Error Corrective Boosting for Learning Fully Convolutional Networks with Limited Data

Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models.Comment: Accepted at MICCAI 201

Plant residue based-composts applied in combination with Trichoderma asperellum improve cacao seedling growth in soil derived from nickel mine area

Cacao is widely grown in Sulawesi close to areas of nickel (Ni) mines indicating a possibility that the plant is affected by this heavy metal. By using soil collected from a Ni mining area, we evaluated three compositions of composted plant residues consisting of firstly gliricidia, billy goat, and rice straw, secondly gliricidia, stalk of palm oil fruit, and rice straw, and thirdly gliricidia, coconut husk, and rice straw, without and with addition of Trichoderma asperellum, in supporting growth of cacao seedling. Treatment with the respective compost types without any addition of T. asperellum caused an increase of seedling height by 18.9%, 28.5%, and 43.8%, stomata opening area by 17.2%, 4.3%, and 41.3%, stomata number by 13.4%, 22.7%, and 14.3%, and leaf Ni content by 3.8%, 12.8%, and 48.8% respectively. Following treatment with the three compost types included T. Asperellum, the increase of seedling height was 36.5%, 45.3%, and 54.7%, stomata opening area 15.9%, 21.3%, and 53.5%, stomata number 5.4%, 7.1%, and 0.0% and leaf Ni content 25.1%, 87.8%, and 161,4% respectively. Leaf analysis indicated that nitrogen content was increased when treated by the combination of composted plant residues and T. asperellum, potassium was increased in all treatments without T. asperellum, while phosphorus was decreased in all treated seedlings. These data suggest that one cause of cacao seedling growth improvement in soil containing Ni by composted plant residues and its combination with T. asperellum was the increase of Ni levels in leaves. Composts treatment could therefore potentially be used for cacao field application around Ni mining areas

Removal of bisphenol A from aqueous media using a highly selective adsorbent of hybridization cyclodextrin with magnetic molecularly imprinted polymer

In this study, a unique magnetic molecularly imprinted polymer (MMIP) adsorbent towards bisphenol A (BPA) as a template molecule was developed by bulk polymerization using β-cyclodextrin (β-CD) as a co-monomer with methacrylic acid (MAA) to form MMIP MAA–βCD as a new adsorbent. β-CD was hybridized with MAA to obtain water-compactible imprinting sites for the effective removal of BPA from aqueous samples. Benzoyl peroxide and trimethylolpropane trimethacrylate were used as the initiator and cross-linker, respectively. The adsorbents were characterized by Fourier transform infrared spectroscopy, scanning electronic microscopy, transmission electron microscopy, vibrating sample magnetometer, Brunauer–Emmett–Teller and X-ray diffraction. 1H nuclear magnetic resonance spectroscopy was used to characterize the MAA–βCD and BPA–MAA–βCD complex. Several parameters influencing the adsorption efficiency of BPA such as adsorbent dosage, pH of sample solution, contact time, initial concentrations and temperature as well as selectivity and reusability study have been evaluated. MMIP MAA–βC

Pulse Sequence Resilient Fast Brain Segmentation

Accurate automatic segmentation of brain anatomy from $T_1$-weighted~($T_1$-w) magnetic resonance images~(MRI) has been a computationally intensive bottleneck in neuroimaging pipelines, with state-of-the-art results obtained by unsupervised intensity modeling-based methods and multi-atlas registration and label fusion. With the advent of powerful supervised convolutional neural networks~(CNN)-based learning algorithms, it is now possible to produce a high quality brain segmentation within seconds. However, the very supervised nature of these methods makes it difficult to generalize them on data different from what they have been trained on. Modern neuroimaging studies are necessarily multi-center initiatives with a wide variety of acquisition protocols. Despite stringent protocol harmonization practices, it is not possible to standardize the whole gamut of MRI imaging parameters across scanners, field strengths, receive coils etc., that affect image contrast. In this paper we propose a CNN-based segmentation algorithm that, in addition to being highly accurate and fast, is also resilient to variation in the input $T_1$-w acquisition. Our approach relies on building approximate forward models of $T_1$-w pulse sequences that produce a typical test image. We use the forward models to augment the training data with test data specific training examples. These augmented data can be used to update and/or build a more robust segmentation model that is more attuned to the test data imaging properties. Our method generates highly accurate, state-of-the-art segmentation results~(overall Dice overlap=0.94), within seconds and is consistent across a wide-range of protocols.Comment: Accepted at MICCAI 201

Search for associated Higgs boson production using like charge dilepton events in p(p)over-bar collisions at root s=1.96 TeV

We present a search for associated Higgs boson production in the process p (p) over bar -> W/ZH -> l(+/-)l'(+/-) + X in ee, e mu, and mu mu final states. The search is based on data collected by the D0 experiment at the Fermilab Tevatron Collider at root s = 1.96 TeV corresponding to 5.3 fb(-1) of integrated luminosity. We require two isolated leptons (electrons or muons) with the same electric charge and additional kinematic requirements. No significant excess above background is observed, and we set 95% C. L. observed (expected) upper limits on ratio of the production cross section to the standard model prediction of 6.4 (7.3) for a Higgs boson mass of 165 GeV and 13.5 (19.8) for a mass of 115 GeV

Extraction of parabens from cosmetic and environmental water samples coupled with uv-visible spectroscopy

