bluuebunny/crossref_metadata_2025 huggingface dataset:
Wind turbine transformer improved design method entailing resonance blocking
Authors: Elhaminia Pedram , Vakilian Mehdi , Lehtonen Matti
Published: July 2018

A wind turbine transformer resonance can occur due to high frequency transients at its terminal i.e.; under its energization through a length of cable. Occurrence of resonance can be addressed by a sophisticated transformer design procedure. The goal is to obtain an optimum design capable of controlling the frequency response of the winding in such a way to avoid occurrence of any resonance under transient conditions. Three insulation clearances parameters which are employed for the wind turbine transformer winding design have been investigated in design of a (800 kVA, 690/20,000 V) wind turbine transformer to determine effect of their variation on its frequency response. It is shown that the best way to control the frequency response is to adjust the distance between LV and HV windings while maintaining other clearances as short as possible; realizing limitations enforced by other insulation constraints. Multiple‐design algorithm is also investigated and found to be effective in control of the amplification factor under resonance frequency condition. Finally a 20 kV/690 V–400 kVA dry type wind turbine transformer is employed to verify the promising features of this design methodology, through comparison of the frequency responses of the real transformer against the model.
Position‐sensorless adaptive positioning control system for IPMSMs
Authors: Kawamura Naoki , Hasegawa Masaru , Liu Kang‐Zhi , Zanma Tadanao
Published: July 2018

Position‐sensorless positioning control system of interior permanent magnet synchronous motors (IPMSMs) has been energetically researched for high reliability and cost reduction. To achieve fast response of positioning servo systems, accurate parameters of IPMSMs are required. The parameters vary due to temperature and/or ageing, which results in degradation of the positioning control performance. Thus, this study proposes a position‐sensorless adaptive positioning control system for IPMSMs using the dynamic certainty equivalence principle for stable parameter identification. In addition, comb filters are used for fast estimation instead of low‐pass filters. Experiments are demonstrated to validate the effectiveness and the feasibility of the proposed method.
Extensive simulation of fibre non‐linearity mitigation in a CO‐OFDM‐WDM long‐haul communication system
Authors: Mhatli Sofien , Mrabet Hichem , Amari Abdelkerim
Published: July 2018

In this study, a performance comparison of fibre non‐linearity mitigation is performed in the context of 10 and 20 Gb/s coherent optical orthogonal frequency‐division multiplexing and wavelength division multiplexing (CO‐OFDM‐WDM). The authors compare two regression methods based on the third‐order Volterra series and least mean square algorithm in terms of the bit error rate (BER) for different transmission distances and modulation formats. They also evaluate the BER as a function of the number of OFDM subcarriers for the Volterra‐based non‐linear equaliser (VNLE). In addition, by increasing the order of the VNLE from third‐order to fifth‐order series, a significant increase of performance is obtained for 100 Gb/s CO‐OFDM‐WDM system. Likewise, a comparison study of 16‐QAM 40 Gb/s CO‐OFDM system is performed as a function of Q‐factor for support vector machine, Volterra equaliser and linear equaliser, respectively.
Sulphur-bearing molecules in AGB stars
Authors: Danilovich T. , Ramstedt S. , Gobrecht D. , Decin L. , De Beck E. , Olofsson H.
Published: July 2018

Context.Sulphur has long been known to form different molecules depending on the chemical composition of its environment. More recently, the sulphur-bearing molecules SO and H2S have been shown to behave differently in oxygen-rich asymptotic giant branch (AGB) circumstellar envelopes of different densities.

Aims.By surveying a diverse sample of AGB stars for CS and SiS emission, we aim to determine in which environments these sulphur-bearing molecules most readily occur. We include sources with a range of mass-loss rates and carbon-rich, oxygen-rich, and mixed S-type chemistries. Where these molecules are detected, we aim to determine their CS and SiS abundances.

Methods.We surveyed 20 AGB stars of different chemical types using the APEX telescope, and combined this with an IRAM 30 m and APEX survey of CS and SiS emission towards over 30 S-type stars. For those stars with detections, we performed radiative transfer modelling to determine abundances and abundance distributions.

Results.We detect CS towards all the surveyed carbon stars, some S-type stars, and the highest mass-loss rate oxygen-rich stars, (Ṁ≥ 5 × 10−6M⊙ yr−1). SiS is detected towards the highest mass-loss rate sources of all chemical types (Ṁ≥ 8 × 10−7M⊙ yr−1). We find CS peak fractional abundances ranging from ~4 × 10−7to ~2 × 10−5for the carbon stars, from ~3 × 10−8to ~1 × 10−7for the oxygen-rich stars, and from ~1 × 10−7to ~8 × 10−6for the S-type stars. We find SiS peak fractional abundances ranging from ~9 × 10−6to ~2 × 10−5for the carbon stars, from ~5 × 10−7to ~2 × 10−6for the oxygen-rich stars, and from ~2 × 10−7to ~2 × 10−6for the S-type stars.

