Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered brain network integrity after childhood maltreatment: A structural connectomic DTI‐study

Childhood maltreatment is associated with alterations in neural architecture that potentially put these children at increased risk for psychopathology. Alterations in white matter (WM) tracts have been reported, however no study to date has investigated WM connectivity in brain networks in maltreated children to quantify global and local abnormalities through graph theoretical analyses of DTI data. We aimed for a multilevel investigation examining the DTI‐based structural connectome and its associations with basal cortisol levels of 25 children with documented maltreatment experiences before age 3, and 24 matched controls (age: 10.6 ± 1.75 years). On the global and lobar level, maltreated children showed significant reductions in global connectivity strength, local connectivity and increased path length, suggesting deviations from the small‐world network architecture previously associated with psychopathology. Reductions in global connectivity were associated with placement instability, attenuated cortisol secretion and higher levels of internalizing and externalizing behaviours. Regional measures revealed lower connectivity strength especially in regions within the ventromedial prefrontal cortex (vMPFC) in maltreated children. These findings show that childhood maltreatment is associated with systemic global neurodevelopmental alterations in WM networks next to regional alterations in areas involved in the regulation of affect. These alterations in WM organization could underlie global functional deficits and multi‐symptom patterns frequently observed in children with maltreatment experiences. Hum Brain Mapp 38:855–868, 2017. © 2016 Wiley Periodicals, Inc.
A sensor platform for outdoor navigation using gyro-assisted odometry and roundly-swinging 3D laser scanner

This paper proposes a light-weight sensor platform that consists of gyro-assisted odometry and a 3D laser scanner for localization of human-scale robots. The gyro-assisted odometry provides highly accurate positioning only by dead-reckoning. The 3D laser scanner has a wide field of view and uniform measuring-point distribution. Robust and computationally inexpensive localization is implemented on the sensor platform using a particle filter on a 2D grid map generated by projecting 3D points on to the ground. The system uses small and low-cost sensors, and can be applied to a variety of mobile robots in human-scale environments. Outdoor navigation experiments were performed at the Tsukuba Challenge 2009, which is an open proving ground for human-scale robots. Our robot successfully navigated the assigned 1-km course in a fully autonomous mode multiple times.
WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models

Learning sparse linear models with two-way interactions is desirable in many application domains such as genomics. l1-regularised linear models are popular to estimate sparse models, yet standard implementations fail to address specifically the quadratic explosion of candidate two-way interactions in high dimensions, and typically do not scale to genetic data with hundreds of thousands of features. Here we present WHInter, a working set algorithm to solve large l1-regularised problems with two-way interactions for binary design matrices. The novelty of WHInter stems from a new bound to efficiently identify working sets while avoiding to scan all features, and on fast computations inspired from solutions to the maximum inner product search problem. We apply WHInter to simulated and real genetic data and show that it is more scalable and two orders of magnitude faster than the state of the art.
Rapid calibration of an intracortical brain–computer interface for people with tetraplegia

Objective. Brain–computer interfaces (BCIs) can enable individuals with tetraplegia to communicate and control external devices. Though much progress has been made in improving the speed and robustness of neural control provided by intracortical BCIs, little research has been devoted to minimizing the amount of time spent on decoder calibration. Approach. We investigated the amount of time users needed to calibrate decoders and achieve performance saturation using two markedly different decoding algorithms: the steady-state Kalman filter, and a novel technique using Gaussian process regression (GP-DKF). Main results. Three people with tetraplegia gained rapid closed-loop neural cursor control and peak, plateaued decoder performance within 3 min of initializing calibration. We also show that a BCI-naïve user (T5) was able to rapidly attain closed-loop neural cursor control with the GP-DKF using self-selected movement imagery on his first-ever day of closed-loop BCI use, acquiring a target 37 s after initiating calibration. Significance. These results demonstrate the potential for an intracortical BCI to be used immediately after deployment by people with paralysis, without the need for user learning or extensive system calibration.
Investigations in GABAA receptor antibody-associated encephalitis

