bluuebunny/crossref_metadata_2025 huggingface dataset:
Pleiotropic signaling evoked by tumor necrosis factor in podocytes
Authors: Abkhezr Mousa , Kim Eun Young , Roshanravan Hila , Nikolos Fotis , Thomas Christoforos , Hagmann Henning , Benzing Thomas , Dryer Stuart E.
Published: May 2015

TNF has been implicated in glomerular diseases, but its actions on podocytes are not well understood. Endogenous TNF expression is markedly increased in mouse podocytes exposed to sera from patients with recurrent focal segmental glomerulosclerosis, and TNF is able to increase its own expression in these cells. Exposure of podocytes to TNF increased phosphorylation of NF-κB p65-RelA followed by increased tyrosine phosphorylation of STAT3. STAT3 activation was blocked by the NF-κB inhibitor JSH-23 and by the STAT3 inhibitor stattic, whereas TNF-evoked NF-κB activation was not affected by stattic. TNF treatment increased nuclear accumulation of nuclear factor of activated T cells (NFAT)c1 in podocytes, a process that occurred downstream of STAT3 activation. TNF also increased expression of cyclin D1 but had no effect on cyclin-dependent kinase 4, p27kip, or podocin. Despite its effects on cyclin D1, TNF treatment for up to 72 h did not cause podocytes to reenter the cell cycle. TNF increased total expression of transient receptor potential (TRP)C6 channels through a pathway dependent on NFATc1 and increased the steady-state expression of TRPC6 subunits on the podocyte cell surface. TNF effects on TRPC6 trafficking required ROS. Consistent with this, La3+-sensitive cationic currents activated by a diacylglycerol analog were increased in TNF-treated cells. The effects of TNF on NFATc1 and TRPC6 expression were blocked by cyclosporine A but were not blocked by the pan-TRP inhibitor SKF-96365. TNF therefore influences multiple pathways previously implicated in podocyte pathophysiology and is likely to sensitize these cells to other insults.
Perceptual decision related activity in the lateral geniculate nucleus
Authors: Jiang Yaoguang , Yampolsky Dmitry , Purushothaman Gopathy , Casagrande Vivien A.
Published: May 2015

Fundamental to neuroscience is the understanding of how the language of neurons relates to behavior. In the lateral geniculate nucleus (LGN), cells show distinct properties such as selectivity for particular wavelengths, increments or decrements in contrast, or preference for fine detail versus rapid motion. No studies, however, have measured how LGN cells respond when an animal is challenged to make a perceptual decision using information within the receptive fields of those LGN cells. In this study we measured neural activity in the macaque LGN during a two-alternative, forced-choice (2AFC) contrast detection task or during a passive fixation task and found that a small proportion (13.5%) of single LGN parvocellular (P) and magnocellular (M) neurons matched the psychophysical performance of the monkey. The majority of LGN neurons measured in both tasks were not as sensitive as the monkey. The covariation between neural response and behavior (quantified as choice probability) was significantly above chance during active detection, even when there was no external stimulus. Interneuronal correlations and task-related gain modulations were negligible under the same condition. A bottom-up pooling model that used sensory neural responses to compute perceptual choices in the absence of interneuronal correlations could fully explain these results at the level of the LGN, supporting the hypothesis that the perceptual decision pool consists of multiple sensory neurons and that response fluctuations in these neurons can influence perception.
Five key factors determining pairwise correlations in visual cortex
Authors: Schulz David P. A. , Sahani Maneesh , Carandini Matteo
Published: May 2015

The responses of cortical neurons to repeated presentation of a stimulus are highly variable, yet correlated. These “noise correlations” reflect a low-dimensional structure of population dynamics. Here, we examine noise correlations in 22,705 pairs of neurons in primary visual cortex (V1) of anesthetized cats, during ongoing activity and in response to artificial and natural visual stimuli. We measured how noise correlations depend on 11 factors. Because these factors are themselves not independent, we distinguished their influences using a nonlinear additive model. The model revealed that five key factors play a predominant role in determining pairwise correlations. Two of these are distance in cortex and difference in sensory tuning: these are known to decrease correlation. A third factor is firing rate: confirming most earlier observations, it markedly increased pairwise correlations. A fourth factor is spike width: cells with a broad spike were more strongly correlated amongst each other. A fifth factor is spike isolation: neurons with worse isolation were more correlated, even if they were recorded on different electrodes. For pairs of neurons with poor isolation, this last factor was the main determinant of correlations. These results were generally independent of stimulus type and timescale of analysis, but there were exceptions. For instance, pairwise correlations depended on difference in orientation tuning more during responses to gratings than to natural stimuli. These results consolidate disjoint observations in a vast literature on pairwise correlations and point towards regularities of population coding in sensory cortex.
Modulation of inhibitory and excitatory fast neurotransmission in the rat CNS by heavy water (D2O)
Authors: Wakita Masahito , Kotani Naoki , Shoudai Kiyomitsu , Yamaga Toshitaka , Akaike Norio
Published: May 2015