Conclusions.Overall, we find that wind density plays an important role in determining the chemical composition of AGB circumstellar envelopes. It is seen that for oxygen-rich AGB stars both CS and SiS are detected only in the highest density circumstellar envelopes and their abundances are generally lower than for carbon-rich AGB stars by around an order of magnitude. For carbon-rich and S-type stars SiS was also only detected in the highest density circumstellar envelopes, while CS was detected consistently in all surveyed carbon stars and sporadically among the S-type stars.
Depletion of 15N in the center of L1544: Early transition from atomic to molecular nitrogen?
Authors: Furuya K. , Watanabe Y. , Sakai T. , Aikawa Y. , Yamamoto S.
Published: July 2018

We performed sensitive observations of the N15ND+(1–0) and 15NND+(1–0) lines toward the prestellar core L1544 using the IRAM 30 m telescope. The lines are not detected down to 3σ levels in 0.2 km s−1 channels of ~6 mK. The non-detection provides the lower limit of the 14N/15N ratio for N2D+ of ~700–800, which is much higher than the elemental abundance ratio in the local interstellar medium of ~200–300. The result indicates that N2 is depleted in 15N in the central part of L1544, because N2D+ preferentially traces the cold dense gas, and because it is a daughter molecule of N2. In situ chemistry is probably not responsible for the 15N depletion in N2; neither low-temperature gas phase chemistry nor isotope selective photodissociation of N2 explains the 15N depletion; the former prefers transferring 15N to N2, while the latter requires the penetration of interstellar far-ultraviolet (FUV) photons into the core center. The most likely explanation is that 15N is preferentially partitioned into ices compared to 14N via the combination of isotope selective photodissociation of N2 and grain surface chemistry in the parent cloud of L1544 or in the outer regions of L1544, which are not fully shielded from the interstellar FUV radiation. The mechanism is most efficient at the chemical transition from atomic to molecular nitrogen. In other words, our result suggests that the gas in the central part of L1544 has previously gone trough the transition from atomic to molecular nitrogen in the earlier evolutionary stage, and that N2 is currently the primary form of gas-phase nitrogen.
Tempered fractional multistable motion and tempered multifractional stable motion
Authors: Fan Xiequan , Lévy Véhel Jacques
Published: July 2018

This work defines two classes of processes, that we term tempered fractional multistable motion and tempered multifractional stable motion. They are extensions of fractional multistable motion and multifractional stable motion, respectively, obtained by adding an exponential tempering to the integrands. We investigate certain basic features of these processes, including scaling property, tail probabilities, absolute moment, sample path properties, pointwise Hölder exponent, Hölder continuity of quasi norm, (strong) localisability and semi-long-range dependence structure. These processes may provide useful models for data that exhibit both dependence and varying local regularity/intensity of jumps.
Evaluation eines neuen elektronischen Handmess geräts zur Messung von β-Hydroxybutyrat bei Milchkühen
Authors: Mahrt A. , Burfeind O. , Voigtsberger R. , Müller A. , Heuwieser W.
Published: July 2018

Gegenstand und Ziel: Die subklinische Ketose (SCK), eine weitverbreitete Stoffwechselkrankheit frischlaktierender Milchkühe, ist definiert durch das Auftreten erhöhter Mengen zirkulierender Ketonkörper bei Fehlen klinischer Symptome. Daher beschränken sich die Möglichkeiten der Diagnostik auf den Nachweis dieser Ketonkörper in verschiedenen Körperflüssigkeiten. Ziel der Studie war die Evaluation eines neuen elektronischen mobilen Messgeräts (NovaVet) zur Messung von β-Hydroxybutyrat (BHB) im Nativblut von Milchkühen. Material und Methoden: Anhand von Blutproben von 155 laktierenden Milchkühen erfolgte ein Vergleich zwischen den mit dem Gerät ermittelten und den in einem kommerziellen Labor gemessenen BHB-Konzentrationen. Zur Auswertung wurden der Rangkorrelationskoeffizient nach Spearman bestimmt, ein Wilcoxon-Test durchgeführt und die gepaarten Messwerte nach Bland und Altman graphisch dargestellt. Ferner wurden für das Gerät spezifische BHB-Grenzwerte im Vergleich zu international anerkannten Grenzwerten zur Diagnose einer SCK mithilfe einer Receiver-Operating-Characteristic(ROC)-Analyse ermittelt und die entsprechenden Testcharakteristika bestimmt. Ergebnisse: Zwischen den vom Gerät und den im Labor gemessenen BHB-Konzentrationen bestand eine hohe Korrelation (rs = 0,87; p < 0,05). Die vom Gerät (Median 1,0 mmol/l; Interquartilsabstand [IQR] 0,7–1,3 mmol/l) und im Labor (Median 0,9 mmol/l; IQR 0,7–1,1 mmol/l) gemessenen BHB-Konzentrationen differierten (Median 0,0 mmol/l; IQR –0,1 bis 0,2 mmol/l; p < 0,05). Mit dem Gerät konnte eine SCK bei einem Grenzwert von 1,2 mmol/l BHB mit einer Sensitivität von 97% und einer Spezifität von 82% diagnostiziert werden. Als Goldstandard diente der Laborwert. Schlussfolgerung und klinische Relevanz: Das BHB-Messgerät zeigte eine gute Übereinstimmung mit dem Labor und gute Testeigenschaften. Seine geringfügige Messabweichung im Vergleich zum Labor kann unter praktischen Bedingungen vernachlässigt werden, doch muss mit einer gewissen Anzahl falsch als erkrankt diagnostizierter Tiere gerechnet werden. Das Gerät kann für die Dia gnostik der SCK beim Rind empfohlen werden.
In-clinic laboratory diagnosis of canine babesiosis (Babesia canis canis) for veterinary practitioners in Central Europe
Authors: Leschnik M. , Hooijberg E. , Tichy A. , Leidinger E. , Kirtz G.
Published: July 2018

