bluuebunny/crossref_metadata_2025 huggingface dataset:
Antenatal Testing for Women With Preexisting Medical Conditions Using Only the Ultrasonographic Portion of the Biophysical Profile
Authors: Zafman Kelly B. , Bruck Efrat , Rebarber Andrei , Saltzman Daniel H. , Fox Nathan S.
Published: August 2018

OBJECTIVE:

To report the utility of the ultrasonographic biophysical profile, which includes all the components of a biophysical profile minus the nonstress test, in women with maternal indications for antepartum surveillance.

METHODS:

We conducted a case series reviewing the records of all women at 32 weeks of gestation or greater with at least one indication for antenatal testing (per the American College of Obstetricians and Gynecologists) delivered by a single maternal–fetal medicine practice between 2006 and 2018. Indications included diabetes, hypertension, lupus, antiphospholipid syndrome, sickle cell disease, renal disease, heart disease, hyperthyroidism, isoimmunization, inherited thrombophilia, and prior intrauterine fetal demise. Weekly ultrasonographic biophysical profiles were initiated at 32 weeks of gestation. We calculated the test-positive rate, the percentage of women delivered for an abnormal ultrasonography biophysical profile, and the intrauterine fetal demise rate (false-negative rate).

RESULTS:

Nine hundred eighty-five women underwent 3,981 ultrasonographic biophysical profiles (four per woman; range 1–11). Sixteen women had an abnormal ultrasonographic biophysical profile, for a test positive rate of 1.6% (95% CI 1.0–2.6%) per woman, or 0.4% (95% CI 0.3–0.7%) per ultrasonographic biophysical profile. Of the 16 women with abnormal ultrasonographic biophysical profiles, 13 were delivered with good outcomes and three women had normal follow-up testing and uncomplicated deliveries at a later date. There were three women with intrauterine fetal demise (false-negative rate of 0.3%, 95% CI 0.1–0.9%). One woman with intrauterine fetal demise had a factor V Leiden mutation, fetal ventriculomegaly, and fetal growth restriction. The second woman with intrauterine fetal demise had advanced maternal age, a factor V Leiden mutation, and fetal growth restriction. The third woman with intrauterine fetal demise had class B diabetes. All three intrauterine fetal demises were diagnosed antepartum with an interval from normal ultrasonographic biophysical profile to intrauterine fetal demise of 7, 7, and 6 days, respectively.

CONCLUSION:

The use of ultrasonographic biophysical profile in a high-risk cohort is associated with a very low test-positive rate and a very low incidence of intrauterine fetal demise. In women with preexisting medical conditions that place them at higher risk for intrauterine fetal demise, ultrasonographic biophysical profile can be used for antenatal testing.
Hormone therapy in postmenopausal women associated with risk of stroke and venous thromboembolism: a population-based cohort study in Taiwan
Authors: Chang Wei-Chuan , Wang Jen-Hung , Ding Dah-Ching
Published: August 2018

Objective:

The aim of the study was to evaluate the risks and benefits of hormone therapy (HT) in postmenopausal women in Taiwan.

Methods:

A retrospective cohort study was conducted using the Taiwan National Health Insurance Research Database, a population-based healthcare claims dataset. Eligible women, aged 40 to 65, were matched 1:1 by age and menopause year to avoid confounding through imbalanced baseline characteristics among the two groups (2,491 pairs). The primary outcomes were acute coronary syndrome (ACS), venous thromboembolism (VTE), and ischemic stroke (IS).

Results:

Mean follow-up in the HT group was 30 months. Mean age of the HT group was 50 years. After adjusting for age, statin and anticoagulant use, hyperlipidemia, diabetes, and hypertension, the hazard ratios (95% CIs) for the HT group were increased: ACS, 3.73 (2.01-6.91); IS, 3.51 (2.41-5.11); and VTE, 2.51 (1.15-5.47).

Conclusions:

In postmenopausal Taiwanese women, HT may be associated with an increased risk of cardiovascular disease. Although the women in our population receiving HT were near menopausal age, their risk of cardiovascular disease was still higher than in the non-HT group.
WISDOM survey: attitudes and behaviors of physicians toward vulvar and vaginal atrophy (VVA) treatment in women including those with breast cancer history
Authors: Kingsberg Sheryl A. , Larkin Lisa , Krychman Michael , Parish Sharon J. , Bernick Brian , Mirkin Sebastian
Published: August 2018

Objective:

To evaluate and compare physicians’ behaviors and attitudes regarding vulvar and vaginal atrophy (VVA) treatment in menopausal women, including women with breast cancer, using an internet-based survey.

Methods:

The WISDOM survey queried obstetricians and gynecologists (OB/GYNs) and primary care physicians (PCPs) with 23 multipart questions assessing behaviors and attitudes towards VVA treatment.

