julilili42/papers huggingface dataset:
The use of a generalized reconstruction by inversion of coupled systems (GRICS) approach for generic respiratory motion correction in PET/MR imaging
2015-03-06

Respiratory motion is a source of artifacts in multimodality imaging such as PET/MR. Solutions include retrospective or prospective gating. They have however found limited use in clinical practice, since their increased overall acquisition duration to maintain overall image quality. More elaborate methods consist of using 4D MR datasets to extract spatial deformations in order to correct for the respiratory motion in PET. The main drawbacks of such approaches is the relatively long acquisition times associated with 4D MR imaging which is often incompatible with clinical PET/MR protocols. The objective of this work was to overcome these limitations by exploiting a generalized reconstruction by inversion of coupled systems (GRICS) approach. The methodology is based on a joint estimation of motion during the MR image reconstruction process, providing internal structure motion and associated deformation matrices for retrospective use in PET respiratory motion correction. This method was first validated on four MR volunteers and two PET/MR patient datasets by comparing GRICS generated MR images to 4D MR series obtained by retrospective gating. In a second step 4D PET datasets corresponding to acquired 4D MR images were simulated using the GATE Monte Carlo simulation platform. GRICS generated deformation matrices were subsequently used to correct respiratory motion in comparison to the 4D MR image based deformations both for the simulated and the two 4D PET/MR patient datasets. Results confirm that GRICS synchronized MR images correlate well with the acquired 4D MR series. Similarly, the use of GRICS for respiratory motion correction allows an equivalent percentage improvement on lesion contrast, position and size, considering the PET simulated tumors as well as PET real tumors. This work demonstrates the potential interest of using GRICS for PET respiratory motion correction in combined PET/MR using shorter duration acquisitions without the need for 4D MRI and associated specific MR sequences.
Effects of the polyphenol resveratrol on contractility of human term pregnant myometrium
2015-03-06

The ideal agent for prevention and treatment of uterine abnormal contractility has not been found. The polyphenol resveratrol possesses a wide spectrum of pharmacologic properties, but its influence on the contractility of human myometrium is not defined. The present study evaluated the effect of resveratrol on the oxytocin-induced contractions of human term pregnant myometrium in vitro and the contribution of different K(+) channels to resveratrol action. Resveratrol induced a concentration-dependent relaxation of myometrium contractions (pD2 value and maximal responses were 4.52 and 82.25%, respectively). Glibenclamide, a selective blocker of ATP-sensitive (KATP), iberiotoxin, a selective blockers of big-calcium sensitive (BK(Ca)) and 4-aminopiridine, a non-selective blocker of voltage-sensitive (Kv) channels induced a significant shift to the right of the concentration-response curves of resveratrol. Inhibition achieved by 0.1 mM resveratrol was insensitive to all K(+) channel blockers. A K(+) channel opener, pinacidil, inhibited oxytocin-induced contractions of pregnant myometrium with comparable potency and efficacy to resveratrol (pD2 values and maximal relaxation were 4.52 and 83.67%, respectively). Based on K(+) channel opener/blocker affinities, it appears that the inhibitory response of resveratrol involves different myometrial K(+) channels. When applied in high concentrations, resveratrol has an additional K(+)-channel-independent mechanism(s) of action. Furthermore, immunohistochemistry staining and western blot analyses detected the presence and distribution of KATP, BK(Ca) and Kv channel proteins in pregnant myometrium.
Dielectrophoretic investigation of Bi2Te3nanowires—a microfabricated thermoelectric characterization platform for measuring the thermoelectric and structural properties of single nanowires
2015-03-06

In this article a microfabricated thermoelectric nanowire characterization platform to investigate the thermoelectric and structural properties of single nanowires is presented. By means of dielectrophoresis (DEP), a method to manipulate and orient nanowires in a controlled way to assemble them onto our measurement platform is introduced. The thermoelectric platform fabricated with optimally designed DEP electrodes results in a yield of nanowire assembly of approximately 90% under an applied peak-to-peak ac signal Vpp = 10 V and frequency f = 20 MHz within a series of 200 experiments. Ohmic contacts between the aligned single nanowire and the electrodes on the platform are established by electron beam-induced deposition. The Seebeck coefficient and electrical conductivity of electrochemically synthesized Bi2Te3 nanowires are measured to be -51 μV K(-1) and (943 ± 160)/(Ω(-1) cm(-1)), respectively. Chemical composition and crystallographic structure are obtained using transmission electron microscopy. The selected nanowire is observed to be single crystalline over its entire length and no grain boundaries are detected. At the surface of the nanowire, 66.1 ± 1.1 at.% Te and 34.9 ± 1.1 at.% Bi are observed. In contrast, chemical composition of 64.2 at.% Te and 35.8 at.% Bi is detected in the thick center of the nanowire.
Usability and Workload of Access Technology for People With Severe Motor Impairment
2015-03-09

