julilili42/papers huggingface dataset:
Beyond Columnar Organization: Cell Type- and Target Layer-Specific Principles of Horizontal Axon Projection Patterns in Rat Vibrissal Cortex
2015-04-01

Vertical thalamocortical afferents give rise to the elementary functional units of sensory cortex, cortical columns. Principles that underlie communication between columns remain however unknown. Here we unravel these by reconstructing in vivo-labeled neurons from all excitatory cell types in the vibrissal part of rat primary somatosensory cortex (vS1). Integrating the morphologies into an exact 3D model of vS1 revealed that the majority of intracortical (IC) axons project far beyond the borders of the principal column. We defined the corresponding innervation volume as the IC-unit. Deconstructing this structural cortical unit into its cell type-specific components, we found asymmetric projections that innervate columns of either the same whisker row or arc, and which subdivide vS1 into 2 orthogonal [supra-]granular and infragranular strata. We show that such organization could be most effective for encoding multi whisker inputs. Communication between columns is thus organized by multiple highly specific horizontal projection patterns, rendering IC-units as the primary structural entities for processing complex sensory stimuli.
Functional imaging for radiotherapy treatment planning: current status and future directions—a review
2015-04-01

In recent years, radiotherapy (RT) has been subject to a number of technological innovations. Today, RT is extremely flexible, allowing irradiation of tumours with high doses, whilst also sparing normal tissues from doses. To make use of these additional degrees of freedom, integration of functional image information may play a key role (i) for better staging and tumour detection, (ii) for more accurate RT target volume delineation, (iii) to assess functional information about biological characteristics and individual radiation resistance and (iv) to apply personalized dose prescriptions. In this article, we discuss the current status and future directions of different clinically available functional imaging modalities; CT, MRI, positron emission tomography (PET) as well as the hybrid imaging techniques PET/CT and PET/MRI and their potential for individualized RT.
Post-processing of structural MRI for individualized diagnostics.
2015-04-01

Currently, a relevant proportion of all histopathologically proven focal cortical dysplasia (FCD) escape visual detection; this shows the need for additional improvements in analyzing MRI data. A positive MRI is still the strongest prognostic factor for postoperative freedom of seizures. Among several post-processing methods voxel-based morphometry (VBM) of T1- and T2-weighted sequences and T2 relaxometry are routinely applied in pre-surgical diagnostics of cryptogenic epilepsy in epilepsy centers. VBM is superior to conventional visual analysis with 9-15% more identified epileptogenic foci, while T2 relaxometry has its main application in (mesial) temporal lobe epilepsy. Further methods such as surface-based morphometry (SBM) or diffusion tensor imaging are promising but there is a lack of current studies comparing their individual diagnostic value. Post-processing methods represent an important addition to conventional visual analysis but need to be interpreted with expertise and experience so that they should be apprehended as a complementary tool within the context of the multi-modal evaluation of epilepsy patients. This review will give an overview of existing post-processing methods of structural MRI and outline their clinical relevance in detection of epileptogenic structural changes.
Automatic Noun Compound Interpretation using Deep Neural Networks and Word Embeddings
2015-04-01

The present paper reports on the results of automatic noun compound interpretation for English using a deep neural network classifier and a selection of publicly available word embeddings to represent the individual compound constituents. The task at hand consists of identifying the semantic relation that holds between the constituents of a compound (e.g. WHOLE+PART_OR_MEMBER_OF in the case of ‘robot arm’, LOCATION in the case of ‘hillside home’). The experiments reported in the present paper use the noun compound dataset described in Tratz (2011), a revised version of the dataset used by Tratz and Hovy (2010) for training their Maximum Entropy classifier. Our experiments yield results that are comparable to those reported in Tratz and Hovy (2010) in a crossvalidation setting, but outperform their system on unseen compounds by a large margin.
Gene expression analysis for evaluation of potential biomarkers in hepatocellular carcinoma.
2015-04-01

