bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical dyssynchrony of the left atrium during sinus rhythm is associated with history of stroke in patients with atrial fibrillation
Authors: Ciuffo Luisa , Inoue Yuko Y , Tao Susumu , Gucuk Ipek Esra , Balouch Muhammad , Lima Joao A C , Nazarian Saman , Spragg David D , Marine Joseph E , Berger Ronald D , Calkins Hugh , Ashikaga Hiroshi
Published: May 2017

Aims

We sought to evaluate the relationship between left atrial (LA) mechanical dyssynchrony and history of stroke or transient ischaemic attack (TIA) in patients with atrial fibrillation (AF). We hypothesized that mechanical dyssynchrony of the LA is associated with history of stroke/TIA independent of LA function and Cardiac failure, Hypertension, Age, Diabetes, Stroke/transient ischaemic attack (TIA), VAscular disease, and Sex category (CHA2DS2-VASc) score in patients with AF.

Methods and results

We conducted a cross-sectional study of 246 patients with a history of AF (59 ± 10 years, 29% female, 26% non-paroxysmal AF) referred for catheter ablation to treat drug-refractory AF who underwent preablation cardiac magnetic resonance (CMR) in sinus rhythm. Using tissue-tracking CMR, we measured the LA longitudinal strain and strain rate in each of 12 equal-length segments in two- and four-chamber views. We defined indices of LA mechanical dyssynchrony, including the standard deviation of the time to the peak longitudinal strain (SD-TPS). Patients with a prior history of stroke or TIA (n = 23) had significantly higher SD-TPS than those without (n = 223) (39.9 vs. 23.4 ms, P < 0.001). Multivariable analysis showed that SD-TPS was associated with stroke/TIA after adjusting for the CHA2DS2-VASc score, LA minimum index volume, and the peak LA longitudinal strain (P < 0.001). The receiver-operating characteristics curve showed that SD-TPS identified patients with stroke/TIA more accurately than CHA2DS2-VASc score alone (c-statistics: 0.82 vs. 0.75, P < 0.001).

Conclusion

Higher mechanical dyssynchrony of the LA during sinus rhythm is associated with a history of stroke/TIA in patients with AF.
Identifying Characteristics of Verticillium Wilt Suppressiveness in Olive Mill Composts
Authors: Avilés Manuel , Borrero Celia
Published: May 2017

The aims of this study were to assess the potential suppressive effects of different olive mill composts on Verticillium wilt and to elucidate the suppressive mechanisms. To this end, four olive mill composts from different crop areas with two maturation levels were selected. After conducting the Verticillium wilt bioassays in cotton, the suppressive effect was observed in only one compost. Compost maturation level did not affect disease development. The standardized area under the disease progress curve and microsclerotia concentration were associated with low API-ZYM enzymatic diversity, β-glucosidase activity, pH, and high electrical conductivity (EC). To assess the nature of suppressiveness in the suppressive compost, additional bioassays were performed with three treated compost-amended growing media (N-supplemented, autoclaved, and heat treated at 60°C for 6 days). Suppressiveness was partially reduced with heat treatments, where N-acetyl-β-glucosaminidase activity disappeared. In this compost, high oligotrophic actinomycete populations were associated with disease reduction. Therefore, plant growth media amended with different olive mill composts do not always show suppressiveness against Verticillium wilt. Enzymatic diversity, β-glucosidase activity, pH, and EC may be sufficient to predict where olive mill compost plant growth media will be effective in reducing Verticillium wilt and microsclerotia concentration. General and specific suppressiveness are involved in the mechanism of compost suppression.
Rebound Deformity After Growth Modulation in Patients With Coronal Plane Angular Deformities About the Knee: Who Gets It and How Much?
Authors: Leveille Lise A. , Razi Ozan , Johnston Charles E.
Published: May 2017

Background:

With observed success and increased popularity of growth modulation techniques, there has been a trend toward use in progressively younger patients. Younger age at growth modulation increases the likelihood of complete deformity correction and need for implant removal before skeletal maturity introducing the risk of rebound deformity. The purpose of this study was to quantify magnitude and identify risk factors for rebound deformity after growth modulation.

Methods:

We performed a retrospective review of all patients undergoing growth modulation with a tension band plate for coronal plane deformity about the knee with subsequent implant removal. Exclusion criteria included completion epiphysiodesis or osteotomy at implant removal, ongoing growth modulation, and <1 year radiographic follow-up without rebound deformity. Mechanical lateral distal femoral angle, mechanical medial proximal tibial angle, hip-knee-ankle angle (HKA), and mechanical axis station were measured before growth modulation, before implant removal, and at final follow-up.

Results:

In total, 67 limbs in 45 patients met the inclusion criteria. Mean age at growth modulation was 9.8 years (range, 3.4 to 15.4 y) and mean age at implant removal was 11.4 years (range, 5.3 to 16.4 y). Mean change in HKA after implant removal was 6.9 degrees (range, 0 to 23 degrees). In total, 52% of patients had >5 degrees rebound and 30% had >10 degrees rebound in HKA after implant removal. Females below 10 years and males below 12 years at time of growth modulation had greater mean change in HKA after implant removal compared with older patients (8.4 vs. 4.7 degrees, P=0.012). Patients with initial deformity >20 degrees had an increased frequency of rebound >10 degrees compared with patients with less severe initial deformity (78% vs. 22%, P=0.002).