The effects of heavy water (deuterium oxide, D2O) on GABAergic and glutamatergic spontaneous and evoked synaptic transmission were investigated in acute brain slice and isolated “synaptic bouton” preparations of rat hippocampal CA3 neurons. The substitution of D2O for H2O reduced the frequency and amplitude of GABAergic spontaneous inhibitory postsynaptic currents (sIPSCs) in a concentration-dependent manner but had no effect on glutamatergic spontaneous excitatory postsynaptic currents (sEPSCs). In contrast, for evoked synaptic responses in isolated neurons, the amplitude of both inhibitory and excitatory postsynaptic currents (eIPSCs and eEPSCs) was decreased in a concentration-dependent manner. This was associated with increases of synaptic failure rate ( Rf) and paired-pulse ratio (PPR). The effect was larger for eIPSCs compared with eEPSCs. These results clearly indicate that D2O acts differently on inhibitory and excitatory neurotransmitter release machinery. Furthermore, D2O significantly suppressed GABAA receptor-mediated whole cell current ( IGABA) but did not affect glutamate receptor-mediated whole cell current ( IGlu). The combined effects of D2O at both the pre- and postsynaptic sites may explain the greater inhibition of eIPSCs compared with eEPSCs. Finally, D2O did not enhance or otherwise affect the actions of the general anesthetics nitrous oxide and propofol on spontaneous or evoked GABAergic and glutamatergic neurotransmissions, or on IGABA and IGlu. Our results suggest that previously reported effects of D2O to mimic and/or modulate anesthesia potency result from mechanisms other than modulation of GABAergic and glutamatergic neurotransmission.
Deep Extreme Learning Machine and Its Application in EEG Classification
Authors: Ding Shifei , Zhang Nan , Xu Xinzheng , Guo Lili , Zhang Jian
Published: May 2015

Recently, deep learning has aroused wide interest in machine learning fields. Deep learning is a multilayer perceptron artificial neural network algorithm. Deep learning has the advantage of approximating the complicated function and alleviating the optimization difficulty associated with deep models. Multilayer extreme learning machine (MLELM) is a learning algorithm of an artificial neural network which takes advantages of deep learning and extreme learning machine. Not only does MLELM approximate the complicated function but it also does not need to iterate during the training process. We combining with MLELM and extreme learning machine with kernel (KELM) put forward deep extreme learning machine (DELM) and apply it to EEG classification in this paper. This paper focuses on the application of DELM in the classification of the visual feedback experiment, using MATLAB and the second brain-computer interface (BCI) competition datasets. By simulating and analyzing the results of the experiments, effectiveness of the application of DELM in EEG classification is confirmed.
Effect of Dehydration Conditions on the Chemical, Physical, and Rehydration Properties of Instant Whole Bean (Phaseolus vulgarisL. var. Azufrado)
Authors: Resendiz Vazquez Juan Alberto , Ulloa José Armando , Rosas Ulloa Petra , Ramírez Ramírez José Carmen
Published: May 2015

The purpose of this study was to evaluate the effect of dehydration conditions on the chemical, physical, and rehydration properties of instant whole beans (Phaseolus vulgarisL. var. Azufrado) using a 22factorial design (air temperature: 25°C and 30°C, air velocity: 0.5 m/s and 1.0 m/s). To determine the kinetic parameters, the rehydration data were fitted to three models: Peleg’s, First Order, and Sigmoid. The protein, fat, and ash contents of the beans were not significantly affected (P>0.05) by the dehydration conditions. Of the 11 physical properties of the instant whole beans, only water activity and splitting were significantly affected by dehydration conditions (P<0.05), with a range from 0.58 to 0.67 and from 2.90% to 5.87%, respectively. Of the three models tested, the First Order model gave the best fit for rehydration, with no significant differences (P>0.05) between the observed and predicted equilibrium moisture contents of the instant whole beans. Regarding the rehydration kinetics for the instant whole beans, the activation energy values ranged from 23.56 kJ/mol to 30.48 kJ/mol, depending on the dehydration conditions. The dehydration conditions had no significant effect (P>0.05) on the rehydration properties of instant whole beans.
Colorectal Cancer Biomarkers: Where Are We Now?
Authors: Gonzalez-Pons Maria , Cruz-Correa Marcia
Published: May 2015

Colorectal cancer is one of the major causes of cancer-related death in the Western world. Patient survival is highly dependent on the tumor stage at the time of diagnosis. Reduced sensitivity to chemotherapy is still a major obstacle in effective treatment of advanced disease. Due to the fact that colorectal cancer is mostly asymptomatic until it progresses to advanced stages, the implementation of screening programs aimed at early detection is essential to reduce incidence and mortality rates. Current screening and diagnostic methods range from semi-invasive procedures such as colonoscopy to noninvasive stool-based tests. The combination of the absence of symptoms, the semi-invasive nature of currently used methods, and the suboptimal accuracy of fecal blood tests results in colorectal cancer diagnosis at advanced stages in a significant number of individuals. Alterations in gene expression leading to colorectal carcinogenesis are reflected in dysregulated levels of nucleic acids and proteins, which can be used for the development of novel, minimally invasive molecular biomarkers. The purpose of this review is to discuss the commercially available colorectal cancer molecular diagnostic methods as well as to highlight some of the new candidate predictive and prognostic molecular markers for tumor, stool, and blood samples.
Comparison of the Effect of Sol‐Gel and Coprecipitation Routes on the Properties and Behavior of Nanocomposite Chitosan‐Bioactive Glass Membranes for Bone Tissue Engineering
Authors: Lemos Elke M. F. , Carvalho Sandhra M. , Patrício Patrícia S. O. , Donnici Claudio L. , Pereira Marivalda M.
Published: May 2015