Objective: Haematological changes in dogs and climatic conditions favourable for the vector may assist in the quick in-house diagnosis of canine babesiosis. Material and methods: Blood samples from 358 dogs suspected to have canine babesiosis were evaluated. The diagnosis was confirmed in 113 dogs by detection of Babesia canis by microscopic examination of a stained blood smear using the concentration line technique. Results: Thrombocytopenia was present in all 113 dogs. Red blood cell count, packed cell volume and haemoglobin values were below the reference range in 62.8%, 61.1% and 46.0% of affected dogs, respectively. An increased reticulocyte count was apparent in five Babesia canis-positive dogs. Leukopenia, lymphopenia, neutropenia and monocytosis were present in 54.9%, 47.8%, 30.4% and 6.5% of the dogs, respectively. Evaluating haematological parameters by CARTanalysis revealed a predictive model (accuracy = 93.5%) for canine babesiosis, when using the leucocyte, thrombocyte, and reticulocyte count. Climatic conditions present at the most probable time of Babesia canis-infection accounted for biseasonal occurrence. Changes of climatic factors during the year influence the vector activity and in conclusion should highlight babesiosis in the ranking of differentials for veterinarians. Conclusion: The results demonstrate that a tentative diagnosis of canine babesiosis can be made based on typical haematological changes. The results recorded match well with the seasonality of the tick vector and were confirmed here by the month of sample submission.
Verabreichung von Antibiotika in Geflügelbeständen
Authors: Hafez H. M. , Böttner A. , Gangl A. , Hartmann K. , Kaske M. , Kehrenberg C. , Kietzmann M. , Klarmann D. , Klein G. , Luhofer G. , Schulz B. , Schwarz S. , Sigge C. , Waldmann K.-H. , Wallmann J. , Werckenthin C. , Richter A. ,   Arbeitsgruppe „Antibiotikaresistenz” der Deutschen Veterinärmedizinischen Gesellschaft e. V.
Published: July 2018

Aus Gründen der Praktikabilität kann auf eine orale Medikation von Antibiotika zur Behandlung bakterieller Erkrankungen in Geflügelbeständen nicht verzichtet werden. Die Verabreichung von Antibiotika über das Futter oder das Trinkwasser ist jedoch mit vielen Problemen behaftet, wie Unterdosierung und Kontamination der Stalleinrichtungen, die eine Selektion von Antibiotikaresistenzen begünstigen. Auch die eingeschränkte Verfügbarkeit zugelassener Arzneimittel für verschiedene Spezies des Wirtschaftsgeflügels erschwert die Therapie bakterieller Erkrankungen in der Geflügelpraxis. Dieser Beitrag soll einen Überblick über die Probleme im Praxisalltag und mögliche Lösungsansätze geben.
Connections and dynamical trajectories in generalised Newton-Cartan gravity. II. An ambient perspective
Authors: Bekaert Xavier , Morand Kevin
Published: July 2018

Connections compatible with degenerate metric structures are known to possess peculiar features: on the one hand, the compatibility conditions involve restrictions on the torsion; on the other hand, torsionfree compatible connections are not unique, the arbitrariness being encoded in a tensor field whose type depends on the metric structure. Nonrelativistic structures typically fall under this scheme, the paradigmatic example being a contravariant degenerate metric whose kernel is spanned by a one-form. Torsionfree compatible (i.e., Galilean) connections are characterised by the gift of a two-form (the force field). Whenever the two-form is closed, the connection is said Newtonian. Such a nonrelativistic spacetime is known to admit an ambient description as the orbit space of a gravitational wave with parallel rays. The leaves of the null foliation are endowed with a nonrelativistic structure dual to the Newtonian one, dubbed Carrollian spacetime. We propose a generalisation of this unifying framework by introducing a new non-Lorentzian ambient metric structure of which we study the geometry. We characterise the space of (torsional) connections preserving such a metric structure which is shown to project to (respectively, embed) the most general class of (torsional) Galilean (respectively, Carrollian) connections.
In vitro assessment of ruminal fermentation, digestibility and methane production of three species of Desmanthus for application in northern Australian grazing systems
Authors: Vandermeulen Sophie , Singh Sultan , Ramírez-Restrepo Carlos Alberto , Kinley Robert D. , Gardiner Christopher P. , Holtum Joseph A. M. , Hannah Iain , Bindelle Jérôme
Published: July 2018