Objective: To report the clinical features, comorbidities, receptor subunit targets, and outcome in patients with anti-GABAA receptor (GABAAR) encephalitis. Methods: Clinical study of 26 patients, including 17 new (April 2013–January 2016) and 9 previously reported patients. Antibodies to α1, β3, and γ2 subunits of the GABAAR were determined using reported techniques. Results: Patients' median age was 40.5 years (interquartile range 48.5 [13.75–62.35] years; the youngest 2.5 months old; 13 female). Symptoms included seizures (88%), alteration of cognition (67%), behavior (46%), consciousness (42%), or abnormal movements (35%). Comorbidities were identified in 11 (42%) patients, including 7 tumors (mostly thymomas), 2 herpesvirus encephalitis (herpes simplex virus 1, human herpesvirus 6; coexisting with NMDAR antibodies), and 2 myasthenia without thymoma. Brain MRI was abnormal in 23 (88%) patients, showing in 20 (77%) multifocal, asynchronous, cortical-subcortical T2/fluid-attenuated inversion recovery abnormalities predominantly involving temporal (95%) and frontal (65%) lobes, but also basal ganglia and other regions. Immunologic or tumor therapy resulted in substantial improvement in 18/21 (86%) assessable patients; the other 3 (14%) died (2 status epilepticus, 1 sepsis). Compared with adults, children were more likely to have generalized seizures (p = 0.007) and movement disorders (p = 0.01) and less likely to have a tumor (p = 0.01). The main epitope targets were in the α1/β3 subunits of the GABAAR. Conclusions: Anti-GABAAR encephalitis is characterized by frequent seizures and distinctive multifocal cortical-subcortical MRI abnormalities that provide an important clue to the diagnosis. The frequency of symptoms and comorbidities differ between children (more viral-related) and adults (more tumor-related). The disorder is severe but most patients respond to treatment.
A Dissipated Energy Approach to Fatigue Evaluation

ABSTRACT The fatigue behaviour of bituminous binders and/or bitumen-filler mastics has been postulated as having a strong correlation with the fatigue behaviour of asphalt mixtures. The binder is one of the major factors controlling fatigue of the asphalt mixture and is considered as the leading media of energy dissipation. It is verified in this paper that the application of the Ratio of Dissipated Energy Change (RDEC) approach in terms of the fatigue characteristics of bituminous binders and mastics produces a unique energy parameter, known as the Plateau Value (PV), similar to the PV previously identified for asphalt mixtures. The relationship between PV and fatigue life (Nf) is found to be unique for asphalt mixtures and binders (mastics). This suggests the RDEC approach is a fundamental approach for fatigue analysis of HMA. Furthermore, the two PV-Nf curves for asphalt mixtures and binders are strongly related, which provides a new way to explain mixture fatigue behaviour from a binder's rheological characteristics.
Considerations for standardizing predictive molecular pathology for cancer prognosis

ABSTRACT Introduction: Molecular tests that were once ancillary to the core business of cyto-histopathology are becoming the most relevant workload in pathology departments after histopathology/cytopathology and before autopsies. This has resulted from innovations in molecular biology techniques, which have developed at an incredibly fast pace. Areas covered: Most of the current widely used techniques in molecular pathology such as FISH, direct sequencing, pyrosequencing, and allele-specific PCR will be replaced by massive parallel sequencing that will not be considered next generation, but rather, will be considered to be current generation sequencing. The pre-analytical steps of molecular techniques such as DNA extraction or sample preparation will be largely automated. Moreover, all the molecular pathology instruments will be part of an integrated workflow that traces the sample from extraction to the analytical steps until the results are reported; these steps will be guided by expert laboratory information systems. In situ hybridization and immunohistochemistry for quantification will be largely digitalized as much as histology will be mostly digitalized rather than viewed using microscopy. Expert commentary: This review summarizes the technical and regulatory issues concerning the standardization of molecular tests in pathology. A vision of the future perspectives of technological changes is also provided.
Pricing Electronic Mail to Solve the Problem of Spam