Recent studies in tissue engineering have highlighted the importance of the development of composite materials based on biodegradable polymers containing bioactive glasses, in particular, composites for high load support and excellent cell viability for potential application in bone regeneration. In this work, hybrid composite films were obtained by combining chitosan with bioactive glass in solution form and in nanoparticle dispersion form obtained by the two different synthesis routes: the sol‐gel method and coprecipitation. The bioactive glass served both as a mechanical reinforcing agent and as a triggering agent with high bioactivity. The results of in vitro assays with simulated body fluid demonstrated the formation of a significant layer of fibrils on the surface of the film, with a typical morphology of carbonated hydroxyapatite, reflecting induction of a favorable bioactivity. Maximum tensile stress increased from 42 to 80 MPa to the sample with 5% wt bioactive glass. In addition, samples containing 5% and 10% wt bioactive glass showed a significant increase in cell viability, 18 and 30% increase compared to the control group. The samples showed significant response, indicating that they could be a potential material for use in bone regeneration through tissue engineering.
Comparison of Malated Ringer’s with Two Other Balanced Crystalloid Solutions in Resuscitation of Both Severe and Moderate Hemorrhagic Shock in Rats
Authors: Keitel Judith , Hussmann Bjoern , Lendemans Sven , de Groot Herbert , Rohrig Ricarda
Published: May 2015

In preclinical treatment of polytraumatized patients crystalloids are preferentially used. To avoid metabolic acidosis, metabolizable anions like lactate or acetate are used to replace chloride in these solutions. We here studied the effects of malated Ringer’s in resuscitation of both shock severities in comparison to lactated and acetated Ringer’s. Male Wistar rats underwent severe (mean arterial blood pressure (MAP) of 25–30 mmHg) or moderate (MAP 40–45 mmHg) hemorrhagic shock. Adjacent to the shock period animals were resuscitated with acetated (AR), lactated (LR), or malated Ringer’s (MR) and observed for 150 min. MR improved survival compared with LR and AR in severe hemorrhagic shock whereas it was equally effective to LR and superior to AR in moderate hemorrhagic shock. In all other parameters tested, MR was also effective similar to the other solutions under these conditions. We conclude that MR is preferable to AR and LR in resuscitation of hemorrhagic shock independent of shock depth. The positive effects of MR may stem from the absence of any adverse impact on energy metabolism under both conditions.
A 3D Porous Gelatin-Alginate-Based-IPN Acts as an Efficient Promoter of Chondrogenesis from Human Adipose-Derived Stem Cells
Authors: Dinescu Sorina , Galateanu Bianca , Radu Eugen , Hermenean Anca , Lungu Adriana , Stancu Izabela Cristina , Jianu Dana , Tumbar Tudorita , Costache Marieta
Published: May 2015

Cartilage has limited regeneration potential. Thus, there is an imperative need to develop new strategies for cartilage tissue engineering (CTE) amenable for clinical use. Recent CTE approaches rely on optimal cell-scaffold interactions, which require a great deal of optimization. In this study we attempt to build a novel gelatin- (G-) alginate- (A-) polyacrylamide (PAA) 3D interpenetrating network (IPN) with superior performance in promoting chondrogenesis from human adipose-derived stem cells (hADSCs). We show that our G-A-PAA scaffold is capable of supporting hADSCs proliferation and survival, with no apparent cytotoxic effect. Moreover, we find that after exposure to prochondrogenic conditions a key transcription factor known to induce chondrogenesis, namely, Sox9, is highly expressed in our hADSCs/G-A-PAA bioconstruct, along with cartilage specific markers such as collagen type II, CEP68, and COMP extracellular matrix (ECM) components. These data suggest that our G-A-PAA structural properties and formulation might enable hADSCs conversion towards functional chondrocytes. We conclude that our novel G-A-PAA biomatrix is a good candidate for prospectivein vivoCTE applications.
Failure to Identify the Left Arcuate Fasciculus at Diffusion Tractography Is a Specific Marker of Language Dysfunction in Pediatric Patients with Polymicrogyria
Authors: Paldino Michael J. , Hedges Kara , Gaab Nadine , Galaburda Albert M. , Grant P. Ellen
Published: May 2015

Background. Polymicrogyric cortex demonstrates interindividual variation with regard to both extent of dyslamination and functional capacity. Given the relationship between laminar structure and white matter fibers, we sought to define the relationship between polymicrogyria (PMG), intrahemispheric association pathways, and network function.Methods. Each arcuate fasciculus (AF) was categorized as present or absent. Language was characterized by a pediatric neurologist. The presence of dysplastic cortex in the expected anatomic locations of Broca’s (BA) and Wernicke’s areas (WA) was evaluated by two pediatric neuroradiologists blinded to DTI and language data.Results. 16 PMG patients and 16 age/gender-matched controls were included. All normative controls had an identifiable left AF. 6/7 PMG patients with dysplastic cortex within BA and/or WA had no left AF; PMG patients without involvement of these regions had a lower frequency of absence of the left AF (p<0.006). All patients without a left AF had some degree of language impairment. PMG patients without a left AF had a significantly greater frequency of language impairment compared to those PMG patients with a left AF (p<0.003).Conclusion. In patients with PMG (1) the presence of dysplastic cortex within WA and/or BA is associated with absence of the left AF and (2) absence of the left AF is associated with language impairment.
Synchronous Multicentric Giant Cell Tumour of Distal Radius and Sacrum with Pulmonary Metastases
Authors: Tandra Varun Sharma , Kotha Krishna Mohan Reddy , Satyanarayana Moorthy Gadisetti Venkata , Vadlamani Kali Varaprasad , Yerravalli Vyjayanthi
Published: May 2015

