Miracle-dz/UniFAR-FTUs huggingface dataset:
Infrared neural stimulation: a new stimulation tool for central nervous system applications

Abstract. The traditional approach to modulating brain function (in both clinical and basic science applications) is to tap into the neural circuitry using electrical currents applied via implanted electrodes. However, it suffers from a number of problems, including the risk of tissue trauma, poor spatial specificity, and the inability to selectively stimulate neuronal subtypes. About a decade ago, optical alternatives to electrical stimulation started to emerge in order to address the shortcomings of electrical stimulation. We describe the use of one optical stimulation technique, infrared neural stimulation (INS), during which short (of the order of a millisecond) pulses of infrared light are delivered to the neural tissue. Very focal stimulation is achieved via a thermal mechanism and stimulation location can be quickly adjusted by redirecting the light. After describing some of the work done in the peripheral nervous system, we focus on the use of INS in the central nervous system to investigate functional connectivity in the visual and somatosensory areas, target specific functional domains, and influence behavior of an awake nonhuman primate. We conclude with a positive outlook for INS as a tool for safe and precise targeted brain stimulation.
Zeroth-Order-Mode Circular Microstrip Antenna With Patch-Like Radiation Pattern

A zeroth-order-mode circular microstrip patch antenna is presented, consisting of two axial symmetrical semicirculars and pins, which are in essential two composite right/left-handed metamaterial unit cells. The patch-like radiation pattern was achieved for the zeroth-order mode by modifying the equivalent magnetic current densities along the perimeter of the proposed antenna. The variations of the resonant frequency affected by the locations of the pins were also investigated. The dispersion diagrams revealed the phase variation on one period, thus validating the existence of the zeroth-order mode. A prototype of the antenna, operative at 5.83 GHz, was designed on a substrate of ${\text{72 mm }}\times \,{\text{50 mm }}\times \,{\text{1.5 mm}}$. Simulations and measurements were made to prove the theory and design concept.
Incorporation of the C-GOLDSTEIN efficient climate model into the GENIE framework: "eb_go_gs" configurations of GENIE

Abstract. A computationally efficient, intermediate complexity ocean-atmosphere-sea ice model (C-GOLDSTEIN) has been incorporated into the Grid ENabled Integrated Earth system modelling (GENIE) framework. This involved decoupling of the three component modules that were re-coupled in a modular way, to allow replacement with alternatives and coupling of further components within the framework. The climate model described here (referred to as "eb_go_gs" for short) is the most basic version of GENIE in which atmosphere, ocean and sea ice all play an active role. Among improvements on the original C-GOLDSTEIN model, latitudinal grid resolution is generalized to allow a wider range of surface grids to be used. The ocean, atmosphere and sea-ice components of the "eb_go_gs" configuration of GENIE are individually described, along with details of their coupling. The setup and results from simulations using four different meshes are presented. The four alternative meshes comprise the widely-used 36 × 36 equal-area-partitioning of the Earth surface with 16 depth layers in the ocean, a version in which horizontal and vertical resolution are doubled, a setup matching the horizontal resolution of the dynamic atmospheric component available in the GENIE framework, and a setup with enhanced resolution in high-latitude areas. Results are presented for a spin-up experiment with a baseline parameter set and wind forcing typically used for current studies in which "eb_go_gs" is coupled with the ocean biogeochemistry module of GENIE, as well as for an experiment with a modified parameter set, revised wind forcing, and additional cross-basin transport pathways (Indonesian and Bering Strait throughflows). The latter experiment is repeated with the four mesh variants, with common parameter settings throughout, except for time-step length. Selected state variables and diagnostics are compared in two regards: (i) between simulations at lowest resolution that are obtained with the baseline and modified configurations, predominantly in order to evaluate the revision of the wind forcing, the modification of some key parameters, and the effect of additional transport pathways across the Arctic Ocean and the Indonesian Archipelago; (ii) between simulations with the four meshes, in order to explore various effects of mesh choice.
Regional effect on urban atmospheric nucleation

Abstract. Secondary aerosol particle production via new particle formation (NPF) has been shown to be a major contributor to the global aerosol load. NPF has also been observed frequently in urban environments. Here, we investigate the effect of regional NPF on urban aerosol load under well-defined atmospheric conditions. The Carpathian Basin, the largest orogenic basin in Europe, represents an excellent opportunity for exploring these interactions. Based on long-term observations, we revealed that NPF seen in a central large city of the basin (Budapest) and its regional background occur in a consistent and spatially coherent way as a result of a joint atmospheric phenomenon taking place on large horizontal scales. We found that NPF events at the urban site are usually delayed by > 1 h relative to the rural site or even inhibited above a critical condensational sink level. The urban processes require higher formation rates and growth rates to be realized, by mean factors of 2 and 1.6, respectively, than the regional events. Regional- and urban-type NPF events sometimes occur jointly with multiple onsets, while they often exhibit dynamic and timing properties which are different for these two event types.
Prognostic models for RPS patients—Attempting to predict patient outcomes