Junk e-mail or spam is rapidly choking off e-mail as a reliable and efficient means of communication over the Internet. Although the demand for human attention increases rapidly with the volume of information and communication, the supply of attention hardly changes. Markets are a social institution for efficiently allocating supply and demand of scarce resources. Charging a price for sending messages may help discipline senders from demanding more attention than they are willing to pay for. Price may also credibly inform recipients about the value of a message to the sender before they read it. This article examines economic approaches to the problem of spam and the results of two laboratory experiments to explore the consequences of a pricing system for electronic mail. Charging postage for e-mail causes senders to be more selective and to send fewer messages. However, recipients did not interpret the postage paid by senders as a signal of the importance of the messages. These results suggest that markets for attention have the potential for addressing the problem of spam but their design needs further development and testing.
Cascades of emotional support in friendship networks and adolescent smoking

Social support from peers and parents provides a key socialization function during adolescence. We examine adolescent friendship networks using a Stochastic Actor-Based modeling approach to observe the flow of emotional support provision to peers and the effect of support from parents, while simultaneously modeling smoking behavior. We utilized one school (n = 976) from The National Longitudinal Study of Adolescent to Adult Health (AddHealth) Study. Our findings suggest that emotional support is transacted through an interdependent contextual system, comprised of both peer and parental effects, with the latter also having distal indirect effects from youths’ friends’ parents.
Cytomorphologic Features of Diffuse Sclerosing Variant of Papillary Carcinoma of the Thyroid

BACKGROUND Diffuse sclerosing papillary carcinoma (DSPC), a variant of papillary carcinoma of thyroid, needs to be differentiated from classical papillary carcinoma and other variants. This variant is characterized by diffuse involvement of one or both thyroid lobes showing such histologic features as prominent sclerosis, an intense lymphocytic infiltrate, numerous psammoma bodies and squamous metaplasia together with the characteristic cytoarchitectural pattern of classical papillary carcinoma. Histologic and immuno-histochemical features have been described in previous publications. Although cytologic features of several variants of papillary carcinoma have been described previously, those of DSPC have not been widely published. The present report is on the cytomorphologic pattern of DSPC in two children, further highlighting the special features. CASES A boy, aged 11 years, presented with diffusely nodular, firm enlargement of the thyroid gland with many palpable lymph nodes, and a girl, aged 12 years, presented with diffusely nodular, firm enlargement of the left lobe with a prominent nodule on the lower pole. Fine needle aspiration biopsy (FNAB) smears stained with hematoxylin and eosin showed numerous psammoma bodies, many lymphocytes, metaplastic squamous cells and absent stringy colloid together with epithelial cells showing classical features of papillary carcinoma, such as nuclear grooves, intranuclear inclusions and papilloid structures. Histologic examination of the thyroidectomy specimens showed features of diffuse sclerosing variant of papillary carcinoma. CONCLUSION A diagnosis of DSPC should be considered when a combination of clinicocytologic features consisting of numerous psammoma bodies, lymphocytes, squamous metaplasia and absence of stringy colloid are noted with otherwise typical cytoarchitectural features of papillary carcinoma in FNAB smears obtained from diffusely nodular, firm thyroid enlargement.
Effects of acute and chronic caffeine on risk-taking behavior in children and adolescents