Results:

Of 2,424 surveys sent, 945 (39%) responded and 644 (27%) were completed. Of the menopausal women seen by OB/GYNs and PCPs, 44% to 55% reported having VVA symptoms. Physicians prescribed VVA treatments primarily because of effectiveness. Only 34% of OB/GYNs and 17% of PCPs felt comfortable prescribing VVA therapies to women with a personal history of breast cancer. In general, the most common VVA treatment recommended by all was prescription therapy (49%; with or without other therapies) in the form of US Food and Drug Administration-approved vaginal estrogen creams. More OB/GYNs (72%) than PCPs (47%) disagreed that VVA was best treated with over the counter than prescription products. Out-of-pocket cost and fear of risks associated with estrogens were believed to be the main barriers for why women choose not to get treated and why they discontinue treatment.

Conclusions:

More OB/GYNs than PCPs prescribed VVA treatment, especially vaginal estrogens, for menopausal women, but both groups generally had similar attitudes and behaviors regarding VVA treatment. Physician comfort was low when prescribing to women with a history of breast cancer, despite women's health medical societies supporting vaginal estrogen use in women with a history of estrogen-dependent breast cancer who were unresponsive to nonhormonal therapies when offered in consultation with their oncologist.
Investigation of Corneal Astigmatism in Chinese Patients With Primary Angle Closure Disease
Authors: Zuo Chengguo , Gong Ruowen , Chen Weirong , Chen Chuyin , Su Jinai , Wei Kun , Gao Xinbo , Lin Mingkai , Ge Jian
Published: August 2018

Purpose:

The purpose of this study was to analyze the demographics and distribution of corneal astigmatism before lens extraction in patients with primary angle closure disease (PACD).

Methods:

Preoperative partial coherence interferometry was performed in patients with PACD. The demographic and biometric data, including corneal astigmatism and keratometry (K), were recorded.

Results:

The study comprised 808 cases (1001 eyes) with a mean age of 67.66±9.07 years, and the mean axial length was 22.55±0.89 mm. The mean corneal astigmatism was 1.08±0.78 diopter (D). Corneal astigmatism was between 0.25 D and 1.25 D in 66.50% of the eyes, 1.25 D or higher in 29.68% of the eyes and <0.25 D in 3.82% of the eyes. The corneal astigmatism of primary angle closure suspect (PACS), primary angle closure (PAC) and primary angle closure glaucoma (PACG) were 1.08±0.77 D, 0.98±0.62 D, and 0.89±0.69 D, respectively. In total, 50.60% of the eyes were classified as astigmatism against the rule (ATR), 28.69% of the eyes were with the rule, and 20.71% of the eyes were oblique. ATR astigmatism increased significantly with age (P<0.001). After matching, corneal astigmatism of PACD was 1.07±0.77 D, although it was statistically significantly higher than that of ARC (0.98±0.66 D, P=0.018), the 2 demonstrated no clinical difference.

Conclusions:

The results provide normative data of corneal astigmatism for PACD patients. Corneal astigmatism was mainly distributed between 0.25 D and 1.25 D. The findings largely concur with published results in age-related cataract subjects.
Factors Associated With Continued Smoking in Lebanese Patients With Acute Coronary Syndrome
Authors: Noureddine Samar , Massouh Angela
Published: August 2018

Background:

Smoking in patients with acute coronary syndrome (ACS) increases their risk for recurrent events and death.

Objectives:

The aim of this study was to describe the smoking trajectory among patients hospitalized with ACS and associated factors.

Methods:

Forty patients with ACS who were smokers were interviewed in the hospital about smoking history, nicotine dependence, depression, self-efficacy, and social support. Phone interviews at 1, 3, 6, and 12 months after discharge assessed smoking status and related factors.

Results:

Most patients (≥80%) were middle-aged married men, with high nicotine dependence (52.5%) and low self-efficacy for smoking cessation (mean [SD], 38.3 [27.19]) at baseline. Although 85% intended to quit after discharge, 62.5% continued smoking after 1 year. Persistent smoking was associated with lower self-efficacy (P < .01) and higher depression (P = .025).

Conclusion:

Smoking cessation intervention must start in the hospital and continue for 6 months. The program must target self-efficacy, manage depression, and involve the patient’s family.
Type 1 and Type 2 Autoimmune Pancreatitis
Authors: Negrelli Riccardo , Boninsegna Enrico , Avesani Giacomo , Zamboni Giulia A. , Brozzi Lorenzo , Frulloni Luca , Manfredi Riccardo , Pozzi Mucelli Roberto
Published: August 2018

Objectives

This study aimed to evaluate magnetic resonance imaging findings of autoimmune pancreatitis (AIP) and to find radiological patterns that could differentiate type 1 and type 2 AIP.

Methods

Eighty-four patients with diagnosis of AIP were enrolled. Image analysis included pancreatic signal intensity abnormalities, enhancement pattern, extrapancreatic involvement, and main pancreatic duct alterations.

