Miracle-dz/UniFAR-FTUs huggingface dataset:
On the integrity of functional brain networks in schizophrenia, Parkinson's disease, and advanced age: Evidence from connectivity‐based single‐subject classification

Previous whole‐brain functional connectivity studies achieved successful classifications of patients and healthy controls but only offered limited specificity as to affected brain systems. Here, we examined whether the connectivity patterns of functional systems affected in schizophrenia (SCZ), Parkinson's disease (PD), or normal aging equally translate into high classification accuracies for these conditions. We compared classification performance between pre‐defined networks for each group and, for any given network, between groups. Separate support vector machine classifications of 86 SCZ patients, 80 PD patients, and 95 older adults relative to their matched healthy/young controls, respectively, were performed on functional connectivity in 12 task‐based, meta‐analytically defined networks using 25 replications of a nested 10‐fold cross‐validation scheme. Classification performance of the various networks clearly differed between conditions, as those networks that best classified one disease were usually non‐informative for the other. For SCZ, but not PD, emotion‐processing, empathy, and cognitive action control networks distinguished patients most accurately from controls. For PD, but not SCZ, networks subserving autobiographical or semantic memory, motor execution, and theory‐of‐mind cognition yielded the best classifications. In contrast, young–old classification was excellent based on all networks and outperformed both clinical classifications. Our pattern‐classification approach captured associations between clinical and developmental conditions and functional network integrity with a higher level of specificity than did previous whole‐brain analyses. Taken together, our results support resting‐state connectivity as a marker of functional dysregulation in specific networks known to be affected by SCZ and PD, while suggesting that aging affects network integrity in a more global way. Hum Brain Mapp 38:5845–5858, 2017. © 2017 Wiley Periodicals, Inc.
Combined Transmission Electron Microscopy and In-Situ Scanning Tunneling Microscopy Characterization of Nanomaterials

The main goal of this thesis has been to apply in-situ Transmission Electron Microscopy (TEM) electrical measurements using a Scanning Tunneling Microscopy (STM) tip, combined with TEM imaging and spectroscopic techniques, in order to address the characterization of relevant nanomaterials. This system has not only been used to measure electrical properties, but also to carry out in-situ experiments with Joule heating and to apply mechanical stresses. A review of the different in-situ TEM techniques, their development over the years and their impact in the scientific community has been presented. Moreover, the instrumental used in this thesis, in particular, the TEM-STM system, has been described. In addition, two techniques for the preparation of specific samples for in-situ TEM-STM experiments have been presented: for nanostructured samples (2D materials, nanowires, etc), and for localized samples (devices, thin layers, bulk samples, etc). A gridcase that allows the use of conventional TEM grids in the TEM-STM system has been designed and fabricated in the context of this thesis. The use of this homemade gridase has allowed us to improve the experiments, offering more reproducibility and versatility. Finally, the calibration of the electrical measurements of the system has been carried out. Using the TEM-STM system, different type of nanostructures have been characterized during the present thesis, from 2D nanostructures, as the elucidation of the effects of electrical current through a single graphene oxide sheet, to functional devices, as the study of the ferroelectric and piezoelectric behavior of structures based on La2WO6, the study of the anisotropic electrical conductivity of GaInP CuPtB type ordering layers used for multijunction solar cells or the study of the conductive filament (CF) formation mechanism in three different Resistive random-access memory (ReRAM) devices. In summary, in-situ microscopy expands the horizons of the characterization and study of materials and, in particular, in the context of this thesis, an in-situ TEM-STM system has been used to electrically characterize samples from nanomaterials to functional devices.
A Delayed Container Organization Approach to Improve Restore Speed for Deduplication Systems

Data deduplication has become necessary to improve the space-efficiency of large-scale distributed storage systems, as the global data have accumulated at an exponential rate and they have significant redundancy. However, the negative impact on restore performance is a main challenge for deduplication systems. One of the key reasons is that when restoring data, the low average useful data ratio (UDR) of containers wastes a considerable part of disk bandwidth to read useless data. This is mainly attributed to the uncontrollable compositions of containers. To solve this problem, we propose a new approach called Delayed Container Organization (DCO) to delay the construction of containers after accumulating some redundant data chunks in fast Non-Volatile Memory (NVM) devices to organize high-UDR containers. For example, data chunks in the intersection of some data segments can be organized together in one container to achieve both high deduplication ratio and high UDRs when restoring these related data segments. DCO is implemented in a prototype deduplication system. The experimental results indicate that compared with Capping, DCO promotes the average UDR of containers by 38.30 percent, improves the restore performance by a factor of 2.2, and achieves better space-efficiency and higher cost performance.
Bedtime Stories that Work: The Effect of Protagonist Liking on Narrative Persuasion