Unlike previous studies, our results did not confirm FUCA1, HGF, IGF1 or CgA as potential markers for HCC. In contrast, OPN, SPINK1, GPC3 and KNPA2 were significantly over-expressed in HCC tissues. These genes may be useful in developing future biomarkers and therapeutic strategies for HCC.
No Dopamine Cell Loss or Changes in Cytoskeleton Function in Transgenic Mice Expressing Physiological Levels of Wild Type or G2019S Mutant LRRK2 and in Human Fibroblasts
2015-04-01

Mutations within the LRRK2 gene have been identified in Parkinson's disease (PD) patients and have been implicated in the dysfunction of several cellular pathways. Here, we explore how pathogenic mutations and the inhibition of LRRK2 kinase activity affect cytoskeleton dynamics in mouse and human cell systems. We generated and characterized a novel transgenic mouse model expressing physiological levels of human wild type and G2019S-mutant LRRK2. No neuronal loss or neurodegeneration was detected in midbrain dopamine neurons at the age of 12 months. Postnatal hippocampal neurons derived from transgenic mice showed no alterations in the seven parameters examined concerning neurite outgrowth sampled automatically on several hundred neurons using high content imaging. Treatment with the kinase inhibitor LRRK2-IN-1 resulted in no significant changes in the neurite outgrowth. In human fibroblasts we analyzed whether pathogenic LRRK2 mutations change cytoskeleton functions such as cell adhesion. To this end we compared the adhesion characteristics of human skin fibroblasts derived from six PD patients carrying one of three different pathogenic LRRK2 mutations and from four age-matched control individuals. The mutant LRRK2 variants as well as the inhibition of LRRK2 kinase activity did not reveal any significant cell adhesion differences in cultured fibroblasts. In summary, our results in both human and mouse cell systems suggest that neither the expression of wild type or mutant LRRK2, nor the inhibition of LRRK2 kinase activity affect neurite complexity and cellular adhesion.
Invasive success and the evolution of enhanced weaponry
2015-04-01

A key hypothesis that has been proposed to explain plants’ invasive success suggests that some invasive species produce allelochemicals that are novel against naïve neighbours at the introduced range and therefore provide an advantage there (novel weapons hypothesis – NWH). However, a seldom‐studied hypothesis suggests that invasive populations could not only possess novel weapons, but might also evolve their enhanced production. Moreover, so far no study has examined both the novelty and evolution of allelopathic effects. Here, we examined these two hypotheses in a set of experiments with the highly invasive plant Impatiens glandulifera . In the first experiment, we examined the evolution of allelopathic ability by comparing the inhibitory effects of leaf extracts from native versus invasive I. glandulifera on the germination success of its dominant neighbour Urtica dioica . In the following experiments, we examined the NWH by comparing the germination success of U. dioica seeds collected at the native versus invasive range of I. glandulifera , in response to either leaf extracts or soil trained with invasive I. glandulifera . The results of the first experiment indicate that invasive I. glandulifera exert a stronger inhibitory effect on the germination of U. dioica compared to their native counterparts, providing support for the hypothesis that allelopathic ability can evolve at the invasive range. However, the results of the two following experiments reveal no difference in the response of U. dioica from the native versus invasive range of I. glandulifera , to the allelopathic effects of either the leaf extracts or the trained soil. These results therefore do not provide support for the NWH, and suggest that increased allelopathy in invasive I. glandulifera might have been selected for by other processes. The results of this study call for biogeographical experiments that will examine not only the novelty but also the evolution of allelopathic effects in invasive plants.
The putative Cationic Amino Acid Transporter 9 is targeted to vesicles and may be involved in plant amino acid homeostasis
2015-04-01