Results

Pancreatic parenchyma resulted in hypointensity on T1-weighted images in 65 (98.5%) of 66 cases in type 1 and in 17 (94.5%) of 18 in type 2 (P > 0.05) and in hyperintensity on T2-weighted images in 41 (62%) of 66 and in 15 (83.4%) of 18, respectively (P > 0.05). Lesions were hypovascular in 64 (97%) of 66 cases in type 1 and in 16 (88.9%) of 18 in type 2 with delayed contrast retention in 56 (84.8%) of 66 and in 17 (94.5%) of 18, respectively (P > 0.05). Autoimmune cholangitis was found in 29 (43.9%) of 66 patients with type 1 and in 3 (16.7%) of 18 with type 2 (P = 0.02); renal involvement was observed in 20 (30.3%) of 66 and 1 (5.5%) of 18, respectively (P = 0.02). Both subtypes presented with multiple stenoses (P > 0.05). Dilation of upstream duct was more frequent in type 1 (P = 0.02).

Conclusions

Magnetic resonance imaging is useful in detecting extrapancreatic involvement, typically seen in type 1. Dilation of the upstream duct suggests type 1 AIP.
Ferroportin Disease Caused by a Heterozygous Variant p.Cys326Phe in the SLC40A1 Gene and the Efficacy of Therapeutic Phlebotomy in Children
Authors: Shimura Masaru , Nishimata Shigeo , Saito Naoko , Tsutsumi Norito , Suzuki Shinji , Morishima Yasuyuki , Kashiwagi Yasuyo , Numabe Hironao , Kawashima Hisashi
Published: August 2018

Therapeutic phlebotomy is recommended for treating hereditary hemochromatosis. However, the procedure and its efficacy for children remain unclear. We describe a young female patient with ferroportin disease, which was confirmed from excess iron deposition within hepatocytes and by identifying a heterozygous variant p.Cys326Phe in SLC40A1. She had been followed without phlebotomy. Liver histology at age 13 years revealed iron deposition progression. Phlebotomy was initiated and her iron markers and imaging findings improved without severe adverse effects. Therapeutic phlebotomy for children is effective and well-tolerated and should be considered as early as possible after a hemochromatosis diagnosis.
Reduced Fear-Conditioned Pain Modulation in Experienced Meditators: A Preliminary Study
Authors: Taylor Véronique A. , Roy Mathieu , Chang Luke , Gill Louis-Nascan , Mueller Christian , Rainville Pierre
Published: August 2018

Objective

Mindfulness-based practice is a form of cognitive/affective training that may help reduce suffering by attenuating maladaptive anticipatory processes. This study's objective was to examine the pain modulating impact of classical fear learning in meditation practitioners.

Methods

The hyperalgesic effects of pain expectation and uncertainty were assessed outside formal meditation in 11 experienced meditators (>1000 hours) compared with meditation-naive controls during a Pavlovian classical fear-conditioning paradigm involving two visual stimuli (CS+/CS−), one of which (CS+) co-terminated with a noxious electrical stimulus (unconditioned stimulus) on 50% of trials. A Rescorla-Wagner/Pearce-Hall hybrid model was fitted onto the conditioned skin conductance responses using computational modeling to estimate two learning parameters: expected shock probability and associability (i.e., uncertainty).

Results

Using a scale ranging between 0 (no pain) and 100 (extremely painful), meditators reported less pain (M = 19.9, SE = 5.1 for meditators, M = 32.4, SE = 2.4 for controls) but had comparable spinal motor responses (nociceptive flexion reflex) to the unconditioned stimulus. Multilevel mediation analyses revealed that meditators also exhibited reduced hyperalgesic effects of fear learning on higher-order pain responses but comparable effects on the nociceptive flexion reflex. These results suggest that mindfulness affects higher-order perceptual processes to a greater extent than from descending inhibitory controls. Furthermore, meditators showed reduced hyperalgesic effects of fear conditioning with no significant group difference in conditioned learning as evidenced by discriminative anticipatory skin conductance responses and learning parameters derived from computational modeling.

Conclusions

These results highlight potential mechanisms underlying mindfulness-related hypoalgesia, relevant to clinical conditions in which repeated pain exposure might reinforce hyperalgesic processes through fear conditioning.
Therapeutic Duplication of Long-Acting Injectable Drugs
Authors: Shao Shih-Chieh , Lai Edward Chia-Cheng , Chan Yuk-Ying , Hung Ming-Jui , Chen Hui-Yu
Published: August 2018

Long-acting medications are widely used to provide convenient ways of managing diseases, but they may cause serious harm to patients when prescribed erroneously. We present a case of hypocalcaemia as a result of therapeutic duplication of 2 long-acting bisphosphonates prescribed within days of each other by different physicians. We describe how we prevented similar medication errors through improvements in medical informatics systems. This case emphasizes the need for enhancements in medical informatics systems to avoid therapeutic duplication of long-acting medications in the interest of patient safety.
The Effect of Histidine-tryptophan-ketoglutarate Solution and University of Wisconsin Solution: An Analysis of the Eurotransplant Registry
Authors: de Boer Jacob D. , Strelniece Agita , van Rosmalen Marieke , de Vries Erwin , Ysebaert Dirk , Guba Markus , Braat Andries Erik , Samuel Undine
Published: August 2018

Background

Both University of Wisconsin (UW) and histidine-tryptophan-ketoglutarate (HTK) solutions are currently used in the Eurotransplant region for preservation of liver allografts. Previous studies on their effect have led to a lot of discussion. This study aims to compare the effect of HTK and UW on graft survival.

