and interrelation of both carbon polymers in non-diazotrophic cyanobacteria are analyzed in a comparative physiological study of single- and double-knockout mutants (ΔglgC; ΔphaC; ΔglgC/ΔphaC), respectively. Most of the observed phenotypes are explicitly related to the knockout of glycogen synthesis, highlighting the metabolic, energetic, and structural impact of this process whenever cells switch from an active, photosynthetic 'protein status' to a dormant 'glycogen status'. The carbon flux regulation into glycogen granules is apparently crucial for both phycobilisome degradation and thylakoid layer disassembly in the presence of light. In contrast, PHB synthesis is definitely not involved in this primary acclimation response. Moreover, the very weak interrelations between the two carbon-polymer syntheses indicate that the regulation and role of PHB synthesis in Synechocystis sp. PCC 6803 is different from glycogen synthesis.
Toward a Unified Sub-symbolic Computational Theory of Cognition
2016-06-21

This paper proposes how various disciplinary theories of cognition may be combined into a unifying, sub-symbolic, computational theory of cognition. The following theories are considered for integration: psychological theories, including the theory of event coding, event segmentation theory, the theory of anticipatory behavioral control, and concept development; artificial intelligence and machine learning theories, including reinforcement learning and generative artificial neural networks; and theories from theoretical and computational neuroscience, including predictive coding and free energy-based inference. In the light of such a potential unification, it is discussed how abstract cognitive, conceptualized knowledge and understanding may be learned from actively gathered sensorimotor experiences. The unification rests on the free energy-based inference principle, which essentially implies that the brain builds a predictive, generative model of its environment. Neural activity-oriented inference causes the continuous adaptation of the currently active predictive encodings. Neural structure-oriented inference causes the longer term adaptation of the developing generative model as a whole. Finally, active inference strives for maintaining internal homeostasis, causing goal-directed motor behavior. To learn abstract, hierarchical encodings, however, it is proposed that free energy-based inference needs to be enhanced with structural priors, which bias cognitive development toward the formation of particular, behaviorally suitable encoding structures. As a result, it is hypothesized how abstract concepts can develop from, and thus how they are structured by and grounded in, sensorimotor experiences. Moreover, it is sketched-out how symbol-like thought can be generated by a temporarily active set of predictive encodings, which constitute a distributed neural attractor in the form of an interactive free-energy minimum. The activated, interactive network attractor essentially characterizes the semantics of a concept or a concept composition, such as an actual or imagined situation in our environment. Temporal successions of attractors then encode unfolding semantics, which may be generated by a behavioral or mental interaction with an actual or imagined situation in our environment. Implications, further predictions, possible verification, and falsifications, as well as potential enhancements into a fully spelled-out unified theory of cognition are discussed at the end of the paper.