Background. Eye trackers are widely used among people with amyotrophic lateral sclerosis, and their benefits to quality of life have been previously shown. On the contrary, Brain-computer interfaces (BCIs) are still quite a novel technology, which also serves as an access technology for people with severe motor impairment. Objective. To compare a visual P300-based BCI and an eye tracker in terms of information transfer rate (ITR), usability, and cognitive workload in users with motor impairments. Methods. Each participant performed 3 spelling tasks, over 4 total sessions, using an Internet browser, which was controlled by a spelling interface that was suitable for use with either the BCI or the eye tracker. At the end of each session, participants evaluated usability and cognitive workload of the system. Results. ITR and System Usability Scale (SUS) score were higher for the eye tracker (Wilcoxon signed-rank test: ITR T = 9, P = .016; SUS T = 12.50, P = .035). Cognitive workload was higher for the BCI ( T = 4; P = .003). Conclusions. Although BCIs could be potentially useful for people with severe physical disabilities, we showed that the usability of BCIs based on the visual P300 remains inferior to eye tracking. We suggest that future research on visual BCIs should use eye tracking–based control as a comparison to evaluate performance or focus on nonvisual paradigms for persons who have lost gaze control.
Source level performance simulation of GPU cores
2015-03-09

Graphic processing units (GPUs) contain a lot of complex architectural features, which make performance analysis and simulation of applications using them for general purpose computation very difficult. Especially when trying to do performance simulations at a higher abstraction level than interpreted instruction set simulators these features are not handled accurately by state of the art simulation techniques. This paper proposes a method for source level performance simulation of the microarchitecture of a GPU core that provides high enough simulation speeds to make testing of large application scenarios possible.
A virtual reconstruction and comparative analysis of the KNM-ER 42700 cranium
2015-03-09

The taxonomic attribution of the 1.55 million year old young adult fossil calvaria KNM-ER 42700 from Ileret, Kenya, is subject to ongoing controversy. It has been attributed to H. erectus based on comparative description and linear measurements. However, 3-D geometric morphometric analysis found that this specimen fell outside the range of variation of H. erectus in its cranial shape, which was intermediate between H. erectus and modern humans. One problem is that analyses so far were conducted on the original specimen, which shows slight post-mortem distortion. Here we use a surface scan of a high resolution cast of KNM-ER 42700 to virtually reconstruct the calvaria and conduct a new 3D geometric morphometric analysis of both its original and its reconstructed shape. Our comparative sample included several specimens of H. erectus (s.l., including the subadult KNM-WT 15000), H. habilis, H. heidelbergenis (s.l.) and H. neanderthalensis, as well as early and Upper Paleolithic H. sapiens. Our principal component analysis results showed that, like the original specimen, our virtual reconstruction of KNM-ER 42700 is also intermediate in shape between fossil Homo and modern humans. Taphonomic distortion, therefore, appears to not have been a major factor affecting previous 3-D geometric morphometric analyses. The intermediate shape of KNM-ER 42700 might instead be related to the young developmental age of the specimen. Further work on reconstructing the original specimen or based on computed tomorgraphic scans is needed to confirm these results.
Spatial and temporal granularity limits of body biasing in UTBB-FDSOI
2015-03-09