Conclusions:

Rebound deformity after growth modulation is common. Growth modulation at a young age and large initial deformity increases risk of rebound. However, rebound does not occur in all at risk patients, therefore, we recommend against routine overcorrection.

Level of Evidence:

Level IV—retrospective study.
Interleukin-10 −592C/A, but not −1082A/G promoter single nucleotide polymorphism, is associated with a decreased risk of colorectal cancer in an ethnic Kashmiri population: a case–control study
Authors: Banday Mujeeb Z. , Sameer Aga S. , Chowdri Nissar A. , Haq Ehtishamul
Published: May 2017

Chronic inflammation influences the development of various cancers including colorectal cancer (CRC). Interleukin-10 (IL-10), an anti-inflammatory cytokine, plays a vital role in several homeostatic physiological processes occurring in the human gastrointestinal tract including intestinal inflammation and is a key regulator of several gastrointestinal tract pathophysiological processes such as inflammatory bowel diseases that are associated with an increased predisposition to CRC. Several studies have reported the association of various polymorphisms in the human IL-10 gene including IL-10 −592C/A and IL-10 −1082A/G single nucleotide polymorphisms (SNPs) with various cancers including CRC, but these SNPs are yet to be studied in a Kashmiri population with respect to CRC risk. The aim of this study was to analyze the association of IL-10 −592C/A and IL-10 −1082A/G promoter SNPs with CRC risk in an ethnic Kashmiri population through a case–control design. The genotype frequencies of IL-10 −592C/A and IL-10 −1082A/G promoter SNPs were compared between 142 CRC patients and 184 individually matched healthy controls using the PCR and restriction fragment length polymorphism method. The association between the IL-10 −592C/A and IL-10 −1082A/G SNPs and CRC risk was examined through conditional logistic regression models adjusted for multiple possible confounding (third) variables. The possible effect measure modification of the association between the relevant SNP genotypes and CRC risk by various CRC risk factors including age, sex, and smoking status was also evaluated. Further, the associations between these SNPs and various clinicopathological parameters, demographic variables, and environmental factors in the case group patients with respect to CRC risk were also analyzed. The overall association between the IL-10 −592C/A SNP and the modulation of CRC risk was found to be significant (P=0.001). The variant genotype (AA) was significantly associated with a decreased risk of CRC (odds ratio: 0.25; 95% confidence interval: 0.11–0.61; P=0.002). Further, the less common IL-10 −592A allele was associated with a decreased risk of CRC (odds ratio: 0.64; 95% confidence interval: 0.46–0.88; P=0.0092). The overall association between the IL-10 −1082A/G SNP and the modulation of CRC risk was not found to be significant (P=0.141). This study has shown that there is a significant association between the IL-10 −592C/A promoter SNP and a decreased risk of CRC in an ethnic Kashmiri population, but the association between IL-10 −1082A/G SNP and the risk of CRC in the population under study is not significant. However, to substantiate our findings, this study needs to be replicated with a larger sample size and with other ethnically defined populations with comparable CRC incidence.
Reinforcing effectiveness of midazolam, ethanol, and sucrose: behavioral economic comparison of a mixture relative to its component solutions
Authors: Townsend E. Andrew , Platt Donna M. , Rowlett James K. , Roma Peter G. , Freeman Kevin B.
Published: May 2017

Benzodiazepines (BZs) are relatively safe when administered alone. However, these drugs can produce severe side effects when coadministered with ethanol. Despite these adverse consequences, rates of concurrent BZ and ethanol misuse are increasing, and it is unclear whether this behavior is maintained by an enhanced reinforcing effect of the mixture. To address this issue, the current study compared the reinforcing effectiveness of sucrose solutions mixed with midazolam, ethanol, or both. Eight male rats were trained to orally self-administer solutions of either sucrose (S), sucrose+midazolam (SM), sucrose+ethanol (SE), or sucrose+midazolam+ethanol (SME). The response requirement was increased between sessions until the number of reinforcers earned was zero and the relationship between response requirement and reinforcers earned was analyzed using the exponential model of demand. Although baseline intake was similar across drug conditions, consumption of SM was least affected by increases in cost, indicating that it possessed the highest reinforcing effectiveness (i.e. least elastic). The reinforcing effectiveness of S, SE, and SME did not differ significantly. The finding that the reinforcing effectiveness of the SME was less than that of SM does not support the supposition that BZ and ethanol coadministration is maintained by a higher reinforcing effectiveness of the mixture.
Behavioural responses of zebrafish larvae to acute ethosuximide exposure
Authors: Ji Yongxia , Lin Jia , Peng Xiaolan , Liu Xiuyun , Li Fei , Zhang Yinglan , Guo Ning , Li Qiang
Published: May 2017