Retroperitoneal sarcoma (RPS) patients can have variable of outcomes after surgery. The chance to recur locally or at distant sites varies according to tumor grade, histologic subtype, and other patient‐ and tumor‐related characteristics. The relative contribution of each prognostic variable on the oncological outcome of RPS patients can be weighted by combining them in prognostic tools such as nomograms. With this review, we critically appraise the available nomograms for RPS patients highlighting pros and cons.
Linear angle based parameterization

In the field of mesh parameterization, the impact of angular and boundary distortion on parameterization quality have brought forward the need for robust and efficient free boundary angle preserving methods. One of the most prominent approaches in this direction is the Angle Based Flattening (ABF) which directly formulates the problem as a constrained nonlinear optimization in terms of angles. Since the original formulation of the ABF, a steady research effort has been dedicated to improving its efficiency. As for any well posed numerical problem, the solution is generally an approximation of the underlying mathematical equations. The economy and accuracy of the solution are to a great extent affected by the kind of approximation used. In this work we reformulate the problem based on the notion of error of estimation. A careful manipulation of the resulting equations yields for the first time a linear version of angle based parameterization. The error induced by this linearization is quadratic in terms of the error in angles and the validity of the approximation is further supported by numerical results. Besides performance speedup, the simplicity of the current setup makes re-implementation and reproduction of our results straightforward.
Traditional and Cyber-Victimization Among Adolescents With and Without Chronic Pain

Objective: Prior research has revealed a link between peer victimization and somatic complaints in healthy youth; however, the peer victimization experiences of youth with clinically significant chronic pain have not been examined. This study aims to determine rates of peer victimization among youth seeking treatment for chronic pain and to compare these rates to a community control group. Relationships between peer victimization, depressive symptoms, and functional disability are also examined. Method: One hundred forty-three adolescents (70 with chronic pain) completed measures assessing their experience of traditional (physical, relational, reputational) and cyber-based peer victimization, as well as measures assessing their depressive symptoms and pain-related functional disability. Results: Peer victimization experiences were common among youth with and without chronic pain. Within the chronic pain group, there were differences in rates of peer victimization as a function of the adolescent’s school setting. Adolescents with chronic pain attending traditional schools reported more frequent peer victimization experiences than adolescents with pain not enrolled in school or attending online/home school. Within the chronic pain sample, peer victimization was moderately associated with depressive symptoms and functional disability. Tests of a simple mediation model revealed a significant indirect effect of peer victimization on functional disability, through depression. Conclusions: These results are the first to systematically document the peer victimization experiences of adolescents with chronic pain. Peer victimization is commonly experienced, particularly for those enrolled in traditional school settings. Associations with depressive symptoms and functional disability suggest that peer victimization may be a useful target for intervention.
Anti-Mullerian hormone, inhibin B, and antral follicle count in young women with ovarian failure.

CONTEXT Ovarian dysfunction is classically categorized on the basis of cycle history, FSH, and estradiol levels. Novel ovarian markers may provide a more direct insight into follicular quantity in hypergonadotropic women. OBJECTIVE The objective of the study was to investigate the distribution of novel ovarian markers in young hypergonadotropic women as compared with normogonadotropic regularly menstruating women. DESIGN This was a nationwide prospective cohort study. SETTING The study was conducted at 10 hospitals in The Netherlands. PATIENTS Women below age 40 yr with regular menses and normal FSH (controls; n = 83), regular menstrual cycles and elevated FSH [incipient ovarian failure (IOF); n = 68]; oligomenorrhea and elevated FSH [referred to as transitional ovarian failure (TOF); n = 79]; or at least 4 months amenorrhea together with FSH levels exceeding 40 IU/liter [premature ovarian failure (POF); n = 112]. MAIN OUTCOME MEASURES Serum levels of anti-Müllerian hormone (AMH), inhibin B, and antral follicle count (AFC) was measured. RESULTS All POF patients showed AMH levels below the fifth percentile (p(5)) of normoovulatory women. Normal AMH levels (>p(5)) could be identified in 75% of IOF, 33% of TOF patients, and 98% of controls. AFC and AMH levels changed with increasing age (P < 0.0001), whereas inhibin B did not (P = 0.26). AMH levels were significantly different between TOF and IOF over the entire age range, whereas AFC became similar for TOF and IOF at higher ages. CONCLUSIONS Compared with inhibin B and AFC, AMH was more consistently correlated with the clinical degree of follicle pool depletion in young women presenting with elevated FSH levels. AMH may provide a more accurate assessment of the follicle pool in young hypergonadotropic patients, especially in the clinically challenging subgroups of patients with elevated FSH and regular menses (i.e. IOF) and in hypergonadotropic women with cycle disturbances not fulfilling the POF diagnostic criteria (i.e. TOF).
Establishment of the First Well-differentiated Human Pancreatic Neuroendocrine Tumor Model