Giant cell tumour (GCT) is an uncommon primary bone tumour, and its multicentric presentation is exceedingly rare. We report a case of a 45-year-old female who presented to us with GCT of left distal radius. On the skeletal survey, osteolytic lesion was noted in her right sacral ala. Biopsy confirmed both lesions as GCT. Pulmonary metastasis was also present. Resection-reconstruction arthroplasty for distal radius and thorough curettage and bone grafting of the sacral lesion were done. Multicentric GCT involving distal radius and sacrum with primary sacral involvement is not reported so far to our knowledge.
Distance Based Multiple Kernel ELM: A Fast Multiple Kernel Learning Approach
Authors: Zhu Chengzhang , Liu Xinwang , Liu Qiang , Ming Yuewei , Yin Jianping
Published: May 2015

We propose a distance based multiple kernel extreme learning machine (DBMK-ELM), which provides a two-stage multiple kernel learning approach with high efficiency. Specifically, DBMK-ELM first projects multiple kernels into a new space, in which new instances are reconstructed based on the distance of different sample labels. Subsequently, anl2-norm regularization least square, in which the normal vector corresponds to the kernel weights of a new kernel, is trained based on these new instances. After that, the new kernel is utilized to train and test extreme learning machine (ELM). Extensive experimental results demonstrate the superior performance of the proposed DBMK-ELM in terms of the accuracy and the computational cost.
Extracting UML Class Diagrams from Object-Oriented Fortran: ForUML
Authors: Nanthaamornphong Aziz , Carver Jeffrey , Morris Karla , Filippone Salvatore
Published: May 2015

Many scientists who implement computational science and engineering software have adopted the object-oriented (OO) Fortran paradigm. One of the challenges faced by OO Fortran developers is the inability to obtain high level software design descriptions of existing applications. Knowledge of the overall software design is not only valuable in the absence of documentation, it can also serve to assist developers with accomplishing different tasks during the software development process, especially maintenance and refactoring. The software engineering community commonly uses reverse engineering techniques to deal with this challenge. A number of reverse engineering-based tools have been proposed, but few of them can be applied to OO Fortran applications. In this paper, we propose a software tool to extract unified modeling language (UML) class diagrams from Fortran code. The UML class diagram facilitates the developers' ability to examine the entities and their relationships in the software system. The extracted diagrams enhance software maintenance and evolution. The experiments carried out to evaluate the proposed tool show its accuracy and a few of the limitations.
Factors Associated with the Use of Drug-Eluting Stents in Patients Presenting with Acute ST-Segment Elevation Myocardial Infarction
Authors: Chavez Jose F. , Doll Jacob A. , Mediratta Anuj , Maffessanti Francesco , Friant Janet , Paul Jonathan D. , Blair John E. A. , Nathan Sandeep , Jolly Neeraj , Shah Atman P.
Published: May 2015

Background. Drug-eluting stents (DES) have proven clinical superiority to bare-metal stents (BMS) for the treatment of patients with ST-segment elevation myocardial infarction (STEMI). Decision to implant BMS or DES is dependent on the patient’s ability to take dual antiplatelet therapy. This study investigated factors associated with DES placement in STEMI patients.Methods. Retrospective analysis was performed on 193 patients who presented with STEMI and were treated with percutaneous coronary intervention at an urban, tertiary care hospital. Independent factors associated with choice of stent type were determined using stepwise multivariate logistic regression. Odds ratio (OR) was used to evaluate factors significantly associated with DES and BMS.Results. 128 received at least one DES, while 65 received BMS. BMS use was more likely in the setting of illicit drug or alcohol abuse ([OR] 0.15, 95% CI 0.05–0.48,p≤0.01), cardiogenic shock (OR 0.26, 95% CI 0.10–0.73,p=0.01), and larger stent diameter (OR 0.28, 95% CI 0.11–0.68,p≤0.01).Conclusions. In this analysis, BMS implantation was associated with illicit drug or alcohol abuse and presence of cardiogenic shock. This study did not confirm previous observations that non-White race, insurance, or income predicts BMS use.
Antiproliferative Effect of Rottlerin on Sk-Mel-28 Melanoma Cells
Authors: Daveri Elena , Valacchi Giuseppe , Romagnoli Roberta , Maellaro Emilia , Maioli Emanuela
Published: May 2015