Consumption of caffeinated beverages is associated with increased risk-taking behavior. The purpose of this study was to determine if acute caffeine administration influences risk-taking behavior in a dose-dependent manner. Participants were pre- (ages 8–9) and post-pubertal (ages 15–17) children who visited the laboratory three times and consumed a beverage containing 0, 1, or 2 mg/kg of caffeine. Thirty minutes later, participants completed the balloon analogue risk task (BART), the Iowa gambling task (IGT), and a delay discounting task. The number of balloons exploded on the BART task was significantly increased after 2 mg/kg of caffeine in moderate caffeine consumers, but was decreased after 2 mg/kg of caffeine in high caffeine consumers. There were no main effects of caffeine dose on the delay discounting task or on the IGT. Post-pubertal participants showed reduced delay discounting compared with pre-pubertal participants. Finally, average daily caffeine use was significantly, positively correlated with scores on a risk-taking questionnaire. These data suggest that caffeine dose-dependently influences decision making and risk taking. More research is needed to determine the mechanism of this difference as well as the extent to which sex and pubertal phase influence these relationships.
Paper‐Based, Capacitive Touch Pads

Metallized paper is patterned to create touch pads of arrayed buttons that are sensitive to contact with both bare and gloved fingers. The paper-based keypad detects the change in capacitance associated with the touch of a finger to one of its buttons. Mounted on an alarmed cardboard box, the keypad requires the appropriate sequence of touches to disarm the system.
T-Bet and Eomes Regulate the Balance between the Effector/Central Memory T Cells versus Memory Stem Like T Cells

Memory T cells are composed of effector, central, and memory stem cells. Previous studies have implicated that both T-bet and Eomes are involved in the generation of effector and central memory CD8 T cells. The exact role of these transcription factors in shaping the memory T cell pool is not well understood, particularly with memory stem T cells. Here, we demonstrate that both T-bet or Eomes are required for elimination of established tumors by adoptively transferred CD8 T cells. We also examined the role of T-bet and Eomes in the generation of tumor-specific memory T cell subsets upon adoptive transfer. We showed that combined T-bet and Eomes deficiency resulted in a severe reduction in the number of effector/central memory T cells but an increase in the percentage of CD62LhighCD44low Sca-1+ T cells which were similar to the phenotype of memory stem T cells. Despite preserving large numbers of phenotypic memory stem T cells, the lack of both of T-bet and Eomes resulted in a profound defect in antitumor memory responses, suggesting T-bet and Eomes are crucial for the antitumor function of these memory T cells. Our study establishes that T-bet and Eomes cooperate to promote the phenotype of effector/central memory CD8 T cell versus that of memory stem like T cells.
Lyotropic Liquid Crystal Phases from Anisotropic Nanomaterials

Liquid crystals are an integral part of a mature display technology, also establishing themselves in other applications, such as spatial light modulators, telecommunication technology, photonics, or sensors, just to name a few of the non-display applications. In recent years, there has been an increasing trend to add various nanomaterials to liquid crystals, which is motivated by several aspects of materials development. (i) addition of nanomaterials can change and thus tune the properties of the liquid crystal; (ii) novel functionalities can be added to the liquid crystal; and (iii) the self-organization of the liquid crystalline state can be exploited to template ordered structures or to transfer order onto dispersed nanomaterials. Much of the research effort has been concentrated on thermotropic systems, which change order as a function of temperature. Here we review the other side of the medal, the formation and properties of ordered, anisotropic fluid phases, liquid crystals, by addition of shape-anisotropic nanomaterials to isotropic liquids. Several classes of materials will be discussed, inorganic and mineral liquid crystals, viruses, nanotubes and nanorods, as well as graphene oxide.
Design of lightweight aggregates composites : an insight into calcium sulphate and cement as binders (part II)

This article addresses the design of lightweight aggregates composites applying different materials (calcium sulphate hemihydrate and cement) as binder. A moderate strength and an excellent thermal conductivity of the lightweight composites are set as the design targets. The designed lightweight aggregates composites are targeted to be used in monolithic facade structure, performing as both load bearing element and thermal insulator. The mixtures are designed based on the insight that superior properties of a granular mix are achieved when a so-called geometric grading line is designed and obtained, applying a model known as the modified Andreasen and Andersen model. The properties of the obtained composites in both fresh and hardened states are investigated. Subsequently, a comparative study on calcium sulphate system and cement as binders is performed.
PRoST: Distributed Execution of SPARQL Queries Using Mixed Partitioning Strategies