The anticonvulsant drug ethosuximide has shown diverse anxiety-related activity in rodents, but research in zebrafish is limited. To evaluate the effects of acute ethosuximide exposure on locomotor activity and anxiety-related thigmotaxis behaviours of zebrafish larvae, the activity of AB strain zebrafish larvae at 5 and 7 days postfertilization (dpf) was analysed under normal constant illumination and stressful light–dark transitions. Under constant illumination, ethosuximide at concentrations of 2, 5 and 10 mmol/l increased the distances travelled and intensified locomotor responses to a novel environment. In addition, 40 mmol/l ethosuximide decreased the travel distance and attenuated the locomotor response to darkness. The effects were age related. Under constant illumination, ethosuximide at 40 mmol/l reduced thigmotaxis behaviours in larvae at both ages. Under the light–dark transition, 5 mmol/l ethosuximide reduced thigmotaxis behaviours in 7-dpf larvae. We concluded that under constant lighting, ethosuximide at low concentrations (2, 5 and 10 mmol/l) stimulated the locomotor activity of zebrafish larvae, whereas a high concentration (40 mmol/l) inhibited the activity. Ethosuximide at a low concentration (5 mmol/l) showed anxiolytic effects during the stressful light–dark transition in 7-dpf larvae. The effects of ethosuximide were age and concentration related.
Knowledge, Attitudes, and Beliefs of Prenursing and Nursing Students About Sexual Assault
Authors: Strunk Judith L.
Published: May 2017

Sexual assault has been identified as a major public health problem in the United States, yet little research has been done regarding nursing students’ knowledge, attitudes, and beliefs about sexual assault. Lack of knowledge, or victim-blaming attitudes held by healthcare providers can be problematic for the care of the sexual assault victim, leaving them feeling upset and distressed after the healthcare encounter. Prenursing and nursing students were surveyed about their knowledge, attitudes, and beliefs about sexual assault. A knowledge test, the Illinois Rape Myth Acceptance scale, and the Attitudes Toward Rape Victims scale were utilized in the survey; 297 students completed the survey. Results indicate that rape myth acceptance is lower for nursing students in their last semester of college than in the prenursing group; and that last-semester nursing students held less victim-blaming attitudes toward rape victims than prenursing students. The knowledge test highlights problem areas that need to be addressed by nursing education to improve the care of sexual assault patients.
A Qualitative Exploration of Sexual Assault Patients’ Barriers to Accessing and Completing HIV Prophylaxis
Authors: Djelaj Valentina , Patterson Debra , Romero Christina M.
Published: May 2017

Sexual assault patients may encounter barriers when accessing, accepting, and completing nonoccupational postexposure prophylaxis (nPEP), such as lacking insurance or an understanding of nPEP. However, less is known about how sexual assault forensic examiner (SAFE) programs’ protocols, approaches to discussing nPEP, and community resources may influence nPEP completion. Utilizing a qualitative case study framework, we conducted semistructured interviews with 10 SAFEs from an urban SAFE program in which emergency department physicians write prescriptions for nPEP before sending patients to the SAFE program. The participants identified barriers encountered by their patients, ranging from emergency department providers inconsistently offering prescriptions for the correct medication, to difficulty locating a local pharmacy stocking nPEP. The SAFEs also expressed concern that uninsured patients had to complete additional steps to access nPEP, while feeling overwhelmed by the immediacy of their assaults. Several participants raised concern that patients’ emotional distress and fear of acquiring HIV may impede their ability to comprehend information and access nPEP. Participants also noted that the 28-day nPEP regimen might be a daily reminder for patients of the sexual assault. The SAFEs identified multiple strategies for discussing HIV and nPEP with these patients. Implications of the SAFE’s role in reducing barriers are discussed.
Cirrhosis has no impact on therapeutic responses of entecavir for chronic hepatitis B
Authors: Wang Pin-Chao , Wei Tao-Yang , Tseng Tai-Chung , Lin Hans Hsienhong , Wang Chia-Chi
Published: May 2017

Objective

As the efficacy of a direct antiviral agent is reduced in cirrhotic chronic hepatitis C patients, prolonged duration of treatment or addition of ribavirin is recommended to improve the rates of sustained virological response. However, the impact of cirrhosis on the efficacy of antiviral treatment for chronic hepatitis B (CHB) remained unclear.

Patients and methods

This retrospective cohort study screened entecavir (ETV)-treated CHB patients in Taipei Tzu Chi Hospital from January 2007 till October 2014. The diagnosis of cirrhosis was made on the basis of clinical/imaging or histologic findings. The primary endpoints were hepatitis B e antigen (HBeAg) loss in HBeAg-positive patients and undetectable hepatitis B virus (HBV) DNA in the overall study population. Initial virological response is defined as undetectable HBV DNA at 1-year ETV treatment.

Results

A total of 381 (262 men; mean age: 49.6±12.9 years) CHB patients were recruited for the final analysis. Of these, 138 were cirrhotic. In 143 HBeAg-positive patients, there was no difference in the rates of 1- and 2-year HBeAg loss between cirrhotic and noncirrhotic patients (P=0.226 and 0.729, respectively). In the overall population, the rate of 1-year undetectable HBV DNA was higher in patients with cirrhosis than those without cirrhosis (76.1 vs. 64.2%, P=0.016). The rate of 2-year undetectable HBV DNA was not different between these two groups. Using multivariate logistic regression analysis, baseline HBV DNA levels (P=0.006) and HBeAg status (P=0.007), were associated with initial virological response, but not cirrhosis.