Three species of Desmanthus adapted to the heavy clay soils of northern Australia were studied to determine their nutritive value and effects on in vitro fermentation with rumen fluid, compared with Rhodes grass (Chloris gayana) hay. Leaves and stems of D. leptophyllus cv. JCU 1, D. virgatus cv. JCU 2 and D. bicornutus cv. JCU 4 were collected in summer, winter and spring of 2014 and analysed for chemical composition. Apparent digestibility as in vitro organic matter digestibility (IVD-OM) and fermentation parameters including methane (CH4) production were measured during 72-h fermentations using rumen fluid from steer donors grazing tropical grasses and legumes. Desmanthus bicornutus was on average more digestible than both D. leptophyllus and D. virgatus at 24, 48 and 72 h of incubation. This species also demonstrated an anti-methanogenic potential, in particular when harvested in summer with a reduction in CH4 production of 26% compared with Rhodes grass hay after 72 h of incubation. At this time point, D. leptophyllus produced higher volatile fatty acids (VFA per g of organic matter fermented) compared with the other forages. This legume also reduced the CH4 production up to 36% compared with the Rhodes grass hay reference. However, D. leptophyllus showed lower IVD-OM. Overall, Desmanthus species produced lower in vitro CH4 and lower volatile fatty acids concentration compared with the reference grass hay. These effects may be due to presence of secondary compounds such as hydrolysable tannins, condensed tannins and/or their combination in Desmanthus species. The IVD-OM was influenced by the season after 72 h of incubation; the digestibility was higher in plants collected in spring. This study suggests that contrasting fermentative profiles in Desmanthus cultivars may offer the opportunity to reduce the greenhouse gas contribution of the beef industry. The next step in demonstration of these promising in vitro results is demonstration of Desmanthus in vivo as proof of concept confirming the productivity and CH4 reduction ability of these legumes in the pastoral systems of northern Australia.
NIH funding longevity by gender
Authors: Hechtman Lisa A. , Moore Nathan P. , Schulkey Claire E. , Miklos Andrew C. , Calcagno Anna Maria , Aragon Richard , Greenberg Judith H.
Published: July 2018

Significance

Diversity of the biomedical workforce is essential to the scientific enterprise, yet women remain underrepresented in academic positions in biomedical sciences and compose less than one-third of National Institutes of Health (NIH) research grantees. We explored NIH grant support as a proxy for participation in academic research. We found that women had similar funding longevity as men after they received their first major NIH grants, contradicting the common assumption that across all career stages, women experience accelerated attrition compared with men. Despite longevity similarities, women composed only 31% of grantees in our analysis. This discrepancy in grantee demographics suggests that efforts may be best directed toward encouraging women to enter academia and supporting their continued grant submissions.
Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan
Authors: Arranz-Otaegui Amaia , Gonzalez Carretero Lara , Ramsey Monica N. , Fuller Dorian Q. , Richter Tobias
Published: July 2018

Significance

Despite being one of the most important foodstuffs consumed in the modern world, the origins of bread are still largely unknown. Here we report the earliest empirical evidence for the preparation of bread-like products by Natufian hunter-gatherers, 4,000 years before the emergence of the Neolithic agricultural way of life. The discovery of charred food remains has allowed for the reconstruction of the
chaîne opératoire
for the early production of bread-like products. Our results suggest the use of the wild ancestors of domesticated cereals (e.g. wild einkorn) and club-rush tubers to produce flat bread-like products. Cereal-based meals such as bread probably become staples when Neolithic farmers started to rely on the cultivation of domesticated cereal species for their subsistence.
Microstructural engineering and strength-impact toughness prediction in ultra-low carbon bainitic steel
Authors: Sk Md. Basiruddin , Chakrabarti Debalay , Chatterjee S.
Published: July 2018

The strength–toughness combination of an ultra-low carbon, low alloyed ‘air-cooled’ steel has been enhanced by developing and refining the granular bainite (GB) structure. Suitable alloy design and thermo-mechanical treatment involving forging, austenitisation (950–1150°C) and air-cooling resulted in the formation of GB matrix along with small islands of martensite–austenite constituents and allotriomorphic ferrite grains. Microstructural characterisation and phase transformation behaviour were studied by scanning electron microscopy and electron backscattered diffraction analysis. The effect of microstructural parameters on the strength-impact toughness combination was investigated. The steel showed an exceptionally low yield ratio, which is beneficial for seismic resistance application.