Melanoma is the most aggressive and chemoresistant form of skin cancer. Mutated, constitutively active B-RAF is believed to play a crucial role, although the selective B-RAF inhibition has shown poor clinical success, since phenomena of resistance usually occur, likely arising from additional genetic aberrations, such as loss of function of p53 and PTEN, overexpression of cyclin D1, hyperactivation of NF-κB, and downregulation of p21/Cip1. Since all of them are present in the Sk-Mel-28 melanoma cells, this cell line could be an ideal, albeit hard to study, model to develop new therapeutic strategies. In the current study, we tested the cytostatic action of Rottlerin on Sk-Mel-28 melanoma cells, on the basis of the known Rottlerin effects on the main proliferative signaling pathways. We presented evidence that the drug inhibits cell growth by an Akt- and p21/Cip1-independent mechanism, involving the dual inhibition of ERK and NF-κB and downregulation of cyclin D1. In addition, we found that Rottlerin increases ERK phosphorylation, but, surprisingly, this resulted in decreased ERK activity. Pull-down experiments, using Rottlerin-CNBr-conjugated Sepharose beads, revealed that Rottlerin binds to ERK, independently from its phosphorylation status. This direct interaction could in part explain the paradoxical blockage of ERK downstream signaling and growth arrest.
Transcriptomic and Immunohistochemical Profiling of SLC6A14 in Pancreatic Ductal Adenocarcinoma
Authors: Penheiter Alan R. , Erdogan Sibel , Murphy Stephen J. , Hart Steven N. , Felipe Lima Joema , Rakhshan Rohakhtar Fariborz , O’Brien Daniel R. , Bamlet William R. , Wuertz Ryan E. , Smyrk Thomas C. , Couch Fergus J. , Vasmatzis George , Bender Claire E. , Carlson Stephanie K.
Published: May 2015

We used a target-centric strategy to identify transporter proteins upregulated in pancreatic ductal adenocarcinoma (PDAC) as potential targets for a functional imaging probe to complement existing anatomical imaging approaches. We performed transcriptomic profiling (microarray and RNASeq) on histologically confirmed primary PDAC tumors and normal pancreas tissue from 33 patients, including five patients whose tumors were not visible on computed tomography. Target expression was confirmed with immunohistochemistry on tissue microarrays from 94 PDAC patients. The best imaging target identified was SLC6A14 (a neutral and basic amino acid transporter). SLC6A14 was overexpressed at the transcriptional level in all patients and expressed at the protein level in 95% of PDAC tumors. Very little is known about the role of SLC6A14 in PDAC and our results demonstrate that this target merits further investigation as a candidate transporter for functional imaging of PDAC.
Evaluation of Different Analysis Methods for the Encapsulation Efficiency of Amylose Inclusion Compound
Authors: Feng Tao , Liu Fangfang , Wang Xu , Zhuang Haining , Ye Ran , Rong Zhiwei , Liu Yi
Published: May 2015

Recently amylose has drawn much attention as a potential vehicle for the nanoencapsulation of different flavor molecules, and the encapsulation efficiency of the complex is an important index for the evaluation of its embedding effect. In this study, three different methods for assessing encapsulation efficiency of amylose-flavor complexes were compared. We chose heptanol and menthone as the flavor molecules, as both of them exhibit a typical odor. The complexes were prepared by the melting method, and their structures were characterized by XRD. In addition, the encapsulation efficiency was determined by thermal gravimetric analysis (TGA), potentiometric titration (PT), and headspace solid phase microextraction gas chromatography (HS-SPME-GC), respectively. The results showed that PT results were within the reported literature range while HS-SPME-GC seemed to overestimate the results and TGA results were the lowest. What is more, the operations of TGA and PT were relatively simple and the results were reproducible, while the HS-SPME-GC method displayed excellent high sensitivity. Therefore, PT method is the best method for assessing encapsulation efficiency of amylose-flavor complexes.
A New Approach for Mining Order-Preserving Submatrices Based on All Common Subsequences
Authors: Xue Yun , Liao Zhengling , Li Meihang , Luo Jie , Kuang Qiuhua , Hu Xiaohui , Li Tiechen
Published: May 2015

Order-preserving submatrices (OPSMs) have been applied in many fields, such as DNA microarray data analysis, automatic recommendation systems, and target marketing systems, as an important unsupervised learning model. Unfortunately, most existing methods are heuristic algorithms which are unable to reveal OPSMs entirely in NP-complete problem. In particular, deep OPSMs, corresponding to long patterns with few supporting sequences, incur explosive computational costs and are completely pruned by most popular methods. In this paper, we propose an exact method to discover all OPSMs based on frequent sequential pattern mining. First, an existing algorithm was adjusted to disclose all common subsequence (ACS) between every two row sequences, and therefore all deep OPSMs will not be missed. Then, an improved data structure for prefix tree was used to store and traverse ACS, and Apriori principle was employed to efficiently mine the frequent sequential pattern. Finally, experiments were implemented on gene and synthetic datasets. Results demonstrated the effectiveness and efficiency of this method.
FPGA-Based Synthesis of High-Speed Hybrid Carry Select Adders
Authors: Kokilavani V. , Preethi K. , Balasubramanian P.
Published: May 2015