Conclusion

Therapeutic responses of ETV are not decreased in cirrhotic CHB patients. Thus, cirrhotic CHB patients can be treated with ETV without the need for dose adjustment.
Examining Drivers of Health Care Spending
Authors: Mitchell Jean M. , Reschovsky James D. , Film Roy J. , Franzini Luisa
Published: May 2017

Background:

Despite the enactment of laws to restrict the practice of self-referral, exceptions in these prohibitions have enabled these arrangements to persist and proliferate. Most research documenting the effects of self-referral arrangements analyzed claims records from Medicare beneficiaries. Empirical evidence documenting the effects of self-referral on use of services and spending incurred by persons with private insurance is sparse.

Objectives:

We analyzed health insurance claims records from a large private insurer in Texas to evaluate the effects of physician self-referral arrangements involving physical therapy on the treatment of patients with frozen shoulder syndrome, elbow tendinopathy or tendinitis, and patellofemoral pain syndrome.

Study Design:

We used regression analysis to evaluate the effects of episode self-referral status on: (1) initiation of physical therapy; (2) physical therapy visits and services for those who had at least 1 visit; and (3) total condition-related insurer allowed amounts per episode.

Results:

For all 3 conditions, we found that patients treated by physician owners were much more likely to be referred for a course of physical therapy when compared with patients seen by physician nonowners. A consistent pattern emerged among patients who had at least 1 physical therapy visit; non–self-referred episodes included more physical therapy visits, and more physical therapy services per episode in comparison with episodes classified as self-referral. Most self-referred episodes were short and the initial visit did not include an evaluation.

Conclusion:

Physician owners of physical therapy services refer significantly higher percentages of patients to physical therapy and many are equivocal cases.
An Unusual Case of Sudden Death
Authors: Aquila Isabella , Boca Silvia , Caputo Fiorella , Sacco Matteo A. , Gratteri Santo , Fineschi Vittorio , Ricci Pietrantonio
Published: May 2017

In adults, the most common cause of sudden death is coronary heart disease or defects in the cardiac conduction system; however, there are many cases of sudden death occurring from other causes such as fatal pulmonary thromboembolism. Several risk factors are recognized, including hospitalization, surgery, obesity, pregnancy, the use of oral contraceptives, traumatic fractures, and genetic conditions, which cause hypercoagulable states such as factor V Leiden mutations. Although many risk factors have been identified, the mortality rate is still high. An association between thyroid disease and coagulation disorders has previously been demonstrated. However, scientific literature does not yet agree on the association between thyroid diseases and pulmonary thromboembolism. Excessive thyroid hormones can determine an alteration in the hemostatic system through different mechanisms, which lead to a hypercoagulable state. In forensic literature, there are no reports of fatal thromboembolism in patients with thyroid disorders. We reported a case of a 41-year-old woman who died during sexual activity. The autopsy findings highlighted the presence of massive pulmonary embolism. Histopathological analysis showed structural anomalies of the thyroid gland. A retrospective analysis of her medical history and possible genetic alterations were performed.
Physical Therapy for a Child With Infantile Idiopathic Scoliosis and Motor Delay
Authors: Hall Rhea K. , Rapport Mary Jane
Published: May 2017

Purpose:

The purpose of this case report is to describe physical therapy (PT) for a child with infantile idiopathic scoliosis and motor delay.

Key Points:

A 10-month-old boy with a 28° left thoracolumbar scoliosis was referred for PT and was seen weekly in his home over a 6-month period following a diagnosis of scoliosis and delayed gross motor milestones. Before the initiation of PT, the child was scheduled to undergo serial casting for correction of the spinal curve and was not yet rolling or transitioning in or out of sitting. By the end of the 6-month intervention period, the spinal curve had resolved to 12° without the need for serial casting and the child was walking independently.

Conclusion:

PT appeared to have a positive effect on reduction of the spinal curve and achievement of gross motor milestones.
The Effect and Safety of Prostaglandin Administration in Pediatric Liver Transplantation
Authors: Lironi Céline , McLin Valérie A. , Wildhaber Barbara E.
Published: May 2017

Background

Prostaglandins are often administered after liver transplantation (LT) to diminish ischemia-reperfusion injury (IRI), to favor liver recovery and to prevent vascular thrombosis. Possible beneficial effects in adult liver recipients are controversial, but the single existing pediatric small case series shows no significant impact of prostaglandin administration after LT. The purpose of this study was to analyze the effect of the prostaglandin dinoprostone in pediatric liver recipients.

Methods

A retrospective analysis of 41 children (<16 years) who underwent LT between March 2008 and December 2013 was performed. Dinoprostone was administered at a rate from 0.1 to a maximum of 0.6 μg/kg per hour immediately after LT and for a maximum of 5 days. Effect of dinoprostone on post-LT IRI and hepatic function up to 60 postoperative days and number of hypotensive episodes were analyzed.