Methods

First liver transplantations in recipients 18 years or older from January 1, 2007, until December 31, 2016, were included. Graft survival was compared for livers preserved with HTK and UW at 30 days, 1, 3, and 5 years. Multivariable analysis of risk factors was performed and outcome was adjusted for important confounders.

Results

Of all 10 628 first liver transplantations, 8176 (77%) and 2452 (23%) were performed with livers preserved with HTK and UW, respectively. Kaplan-Meier curves showed significant differences in graft survival between HTK and UW at 30 days (89% vs 93%, P=<0.001), 1 year (75% vs 82%, P=<0.001), 3 years (67% vs 72%, P<0.001), and at 5 years (60% vs 67%, P<0.001). No significant differences in outcome were observed in separate analyses of Germany or non-German countries. In multivariable analysis, UW was associated with a decreased risk of graft loss at 30 days (HR 0.772, P=0.002) and at 1 year (0.847 (0.757-0.947). When adjusted for risk factors, no differences in long term outcome could be detected.

Conclusions

Because the use of preservation fluids is clustered geographically, differences in outcome by preservation fluids are strongly affected by regional differences in donor and recipient characteristics. When adjusted for risk factors, no differences in graft survival exist between transplantations performed with livers preserved with either HTK or UW.
Outcomes in Third and Fourth Kidney Transplants Based on the Type of Donor
Authors: Dabare Dilan , Kassimatis Theodoros , Hodson James , Khurram Muhammad Arslan , Papadakis Georgios , Rompianesi Gianluca , Shaw Olivia , Karydis Nikolaos , Callaghan Chris , Olsburgh Jonathon , Mamode Nizam , Kessaris Nicos , Loukopoulos Ioannis
Published: August 2018

Background.

An increasing number of patients are requiring multiple retransplants. We assessed outcomes of third and fourth kidney transplants, to aid decision making on the most suitable donor type.

Methods.

Data were collected retrospectively for 2561 transplants, including 69 third and 8 fourth, performed from 2000 to 2017. Demographics and outcomes for the combined third/fourth group were compared to first and second transplants. Within the third/fourth kidney transplant group, comparisons were made between deceased donors (n = 39), live donor HLA-compatible (n = 23) and -incompatible (n = 13) transplants, as well as between standard (n = 25) and extended-criteria (n = 14) deceased donor transplants.

Results.

Patient survival did not differ significantly by transplant number (P = 0.532), whereas death-censored graft survival declined progressively, from 89% at 5 years in first, 85% in second and 74% in the third/fourth transplant group (P < 0.001). Within the combined third/fourth transplant subgroup, 5-year graft survival was found to be 100% in recipients of HLA-compatible live donors, compared to 75% in deceased donors and 53% in HLA-incompatible live donors, although this difference did not reach statistical significance (P = 0.083). No significant difference in patient survival (P = 0.356) or complication rates (P = 0.757) were detected between these groups. For recipients of deceased donors in the third/fourth transplant group, there were no significant differences between standard versus extended-criteria donors for any of the outcomes considered.

Conclusions.

Despite variable functional outcomes, third and fourth kidney transplant recipients experience comparable patient survival rates to first and second transplants, regardless of the donor type. In selected patients, HLA-incompatible live donors and extended-criteria deceased donors should be considered.
Movement context modulates neuronal activity in motor and limbic-associative domains of the human subthalamic nucleus
Authors: Marmor Odeya , Rappel Pnina , Valsky Dan , Bick Atira S , Arkadir David , Linetzky Eduard , Peled Or , Tamir Idit , Bergman Hagai , Israel Zvi , Eitan Renana
Published: August 2018

To better understand the mechanism of movement facilitation and inhibition in the subthalamic nucleus (STN), we recorded subthalamic multiunit activity intra-operatively while parkinsonian patients (n=43 patients, 173 sites) performed increasingly complex oddball paradigms: auditory (‘None-Go’, n=7, 28), simple movement (‘All-Go’, n=7, 26) and movement inhibition (‘Go-NoGo’, n=29, 119) tasks. To enable physiological sampling of the different subthalamic nucleus domains in both hemispheres, each patient performed one of the oddball paradigms several times.

The human STN responded mainly to movement-involving tasks: movement execution at the motor STN and movement planning at the limbic-associative STN. In the limbic-associative STN, responses to the inhibitory cue (deviant tone) in the movement inhibition task were not significantly different from the simple movement task. However, responses to the go cue (frequent tone) were significantly reduced. The reduction was mainly in the negative component of the evoked response amplitude. Successful movement inhibition was correlated with higher baseline activity before the inhibitory cue.

We suggest that the STN adapts to movement inhibition context by selectively decreasing the amplitude of neuronal activity. Thus, the STN enables movement inhibition not by increasing responses to the inhibitory cue but by reducing responses to the release cue. The negative component of the evoked response probably facilitates movement and a higher baseline activity enables successful inhibition of movement. These discharge modulations were found in the ventromedial, non-motor domain of the STN and therefore suggest a significant role of the associative-limbic domains in movement planning and in global movement regulation.
Prescription Opioid Analgesic Use and Mortality in Systemic Lupus Erythematosus
Authors: Cabacungan Romy J. , Qualls Clifford R. , Sibbitt Wilmer L , Hayward William A. , Gibb James I. , Kettwich Selma D. , Fields Roderick A. , Emil N. Suzanne , Fangtham Monthida , Bankhurst Arthur D
Published: August 2018

Objectives

This research investigated the prevalence of opioid analgesic use in patients with systemic lupus erythematosus (SLE).