Carry select adder is a square-root time high-speed adder. In this paper, FPGA-based synthesis of conventional and hybrid carry select adders are described with a focus on high speed. Conventionally, carry select adders are realized using the following: (i) full adders and 2 : 1 multiplexers, (ii) full adders, binary to excess 1 code converters, and 2 : 1 multiplexers, and (iii) sharing of common Boolean logic. On the other hand, hybrid carry select adders involve a combination of carry select and carry lookahead adders with/without the use of binary to excess 1 code converters. In this work, two new hybrid carry select adders are proposed involving the carry select and section-carry based carry lookahead subadders with/without binary to excess 1 converters. Seven different carry select adders were implemented in Verilog HDL and their performances were analyzed under two scenarios, dual-operand addition and multioperand addition, where individual operands are of sizes 32 and 64-bits. In the case of dual-operand additions, the hybrid carry select adder comprising the proposed carry select and section-carry based carry lookahead configurations is the fastest. With respect to multioperand additions, the hybrid carry select adder containing the carry select and conventional carry lookahead or section-carry based carry lookahead structures produce similar optimized performance.
Synthesis and Characterization of Bioactive Acylpyrazolone Sulfanilamides and Their Transition Metal Complexes: Single Crystal Structure of 4-Benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one Sulfanilamide
Authors: Idemudia Omoruyi G. , Sadimenko Alexander P. , Afolayan Anthony J. , Hosten Eric C.
Published: May 2015

Two Schiff base ligands Ampp-Sn1and Bmpp-Sn2, afforded by a condensation reaction between sulfanilamide and the respective acylpyrazolone carbonyl precursors, their Mn(II), Co(II), Ni(II), and Cu(II) complexes prepared by the reaction of ligands and corresponding metal salts in aqueous solutions, were synthesized and then characterized by both analytical and spectroscopic methods, in a view to developing new improved bioactive materials with novel properties. On the basis of elemental analysis, spectroscopic and TGA results, transition metal complexes, with octahedral geometry having two molecules of the bidentate keto-imine ligand each, have been proposed. The single crystal structure of Bmpp-Sn according to X-ray crystallography showed a keto-imine tautomer type of Schiff base, having three intramolecular bonds, one short N2⋯H2⋯O3 hydrogen bond of 1.90 Å and two long C13⋯H13⋯O2 and C32⋯H32⋯O3 hydrogen bonds of 2.48 Å. A moderate to low biological activities have been exhibited by synthesized compounds when compared with standard antimicrobial agents on screening the synthesized compounds againstStaphylococcus aureus,Bacillus pumilus,Proteus vulgaris, andAeromonas hydrophilafor antibacterial activity and against free radical 1, 1-diphenyl-2-picryl-hydrazyl (DPPH) for antioxidant activity.
Fucoxanthin: A Promising Medicinal and Nutritional Ingredient
Authors: Zhang Hui , Tang Yibo , Zhang Ying , Zhang Shuofeng , Qu Jing , Wang Xu , Kong Ran , Han Chunchao , Liu Zhenquan
Published: May 2015

Fucoxanthin, an allenic carotenoid, can be isolated from edible brown seaweeds. Recent studies have reported that fucoxanthin has many physiological functions and biological properties, such as antiobesity, antitumor, antidiabetes, antioxidant, anti-inflammatory, and hepatoprotective activities, as well as cardiovascular and cerebrovascular protective effects. Therefore, fucoxanthin can be used as both medicinal and nutritional ingredient to prevent and treat chronic diseases. Although fucoxanthin possesses many medicinal ingredient and nutritional qualities, studies indicated that its structure was unstable. In this paper, we consulted the current documents and reviewed structural properties and factors affecting the stability of fucoxanthin. We also reported the metabolism, safety, pharmacological activities, and the methods of improving the bioavailability of fucoxanthin. Based on these studies providing essential background knowledge, fucoxanthin can be developed into marine drugs and nutritional products.
Inflammation, Iron, Energy Failure, and Oxidative Stress in the Pathogenesis of Multiple Sclerosis
Authors: Haider Lukas
Published: May 2015

Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system. Different trigger pathologies have been suggested by the primary cytodegenerative “inside-out” and primary inflammation-driven “outside-in” hypotheses. Recent data indicate that mitochondrial injury and subsequent energy failure are key factors in the induction of demyelination and neurodegeneration. The brain weighs only a few percent of the body mass but accounts for approximately 20% of the total basal oxygen consumption of mitochondria. Oxidative stress induces mitochondrial injury in patients with multiple sclerosis and energy failure in the central nervous system of susceptible individuals. The interconnected mechanisms responsible for free radical production in patients with multiple sclerosis are as follows: (i) inflammation-induced production of free radicals by activated immune cells, (ii) liberation of iron from the myelin sheets during demyelination, and (iii) mitochondrial injury and thus energy failure-related free radical production. In the present review, the different sources of oxidative stress and their relationships to patients with multiple sclerosis considering tissue injury mechanisms and clinical aspects have been discussed.
Assessment of Liver Remnant Using ICG Clearance Intraoperatively during Vascular Exclusion: Early Experience with the ALIIVE Technique
Authors: Lau Lawrence , Christophi Christopher , Nikfarjam Mehrdad , Starkey Graham , Goodwin Mark , Weinberg Laurence , Ho Loretta , Muralidharan Vijayaragavan
Published: May 2015