ABSTRACT The experiment described in this article draws on affective disposition theory to clarify how protagonist likeability influences participants’ sleep hygiene-related self-efficacy and outcome expectations immediately after media exposure and 3 days later. Results indicate that protagonist likeability is an important factor in narrative persuasion. Protagonist likeability did not directly affect participants’ sleep hygiene-related self-efficacy immediately postexposure, but it did influence self-efficacy 3 days later. The dislikeable protagonist influenced self-efficacy more than the likeable protagonist. Further, protagonist likeability did not directly affect outcome expectations either immediately postexposure or 3 days later. However, mediation analyses demonstrated that protagonist likeability indirectly influenced both self-efficacy and outcome expectations via perceived liking of the protagonist immediately after exposure and 3 days later. Implications of these findings are further discussed.
Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types

Abstract Thyroid hormones, thyroxine, and triiodothyronine (T3) are crucial for cerebral cortex development acting through regulation of gene expression. To define the transcriptional program under T3 regulation, we have performed RNA‐Seq of T3‐treated and untreated primary mouse cerebrocortical cells. The expression of 1145 genes or 7.7% of expressed genes was changed upon T3 addition, of which 371 responded to T3 in the presence of cycloheximide indicating direct transcriptional regulation. The results were compared with available transcriptomic datasets of defined cellular types. In this way, we could identify targets of T3 within genes enriched in astrocytes and neurons, in specific layers including the subplate, and in specific neurons such as prepronociceptin, cholecystokinin, or cortistatin neurons. The subplate and the prepronociceptin neurons appear as potentially major targets of T3 action. T3 upregulates mostly genes related to cell membrane events, such as G‐protein signaling, neurotransmission, and ion transport and downregulates genes involved in nuclear events associated with the M phase of cell cycle, such as chromosome organization and segregation. Remarkably, the transcriptomic changes induced by T3 sustain the transition from fetal to adult patterns of gene expression. The results allow defining in molecular terms the elusive role of thyroid hormones on neocortical development.
Survey of diagnostic and treatment practices for multiple sclerosis (MS) in Europe. Part 2: Progressive MS, paediatric MS, pregnancy and general management

The European Charcot Foundation supported the development of a set of surveys to understand current practice patterns for the diagnosis and management of multiple sclerosis (MS) in Europe. Part 2 of the report summarizes survey results related to secondary progressive MS (SPMS), primary progressive MS (PPMS), pregnancy, paediatric MS and overall patient management.
A project to measure and model pyrolysis to improve prediction of prescribed fire behavior

Laboratory and field experiments focused on pyrolysis and ignition coupled with sufficient description of fuel characteristics and physics-based modeling are being used to improve our understanding of combustion processes in mixed (heterogeneous) fuel beds managed with prescribed fire in the southern United States. Previous pyrolysis work has typically used ground-up samples, thus eliminating any effects caused by moisture content, fuel particle shape, or heating mode. We are measuring pyrolysis at bench, laboratory and field-scale using intact fuels from living plants. Pyrolysis products being measured include light gases and tars using off-line and real-time spectroscopic instruments. 3-D fuel description, heat transfer to the fuels, and air flow around the fuels are being determined using a variety of intrusive and nonintrusive methods. The ability of high fidelity physics-based FDS, WFDS, and GPYRO3D to reproduce experimental results and to study conditions outside the range of the experimental data is being examined. This presentation will present an overview of the project and the questions being addressed. Preliminary results from initial attempts to measure pyrolysis at field-scale and results from early modeling of pyrolysis of live leaves using coupled GPYRO3D and FDS models are presented.
Transcriptome analysis reveals intermittent fasting-induced genetic changes in ischemic stroke.

Transcriptome analysis reveals intermittent fasting-induced genetic changes in ischemic stroke Joonki Kim, Sung-Wook Kang, Karthik Mallilankaraman, Sang-Ha Baik, James C. Lim, Priyanka Balaganapathy, David T. She, Ker-Zhing Lok David Y. Fann, Uma Thambiayah, Sung-Chun Tang, Alexis M. Stranahan, S. Thameem Dheen, Mathias Gelderblom, Raymond C. Seet, Vardan T. Karamyan, Raghu Vemuganti, Christopher G. Sobey, Mark P. Mattson, Dong-Gyu Jo and Thiruma V. Arumugam* Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore, Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do 25451, Republic of Korea, Department of Neurology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan, Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA, Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 117594, Singapore, Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany, Division of Neurology, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore, Department of Pharmaceutical Sciences, Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA, Department of Neurological Surgery, University of Wisconsin, Madison, WI 53792, USA, Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, 3086 VIC, Australia, Intramural Research Program, Laboratory of Neurosciences, National Institute on Aging, Baltimore, MD 21224, USA, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, School of Pharmacy, Sungkyunkwan University, Suwon, 16419 Republic of Korea and Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, 117456, Singapore
Hippocampal low-frequency stimulation inhibits afterdischarge and increases GABA (A) receptor expression in amygdala-kindled pharmacoresistant epileptic rats