Methods

This 5-year prospective cohort study of 275 SLE patients focused on prescription opioid use and 5-year outcome. Associations were determined with univariable regression analysis and then multivariable models were created to determine independent effects on dependent variables

Results

Prescription opioid use was common in SLE with 24% using opioid analgesics chronically and 76% not using opioids. Opioid users had a higher rate of tobacco use (p<0.01), cocaine use (p<0.002), mean pain scores (p<0.001), disease activity (SLEDAI-2K) (p<0.001), disease damage (SLICC/ACRDI) (p<0.001), non-adherence to medical therapy (p<0.01), and total deaths at 5 years (opioids: 48.0%, no opioids 19.0%, p<0.001). Logistic regression analysis predicting death revealed opioid use (hazard ratio 2.6, p<0.001) and SLEDAI-2K (1.1, p<0.001) respectively; and opioid use (hazard ratio 2.5, p<0.002), SLEDAI-2K (hazard ratio 1.1, p<0.001), and non-adherence (hazard ratio 1.6, p=0.11), respectively. Multivariable Cox Model analysis estimating probability of death with covariates: opioid use (hazard ratio 2.6, p<0.001) and SLEDAI-2K (hazard ratio 1.1, p<0.001); opioid use (hazard ratios 3.0, p<0.001), and cocaine use (hazard ratio 3.2, p<0.001). The Kaplan-Meir survival analysis revealed a significantly higher probability of death for SLE patients using opioid analgesics.

Conclusions

Prescription opioid analgesic use is common in SLE and is associated with markedly increased mortality. Preferably, non-opioid approaches to treat chronic pain should be used in SLE patients.

Clinical trial registration number

This was not a clinical trial.

KEY MESSAGES:

1. Chronic opioid analgesic use is common in SLE (24%).

2. Opioid use is associated with greater disease severity, tobacco use, non-adherence, and increased mortality.

3. Opioids should be used cautiously in SLE; alternative non-opioid management of pain is recommended.

ACKNOWLEDGMENTS AND FUNDING INFORMATION:

This work was supported by US National Institutes of Health research grants to Dr. Sibbitt (R01 NS035708) and to the Clinical and Translational Research Center (UL1TR001449).
Somatically Mutated Genes Under Positive and Negative Selection Found by Transcriptome Sequence Analysis Include Oncogene and Tumor Suppressor Candidates
Authors: Drubin Casey W. , Ramu Avinash , Rockweiler Nicole B. , Conrad Donald F.
Published: August 2018

Introduction

Oncogenic somatic mutations confer proliferative advantage and undergo positive clonal selection. We developed software and applied new analytical approaches to identify: (1) somatic mutations in diverse tissues, (2) somatically mutated genes under positive and negative selection, (3) post-transcriptional modifications in the mitochondrial transcriptome, and (4) inherited germline alleles predisposing people to higher somatic mutation burden or higher levels of post-transcriptional modification.

Methods

Transcriptome sequence data (Genotype Tissue Expression project) for 7051 tissue samples from 549 postmortem donors and representing 44 tissue types were used. Germline mutations were inferred from whole-exome DNA sequencing and SNP arrays. DNA somatic mutations were inferred from variant allele frequencies (VAF) in RNA-seq data. Post-transcriptional modifications were inferred from Polymorphism Information Content (PIC) at the p9 sites of mitochondrial tRNA sequences. Positive and negative clonal selection was evaluated using a nonsynonomous/synonomous mutation rate (dN/dS) model. Genome-wide association studies (GWAS) were assessed with mitochondrial PIC for post-transcriptional modification level, or using the total number of somatic mutations observed per donor for somatic mutation burden.

Results

Our dN/dS model identified 78 genes under negative selection for somatic mutations (dN/dS < 1, padj< 0.05) and 14 under positive selection (dN/dS > 1, padj<0.05). Our GWAS identified 2 sites associated with post-transcriptional modification (1 approaching significance with p=5.99×10−8, 1 with p<5×10−8) and ∼20 sites associated with somatic mutation burden (p<5×10−8).

Conclusions

To our knowledge these are the first genome-wide association studies on normal somatic mutation burden. These studies were an attempt to increase understanding of the somatic mutation process. Our work identified somatic mutations at the global organismal level that may promote cell proliferation in a tissue-specific manner. By identifying tissue-specific mutations in actively expressed genes that appear before cancer phenotype is detected, this work also identifies gene candidates that might initiate tumorigenesis.
tmap: topological analysis of population-scale microbiome data
Authors: Liao Tianhua , Wei Yuchen , Luo Mingjing , Zhao Guoping , Zhou Haokui
Published: August 2018

Population-scale microbiome study poses specific challenges in data analysis, from enterotype analysis, identification of driver species, to microbiome-wide association of host covariates. Application of advanced data mining techniques to high-dimensional complex dataset is expected to meet the rapid advancement in large scale and integrative microbiome research. Here, we present tmap, a topological data analysis framework for population-scale microbiome study. This framework can capture complex shape of large scale microbiome data into a compressive network representation. We also develop network-based statistical analysis for driver species identification and microbiome-wide association analysis. tmap can be used for exploring variations in a population-scale microbiome landscape to study host-microbiome association.