Background. The most significant risk following major hepatectomy is postoperative liver insufficiency. Current preoperative assessment of the future liver remnant relies upon assumptions which may not be valid in the setting of advanced resection strategies. This paper reports the feasibility of the ALIIVE technique which assesses the liver remnant with ICG clearance intraoperatively during vascular exclusion. Methods. 10 patients undergoing planned major liver resection (hemihepatectomy or greater) were recruited. Routine preoperative assessment included CT and standardized volumetry. ICG clearance was measured noninvasively using a finger spectrophotometer at various time points including following parenchymal transection during inflow and outflow occlusion before vascular division, the ALIIVE step. Results. There were one case of mortality and three cases of posthepatectomy liver failure. The patient who died had the lowest ALIIVE ICG clearance (7.1%/min versus 14.4 ± 4.9). Routine preoperative CT and standardized volumetry did not predict outcome. Discussion/Conclusion. The novel ALIIVE technique is feasible and assesses actual future liver remnant function before the point of no return during major hepatectomy. This technique may be useful as a check step to offer a margin of safety to prevent posthepatectomy liver failure and death. Further confirmatory studies are required to determine a safety cutoff level.
Life-Threatening Postpneumonectomy Syndrome Complicated with Right Aortic Arch after Left Pneumonectomy
Authors: Karasaki Takahiro , Tanaka Makoto
Published: May 2015

A 54-year-old man with right aortic arch underwent left lower lobectomy and lingular segmentectomy, followed by complete pneumonectomy, for refractory nontuberculous mycobacterial infection. Three months after the pneumonectomy, he developed acute respiratory distress. Computed tomography showed an excessive mediastinal shift with an extremely narrowed bronchus intermedius and right lower bronchus compressed between the right pulmonary artery and the right descending aorta. Soon after the nearly obstructed bronchus intermedius was observed by bronchoscopy, he began to exhibit frequent hypoxic attacks, perhaps due to mucosal edema. Emergent surgical repositioning of the mediastinum and decompression of the bronchus was indicated. After complete adhesiolysis of the left thoracic cavity was performed, to maintain the proper mediastinal position, considering the emergent setting, an open wound thoracostomy was created and piles of gauze were inserted, mildly compressing the heart and the mediastinum to the right side. Thoracoplasty was performed three months later, and he was eventually discharged without any dressings needed. Mediastinal repositioning under thoracostomy should be avoided in elective cases because of its extremely high invasiveness. However, in the case of life-threatening postpneumonectomy syndrome in an emergent setting, mediastinal repositioning under thoracostomy may be an option to save life, which every thoracic surgeon could attempt.
The Role of Overweight and Obesity in In Vitro Fertilization Outcomes of Poor Ovarian Responders
Authors: Vural Fisun , Vural Birol , Çakıroğlu Yiğit
Published: May 2015

Objective. Obesity is a worldwide concern with detrimental health effects including decreased fecundity. However, obesity’s impact on in vitro fertilization (IVF) is inconclusive and there is little data concerning poor ovarian responders (POR). This study explored the effects of overweight and obesity on IVF outcomes of POR.Design. We retrospectively evaluated 188 POR undergoing IVF cycles.Methods. Patients were categorized into three groups. Group 1 was normal weight POR (18.5–24.9 kg/m2,n=96); Group 2 was overweight POR (25.0–29.9 kg/m2,n=52); and Group 3 was obese POR (≥30.0 kg/m2,n=40). Main measured outcomes included IVF outcomes.Results. The oocyte maturity, total gonadotropin dose-duration, and cycle cancellation rates were similar. Obese women had significantly decreased LH levels. LH < 4 mIU/mL had a sensitivity (62%) and a specificity (86%) for IVF failure (AUC: 0.71). Fertilization rates of obese subjects were significantly lower than normal and overweight subjects (p=0.04). Obese women’s clinical pregnancy rates were significantly lower (15%) than normal weight women (33.3%,p=0.01).Conclusions. Despite similar counts of recruited mature oocytes, obese POR women had decreased fertilization and clinical pregnancy rates. Obesity rather than overweight significantly decreased IVF outcomes in POR.
Density Functional Study of Electronic and Structural Properties of Gold-Cadmium Selenide/Telluride Nanoclusters
Authors: Bulbula Shimeles T. , Zeweldi Hagos W.
Published: May 2015

Semiconductor nanowires are one class of building blocks that show promise for application in nanoscale electronics. Metal-semiconductor nanowire helps to improve the electrical properties or create unique ones. Electronic and structural properties of cadmium selenide/telluride connected to gold electrode clusters have been the focus of this research due to their importance in constructing fast microelectric devices. The simulations were carried out by using VASP (ViennaAb-InitioSimulation Package) which utilizes the method of density functional theory (DFT) and plane wave basis set. Optimization was performed to obtain the minimum energy structure. In this research paper the result shows that the HOMO-LUMO gaps for the minimum energy cadmium selenide/telluride connected to gold electrodes decrease as cluster size increases, whereas the binding energy shows a reverse relationship with the cluster size. However, a few clusters show special properties like AuCd2Se3and AuCd2Te3clusters.
Using Coarrays to Parallelize Legacy Fortran Applications: Strategy and Case Study
Authors: Radhakrishnan Hari , Rouson Damian W. I. , Morris Karla , Shende Sameer , Kassinos Stavros C.
Published: May 2015