Advances in SOI technology such as STMicro's 28nm UTBB-FDSOI enabled a renaissance of body biasing. Body biasing is a fast and efficient technique to change power and performance characteristics. As the electrical task to change the substrate potential is small compared to Dynamic Voltage Scaling, much finer island sizes are conceivable. This however creates new challenges in regard to design partitioning into body bias islands and body bias combinations across such designs. These combinations should be chosen so that energy efficiency improves while maintaining timing constraints. We introduce a combination based analysis tool to find optimized body bias island partitions and body biasing levels. For such partitions, optimized body bias assignments for static, programmable and dynamic body biasing can be computed. The overheads incurred by dynamically switching body biases are estimated to yield actual improvements and to give an upper bound for the power consumption of required additional circuitry. Based on these partitionings and the switching overheads, optimized application specific switching strategies are computed. The effectiveness of this method is demonstrated in a frequency scaling scenario using forward body biasing on a Dynamic Reconfigurable Processor (DRP) design. We show that leakage can be greatly reduced using the proposed methods and that dynamic body biasing can be beneficial even at small time periods.
Anticoagulation after Catheter Ablation of Atrial Fibrillation Guided by Implantable Cardiac Monitors
2015-03-10

Background Discontinuation of oral anticoagulation (OAC) after catheter ablation of atrial fibrillation (AF) is not recommended in patients with elevated CHADS 2 scores. However, a low incidence of thromboembolic events is reported when OAC is stopped in these patients. We introduce an algorithm for discontinuation of OAC after ablation based on the AF burden documented by implantable cardiac monitors (ICM). Methods Sixty‐five patients with CHADS 2 scores 1–3 free from AF 3 months after ablation (AF ablation [n = 49] or ablation of possible AF triggers [n = 16]) were included. One day after implantation of the ICM, OAC was stopped. Patients performed a daily interrogation of the ICM which was programmed to alarm the patient if daily AF burden exceeded 1 hour. Study end point was the first recurrence of a daily AF burden ≥1 hour or a thromboembolic event, which both triggered reinitiation of OAC. Results During a follow‐up time of 32 ± 12 months (126 patient‐years), 41 of the 65 patients (63%) had an AF burden &lt;1 h/day and were able to stay off OAC. Twenty‐one patients (32%) had to reinitiate OAC due to an AF burden ≥1 hour and three patients due to other reasons. No stroke, transitory ischemic attack, or other thromboembolic event was observed during follow‐up. Conclusions Rhythm monitoring by ICM in patients who have stopped OAC after catheter ablation of AF or ablation of possible AF triggers seems to be a safe and promising method to monitor for AF recurrence. Within 1.3 years after ablation, about two‐thirds of patients were able to stay off OAC.
Does our Brain House a „Mental Syllabary“? An fMRI Study
2015-03-10

The present study combines functional magnetic resonance imaging (fMRI) and reaction time (RT) measurements to further elucidate the influence of syllable frequency and complexity on the production of pseudo-words. Similar to a recent fMRI investigation of our group, the present study was based on the concept of a mental syllabary, housing ready-made motor plans of high- (HF), but not low-frequency (LF) syllables. The fMRI data provided no evidence for a frequency effect, revealed, however, an impact of syllable structure: Compared to CV-items, syllables with a more complex onset (CCV) yielded higher hemodynamic activation in motor “execution ” areas, i.e., left sensorimotor cortex and right inferior cerebellum. These results are consistent with our previous study, although the areas associated with the complexity effect show only a partial overlap. In contrast to the fMRI data, RT analyses disclosed a significant impact of syllable frequency, an observation supporting the concept of a mental syllabary. However, a significant interaction between frequency and complexity could be observed, i.e., LF-items- but not HF-syllables- were influenced by syllable structure. These latter findings are at variance with the hypothesis that both simple and complex HF syllables are stored as ready-made motor plans, equally accessible during speech production. 1
Identifying close binary central stars of PN with Kepler
2015-03-11