Availability and implementation

tmap is available at GitHub (https://github.com/GPZ-Bioinfo/tmap), accompanied with online documentation and tutorial (http://tmap.readthedocs.io).

Contact

http://hk.zhou@siat.ac.cn
CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage
Authors: Soczek Katarzyna M. , Grant Tim , Rosenthal Peter B. , Mondragon Alfonso
Published: August 2018

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.16 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.
Mutual synchronization pattern as a complementary indicator of the short-term blood pressure – heart rate feedback regulation activity
Authors: Pyko Nikita S , Pyko Svetlana A , Markelov Oleg A , Mamontov Oleg V , Bogachev Mikhail I
Published: August 2018

We suggest a complementary indicator of the blood pressure – heart rate feedback regulation based on their synchronization pattern assessed by Hilbert transform. We determine the synchronization coefficient Sync as the fraction of time fragments where the standard deviation of the differences between instantaneous phases of blood pressure and pulse intervals are below a certain threshold. While BRS characterizes the intensity of the pulse intervals response to the blood pressure changes during observed feedback responses, the Sync likely indicates how often such responses are activated in the first place. Data from 95 tilt test records indicate that in both healthy subjects and patients with moderate autonomic dysfunction BRS and Sync are typically reciprocal suggesting that low intensity of the feedback responses characterized by low BRS is rather compensated by their more frequent activation indicated by higher Sync. In contrast, in diabetes patients with autonomic neuropathy BRS and Sync are positively correlated likely indicating the breakdown of this compensation in some of the diabetic patients. Therefore we suggest that Sync could be used as an additional indicator of the blood pressure – heart rate feedback regulation activity that is complementary to the widely used baroreflex sensitivity (BRS).
Regional low-frequency oscillations in human rapid-eye movement sleep
Authors: Bernardi Giulio , Betta Monica , Ricciardi Emiliano , Pietrini Pietro , Tononi Giulio , Siclari Francesca
Published: August 2018

Although the EEG slow wave of sleep is typically considered to be a hallmark of Non Rapid Eye Movement (NREM) sleep, recent work in mice has shown that slow waves can also occur in REM sleep. Here we investigated the presence and cortical distribution of low-frequency (1-4 Hz) oscillations in human REM sleep by analyzing high-density EEG sleep recordings obtained in 28 healthy subjects. We identified two clusters of low-frequency oscillations with distinctive properties: 1) a fronto-central cluster characterized by ∼2.5-3.0 Hz, relatively large, notched delta waves (so-called ‘sawtooth waves’) that tended to occur in bursts, were associated with increased gamma activity and rapid eye movements, and upon source modeling, displayed an occipito-temporal and a fronto-central component; and 2) a medial occipital cluster characterized by more isolated, slower (<2 Hz) and smaller waves that were not associated with rapid eye movements, displayed a negative correlation with gamma activity and were also found in NREM sleep. Thus, low-frequency oscillations are an integral part of REM sleep in humans, and the two identified subtypes (sawtooth and medial-occipital slow waves) may reflect distinct generation mechanisms and functional roles. Sawtooth waves, which are exclusive to REM sleep, share many characteristics with ponto-geniculo-occipital (PGO) waves described in animals and may represent the human equivalent or a closely related event while medio-occipital slow waves appear similar to NREM sleep slow waves.
Crystal structure and Hirshfeld surface analysis of (E)-5-phenyl-3-[(pyridin-4-ylmethylidene)amino]thiazolidin-2-iminium bromide monohydrate
Authors: Akkurt Mehmet , Maharramov Abel M. , Duruskari Gulnara Sh. , Toze Flavien A. A. , Khalilov Ali N.
Published: August 2018

In the cation of the title salt, C15H15N4S+·Br−·H2O, the central thiazolidine ring adopts an envelope conformation with puckering parameters Q(2) = 0.279 (4) Å and φ(2) = 222.5 (9)°. The mean plane of the thiazolidine ring makes dihedral angles of 12.4 (2) and 66.8 (3)° with the pyridine and phenyl rings, respectively. The pyridine ring in the title molecule is essentially planar (r.m.s deviation = 0.005 Å). In the crystal, the cations, anions and water molecules are linked into a three-dimensional network, which forms cross layers parallel to the (120) and (\overline{1}20) planes via O—H...Br, N—H...Br and N—H...N hydrogen bonds. C—H...π interactions also help in the stabilization of the molecular packing. Hirshfeld surface analysis and 2D (two-dimensional) fingerprint plots indicate that the most important contributions to the crystal packing are from H...H (35.5%), C...H/H...C (23.9%), Br...H/H...Br (16.4%), N...H/H...N (10.6%) and S...H/H...S (7.9%) interactions.
Research of leakage magnetic field in deenergized transformer
Authors: Horiszny Jacek
Published: August 2018

Purpose

The paper presents the analysis of magnetic field that surrounds the power transformer after it has been switched off. The purpose of this paper is to determine the possibility of defining the residual fluxes in the legs of the transformer based on the measurement of this field. It was also intended to determine the type and the location of magnetic sensors.