Amino acids are major primary metabolites. Their uptake, translocation, compartmentation, and re-mobilization require a diverse set of cellular transporters. Here, the broadly expressed gene product of CATIONIC AMINO ACID TRANSPORTER 9 (CAT9) was identified as mainly localized to vesicular membranes that are involved in vacuolar trafficking, including those of the trans-Golgi network. In order to probe whether and how these compartments are involved in amino acid homeostasis, a loss-of-function cat9-1 mutant and ectopic over-expressor plants were isolated. Under restricted nitrogen supply in soil, cat9-1 showed a chlorotic phenotype, which was reversed in the over-expressors. The total soluble amino acid pools were affected in the mutants, but this was only significant under poor nitrogen supply. Upon nitrogen starvation, the soluble amino acid leaf pools were lower in the over-expressor, compared with cat9-1. Over-expression generally affected total soluble amino acid concentrations, slightly delayed development, and finally improved the survival upon severe nitrogen starvation. The results potentially identify a novel function of vesicular amino acid transport mediated by CAT9 in the cellular nitrogen-dependent amino acid homeostasis.
Experience-Related Structural Changes of Degenerated Occipital White Matter in Late-Blind Humans – A Diffusion Tensor Imaging Study
2015-04-01

Late-blind humans can learn to understand speech at ultra-fast syllable rates (ca. 20 syllables/s), a capability associated with hemodynamic activation of the central-visual system. Thus, the observed functional cross-modal recruitment of occipital cortex might facilitate ultra-fast speech processing in these individuals. To further elucidate the structural prerequisites of this skill, diffusion tensor imaging (DTI) was conducted in late-blind subjects differing in their capability of understanding ultra-fast speech. Fractional anisotropy (FA) was determined as a quantitative measure of the directionality of water diffusion, indicating fiber tract characteristics that might be influenced by blindness as well as the acquired perceptual skills. Analysis of the diffusion images revealed reduced FA in late-blind individuals relative to sighted controls at the level of the optic radiations at either side and the right-hemisphere dorsal thalamus (pulvinar). Moreover, late-blind subjects showed significant positive correlations between FA and the capacity of ultra-fast speech comprehension within right-hemisphere optic radiation and thalamus. Thus, experience-related structural alterations occurred in late-blind individuals within visual pathways that, presumably, are linked to higher order frontal language areas.
UAV energy extraction with incomplete atmospheric data using MPC
2015-04-01

A nonlinear model predictive control strategy is presented for unmanned aerial vehicle (UAV) trajectory determination. The objective is to find optimal paths in the atmosphere by maximizing the UAV's energy (kinetic and potential) over a finite but receding horizon. The main assumption is that the updraft distribution is unknown, creating a realistic situation. The updrafts are only estimated online using standard on-board inertial sensors. Real-time implementation of the algorithm is shown to be possible in principle.
Series and Contact Resistance Measurements between 80 K and Room Temperature for Industrial Solar Cells
2015-04-01

Cells with different front side pastes, processing parameters and substrate orientation were electrically characterized especially with regard to the series and contact resistance. Such cells were used for electrical measurements in an optical cryostat: VOC, dark current and I-V curves under illumination were acquired. Care was taken to provide optimum contacting of the cells and reproducible results could be obtained. Pastes of two different suppliers were processed and yielded significantly different microstructure and electrical properties. A large hysteresis in VOC of about 100 mV at 80 K was found for an overfired cell, the identical cell processed at optimum temperature yielded no hysteresis in VOC. Dark current measurements yielded differences for cells processed with different pastes, these differences increased with decreasing temperature. The temperature dependent series resistance was determined: at low temperatures (80 K) a metallic behaviour was seen that switched to semiconducting close to room temperature. From such measurements conclusions with respect to the current path can be drawn and are discussed. Planar cells were investigated for two different surface orientations, i.e. 〈100〉 and 〈111〉. Pyramidal shaped Ag crystallites form only in the 〈100〉 orientation, not in 〈111〉. The density of Ag colloids in the glass layer is significantly larger in the 〈111〉 orientation. The contact resistance of planar 〈111〉 cells was in the range of textured surfaces and was found to be smaller as compared to 〈100〉 orientation. This indicates that pyramidal Ag crystallites are not necessary for a low contact resistance and a percolative current path along the Ag colloids in the glass layer is proposed.
Scalable resilience for Software-Defined Networking using Loop-Free Alternates with loop detection
2015-04-01