This paper summarizes a strategy for parallelizing a legacy Fortran 77 program using the object-oriented (OO) and coarray features that entered Fortran in the 2003 and 2008 standards, respectively. OO programming (OOP) facilitates the construction of an extensible suite of model-verification and performance tests that drive the development. Coarray parallel programming facilitates a rapid evolution from a serial application to a parallel application capable of running on multicore processors and many-core accelerators in shared and distributed memory. We delineate 17 code modernization steps used to refactor and parallelize the program and study the resulting performance. Our initial studies were done using the Intel Fortran compiler on a 32-core shared memory server. Scaling behavior was very poor, and profile analysis using TAU showed that the bottleneck in the performance was due to our implementation of a collective, sequential summation procedure. We were able to improve the scalability and achieve nearly linear speedup by replacing the sequential summation with a parallel, binary tree algorithm. We also tested the Cray compiler, which provides its own collective summation procedure. Intel provides no collective reductions. With Cray, the program shows linear speedup even in distributed-memory execution. We anticipate similar results with other compilers once they support the new collective procedures proposed for Fortran 2015.
Bayesian Method for Shape Reconstruction in the Inverse Interior Scattering Problem
Authors: Wang Yujie , Ma Fuming , Zheng Enxi
Published: May 2015

The inverse scattering problem of an interior cavity with three different boundary conditions is considered. Bayesian method is used to reconstruct the shape of the cavity from scattered fields incited by point source(s) and measured on a closed curve inside the cavity. We prove the well-posedness in Bayesian perspective and present numerical examples to show the viability of the method.
High-Performance Design Patterns for Modern Fortran
Authors: Haveraaen Magne , Morris Karla , Rouson Damian , Radhakrishnan Hari , Carson Clayton
Published: May 2015

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented these patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow.
Stroboscopic Surface Thermal Lensing for Fast Detection of Thermal Defects in Large‐Scaled Coating Films
Authors: Tao Chunxian , Zhang Dawei , Hong Ruijin , Wang Zhongfei
Published: May 2015

A stroboscopic surface thermal lensing (SSTL) system for the fast detection of thermal‐induced defects in large‐scaled optical coating films was constructed. The SSTL signal was generated by a set of double‐modulators and captured by a high speed matrix camera, respectively. The spot size of both pump laser and probe laser expanded for larger detection area was finished in a single step. Based on the STL technique, both the mapping of amplitude and the phase of SSTL signal on the whole area of the coatings can be achieved simultaneously.
Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools
Authors: Orduña Patricia , Castillo-Rodal Antonia I. , Mercado Martha E. , Ponce de León Samuel , López-Vidal Yolanda
Published: May 2015

Nontuberculous mycobacteria (NTM) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. Although most NTM are saprophytes, approximately one-third of NTM have been associated with human diseases. In this study, we did a comparative proteomic analysis among five NTM strains isolated from several sources. There were different numbers of protein spots fromM. gordonae(1,264),M. nonchromogenicumtype I (894),M. nonchromogenicumtype II (935),M. peregrinum(806), andM. scrofulaceum/Mycobacterium mantenii(1,486) strains, respectively. We identified 141 proteins common to all strains and specific proteins to each NTM strain. A total of 23 proteins were selected for its identification. Two of the common proteins identified (short-chain dehydrogenase/reductase SDR and diguanylate cyclase) did not align withM. tuberculosiscomplex protein sequences, which suggest that these proteins are found only in the NTM strains. Some of the proteins identified as common to all strains can be used as markers of NTM exposure and for the development of new diagnostic tools. Additionally, the specific proteins to NTM strains identified may represent potential candidates for the diagnosis of diseases caused by these mycobacteria.
Evidence Suggesting That Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors
Authors: Amin Amit Dipak , Rajan Soumya S. , Liang Winnie S. , Pongtornpipat Praechompoo , Groysman Matthew J. , Tapia Edgar O. , Peters Tara L. , Cuyugan Lori , Adkins Jonathan , Rimsza Lisa M. , Lussier Yves A. , Puvvada Soham D. , Schatz Jonathan H.
Published: May 2015

The anaplastic lymphoma kinase (ALK) is chromosomally rearranged in a subset of certain cancers, including 2% to 7% of non–small cell lung cancers (NSCLC) and ∼70% of anaplastic large cell lymphomas (ALCL). The ALK kinase inhibitors crizotinib and ceritinib are approved for relapsed ALK+ NSCLC, but acquired resistance to these drugs limits median progression-free survival on average to ∼10 months. Kinase domain mutations are detectable in 25% to 37% of resistant NSCLC samples, with activation of bypass signaling pathways detected frequently with or without concurrent ALK mutations. Here we report that, in contrast to NSCLC cells, drug-resistant ALCL cells show no evidence of bypassing ALK by activating alternate signaling pathways. Instead, drug resistance selected in this setting reflects upregulation of ALK itself. Notably, in the absence of crizotinib or ceritinib, we found that increased ALK signaling rapidly arrested or killed cells, allowing a prolonged control of drug-resistant tumors in vivo with the administration of discontinuous rather than continuous regimens of drug dosing. Furthermore, even when drug resistance mutations were detected in the kinase domain, overexpression of the mutant ALK was toxic to tumor cells. We confirmed these findings derived from human ALCL cells in murine pro-B cells that were transformed to cytokine independence by ectopic expression of an activated NPM–ALK fusion oncoprotein. In summary, our results show how ALK activation functions as a double-edged sword for tumor cell viability, with potential therapeutic implications. Cancer Res; 75(14); 2916–27. ©2015 AACR.