Design/methodology/approach

Numerical analysis of the magnetic field was performed. A three-dimensional model of the transformer’s magnetic core was created in the Flux 3D simulation program. The analysis was concerned with an oil-filled transformer and a dry transformer. The magnetic field of Earth was taken into account.

Findings

The research has shown that magnetic induction of the leakage field produced by residual magnetization of the core is comparable to the magnetic induction of the Earth’s field. It was also found that the measurement of the magnetic induction should be performed as close as possible to the core. The interior of the tank turned out to be a convenient space for the placement of the sensors.

Research limitations/implications

The influence of external ferromagnetic objects, and devices generating magnetic field, on the measurement was not considered. It should be taken into account in the future work.

Originality/value

On the basis of the analysis, it was proposed to measure the magnetic induction vector of the leakage field at three points. The sensors should be placed in front of the columns at a position that is half of their height. The measurement can be performed with satisfactory accuracy by sensors located on the surface of the windings.
A passive SPICE model for rectennas
Authors: Pereira Polyanna Mara , Campelo Felipe , Mori Takuya , Igarashi Hajime , Adriano Ricardo
Published: August 2018

Purpose

This paper aims to present a SPICE model to represent antennas in receiving mode. The model can be used to evaluate the performance of the antenna when it is coupled to several different nonlinear electric circuits. The proposed methodology is particularly suitable for rectenna applications, as it allows the analysis of different configurations for a rectenna more efficiently than using full-wave analysis simulators coupled directly to each rectifier circuit.

Design/methodology/approach

The model presented uses reciprocity theory to calculate the ideal voltage source of the Thevenin-equivalent circuit for an antenna. Vector fitting is then used to approximate the model to rational functions that can be converted to Resistor, Inductor and Capacitor circuits. Additional components are added to the circuit to prevent numerical instability.

Findings

Two rectennas are used to illustrate the performance of the proposed model, one based on a 2.45-GHz rectangular patch antenna and another based on a planar spiral antenna. The second antenna has impedance with positive and negative real parts along the frequency range, which could lead to numerical instabilities. The proposed method is shown to be stable while working with these negative resistance values, which may appear during circuit parameterization.

Research limitations/implications

The equivalent SPICE circuit model for the antenna makes it easy to simulate nonlinear circuits connected to the antenna and perform transient analyses. The computational cost of antenna analysis is reduced, being more computationally efficient than methods that involve full-wave simulation. This characteristic makes it an interesting approach for working with rectennas, or any application where the time constant of the circuit is much longer than the period of the incident wave.

Originality/value

For most antenna applications, the numerical stability of the circuit can be achieved using passive enforcement. However, depending on the phase response of the antenna, the impedance that represents its far-field characteristic may present a negative real part, in which case, passive enforcement will fail. In this paper, the problem of numerical instability is solved by introducing an offset resistance and a current-controlled voltage source to the model.
Risk reliability-based underwater inspection method for jacket platforms in Indonesia
Authors: Tawekal Jessica Rikanti , Tawekal Ricky Lukman
Published: August 2018

Purpose

The purpose of this paper is to carry out the application of risk reliability-based underwater inspection (RReBUI).

Design/methodology/approach

The consequence of failure factor is calculated qualitatively in accordance with the risk-based underwater inspection (RBUI) method but the criteria are modified as an adjustment to the addition and combination of production and reliability information of the analyzed platforms. The probability of failure (PoF) is determined quantitatively by calculating the structure reliability index based on collapse failure mechanism in which the uncertainty of wave load is considered. The PoF criteria from the RBUI are re-modified to adjust the criterion with the highest and lowest reliability indexes obtained in RReBUI study. Selection of exposure category of the platform is still the same as the RBUI method.

Findings

The models of three offshore jacket platforms located in each of Java Sea and Natuna Sea were used for the RReBUI application. These six models were previously used in the traditional RBUI application. The results of RReBUI analysis indicated that including the environmental characteristics in the risk assessment resulted in more reliable inspection interval plans.

Originality/value

The drawback of RBUI is that it cannot be used for platforms spread over a distance or different areas, as the failure parameters of these platforms cannot be compared. Furthermore, the RBUI method does not consider the environmental characteristics in its risk assessment. Unlike RBUI, the purpose of RReBUI method is to assess the reliability of a platform based on both structural and environment characteristics. Therefore, the RReBUI method determines the risk of every platform quantitatively without having to compare the failure parameters based on expert justification. The application of RReBUI for jacket platforms has never been developed in Indonesia.
Method for computing the shear capacity of prestressed reinforced concrete beams based on truss-arch model
Authors: Wang Jiawei , Liu Jinliang , Zhang Guanhua , Jia Yanmin
Published: August 2018

Purpose

The calculation of the shear capacity of inclined section for prestressed reinforced concrete beams is an important topic in the design of concrete members. The purpose of this paper, based on the truss-arch model, is to analyze the shear mechanism in prestressed reinforced concrete beams and establish the calculation formula for shear capacity.