Abstract Objective: The purpose of the present study was to observe the effects of hippocampal low-frequency stimulation (Hip-LFS) on amygdala afterdischarge and GABA (A) receptor expression in pharmacoresistant epileptic (PRE) rats. Methods: A total of 110 healthy adult male Wistar rats were used to generate a model of epilepsy by chronic stimulation of the amygdala. Sixteen PRE rats were selected from 70 amygdala-kindled rats by testing their response to Phenytoin and Phenobarbital, and they were randomly assigned to a pharmacoresistant stimulation group (PRS group, 8 rats) or a pharmacoresistant control group (PRC group, 8 rats). A stimulation electrode was implanted into the hippocampus of all of the rats. Hip-LFS was administered twice per day in the PRS group for two weeks. Simultaneously, amygdala stimulus-induced seizures and afterdischarge were recorded. After the hippocampal stimulation was terminated, the brain tissues were obtained to determine the GABA (A) receptors by a method of immumohistochemistry and a real-time polymerase chain reaction. Results: The stages and duration of the amygdala stimulus-induced epileptic seizures were decreased in the PRS group. The afterdischarge threshold was increased and the duration as well as the afterdischarge frequency was decreased. Simultaneously, the GABA (A) expression was significantly increased in the PRS group. Conclusions: Hip-LFS may inhibit amygdala stimulus-induced epileptic seizures and up-regulate GABA (A) receptor expression in PRE rats. The antiepileptic effects of hippocampal stimulation may be partly achieved by increasing the GABA (A) receptor.
Deficient Event-Related Theta Oscillations in Individuals at Risk for Alcoholism: A Study of Reward Processing and Impulsivity Features

Background Individuals at high risk to develop alcoholism often manifest neurocognitive deficits as well as increased impulsivity. Event-related oscillations (EROs) have been used to effectively measure brain (dys)function during cognitive tasks in individuals with alcoholism and related disorders and in those at risk to develop these disorders. The current study examines ERO theta power during reward processing as well as impulsivity in adolescent and young adult subjects at high risk for alcoholism. Methods EROs were recorded during a monetary gambling task (MGT) in 12–25 years old participants (N = 1821; males = 48%) from high risk alcoholic families (HR, N = 1534) and comparison low risk community families (LR, N = 287) from the Collaborative Study on the Genetics of Alcoholism (COGA). Impulsivity scores and prevalence of externalizing diagnoses were also compared between LR and HR groups. Results HR offspring showed lower theta power and decreased current source density (CSD) activity than LR offspring during loss and gain conditions. Younger males had higher theta power than younger females in both groups, while the older HR females showed more theta power than older HR males. Younger subjects showed higher theta power than older subjects in each comparison. Differences in topography (i.e., frontalization) between groups were also observed. Further, HR subjects across gender had higher impulsivity scores and increased prevalence of externalizing disorders compared to LR subjects. Conclusions As theta power during reward processing is found to be lower not only in alcoholics, but also in HR subjects, it is proposed that reduced reward-related theta power, in addition to impulsivity and externalizing features, may be related in a predisposition to develop alcoholism and related disorders.
Solving Constraint-Satisfaction Problems with Distributed Neocortical-Like Neuronal Networks

Finding actions that satisfy the constraints imposed by both external inputs and internal representations is central to decision making. We demonstrate that some important classes of constraint satisfaction problems (CSPs) can be solved by networks composed of homogeneous cooperative-competitive modules that have connectivity similar to motifs observed in the superficial layers of neocortex. The winner-take-all modules are sparsely coupled by programming neurons that embed the constraints onto the otherwise homogeneous modular computational substrate. We show rules that embed any instance of the CSP's planar four-color graph coloring, maximum independent set, and sudoku on this substrate and provide mathematical proofs that guarantee these graph coloring problems will convergence to a solution. The network is composed of nonsaturating linear threshold neurons. Their lack of right saturation allows the overall network to explore the problem space driven through the unstable dynamics generated by recurrent excitation. The direction of exploration is steered by the constraint neurons. While many problems can be solved using only linear inhibitory constraints, network performance on hard problems benefits significantly when these negative constraints are implemented by nonlinear multiplicative inhibition. Overall, our results demonstrate the importance of instability rather than stability in network computation and offer insight into the computational role of dual inhibitory mechanisms in neural circuits.
Computation Error Analysis of Block Floating Point Arithmetic Oriented Convolution Neural Network Accelerator Design