GRAPHICAL ABSTRACT
Perspectives of applied collaborative sport science research within professional team sports
Authors: Malone James J. , Harper Liam D. , Jones Ben , Perry John , Barnes Chris , Towlson Chris
Published: July 2018

The purpose of the study was to examine the perspectives of both academics and practitioners in relation to forming applied collaborative sport science research within team sports. Ninety‐three participants who had previously engaged in collaborative research partnerships within team sports completed an online survey which focused on motivations and barriers for forming collaborations using blinded sliding scale (0–100) and rank order list. Research collaborations were mainly formed to improve the team performance (Academic: 73.6 ± 23.3; Practitioner: 84.3 ± 16.0; effect size (ES = 0.54), small). Academics ranked journal articles’ importance significantly higher than practitioners did (Academic: Mrank = 53.9; Practitioner: 36.0; z = −3.18, p = .001, p < q). However, practitioners rated one‐to‐one communication as more preferential (Academic: Mrank = 41.3; Practitioner 56.1; z = −2.62, p = .009, p < q). Some potential barriers were found in terms of staff buy in (Academic: 70.0 ± 25.5; Practitioner: 56.8 ± 27.3; ES = 0.50, small) and funding (Academic: 68.0 ± 24.9; Practitioner: 67.5 ± 28.0; ES = 0.02, trivial). Both groups revealed low motivation for invasive mechanistic research (Academic: 36.3 ± 24.2; Practitioner: 36.4 ± 27.5; ES = 0.01, trivial), with practitioners have a preference towards ‘fast’ type research. There was a general agreement between academics and practitioners for forming research collaborations. Some potential barriers still exist (e.g. staff buy in and funding), with practitioners preferring ‘fast’ informal research dissemination compared to the ‘slow’ quality control approach of academics.
Influence of upright versus time trial cycling position on determination of critical power and W′ in trained cyclists
Authors: Kordi Mehdi , Fullerton Chris , Passfield Louis , Parker Simpson Len
Published: July 2018

Body position is known to alter power production and affect cycling performance. The aim of this study was to compare mechanical power output in two riding positions, and to calculate the effects on critical power (CP) and W′ estimates. Seven trained cyclists completed three peak power output efforts and three fixed‐duration trial (3‐, 5‐ and 12‐min) riding with their hands on the brake lever hoods (BLH), or in a time trial position (TTP). A repeated‐measures analysis of variance showed that mean power output during the 5‐min trial was significantly different between BLH and TTP positions, resulting in a significantly lower estimate of CP, but not W′, for the TTP trial. In addition, TTP decreased the performance during each trial and increased the percentage difference between BLH and TTP with greater trial duration. There were no differences in pedal cadence or heart rate during the 3‐min trial; however, TTP results for the 12‐min trial showed a significant fall in pedal cadence and a significant rise in heart rate. The findings suggest that cycling position affects power output and influences consequent CP values. Therefore, cyclists and coaches should consider the cycling position used when calculating CP.
Rwanda’s post-genocide foreign aid relations: Revisiting notions of exceptionalism
Authors: Desrosiers Marie-Eve , Swedlund Haley J
Published: July 2018

This article studies donor–government relations in Rwanda since the end of the 1994 genocide. The notion that Rwanda enjoyed or enjoys exceptional relations with donors because of guilt regarding their inaction during the genocide is widespread in the literature and in policy circles. To assess this myth, the article first looks at aid trends for Rwanda and comparable countries, and then takes an in-depth look at aid relations with two average-size donors: Canada and the Netherlands. It demonstrates that Rwanda is not as exceptional as claimed, but instead should be considered one amongst a group of exceptional cooperation partners. The article further highlights that donors operated informally immediately following the genocide, but soon renormalized aid relations, and that there has always been a complex set of rationales determining donor behaviour regarding Rwanda.
Uncontrolled Hypertension Is Common in Glaucoma Clinics
Authors: Varadaraj Varshini , Vardhan Ashok , Mudie Lucy I , LaBarre Sophie , Ong Yuhan , Wang Bingsong , Sherrod Cheryl , Friedman David S
Published: July 2018

BACKGROUND

To determine the magnitude of uncontrolled hypertension and smoking among patients visiting an eye clinic, and ascertain if referral to care providers is effective.

METHODS

Information on smoking status and blood pressure (BP) was collected among patients ≥18 years visiting an eye clinic. Those with high BP (systolic: ≥140 mm Hg and/or diastolic: ≥90 mm Hg) received a pamphlet on harms of hypertension on vision and were referred to a primary care physician. Smokers received a pamphlet on negative effects of smoking on vision and were offered referral to a tobacco quitline. Patients were followed up for referral outcome within 10 weeks from screening.

RESULTS

Screening: A total of participants screened included 140 (29.5%) with high BP and 31 (6.6%) current smokers. In the high BP group, 92 (66%) subjects were previously diagnosed with hypertension. Follow-up: Of the 140 participants with elevated BP, 84 (60%) responded to follow-up. Among these 84 participants, 57 (67.9%) had consulted primary care, of whom 5 (8.8%) reported being newly diagnosed with hypertension, and 11 (19.3%) reported a change in their antihypertensive prescription. Among the 31 smokers, 24 (77.4%) were willing for quitline referral. Sixteen (66.7%) of these patients responded to follow-up, 8 (50%) of whom reported participation in a smoking-cessation program with 1 patient (6.3%) successfully quitting smoking.