Results

The median cumulative dose of dinoprostone was 28 μg/kg (interquartile range, 23.2). Dinoprostone had no significant effect on post-LT liver function tests and factor V levels at any of the administered dosages. There was no significant association between the total quantity of vasopressor given and the number of hypotensive episodes observed in 8 patients. One patient showed a short-lasting hypotension, possibly related to the administration of dinoprostone.

Conclusions

This study did not show, at any dosage between 0.1 and 0.6 μg/kg per hour, any differences in beneficial or harmful effects of high- or low-dose dinoprostone administered immediately after pediatric LT on markers of IRI, hepatic function, or hypotension.
Network analysis of high-density microelectrode recordings
Authors: Bullmann Torsten , Radivojevic Milos , Huber Stefan , Deligkaris Kosmas , Hierlemann Andreas , Frey Urs
Published: May 2017

A high-density microelectrode arrays (HDMEA) with 3,150 electrodes per square millimetre was used to capture neuronal activity across various scales, including axons, dendrites, and networks. We present a new method for high-throughput segmentation of axons based on the spatial smoothness of signal delays. Comparison with both ground truth and receiver operator characteristics shows that the new segmentation method outperforms previous methods based on the signal-amplitude-to-noise ratio. Structural and functional neuronal network connectivity were reconstructed using a common extension of “Peter’s rule” and a inter-spike histogram method, respectively. Approximately one third of these connections are putative chemical synapses. We evaluated the spike patterns but did not find evidence for “polychronisation” (non-synchronous but precisely timed spike sequences). The developed framework can be used to investigate the relationship between the topology of neuronal connections and emerging temporal spike patterns observed in dissociated neuronal cultures.
Individual differences in perceptual decision making reflect neural variability in medial frontal cortex
Authors: Kurikawa Tomoki , Handa Takashi , Fukai Tomoki
Published: May 2017

Decision making obeys common neural mechanisms, but there is considerable variability in individuals’ decision making behavior particularly under uncertainty. How individual differences arise within common decision making brain systems is not known. Here, we explored this question in the medial frontal cortex (MFC) of rats performing a sensory-guided choice task. When rats trained on familiar stimuli were exposed to unfamiliar stimuli, choice responses varied significantly across individuals. We examined how variability in MFC neural processing could mediate this individual difference and constructed a network model to replicate this. Our model suggested that susceptibility of neural trajectories is a crucial determinant of the observed choice variability. The model predicted that trial-by-trial variability of trajectories are correlated with the susceptibility, and hence also correlated with the individual difference. This prediction was confirmed by experiment. Thus, our results suggest that variability in neural dynamics in MFC networks underlies individual differences in decision making.
Quantitative MRI provides markers of intra-, inter-regional, and age-related differences in young adult cortical microstructure
Authors: Carey Daniel , Caprini Francesco , Allen Micah , Lutti Antoine , Weiskopf Nikolaus , Rees Geraint , Callaghan Martina F. , Dick Frederic
Published: May 2017

Measuring the structural composition of the cortex is critical to understanding typical development, yet few investigations in humans have charted markers in vivo that are sensitive to tissue microstructural attributes. Here, we used a well-validated quantitative MR protocol to measure four parameters (R1, MT, R2*, PD*) that differ in their sensitivity to facets of the tissue microstructural environment (R1, MT: myelin, macromolecular content; R2*: paramagnetic ions, i.e., iron; PD*: free water content). Mapping these parameters across cortical regions in a young adult cohort (18-30 years, N=93) revealed expected patterns of increased macromolecular content as well as reduced tissue water content in primary and primary adjacent cortical regions. Mapping across cortical depth within regions showed decreased expression of myelin and related processes – but increased tissue water content – when progressing from the grey/white to the grey/pial boundary, in all regions. Charting developmental change in cortical microstructure, we found that parameters with the greatest sensitivity to tissue myelin (R1& MT) showed linear increases with age across frontal and parietal cortex (change 0.5-1.0% per year). Overlap of robust age effects for both parameters emerged in left inferior frontal, right parietal and bilateral pre-central regions. Our findings afford an improved understanding of ontogeny in early adulthood and offer normative quantitative MR data for inter- and intra-cortical composition, which may be used as benchmarks in further studies.