The heavy burdens of computation and off-chip traffic impede deploying the large scale convolution neural network on embedded platforms. As CNN is attributed to the strong endurance to computation errors, employing block floating point (BFP) arithmetics in CNN accelerators could save the hardware cost and data traffics efficiently, while maintaining the classification accuracy. In this paper, we verify the effects of word width definitions in BFP to the CNN performance without retraining. Several typical CNN models, including VGG16, ResNet-18, ResNet-50 and GoogLeNet, were tested in this paper. Experiments revealed that 8-bit mantissa, including sign bit, in BFP representation merely induced less than 0.3% accuracy loss. In addition, we investigate the computational errors in theory and develop the noise-to-signal ratio (NSR) upper bound, which provides the promising guidance for BFP based CNN engine design.
Towards traffic minimization for data placement in online social networks

With the increasing number of users and a huge scale of data, the service providers of Online Social Networks (OSNs) are facing the problem of how to place users' data to multiple servers. Key‐value stores solve the problem based on consistent hashing, and have become a defacto standard. However, random placement manner of hashing cannot preserve social locality, which leads to high intra‐data center traffic and unpredictable response time. Many existing works solve the problem by using graph partitioning algorithms. These works have two drawbacks: First, the social graph is constructed with ordinary pairwise graph that cannot fully reflect multi‐participant interactions often occurring in OSNs. Second, the underlying network topologies of data center have never been considered. This paper investigates the problem of traffic minimization for OSNs data storage. Motivated by maximally preserving both social locality and distance locality, we formulate the problem as two sub‐problems — hypergraph partitioning and partition‐to‐server mapping, and propose a two‐phase data placement (TDP) scheme. Specifically we present two algorithms to solve partition‐to‐server mapping over two widely used network topologies (i.e., tree and BCube). Evaluations with a large scale Facebook trace show that TDP significantly reduces intra‐data center traffic as well as load balancing across servers. Copyright © 2016 John Wiley & Sons, Ltd.
Quality of life after bone sarcoma surgery around the knee: A long‐term follow‐up study

It remains unclear if quality of life (QoL) improvements could be expected in young patients after malignant bone tumour surgery after 2 years. To assess the course of QoL over time during a long-term follow-up, malignant bone tumour survivors of a previous short-term study were included. Assessments were done at least 5 years after surgery. QoL was measured with Short-form (SF)-36, TNO-AZL Questionnaire for Adult's Quality of Life (TAAQOL) and Bone tumour (Bt)-DUX. QoL throughout the follow-up was analysed by linear mixed model analysis. From the original cohort of 44 patients; 20 patients were included for this study, 10 males; mean age at surgery 15.1 years and mean follow-up 7.2 years. Twenty-one patients of the initial cohort (47%) deceased. Fifteen patients (75%) underwent limb-salvage and five (25%) ablative surgery. QoL improved significantly during follow-up at Physical Component Summary Scale scale of the SF-36 and TAAQOL and all subscales of the Bt-DUX (p < .01). No significant differences were found between current evaluations and previous evaluations at 2 years after surgery (p = .41-.98). Significant advantages after limb-salvage were seen at the PCS scale of the SF-36 (MD 13.7, p = .05) and the cosmetic scale of the Bt-DUX (MD 17.7, p = .04).
Rapid and Direct VHH and Target Identification by Staphylococcal Surface Display Libraries

Unbiased and simultaneous identification of a specific antibody and its target antigen has been difficult without prior knowledge of at least one interaction partner. Immunization with complex mixtures of antigens such as whole organisms and tissue extracts including tumoral ones evokes a highly diverse immune response. During such a response, antibodies are generated against a variety of epitopes in the mixture. Here, we propose a surface display design that is suited to simultaneously identify camelid single domain antibodies and their targets. Immune libraries of single-domain antigen recognition fragments from camelid heavy chain-only antibodies (VHH) were attached to the peptidoglycan of Gram-positive Staphylococcus aureus employing its endogenous housekeeping sortase enzyme. The sortase transpeptidation reaction covalently attached the VHH to the bacterial peptidoglycan. The reversible nature of the reaction allowed the recovery of the VHH from the bacterial surface and the use of the VHH in downstream applications. These staphylococcal surface display libraries were used to rapidly identify VHH as well as their targets by immunoprecipitation (IP). Our novel bacterial surface display platform was stable under harsh screening conditions, allowed fast target identification, and readily permitted the recovery of the displayed VHH for downstream analysis.