CONCLUSIONS

Nearly one-third of patients attending an eye clinic had elevated BP, and a smaller, but substantial, number of patients were current smokers. Eye clinics may serve as point for identification and referral of these patients with unmet needs.
Racial Residential Segregation and Hypertensive Disorder of Pregnancy Among Women in Chicago: Analysis of Electronic Health Record Data
Authors: Mayne Stephanie L , Yellayi Disha , Pool Lindsay R , Grobman William A , Kershaw Kiarri N
Published: July 2018

BACKGROUND

Racial residential segregation is associated with higher rates of chronic hypertension, as well as greater risk of preterm birth and low birthweight. However, few studies have examined associations between segregation and hypertensive disorder of pregnancy (HDP).

METHODS

Electronic health records from 4,748 singleton births among non-Hispanic black women at Prentice Women’s Hospital in Chicago, IL (2009–2013) were geocoded to the census tract level. Residential segregation was measured using the Gi* statistic, a z-score measuring the extent to which each individual’s neighborhood composition deviates from the composition of the larger surrounding area. Segregation was categorized as low (z < 0), medium (z = 0–1.96) or high (z > 1.96). We estimated cross-sectional associations of segregation with HDP using multilevel logistic regression models with census tract random intercepts. Models adjusted for neighborhood poverty and maternal characteristics. We also examined effect modification by neighborhood poverty.

RESULTS

Overall, 27.2% of women lived in high segregation, high-poverty neighborhoods. Racial residential segregation was not associated as a main effect with HDP in models adjusting for neighborhood poverty and maternal characteristics. However, at higher levels of neighborhood poverty (>20%), women living in high- and medium-segregated neighborhoods had greater odds of HDP relative to those in low-segregation neighborhoods (P interaction: 0.002).

CONCLUSIONS

In this sample of non-Hispanic black women in Chicago, racial residential segregation was associated with greater prevalence of HDP among those living in higher poverty neighborhoods. Understanding sources of heterogeneity in the relationship between segregation and health will help refine targeted intervention efforts to reduce disparities.
The Impact on Mortality and Societal Costs From Smoking Cessation in Aesthetic Plastic Surgery in the United States
Authors: Bloom Joshua A , Rashad Ramy , Chatterjee Abhishek
Published: July 2018

Background

It is common practice to require patients to stop smoking prior to elective plastic surgery procedures. Scarce research exists describing the impact on mortality and associated societal cost savings with regard to smoking cessation in aesthetic surgery.

Objectives

Our objective is to demonstrate that smoking cessation in anticipation for aesthetic surgery significantly reduces mortality and increases societal cost savings.

Methods

We performed a systematic literature review of 5 common aesthetic procedures (reduction mammaplasty, breast augmentation, facelift, rhinoplasty, and abdominoplasty) to determine patient smoking rates and subsequent recidivism. Sensitivity analyses estimated life years saved using ranges of recidivism from our literature review and assessed total lifetime savings, including direct and productivity costs, while adjusting for inflation (3%) and interest (5%). One life saved was equated to 45 life years saved.

Results

Between May 2008 and May 2013, 7867 patients stopped smoking prior to undergoing aesthetic plastic surgery procedures. Assuming a reported recidivism rate of 68%, smoking cessation prior to aesthetic plastic surgery is associated with 429 lives saved and a total lifetime savings of $524.4 million over the five-year period. Total lives saved ranged from 214 (84% recidivism) to 885 (34% recidivism), and total lifetime cost savings ranged from $262.2 million (84% recidivism) to $1.08 billion (34% recidivism).

Conclusions

Presently, smoking cessation before aesthetic surgery significantly saves patient lives with yearly $104.9 million of societal cost savings in the United States. Future reductions in the presently high recidivism rate would lead to additional lives saved and reduced societal costs.

Level of Evidence: 4
Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies
Authors: Ghoshdastidar Debostuti , Bansal Manju
Published: July 2018

DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes
Authors: Parca Luca , Ariano Bruno , Cabibbo Andrea , Paoletti Marco , Tamburrini Annalaura , Palmeri Antonio , Ausiello Gabriele , Helmer-Citterich Manuela
Published: July 2018

Motivation

Signaling and metabolic pathways are finely regulated by a network of protein phosphorylation events. Unraveling the nature of this intricate network, composed of kinases, target proteins and their interactions, is therefore of crucial importance. Although thousands of kinase-specific phosphorylations (KsP) have been annotated in model organisms their kinase-target network is far from being complete, with less studied organisms lagging behind.

Results

In this work, we achieved an automated and accurate identification of kinase domains, inferring the residues that most likely contribute to peptide specificity. We integrated this information with the target peptides of known human KsP to predict kinase-specific interactions in other eukaryotes through a deep neural network, outperforming similar methods. We analyzed the differential conservation of kinase specificity among eukaryotes revealing the high conservation of the specificity of tyrosine kinases. With this approach we discovered 1590 novel KsP of potential clinical relevance in the human proteome.