An effective and fast vortex-assisted dispersive liquid–liquid extraction method was developed for the extraction of paraben in cosmetic samples and water samples. The paraben was determined and quantifi ed using ultraviolet-visible (UV-Vis) spectrometry. A response surface methodology (RSM) based on the central composite design was used for the optimization of factors (composition of the extractant, volume of extractant, extraction time, centrifugation time, and centrifugation velocity) affecting the extraction effi ciency of the procedure. The optimum parameters for vortexassisted dispersive liquid–liquid extraction (VA-DLLE) are: chloroform used as the extractant solvent, 5 ml volume of extractant, 3 min extraction time, 5 min centrifugation time, and 2400 rpm centrifugation velocity. The limit of detection (LOD) and the limit of quantifi cation (LOQ) for paraben are 0.0476 and 0.1442 μg/mL, respectively. Spiked cosmetic samples have the extraction recoveries in the range of 81.2–96.8%, whereas spiked water sample extraction recoveries were in the range of 88.8–100.63%. Each sample was repeated (n = 2), with a relative standard deviation of <5.74% for cosmetic samples and <9.03% for water samples. In conclusion, this extraction method is fast and inexpensive for the extraction of paraben

Study of Zγ events and limits on anomalous ZZγ and Zγγ couplings in pp̄ collisions at s=1.96TeV

We present a measurement of the Zγ production cross section and limits on anomalous ZZγ and Zγγ couplings for form-factor scales of Λ=750 and 1000 GeV. The measurement is based on 138 (152) candidates in the eeγ (μμγ) final state using 320(290)pb-1 of pp̄ collisions at s=1.96TeV. The 95% C.L. limits on real and imaginary parts of individual anomalous couplings are |h10,30Z|<0.23, |h20,40Z|<0.020, |h10,30γ|<0.23, and |h20,40γ|<0.019 for Λ=1000GeV. © 2005 The American Physical Society

mTOR Kinase Inhibition Effectively Decreases Progression of a Subset of Neuroendocrine Tumors that Progress on Rapalog Therapy and Delays Cardiac Impairment

Inhibition of mTOR signaling using the rapalog everolimus is an FDA-approved targeted therapy for patients with lung and gastroenteropancreatic neuroendocrine tumors (NET). However, patients eventually progress on treatment, highlighting the need for additional therapies. We focused on pancreatic NETs (pNET) and reasoned that treatment of these tumors upon progression on rapalog therapy, with an mTOR kinase inhibitor (mTORKi), such as CC-223, could overcome a number of resistance mechanisms in tumors and delay cardiac carcinoid disease. We performed preclinical studies using human pNET cells in vitro and injected them subcutaneously or orthotopically to determine tumor progression and cardiac function in mice treated with either rapamycin alone or switched to CC-223 upon progression. Detailed signaling and RNA sequencing analyses were performed on tumors that were sensitive or progressed on mTOR treatment. Approximately 57% of mice bearing pNET tumors that progressed on rapalog therapy showed a significant decrease in tumor volume upon a switch to CC-223. Moreover, mice treated with an mTORKi exhibited decreased cardiac dilation and thickening of heart valves than those treated with placebo or rapamycin alone. In conclusion, in the majority of pNETs that progress on rapalogs, it is possible to reduce disease progression using an mTORKi, such as CC-223. Moreover, CC-223 had an additional transient cardiac benefit on valvular fibrosis compared with placebo- or rapalog-treated mice. These results provide the preclinical rationale to further develop mTORKi clinically upon progression on rapalog therapy and to further test their long-term cardioprotective benefit in those NET patients prone to carcinoid syndrome

The proportion of individuals likely to benefit from customized optic nerve head structure-function mapping

yesPurpose: Inter-individual variance in optic nerve head (ONH) position, axial length and location of the temporal raphe suggest that customizing mapping between visual field locations and optic nerve head sectors for individuals may be clinically useful. Here we quantify the proportion of the population predicted to have structure-function mappings that markedly deviate from “average”, and thus would benefit from customized mapping. Design: Database study and case report Participants: Population database of 2836 eyes from the Beijing Eye Study; single case report of an individual with primary open angle glaucoma Methods: Using the morphometric fundus data of the Beijing Eye Study on 2836 eyes and applying a recently developed model based on axial length and ONH position relative to the fovea, we determined for each measurement location in the 24-2 Humphrey visual field the proportion of eyes for which, in the customized approach as compared to the generalized approach, the mapped ONH sector was shifted into a different sector. We determined the proportion of eyes for which the mapped ONH location was shifted by 15°, 30° or 60°. Main outcome measures: Mapping correspondence between locations in visual field space to localized sectors on the optic nerve head Results: The largest inter-individual differences in mapping are in the nasal step region where the same visual field location can map to either the superior or inferior ONH depending on other anatomical features. For these visual field locations, approximately 12% of eyes showed a mapping opposite to conventional expectations. Conclusions: Anatomically customised mapping shifts the map markedly in approximately 12% of the general population in the nasal step region where visual field locations can map to the opposite pole of the ONH than conventionally considered. Early glaucomatous damage commonly affects this region, hence individually matching structure to function may prove clinically useful for the diagnosis and monitoring of progression within individuals.Australian Research Council Linkage Project 130100055 (industry partner, Heidelberg Engineering, GmBH, Germany)