Highlights

We mapped multi-parameter maps (MPMs) across and within cortical regions

We charted age effects on myelin and related processes at mid-cortical depth

Inter- and intra-regional differences in MPMs emerged at primary and association cortex

Iron-sensitive R2* map foci tended to overlap MPMs sensitive to myelin (R1, MT)

R1and MT increased with age (0.5-1.0% per year) in frontal and parietal cortex
Evaluation of classifier performance for multiclass phenotype discrimination in untargeted metabolomics
Authors: Trainor Patrick J. , DeFilippis Andrew P. , Rai Shesh N.
Published: May 2017

Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes and for furnishing diagnostic and prognostic phenotype predictions in medicine. Despite this, a comprehensive and rigorous evaluation of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics data, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines, and Neural Network classification techniques for discriminating phenotype. We evaluated the techniques on simulated data generated to mimic global untargeted metabolomics data by incorporating realistic block-wise correlation and partial correlation structures for mimicking the correlations and metabolite clustering generated by biological processes. Over the simulation studies, covariance structures, means, and effect sizes were randomly simulated to provide consistent estimates of classifier performance over a wide range of possible scenarios. The presence of non-normal error distributions and the effect of prior-significance filtering (dimension reduction) were evaluated. In each simulation, classifier parameters (such as the number of hidden nodes in a neural network) were tuned by cross-validation to minimize the probability of detecting spurious results due to poorly tuned classifiers. Classifier performance was then evaluated using real clinical metabolomics datasets of varying sample medium, sample size, and experimental design. We report that in the scenarios without a significant presence of non-normal error distributions over metabolite clusters, Neural Network and PLS-DA classifiers performed poorly relative to Sparse PLS-DA (sPLS-DA), Support Vector Machine (SVM), and Random Forest classifiers. When non-normal error distributions were introduced, the performance of PLS-DA classifiers deteriorated further relative to the remaining techniques. Simultaneously, while the relative performance of Neural Network classifiers improved relative to PLS-DA classifiers, Neural Network classifier performance remained poor compared sPLS-DA, SVM, and Random Forest classifiers. Over the real datasets, a trend of better performance of SVM and Random Forest classifier performance was observed.
Purification of the mammalian NgBR/hCITcis-prenyltransferase complex: Identification of a conserved carboxyterminal RxG motif crucial for enzymatic activity
Authors: Grabińska Kariona A. , Edani Ban H. , Park Eon Joo , Kraehling Jan R. , Sessa William C.
Published: May 2017

Cis-Prenyltransferases (cisPTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. In eukaryotes and archaea,cisPT is the first enzyme committed to the synthesis of dolichyl-phosphate (DolP). DolP is obligate lipid carrier in protein glycosylation reactions in mammals. The homodimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS) generates 11 isoprene units and has been structurally and mechanistically characterized in great detail. Recently our group discovered that unlike UPPS, mammaliancisPT is a heteromer consisting of NgBR (NUS1) and hCIT (DHDDS) subunits and this composition has been confirmed in plants and fungalcisPTs. Here, we establish the first purification system for heteromericcisPT and show that both NgBR and hCIT subunits function in catalysis and substrate binding. Finally, we identified a critical RxG sequence in the C-terminal tail of NgBR that is conserved and essential for enzyme activity across phyla.
Cohesin loss eliminates all loop domains, leading to links among superenhancers and downregulation of nearby genes
Authors: Rao Suhas S. P. , Huang Su-Chen , Glenn St Hilair Brian , Engreitz Jesse M. , Perez Elizabeth M. , Kieffer-Kwon Kyong-Rim , Sanborn Adrian L. , Johnstone Sarah E. , Bochkov Ivan D. , Huang Xingfan , Shamim Muhammad S. , Omer Arina D. , Bernstein Bradley E. , Casellas Rafael , Lander Eric S. , Lieberman Aiden Erez
Published: May 2017

The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci - almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loci in different compartments that had been in the same loop domain become more segregated. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. Cohesin restoration quickly reverses these effects, consistent with a model where loop extrusion is rapid.
Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
Authors: Sun Hai-Xi , Li Yan , Niu Qi-Wen , Chua Nam-Hai
Published: May 2017

The 3′ untranslated regions (3′ UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation, and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3′ UTRs, but the involvement of this process in stress response has not yet been clarified. Here, we report that a subset of stress-related genes exhibits 3′ UTR extensions of their mRNAs during dehydration stress. These extended 3′ UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can act as antisense transcripts to repress expression levels of sense genes from the opposite strand or can activate the transcription or lead to read-through transcription of their downstream genes. Further analysis suggests that transcripts with 3′ UTR extensions have weaker poly(A) signals than those without 3′ UTR extensions. Finally, we show that their biogenesis is partially dependent on a trans-acting factor FPA. Taken together, we report that dehydration stress could induce transcript 3′ UTR extensions and elucidate a novel function for these stress-induced 3′ UTR extensions as long noncoding RNAs in the regulation of their neighboring genes.
A new example of intramolecular C—H...Ni anagostic interactions: synthesis, crystal structure and Hirshfeld analysis of cis-bis[4-methyl-2-(1,2,3,4-tetrahydronaphthalen-1-ylidene)hydrazinecarbothioamidato-κ2
N
1,S]nickel(II) dimethylformamide monosolvate
Authors: Oliveira Adriano Bof de , Beck Johannes , Mellone Sônia Elizabeth Brown S. , Daniels Jörg
Published: May 2017