Availability and implementation

http://akid.bio.uniroma2.it

Supplementary information

Supplementary data are available at Bioinformatics online.
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
Authors: Schmidt Florian , List Markus , Cukuroglu Engin , Köhler Sebastian , Göke Jonathan , Schulz Marcel H
Published: July 2018

Motivation

International consortia such as the Genotype-Tissue Expression (GTEx) project, The Cancer Genome Atlas (TCGA) or the International Human Epigenetics Consortium (IHEC) have produced a wealth of genomic datasets with the goal of advancing our understanding of cell differentiation and disease mechanisms. However, utilizing all of these data effectively through integrative analysis is hampered by batch effects, large cell type heterogeneity and low replicate numbers. To study if batch effects across datasets can be observed and adjusted for, we analyze RNA-seq data of 215 samples from ENCODE, Roadmap, BLUEPRINT and DEEP as well as 1336 samples from GTEx and TCGA. While batch effects are a considerable issue, it is non-trivial to determine if batch adjustment leads to an improvement in data quality, especially in cases of low replicate numbers.

Results

We present a novel method for assessing the performance of batch effect adjustment methods on heterogeneous data. Our method borrows information from the Cell Ontology to establish if batch adjustment leads to a better agreement between observed pairwise similarity and similarity of cell types inferred from the ontology. A comparison of state-of-the art batch effect adjustment methods suggests that batch effects in heterogeneous datasets with low replicate numbers cannot be adequately adjusted. Better methods need to be developed, which can be assessed objectively in the framework presented here.

Availability and implementation

Our method is available online at https://github.com/SchulzLab/OntologyEval.

Supplementary information

Supplementary data are available at Bioinformatics online.
DeepDTA: deep drug–target binding affinity prediction
Authors: Öztürk Hakime , Özgür Arzucan , Ozkirimli Elif
Published: July 2018

Motivation

The identification of novel drug–target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein–ligand interactions assume a continuum of binding strength values, also called binding affinity and predicting this value still remains a challenge. The increase in the affinity data available in DT knowledge-bases allows the use of advanced learning techniques such as deep learning architectures in the prediction of binding affinities. In this study, we propose a deep-learning based model that uses only sequence information of both targets and drugs to predict DT interaction binding affinities. The few studies that focus on DT binding affinity prediction use either 3D structures of protein–ligand complexes or 2D features of compounds. One novel approach used in this work is the modeling of protein sequences and compound 1D representations with convolutional neural networks (CNNs).

Results

The results show that the proposed deep learning based model that uses the 1D representations of targets and drugs is an effective approach for drug target binding affinity prediction. The model in which high-level representations of a drug and a target are constructed via CNNs achieved the best Concordance Index (CI) performance in one of our larger benchmark datasets, outperforming the KronRLS algorithm and SimBoost, a state-of-the-art method for DT binding affinity prediction.

Availability and implementation

https://github.com/hkmztrk/DeepDTA

Supplementary information

Supplementary data are available at Bioinformatics online.
DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications
Authors: Sekhon Arshdeep , Singh Ritambhara , Qi Yanjun
Published: July 2018

Motivation

Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing differential gene regulation. Recent studies either failed to capture combinatorial effects on differential prediction or primarily only focused on cell type-specific analysis. In this paper we develop a novel attention-based deep learning architecture, DeepDiff, that provides a unified and end-to-end solution to model and to interpret how dependencies among histone modifications control the differential patterns of gene regulation. DeepDiff uses a hierarchy of multiple Long Short-Term Memory (LSTM) modules to encode the spatial structure of input signals and to model how various histone modifications cooperate automatically. We introduce and train two levels of attention jointly with the target prediction, enabling DeepDiff to attend differentially to relevant modifications and to locate important genome positions for each modification. Additionally, DeepDiff introduces a novel deep-learning based multi-task formulation to use the cell-type-specific gene expression predictions as auxiliary tasks, encouraging richer feature embeddings in our primary task of differential expression prediction.

Results

Using data from Roadmap Epigenomics Project (REMC) for ten different pairs of cell types, we show that DeepDiff significantly outperforms the state-of-the-art baselines for differential gene expression prediction. The learned attention weights are validated by observations from previous studies about how epigenetic mechanisms connect to differential gene expression.

Availability and implementation

Codes and results are available at deepchrome.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hierarchical HotNet: identifying hierarchies of altered subnetworks
Authors: Reyna Matthew A , Leiserson Mark D M , Raphael Benjamin J
Published: July 2018

Motivation

The analysis of high-dimensional ‘omics data is often informed by the use of biological interaction networks. For example, protein–protein interaction networks have been used to analyze gene expression data, to prioritize germline variants, and to identify somatic driver mutations in cancer. In these and other applications, the underlying computational problem is to identify altered subnetworks containing genes that are both highly altered in an ‘omics dataset and are topologically close (e.g. connected) on an interaction network.