Clinical options for systemic therapy of neuroendocrine tumors (NET) are limited. Development of new drugs requires suitable representative in vitro and in vivo model systems. So far, the unavailability of a human model with a well-differentiated phenotype and typical growth characteristics has impaired preclinical research in NET. Herein, we establish and characterize a lymph node–derived cell line (NT-3) from a male patient with well-differentiated pancreatic NET. Neuroendocrine differentiation and tumor biology was compared with existing NET cell lines BON and QGP-1. In vivo growth was assessed in a xenograft mouse model. The neuroendocrine identity of NT-3 was verified by expression of multiple NET-specific markers, which were highly expressed in NT-3 compared with BON and QGP-1. In addition, NT-3 expressed and secreted insulin. Until now, this well-differentiated phenotype is stable since 58 passages. The proliferative labeling index, measured by Ki-67, of 14.6% ± 1.0% in NT-3 is akin to the original tumor (15%–20%), and was lower than in BON (80.6% ± 3.3%) and QGP-1 (82.6% ± 1.0%). NT-3 highly expressed somatostatin receptors (SSTRs: 1, 2, 3, and 5). Upon subcutaneous transplantation of NT-3 cells, recipient mice developed tumors with an efficient tumor take rate (94%) and growth rate (139% ± 13%) by 4 weeks. Importantly, morphology and neuroendocrine marker expression of xenograft tumors resembled the original human tumor. Implications: High expression of somatostatin receptors and a well-differentiated phenotype as well as a slow growth rate qualify the new cell line as a relevant model to study neuroendocrine tumor biology and to develop new tumor treatments. Mol Cancer Res; 16(3); 496–507. ©2018 AACR.
N-body Networks: a Covariant Hierarchical Neural Network Architecture for Learning Atomic Potentials

We describe N-body networks, a neural network architecture for learning the behavior and properties of complex many body physical systems. Our specific application is to learn atomic potential energy surfaces for use in molecular dynamics simulations. Our architecture is novel in that (a) it is based on a hierarchical decomposition of the many body system into subsytems, (b) the activations of the network correspond to the internal state of each subsystem, (c) the "neurons" in the network are constructed explicitly so as to guarantee that each of the activations is covariant to rotations, (d) the neurons operate entirely in Fourier space, and the nonlinearities are realized by tensor products followed by Clebsch-Gordan decompositions. As part of the description of our network, we give a characterization of what way the weights of the network may interact with the activations so as to ensure that the covariance property is maintained.
Identifying Terms in Open Source Software License Texts

Open source software is nowadays widely used and any open source software must carry a prominent license. However, the legal, natural language text of open source licenses is not always easy to interpret and an extensive manual analysis of the text may be required, in order to fully understand its content. Existing approaches present license content based on such manual interpretation. In this paper, we propose an automated license term extraction system (FOSS-LTE) for the identification of the license terms from a specific license text and the creation of a representation of these terms divided into rights, obligations and additional conditions. We present the process employed for the creation of the license term extraction system using NLP techniques and we evaluate its accuracy on a set of sentences from available licenses collected for this purpose.
Versajet Hydrosurgery Versus Classic Escharectomy for Burn Débridment: A Prospective Randomized Trial

Our purpose was to conduct a prospective randomized trial to compare the Versajet system (Smith & Nephew, London, UK) vs hand-held dermatome escharectomy for burn débridment. All patients admitted over the course of 1 year at our burn center were recruited and randomly assigned to Versajet or hand-held dermatome escharectomy. We evaluated the 1) time for complete débridment and 2) the efficacy of Versajet in reaching the correct dermal plane. Secondary end points were the assessment of postoperative pain (evaluated with the visual analog scale), adverse effects, complete healing times, and contractures rates (after 6 months). A total of 87 patients were analyzed in two homogeneous groups of 42 (Versajet) and 45 (escharectomy) patients. All of them received adequate débridment, but the Versajet procedure was faster (P < .05) and more precise in obtaining the correct plane. One Versajet patient required ligation of a large subcutaneous vessel, which inadvertently was cut during the procedure. Versajet is a feasible, simple, and safe technique that hastens surgical débridment of burns and adds more precision to the procedure.
Evolution of Directed Triangle Motifs in the Google+ OSN