The reaction of NiII acetate tetrahydrate with 4-methyl-2-(1,2,3,4-tetrahydronaphthalen-1-ylidene)hydrazinecarbothioamide in a 2:1 molar ratio and recrystallization from dimethylformamide yielded the title compound, [Ni(C12H14N3S)2]·C3H7NO. The ligands act as monoanionic κ2
N
1,S-donors, forming five-membered metallarings. The NiII ion is fourfold coordinated in a distorted square-planar cis-configuration, which is rather uncommon for monothiosemicarbazone complexes. Intramolecular H...Ni trans-interactions are observed [H...Ni distances are 2.50 and 2.57 Å] and thus anagostic interactions can be suggested. The Hirshfeld surface analysis indicates that the major contributions for the crystal packing are H...H (66.6%), H...S (12.3%) and H...C (10.9%) interactions. In the crystal, the complex molecules are linked by dimethylformamide solvent molecules through N—H...O interactions into one-dimensional hydrogen-bonded polymers along [010].
Crystal structure of 4,4′-bis[3-(piperidin-1-yl)prop-1-yn-1-yl]-1,1′-biphenyl
Authors: Walbaum Anqi , Fifer E. Kim , Parkin Sean , Crooks Peter A.
Published: May 2017

The title compound, C28H32N2, (I), is one of a second generation of compounds designed and synthesized based on a very potent and selective α9α10 nicotinic acetylcholine receptor antagonist ZZ161C {1,1′-[[1,1′-biphenyl]-4,4′-diylbis(prop-2-yne-3,1-diyl)]bis(3,4-dimethylpyridin-1-ium) bromide}, which has shown analgesic effects in a chemotherapy-induced neuropathy animal model. Compound (I) was synthesized by the reaction of 4,4′-bis(3-bromoprop-1-yn-1-yl)-1,1′-biphenyl with piperidine at room temperature in acetonitrile. The single-crystal used for X-ray analysis was obtained by dissolving (I) in a mixture of dichloromethane and methanol, followed by slow evaporation of the solvent. In the crystal of (I), the biphenyl moiety has a twisted conformation, with a dihedral angle of 25.93 (4)° between the benzene rings. Both piperidine head groups in (I) are in the chair conformation and are oriented so that the N-atom lone pairs of each piperidine group point away from the central biphenyl moiety.
N,N-Diethyl-2-[5-(4-methoxybenzylidene)-2,4-dioxo-1,3-thiazolidin-3-yl]acetamide
Authors: Viswanathan Vijayan , Yasmin Sabina , Jayaprakash Venkatesan , Velmurugan Devadasan
Published: May 2017

In the title compound, C17H20N2O4S, the thiazolidine (r.m.s. deviation = 0.022 Å) and phenyl rings (major and minor occupancies) are inclined to one another by 6.3 (3) and 10.5 (3)°, respectively. The molecular conformation is stabilized by an intramolecular C—H...S interaction. In the crystal, molecules are linked by C—H...O hydrogen bonds, which generateR22(18),R22(24) andR21(7) ring motifs. Aromatic π–π stacking interactions are also observed.
3-(4-Methoxyphenyl)-4-methyl-N-[4-(4-methylphenyl)-1,3-thiazol-2-yl]benzamide
Authors: Archana K. , Saravanan K. , Lakshmithendral K. , Kabilan S. , Selvanayagam S.
Published: May 2017

In the title compound, C25H22N2O2S, the methylphenyl rings are oriented with a dihedral angle of 19.4 (1)° with respect to each other. In the crystal, molecules are linkedviastrong N—H...O hydrogen bonds, which formC(11) chains propagating along [001]. In addition, weak C—H...O and C—H...π interactions are observed in the structure.
3,5-Dibromo-6-methylpyridin-2-amine
Authors: Krishna Murthy P. , Sreenivasa Rao R. , Suneetha V. , Giri L. , Suchetan P. A.
Published: May 2017

The title molecule, C6H6Br2N2, is almost planar (r.m.s. deviation for the non-H atoms = 0.012 Å). In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generateR22(8) loops.
Calculation of Lorentz force in planar EMAT for thickness measurement of steel plate
Authors: Tu Jun , Chen Tao , Xiong Zhi , Song Xiaochun , Huang Songling
Published: May 2017

Purpose

The aim of this paper is to better understand the generation and transmission mechanism of the electromagnetic acoustic transducer (EMAT).

Design/methodology/approach

A semi-analytical method was used to calculate the Lorentz force. Both the hypothetical magnetic field mirror method and the diffusion equation were adopted to solve the eddy current distribution by variables separation method in time domain. A three-dimension magnetostatic finite element model was used to calculate the static magnetic field and the relative permeability. And an experimental platform with a piezoelectric probe to generate and an EMAT to receive, the ultrasonic wave was set up to verify the distribution of the Lorentz force.

Findings

The Lorentz force at different time and in different positions of the steel plate can be easily calculated. The experimental results show a good agreement with the analytical results.

Originality/value

The accurate prediction of the Lorentz force provides an insight into the physical phenomenon of EMAT and a powerful tool to design optimum EMAT.
Reinforcement learning based PID controller design for LFC in a microgrid
Authors: Esmaeili Mehran , Shayeghi Hossein , Mohammad Nejad Hamid , Younesi Abdollah
Published: May 2017

Purpose

This paper aims to propose an improved reinforcement learning-based fuzzy-PID controller for load frequency control (LFC) of an island microgrid.