The rapidly growing size of RDF graphs in recent years necessitates distributed storage and parallel processing strategies. To obtain efficient query processing using computer clusters a wide variety of different approaches have been proposed. Related to the approach presented in the current paper are systems built on top of Hadoop HDFS, for example using Apache Accumulo or using Apache Spark. We present a new RDF store called PRoST (Partitioned RDF on Spark Tables) based on Apache Spark. PRoST introduces an innovative strategy that combines the Vertical Partitioning approach with the Property Table, two preexisting models for storing RDF datasets. We demonstrate that our proposal outperforms state-of-the-art systems w.r. t. the runtime for a wide range of query types and without any extensive precomputing phase.
In‐scan and scan–rescan assessment of LV in‐ and outflow volumes by 4D flow MRI versus 2D planimetry

To evaluate the in‐scan and scan–rescan consistency of left ventricular (LV) in‐ and outflow assessment from 1) 2D planimetry; 2) 4D flow magnetic resonance imaging (MRI) with retrospective valve tracking, and 3) 4D flow MRI with particle tracing.
Vaccinating healthcare workers: Level of implementation, barriers and proposal for evidence-based policies in Turkey

ABSTRACT The role of healthcare workers in life-long vaccination is very important in the means of 2 sided infection, rising patient awareness and being a role model for the patients. Numerous organizations publish guidelines for vaccination of HCWs, while healthcare facilities develop vaccination policies according to the accreditation standards. Nevertheless, vaccination rates among HCWs are far below targets. The obstacles to getting vaccinated or recommending vaccination may include rather universal factors such as the vaccine paradox, however in the case of HCWs, probably a different set of factors are included. The aims of this article are to gain an overview of vaccination strategies for HCWs, to assess the coverage rates of HCWs and make in-depth analyses of the potential barriers to vaccination and potential factors to motivate HCWs for vaccination in Turkey and to compare them with the global picture to improve implementation of policies concerning vaccination of HCWs.
Finding duplicate images in biology papers

Duplicated images in biology papers are a possible indicator for plagiarism or data fabrication. A manual detection of such duplicates can be time consuming or even infeasible for huge image collections. In this paper, a semi-automatic duplicate detection approach is proposed. The approach can be used for the detection of duplicates that cover only a fraction of the full image, are transformed (e.g. rotation), occur between images or within single images (i.e. single-image-duplicates). In the proposed approach, single-image-duplicates are detected between sub-images (i.e. sub-figures) based on a connected component approach and duplicates between images are detected via the min-hashing technique. The approach was evaluated on 1.7 million images extracted from biology papers. By application of various filtering methods to remove false positive detections, only a small amount of manual effort was necessary to find 3041 potentially serious duplicates in so far non-retracted papers.
Comparison of two measurement methods of dissolved gaseous mercury concentrations and estimations of supersaturation grade and mercury fluxes during a research campaign at the Mediterranean Sea

Dissolved gaseous mercury (DGM) concentrations and gaseous elemental mercury (GEM) concentrations were measured during an oceanographic campaign in the Mediterranean Sea. The DGM concentrations were measured using two different methods, a manual-and an automated method. The manual method was used to obtain DGM depth profiles at several stations throughout the campaign. The automated device measured DGM concentrations continuously at a depth of 4 m. Gaseous elemental mercury (GEM) concentrations in air were measured continuously at the bridge deck. The objectives were to achieve DGM depth profiles, compare the manual-and automated DGM measurement methods, to calculate the supersaturation grades of the sea and the evasional fluxes from the sea surface. Depth profiles of the four measured stations show no diurnal variations. The manual-and the automated method show good compliance. Supersaturation grades are high due to high DGM values and low GEM concentrations. Fluxes of Hg from the sea surface are more dependent on the wind speed than on the supersaturation grade according to the flux models used.