Six planetary nebulae (PN) are known in the Kepler space telescope field of\\nview, three newly identified. Of the 5 central stars of PN with useful Kepler\\ndata, one, J193110888+4324577, is a short-period, post common envelope binary\\nexhibiting relativistic beaming effects. A second, the central star of the\\nnewly identified PN Pa5, has a rare O(He) spectral type and a periodic\\nvariability consistent with an evolved companion, where the orbital axis is\\nalmost aligned with the line of sight. The third PN, NGC~6826 has a fast\\nrotating central star, something that can only be achieved in a merger. Fourth,\\nthe central star of the newly identified PN Kn61, has a PG1159 spectral type\\nand a mysterious semi-periodic light variability which we conjecture to be\\nrelated to the interplay of binarity with a stellar wind. Finally, the central\\nstar of the circular PN A61 does not appear to have a photometric variability\\nabove 2 mmag. With the possible exception of the variability of Kn61, all other\\nvariability behaviour, whether due to binarity or not, would not easily have\\nbeen detected from the ground. We conclude, based on very low numbers, that\\nthere may be many more close binary or close binary products to be discovered\\nwith ultra-high precision photometry. With a larger number of high precision\\nphotometric observations we will be able to determine how much higher than the\\ncurrently known 15 per cent, the short period binary fraction for central stars\\nof PN is likely to be.\\n
The Novel Lipopeptide Poaeamide of the EndophytePseudomonas poaeRE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization
2015-03-11

Endophytic Pseudomonas poae strain RE*1-1-14 was originally isolated from internal root tissue of sugar beet plants and shown to suppress growth of the fungal pathogen Rhizoctonia solani both in vitro and in the field. To identify genes involved in its biocontrol activity, RE*1-1-14 random mutagenesis and sequencing led to the identification of a nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode a lipopeptide (LP) with a 10-amino-acid peptide moiety. The two unlinked gene clusters consisted of three NRPS genes, designated poaA (cluster 1) and poaB and poaC (cluster 2), spanning approximately 33.7 kb. In silico analysis followed by chemical analyses revealed that the encoded LP, designated poaeamide, is a structurally new member of the orfamide family. Poaeamide inhibited mycelial growth of R. solani and different oomycetes, including Phytophthora capsici, P. infestans, and Pythium ultimum. The novel LP was shown to be essential for swarming motility of strain RE*1-1-14 and had an impact on root colonization of sugar beet seedlings The poaeamide-deficient mutant colonized the rhizosphere and upper plant cortex at higher densities and with more scattered colonization patterns than the wild type. Collectively, these results indicate that Pseudomonas poae RE*1-1-14 produces a structurally new LP that is relevant for its antagonistic activity against soilborne plant pathogens and for colonization of sugar beet roots.
Three‐layered radio frequency coil arrangement for sodium MRI of the human brain at 9.4 Tesla
2015-03-11

Purpose A multinuclei imaging setup with the capability to acquire both sodium ( 23 Na) and proton ( 1 H) signals at 9.4 Tesla is presented. The main objective was to optimize coil performance at the 23 Na frequency while still having the ability to acquire satisfactory 1 H images. Methods The setup consisted of a combination of three radio frequency (RF) coils arranged in three layers: the innermost layer was a 27‐channel 23 Na receive helmet which was surrounded by a four‐channel 23 Na transceiver array. The outer layer consisted of a four‐channel 1 H dipole array for B 0 shimming and anatomical localization. Transmit and receive performance of the 23 Na arrays was compared to a single‐tuned 23 Na birdcage resonator. Results While the transmit efficiency of the 23 Na transceiver array was comparable to the birdcage, the 23 Na receive array provided substantial signal‐to‐noise ratio (SNR) gain near the surface and comparable SNR in the center. The utility of this customized setup was demonstrated by 23 Na images of excellent quality. Conclusion High SNR, efficient transmit excitation and B 0 shimming capability can be achieved for 23 Na MRI at 9.4T using novel coil combination. This RF configuration is easily adaptable to other multinuclei applications at ultra high field (≥ 7T). Magn Reson Med 75:906–916, 2016. © 2015 Wiley Periodicals, Inc.
A Neural Mechanism for Time-Window Separation Resolves Ambiguity of Adaptive Coding
2015-03-11

The senses of animals are confronted with changing environments and different contexts. Neural adaptation is one important tool to adjust sensitivity to varying intensity ranges. For instance, in a quiet night outdoors, our hearing is more sensitive than when we are confronted with the plurality of sounds in a large city during the day. However, adaptation also removes available information on absolute sound levels and may thus cause ambiguity. Experimental data on the trade-off between benefits and loss through adaptation is scarce and very few mechanisms have been proposed to resolve it. We present an example where adaptation is beneficial for one task--namely, the reliable encoding of the pattern of an acoustic signal-but detrimental for another--the localization of the same acoustic stimulus. With a combination of neurophysiological data, modeling, and behavioral tests, we show that adaptation in the periphery of the auditory pathway of grasshoppers enables intensity-invariant coding of amplitude modulations, but at the same time, degrades information available for sound localization. We demonstrate how focusing the response of localization neurons to the onset of relevant signals separates processing of localization and pattern information temporally. In this way, the ambiguity of adaptive coding can be circumvented and both absolute and relative levels can be processed using the same set of peripheral neurons.
Tracing formation and durability of calcite in a Punic–Roman cistern mortar (Pantelleria Island, Italy)
2015-03-11