Results

We introduce Hierarchical HotNet, an algorithm that finds a hierarchy of altered subnetworks. Hierarchical HotNet assesses the statistical significance of the resulting subnetworks over a range of biological scales and explicitly controls for ascertainment bias in the network. We evaluate the performance of Hierarchical HotNet and several other algorithms that identify altered subnetworks on the problem of predicting cancer genes and significantly mutated subnetworks. On somatic mutation data from The Cancer Genome Atlas, Hierarchical HotNet outperforms other methods and identifies significantly mutated subnetworks containing both well-known cancer genes and candidate cancer genes that are rarely mutated in the cohort. Hierarchical HotNet is a robust algorithm for identifying altered subnetworks across different ‘omics datasets.

Availability and implementation

http://github.com/raphael-group/hierarchical-hotnet.

Supplementary information

Supplementary material are available at Bioinformatics online.
Automatic recognition of ligands in electron density by machine learning
Authors: Kowiel Marcin , Brzezinski Dariusz , Porebski Przemyslaw J , Shabalin Ivan G , Jaskolski Mariusz , Minor Wladek
Published: July 2018

Motivation

The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting.

Results

Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes.

Availability and implementation

Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob.

Supplementary information

Supplementary data are available at Bioinformatics online.
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Authors: Paradis Emmanuel , Schliep Klaus
Published: July 2018

After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for ‘big data’ (R’s long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.

Availability and implementation

ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.
Absolute quantitation of poly(R)-3-hydroxybutyric acid using spectrofluorometry in recombinant Escherichia coli
Authors: Rajankar Mayooreshwar P , Ravindranathan Sapna , Rajamohanan P R , Raghunathan Anu
Published: July 2018

Poly(R)-3-hydroxybutyric acid (PHB) is a biodegradable natural polymer produced by microorganisms and plants under nitrogen deprivation and physiological stress. Metabolic engineering and synthetic biology approaches are underway to develop strains that can produce PHB and its co-polymers. One of the major limitations to the scaling and success of strain development for biosynthesis of PHB is the absence of fast, accurate, quantitative and scalable methods to estimate PHB in polymer producing cells. In this study, a Nile red-based spectrofluorometric method is developed for absolute quantitation of PHB in recombinant Escherichia coli. The method is a modification of an existing Nile red-based method currently only used for relative quantitation. The two added steps of sonication and ethanol extraction increase the dynamic range of the assay and limit of detection/quantitation. Sonication of PHB standards provides uniform distribution of surface area to volume ratios. This ensures reproducibility and accuracy (lower %relative error) of quantitative staining of granules by Nile red even in a higher dynamic concentration range of 125–1000 µg/ml. Ethanolic extraction of the PHB bound Nile red allows higher recovery and accurate absolute quantitation. To reproduce high recovery and ensure accuracy and precision of the analytical method directly using cells, a protein digestion step was added. This accounted for fluorescence from over-expressed protein and resulted in screening of nonproducers of PHB amongst samples. Thus, the method developed is rapid, accurate, and reproducible, requires low sample volumes and processing compared to other conventional methods. This method is scalable to other PHA’s and diverse plastics.
Hybrid principal components analysis for region-referenced longitudinal functional EEG data
Authors: Scheffler Aaron , Telesca Donatello , Li Qian , Sugar Catherine A , Distefano Charlotte , Jeste Shafali , Şentürk Damla
Published: July 2018

Electroencephalography (EEG) data possess a complex structure that includes regional, functional, and longitudinal dimensions. Our motivating example is a word segmentation paradigm in which typically developing (TD) children, and children with autism spectrum disorder (ASD) were exposed to a continuous speech stream. For each subject, continuous EEG signals recorded at each electrode were divided into one-second segments and projected into the frequency domain via fast Fourier transform. Following a spectral principal components analysis, the resulting data consist of region-referenced principal power indexed regionally by scalp location, functionally across frequencies, and longitudinally by one-second segments. Standard EEG power analyses often collapse information across the longitudinal and functional dimensions by averaging power across segments and concentrating on specific frequency bands. We propose a hybrid principal components analysis for region-referenced longitudinal functional EEG data, which utilizes both vector and functional principal components analyses and does not collapse information along any of the three dimensions of the data. The proposed decomposition only assumes weak separability of the higher-dimensional covariance process and utilizes a product of one dimensional eigenvectors and eigenfunctions, obtained from the regional, functional, and longitudinal marginal covariances, to represent the observed data, providing a computationally feasible non-parametric approach. A mixed effects framework is proposed to estimate the model components coupled with a bootstrap test for group level inference, both geared towards sparse data applications. Analysis of the data from the word segmentation paradigm leads to valuable insights about group-region differences among the TD and verbal and minimally verbal children with ASD. Finite sample properties of the proposed estimation framework and bootstrap inference procedure are further studied via extensive simulations.