Design/methodology/approach

Considering the effect of the prestressed reinforcement axial force on the angle of the diagonal struts and regression coefficient of softening cocalculation of shear capacity is established. According to the shape of the cracks of prestressed reinforced concrete beams under shear compression failure, the tie-arch model for the calculation of shear capacity is established. Shear-failure-test beam results are collected to verify the established formula for shear bearing capacity.

Findings

Through theoretical analysis and experimental beam verification, it is confirmed in this study that the truss-arch model can be used to analyze the shear mechanism of prestressed reinforced concrete members accurately. The calculation formula for the angle of the diagonal struts chosen by considering the effect of prestress is accurate. The relationship between the softening coefficient of concrete and strength of concrete that is established is correct. Considering the effect of the destruction of beam shear plasticity of the concrete on the surface crack shape, the tie-arch model, which is established where the arch axis is parabolic, is applicable.

Originality/value

The formula for shear capacity of prestressed reinforced concrete beams based on this theoretical model can guarantee the effectiveness of the calculation results when the structural properties vary significantly. Engineers can calculate the parameters of prestressed reinforced concrete beams by using the shear capacity calculation formula proposed in this paper.
Study on behaviour of geometrically scaled glass reinforced epoxy tubes subjected to non-coincident quasi static-indentation
Authors: Almaskari Fahad , Hafeez Farrukh
Published: August 2018

Purpose

The purpose of this paper is to study the behaviour of glass reinforced epoxy tubes subjected to repeated indentation loads at two non-coincident indentations 180° apart.

Design/methodology/approach

Four geometrically scaled specimens ranging from 100 to 400 mm diameter were used in repeated indentation tests. Force, displacement and damage growth were recorded for loading and unloading until the indenter returned to its original starting point.

Findings

Similar scaled trends were observed between the non-coincidental loadings. Unlike reported response form coincidental loadings, the responses from non-coincidental loadings yield lower values for bending stiffness and peak load.

Research limitations/implications

The differences in behaviour of the specimen between non-coincident loadings were attributed to reductions in fracture toughness and circumferential modulus.

Practical implications

Distant non-interacting damage and delamination around the circumference does reduce the structural performance.

Originality/value

Behaviour of composite tubes under different loading conditions, for example low speed impact or quasi static indentation, is widely studied, however little attention has been given to the repeated loading incidents.
Non-linear delamination in two-dimensional functionally graded multilayered beam
Authors: Rizov Victor
Published: August 2018

Purpose

A delamination fracture analysis of two-dimensional functionally graded multilayered end-loaded split beam configuration with non-linear mechanical behaviour of material is conducted. The beam is made of an arbitrary number of longitudinal layers. Perfect adhesion between layers is assumed. The material is two-dimensional functionally graded in the cross-section of each layer. Also, each layer has individual thickness and material properties. A delamination crack is located arbitrary along the beam height. The paper aims to discuss these issues.

Design/methodology/approach

The delamination fracture behaviour is investigated analytically in terms of the strain energy release rate by analysing the balance of the energy. An additional analysis of the delamination fracture is performed by applying the J-integral approach for verification.

Findings

The solutions derived are used to evaluate the effects of crack location, material gradients and material non-linearity on the delamination fracture behaviour of end-loaded split beam. The effect of material gradient on the distribution of the J-integral value along the crack front is elucidated too.

Originality/value

Delamination in the multilayered functionally graded end-loaded split beam exhibiting non-linear mechanical behaviour of the material is analysed assuming that the material property is distributed non-linearly in both thickness and width directions in each layer.
The narrative rhythm of terror: a study of the Stockholm terrorist attack and the “Last Night in Sweden” event
Authors: Cassinger Cecilia , Eksell Jorgen , Mansson Maria , Thufvesson Ola
Published: August 2018

Purpose

The purpose of this paper is to examine how the mediatisation of terror attacks affects the brand image of tourism cities.

Design/methodology/approach

Informed by theories of mediatisation and space, the study analyses two different types of terror attacks in Sweden during 2017 as media events. The focus of analysis is on identifying spatial and temporal patterns that underpin the narrative rhythm of the discussions of the events on Twitter and online news platforms.

Findings

The findings demonstrate that the unfolding of the events can be divided into three phases of varying intensity in rhythm and implications for city brand image. The manifestation of an imaginary terror attack in a digital environment had a greater impact on the narratives of the city than an actual one.

Research limitations/implications

Rythmanalysis is introduced as a useful device to examine how urban space is mediatised through social media and online news flows.

Originality/value

The study contributes with novel knowledge on the mediatisation of city space on digital media platforms in a post-truth world. It shows that city administrations need to deal with both real and imaginary terror attacks, especially when there is an already established negative image of the city.