Ancient hydraulic lime mortar preserves chemical and isotopic signatures that provide important information about historical processing and its durability. The distribution and isotopic composition of calcite in a mortar of a well-preserved Punic-Roman cistern at Pantelleria Island (Italy) was used to trace the formation conditions, durability, and individual processing periods of the cistern mortar. The analyses of stable carbon and oxygen isotopes of calcite revealed four individual horizons, D, E, B-1 and B-2, of mortar from the top to the bottom of the cistern floor. Volcanic and ceramic aggregates were used for the production of the mortar of horizons E/D and B-1/B-2, respectively. All horizons comprise hydraulic lime mortar characterized by a mean cementation index of 1.5 ± 1, and a constant binder to aggregate ratio of 0.31 ± 0.01. This suggests standardized and highly effective processing of the cistern. The high durability of calcite formed during carbonation of slaked lime within the matrix of the ancient mortar, and thus the excellent resistance of the hydraulic lime mortar against water, was documented by (i) a distinct positive correlation of δ(18)Ocalcite and δ(13)Ccalcite; typical for carbonation through a mortar horizon, (ii) a characteristic evolution of δ(18)Ocalcite and δ(13)Ccalcite through each of the four mortar horizons; lighter follow heavier isotopic values from upper to lower part of the cistern floor, and (iii) δ(18)Ocalcite varying from -10 to -5 ‰ Vienna Pee Dee belemnite (VPDB). The range of δ(18)Ocalcite values rule out recrystallization and/or neoformation of calcite through chemical attack of water stored in cistern. The combined studies of the chemical composition of the binder and the isotopic composition of the calcite in an ancient mortar provide powerful tools for elucidating the ancient techniques and processing periods. This approach helps to evaluate the durability of primary calcite and demonstrates the importance of calcite as a proxy for chemical attack and quality of the ancient inorganic binder.
Neutrophils: Between Host Defence, Immune Modulation, and Tissue Injury
2015-03-12

Neutrophils, the most abundant human immune cells, are rapidly recruited to sites of infection, where they fulfill their life-saving antimicrobial functions. While traditionally regarded as short-lived phagocytes, recent findings on long-term survival, neutrophil extracellular trap (NET) formation, heterogeneity and plasticity, suppressive functions, and tissue injury have expanded our understanding of their diverse role in infection and inflammation. This review summarises our current understanding of neutrophils in host-pathogen interactions and disease involvement, illustrating the versatility and plasticity of the neutrophil, moving between host defence, immune modulation, and tissue damage.
Pathogenic Fungi Regulate Immunity by Inducing Neutrophilic Myeloid-Derived Suppressor Cells
2015-03-12

Despite continuous contact with fungi, immunocompetent individuals rarely develop pro-inflammatory antifungal immune responses. The underlying tolerogenic mechanisms are incompletely understood. Using both mouse models and human patients, we show that infection with the human pathogenic fungi Aspergillus fumigatus and Candida albicans induces a distinct subset of neutrophilic myeloid-derived suppressor cells (MDSCs), which functionally suppress T and NK cell responses. Mechanistically, pathogenic fungi induce neutrophilic MDSCs through the pattern recognition receptor Dectin-1 and its downstream adaptor protein CARD9. Fungal MDSC induction is further dependent on pathways downstream of Dectin-1 signaling, notably reactive oxygen species (ROS) generation as well as caspase-8 activity and interleukin-1 (IL-1) production. Additionally, exogenous IL-1β induces MDSCs to comparable levels observed during C. albicans infection. Adoptive transfer and survival experiments show that MDSCs are protective during invasive C. albicans infection, but not A. fumigatus infection. These studies define an innate immune mechanism by which pathogenic fungi regulate host defense.