In this paper we propose a novel resilience scheme for OpenFlow-based Software-Defined Networking (SDN). To forward packets in line speed, OpenFlow switches store their flow tables in expensive, limited TCAM due to which the stored tables cannot be large. Most resilience mechanisms require additional entries thus the implementation in OpenFlow may quickly exceed the available TCAM. Loop-Free Alternates (LFAs) are a standardized mechanism for fast reroute in IP networks which do not require additional entries. However, LFAs cannot protect against all single link and node failures. Moreover, some LFAs even cause loops in case of some node failures or multiple failures, making additional links unusable. Excluding such LFAs reduces the fraction of protected destinations (protection coverage) in nodes even further. We suggest a scheme for detection of loops caused by LFAs. It maximizes the protection coverage because it allows all LFAs to be used without creating loops. We describe how LFAs and the loop detection scheme can be implemented in OpenFlow networks with only little packet overhead and a single additional entry per switch. We evaluate our proposal on real network topologies of varying size and connectivity. In particular, we quantify the benefit gained from loop detection. Amongst others, we study the percentage of failures that cannot be protected by LFAs at all, and the percentage of failures in which conventional LFAs cause extra loops.
Loa loaInfection in Pregnant Women, Gabon
2015-04-01

Loa loa, the African eye worm, is a filarial pathogen of Central African rainforest regions. As of 2013, it had affected an estimated 2–3 million persons in Central Africa (1,2). Adult worm migrations in humans may intermittently cause Calabar swelling, and microfilariae are commonly found in blood and body fluids. Loiasis is a chronic infection persisting for many years; a considerable proportion of women in loiasis-endemic regions are infected during gestation. To date, the epidemiology of loiasis in pregnant women has not been investigated, and the effects of loiasis on maternal and fetal health outcomes are unknown. We investigated the epidemiology of loiasis in a cohort of pregnant women participating in a drug trial for preventing malaria during pregnancy.
To what extent can retinal prostheses restore vision?
2015-04-01

After a general consideration of the various approaches to electrical stimulation of the retina, a thorough in vitro investigation of retinal responses to voltage-controlled stimuli is discussed within the context of the Alpha IMS subretinal implant (Retina Implant AG, Reutlingen, Germany). This is supplemented by a clinical trial interim report describing results obtained in 29 patients blind from retinitis pigmentosa who have received the Alpha IMS implant. It is concluded that the surgical procedure is safe and blind patients can benefit in visual tasks of daily life with this device that has meanwhile received approval for commercial use in Europe.
Combining Compressed Sensing with motion correction in acquisition and reconstruction for PET/MR
2015-04-01

In the field of oncology, simultaneous Positron-Emission-Tomography/Magnetic Resonance (PET/MR) scanners offer a great potential for improving diagnostic accuracy. However, to achieve a high Signal-to-Noise Ratio (SNR) for an accurate lesion detection and quantification in the PET/MR images, one has to overcome the induced respiratory motion artifacts. The simultaneous acquisition allows performing a MR-based non-rigid motion correction of the PET data. It is essential to acquire a 4D (3D + time) motion model as accurate and fast as possible to minimize additional MR scan time overhead. Therefore, a Compressed Sensing (CS) acquisition by means of a variable-density Gaussian subsampling is employed to achieve high accelerations. Reformulating the sparse reconstruction as a combination of the inverse CS problem with a non-rigid motion correction improves the accuracy by alternately projecting the reconstruction results on either the motion-compensated CS reconstruction or on the motion model optimization. In-vivo patient data substantiates the diagnostic improvement.
Treatment escalation options for patients with type 2 diabetes after failure of exenatide twice daily or glimepiride added to metformin: results from the prospective E uropean E xenatide ( EUREXA ) study
2015-04-01