Design/methodology/approach

To evaluate the performance of the proposed controller, three different types of controllers including optimal proportional-integral-derivative (PID) controller, optimal fuzzy PID controller and the proposed reinforcement learning-based fuzzy-PID controller are compared. Optimal PID controller and classic fuzzy-PID controller parameters are tuned using Non-dominated Sorting Genetic Algorithm-II algorithm to minimize overshoot, settling time and integral square error over a wide range of load variations. The simulations are carried out using MATLAB/SIMULINK package.

Findings

Simulation results indicated the superiority of the proposed reinforcement learning-based controller over fuzzy-PID and optimal-PID controllers in the same operational conditions.

Originality/value

In this paper, an improved reinforcement learning-based fuzzy-PID controller is proposed for LFC of an island microgrid. The main advantage of the reinforcement learning-based controllers is their hardiness behavior along with uncertainties and parameters variations. Also, they do not need any knowledge about the system under control; thus, they can control any large system with high nonlinearities.
Analysis of AFPM machines with cylindrically shaped magnets using quasi-3D method
Authors: Rostami Naghi , Rostami Majid
Published: May 2017

Purpose

The purpose of this paper is the fast and accurate modelling of surface-mounted Axial-Flux Permanent-Magnet (AFPM) machines equipped with cylindrical magnets using quasi-3D approach. Furthermore, the accuracy of the method is improved by using leakage coefficient, saturation coefficient and an appropriate permeance function.

Design/methodology/approach

Quasi-3D approach is used for fast and accurate modelling of AFPM machines. Air-gap flux density distribution, induced back EMF, and produced cogging torque are calculated using the proposed method with reasonable accuracy.

Findings

The results obtained by quasi-3D approach compared to Finite-Element-Analyses (FEA) shows how accurate, fast and efficient this method is. It is proved that, this method can be successfully applied to evaluate the performance of the AFPM machines.

Originality/value

Effectiveness and accuracy of quasi-3D approach is assessed on different AFPM machines. Furthermore, to increase the accuracy of computations, the effects of the magnetic potential drop at iron parts of the machine are taken into account by using a saturation coefficient. Besides, the influence of the slot opening on the flux density distribution is taken into account by using an appropriate relative permeance function.
GPU-based parallelization for bubble mesh generation
Authors: Dinh Van Quang , Marechal Yves
Published: May 2017

Purpose

In FEM computations, the mesh quality improves the accuracy of the approximation solution and reduces the computation time. The dynamic bubble system meshing technique can provide high-quality meshes, but the packing process is time-consuming. This paper aims to improve the running time of the bubble meshing by using the advantages of parallel computing on graphics processing unit (GPU).

Design/methodology/approach

This paper is based on the analysis of the processing time on CPU. A massively parallel computing-based CUDA architecture is proposed to improve the bubble displacement and database updating. Constraints linked to hardware considerations are taken into account. Finally, speedup factors are provided on test cases and real scale examples.

Findings

The numerical experiences show the efficiency of parallel performance reaches a speedup of 35 compared to the serial implementation.

Research limitations/implications

This contribution is so far limited to two-dimensional (2D) geometries although the extension to three-dimension (3D) is straightforward regarding the meshing technique itself and the GPU implementation. The authors’ works are based on a CUDA environment which is widely used by developers. C\C++ and Java were the programming languages used. Other languages may of course lead to slightly different implementations.

Practical implications

This approach makes it possible to use bubble meshing technique for both initial design and optimization, as excellent meshes can be built in few seconds.

Originality/value

Compared to previous works, this contribution shows that the scalability of the bubble meshing technique needs to solve two key issues: reach a T(N) global cost of the implementation and reach a very fast size map interpolation strategy.
A simple turn-on and turn-off angles searching method for copper loss minimization of the switched reluctance motor
Authors: Chen Hai-Jin , Li Jin-Yang
Published: May 2017

Purpose

The purpose of this paper is to present a simple and effective method to search the optimal turn-on and turn-off angles on-line for the control of the switched reluctance motor (SRM). The optimal turn-on and turn-off angles are defined as the ones that can meet torque production requirements with minimum copper loss.

Design/methodology/approach

The optimal turn-on and turn-off angles are first defined based on the analysis of the SRM losses and torque production principles. Then the algorithm for optimal angles searching is developed, and the searching parameters are determined through analytical computation. The optimal angles are approached on-line with iterative process. Simulation and experiments are finally performed to verify the proposed method.

Findings

The presented method can meet torque production requirements while copper loss is minimized. The optimal turn-on and turn-off angles are generally approached within five phase cycles for most of the SRM operation modes. Furthermore, the SRM drive system using the presented method exhibits good dynamics during starting and sudden load operations.

Practical implications

The presented method is simple, and implementation of it is easy. It is an eligible candidate for industrial applications where energy conversion efficiency is crucial.

Originality/value

The optimal turn-off angle definition that considers both torque production and copper loss minimization is proposed. The turn-on and turn-off angles are searched independently on-line with little SRM geometrical information. The searching steps are derived through analytical computation and qualitative analysis so that both the searching speed and algorithm convergence are balanced.