Motifs are a fundamental building block and distinguishing feature of networks. While characteristic motif distribution have been found in many networks, very little is known today about the evolution of network motifs. This paper studies the most important motifs in social networks, triangles, and how directed triangle motifs change over time. Our chosen subject is one of the largest Online Social Networks, Google+. Google+ has two distinguishing features that make it particularly interesting: (1) it is a directed network, which yields a rich set of triangle motifs, and (2) it is a young and fast evolving network, whose role in the OSN space is still not fully understood. For the purpose of this study, we crawled the network over a time period of six weeks, collecting several snapshots. We find that some triangle types display significant dynamics, e.g., for some specific initial types, up to 20% of the instances evolve to other types. Due to the fast growth of the OSN in the observed time period, many new triangles emerge. We also observe that many triangles evolve into less-connected motifs (with less edges), suggesting that growth also comes with pruning. We complement the topological study by also considering publicly available user profile data (mostly geographic locations). The corresponding results shed some light on the semantics of the triangle motifs. Indeed, we find that users in more symmetric triangle motifs live closer together, indicating more personal relationships. In contrast, asymmetric links in motifs often point to faraway users with a high in-degree (celebrities).
PHRAPL: Phylogeographic Inference Using Approximate Likelihoods

Abstract. — The demographic history of most species is complex, with multiple evolutionary processes combining to shape the observed patterns of genetic diversity. To infer this history, the discipline of phylogeography has (to date) used models that simplify the historical demography of the focal organism, for example by assuming or ignoring ongoing gene flow between populations or by requiring a priori specification of divergence history. Since no single model incorporates every possible evolutionary process, researchers rely on intuition to choose the models that they use to analyze their data. Here, we describe an approximate likelihood approach that reduces this reliance on intuition. PHRAPL allows users to calculate the probability of a large number of complex demographic histories given a set of gene trees, enabling them to identify the most likely underlying model and estimate parameters for a given system. Available model parameters include coalescence time among populations or species, gene flow, and population size. We describe the method and test its performance in model selection and parameter estimation using simulated data. We also compare model probabilities estimated using our approximate likelihood method to those obtained using standard analytical likelihood. The method performs well under a wide range of scenarios, although this is sometimes contingent on sampling many loci. In most scenarios, as long as there are enough loci and if divergence among populations is sufficiently deep, PHRAPL can return the true model in nearly all simulated replicates. Parameter estimates from the method are also generally accurate in most cases. PHRAPL is a valuable new method for phylogeographic model selection and will be particularly useful as a tool to more extensively explore demographic model space than is typically done or to estimate parameters for complex models that are not readily implemented using current methods. Estimating relevant parameters using the most appropriate demographic model can help to sharpen our understanding of the evolutionary processes giving rise to phylogeographic patterns. [AIC; grid search; isolation‐with‐migration; migration rate; multispecies coalescent; parameter optimization; population genetics; tree topologies. ]
Restricted nutrition-induced low birth weight, low number of nephrons and glomerular mesangium injury in Japanese quail

Insufficient nutrition during the perinatal period causes structural alterations in humans and experimental animals, leading to increased vulnerability to diseases in later life. Japanese quail, Coturnix japonica, in which partial (8–10%) egg white was withdrawn (EwW) from eggs before incubation had lower birth weights than controls (CTs). EwW birds also had reduced hatching rates, smaller glomeruli and lower embryo weight. In EwW embryos, the surface condensate area containing mesenchymal cells was larger, suggesting that delayed but active nephrogenesis takes place. In mature EwW quail, the number of glomeruli in the cortical region (mm2) was significantly lower (CT 34.7±1.4, EwW 21.0±1.2); capillary loops showed focal ballooning, and mesangial areas were distinctly expanded. Immunoreactive cell junction proteins, N-cadherin and podocin, and slit diaphragms were clearly seen. With aging, the mesangial area and glomerular size continued to increase and were significantly larger in EwW quail, suggesting compensatory hypertrophy. Furthermore, apoptosis measured by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling analysis was higher in EwWs than in CTs on embryonic day 15 and postnatal day 4 (D4). Similarly, plasma glucocorticoid (corticosterone) was higher (P<0.01) on D4 in EwW quail. These results suggest that although nephrogenic activity is high in low-nutrition quail during the perinatal period, delayed development and increased apoptosis may result in a lower number of mature nephrons. Damaged or incompletely mature mesangium may trigger glomerular injury, leading in later life to nephrosclerosis. The present study shows that birds serve as a model for ‘fetal programming,’ which appears to have evolved phylogenetically early.
Homeopathic treatment of chronic headache: a critique

Abstract The author critically reviews a randomised controlled trial by homeopathy for chronic headache and an observational follow-up study of the same patient cohort. The results showed no difference between homeopathy and placebo. The author believes that these results were a ‘false negative’ due to inadequate homeopathic treatment, particularly relating to the duration of symptoms and handling of homeopathic aggravations. Guidelines for future studies are proposed.