Aims To evaluate third‐line thiazolidinedione ( TZD ) or glimepiride therapy in patients inadequately controlled on metformin + exenatide twice daily, and third‐line exenatide twice daily in patients inadequately controlled on metformin + glimepiride. Methods In this randomized, open‐label, multicentre trial, 144 patients with type 2 diabetes inadequately controlled [glycated haemoglobin ( HbA1c ) &gt;9% (75 mmol/mol) after 3 months' treatment or &gt;7% (53 mmol/mol) at two consecutive visits 3 months apart, after 6 months' treatment] on metformin + exenatide twice daily were re‐randomized to add‐on TZD or glimepiride, and 166 patients inadequately controlled on metformin + glimepiride received add‐on exenatide twice daily. Changes in HbA1c , body mass index ( BMI ), lipids, hypoglycaemia and vital signs were evaluated. Results The median duration of triple therapy was ∼2 years. In patients inadequately controlled on metformin + exenatide twice daily, add‐on TZD decreased HbA1c levels significantly better than add‐on glimepiride: 130‐week difference 0.48% [95% confidence interval ( CI ) 0.19–0.77] or 5.2 mmol/mol (95% CI 2.1–8.4; p = 0.001), but with significantly increased BMI and systolic blood pressure. The ratio of documented symptomatic (blood glucose ≤70 mg/dl [3.9 mmol/l]) hypoglycaemia rates for add‐on glimepiride to add‐on TZD was 8.48 (p &lt; 0.0001). Add‐on exenatide twice daily after metformin + glimepiride significantly reduced HbA1c levels: mean [standard deviation (s.d.)] change from baseline −0.35 (0.89)% [−3.8 (9.7) mmol/mol] and BMI : mean (s.d.) change from baseline −0.82 (1.9) kg/m 2 at 130 weeks, with a slightly increased rate of documented symptomatic hypoglycaemia from metformin + glimepiride (ratio 1.49). Conclusions TZD , but not glimepiride, was an effective and well tolerated third‐line therapy in patients without glycaemic control after long‐term therapy with metformin + exenatide twice daily. Exenatide twice daily was an effective and well tolerated third‐line therapy in patients inadequately controlled on metformin + glimepiride.
Fined-grained body biasing for frequency scaling in advanced SOI processes
2015-04-01

New SOI processes offer unprecedented flexibility in regard to low-power and performance. The use of fine-grained body biasing in STMicro's 28nm UTBB-FDSOI is evaluated for a Dynamically Reconfigurable Processor design in a frequency scaling scenario. Three different strategies are evaluated for Processing Elements: Static, programmable and dynamic body biasing. Fine-grained body biasing significantly mitigates increased leakage currents of forward body biasing between 42.85% to 64.5% on average. This makes static body biasing a viable low-cost option and makes dynamic body biasing worthwhile even at short time periods.
Temporally‐controlled Cell Labelling Reveals Transdifferentiation of Smooth Muscle Cells during Atherogenesis
2015-04-01

Atherosclerosis and its secondary disorders, heart attack and stroke, are the major causes of death in the western world, but their pathogenesis is poorly understood. One question is how vascular smooth muscle cells (VSMCs) contribute to atherogenesis. In this study, temporally‐controlled Cre/lox‐mediated cell fate mapping was used to investigate the role of VSMCs in atherosclerotic plaque formation in apolipoprotein E‐deficient mice. Prior to development of atherosclerosis, VSMCs were genetically labelled and their fate was followed during disease progression. Our in vivo analyses showed that distinct plaque regions are composed of clonally growing VSMC‐derived cells, which drastically changed their phenotype. These phenotypic changes were further evaluated by expression profiling of cultured VSMCs as an in vitro model of atherogenesis. Both the synthetic/dedifferentiated VSMCs in cell culture and the VSMC‐derived plaque cells in vivo lost typical smooth muscle markers (e.g., SM alpha‐actin) and instead expressed macrophage markers (e.g., Mac‐2 and CD68) and proteins associated with cellular growth and stress. Interestingly, we found that cGMP signalling via cGMP‐dependent protein kinase I might be involved in the development of the VSMC‐derived plaque cells. These findings provide strong in vivo evidence for smooth muscle‐to‐macrophage transdifferentiation and support important roles of cGMP and VSMC plasticity in atherogenesis. Targeting this type of VSMC phenotypic conversion might be a novel strategy for the treatment of atherosclerosis as well as other diseases with a smooth muscle component.