bluuebunny/crossref_metadata_2025 huggingface dataset:
Neonatal Seizures—Are We there Yet?
Authors: Ramantani Georgia , Schmitt Bernhard , Plecko Barbara , Pressler Ronit M. , Wohlrab Gabriele , Klebermass-Schrehof Katrin , Hagmann Cornelia , Pisani Francesco , Boylan Geraldine B.
Published: July 2019

Neonatal seizures are the most prevalent and distinctive sign of neurologic dysfunction in early life and pose an immense challenge for clinicians. Improvements in neonatal care have increased the survival rate of extremely premature infants, considerably changing the spectrum of underlying etiologies, and instigating a gradual shift from mortality to morbidity. Recognizing neonatal seizures can be challenging due to variability in presentation but clinical features can often provide valuable clues about etiology. Yet, the majority of neonatal seizures are subclinical. Even though conventional electroencephalography (EEG) with simultaneous video detection of seizures still represents the diagnostic gold standard, continuous monitoring using a one- to two-channel amplitude-integrated EEG with concurrent unprocessed EEG can be crucial for early recognition and intervention. Furthermore, tremendous progress has been made in neuroimaging, and all infants with seizures should have a magnetic resonance imaging (MRI) to help identify the underlying etiology. While the majority of neonatal seizures are caused by hypoxic-ischemic events, stroke, hemorrhage, or infection, approximately 15% of patients will require more sophisticated algorithms for diagnostic workup, including metabolic and genetic screening. These recent developments have led to renew interest in the classification of neonatal seizures, which aim to help identify etiology and guide appropriate therapeutic and prognostic decisions. In this review, we outline recent progress made in the etiology, diagnosis, and treatment of neonatal seizures and highlight areas that deserve further research.
Progress in optical Thomson scattering diagnostics for ICF gas-filled hohlraums
Authors: Zhao Hang , Li Zhichao , Yang Dong , Li Xin , Chen Yaohua , Jiang Xiaohua , Liu Yonggang , Gong Tao , Guo Liang , Li Sanwei , Li Qi , Wang Feng , Liu Shenye , Yang Jiamin , Jiang Shaoen , Zheng Wanguo , Zhang Baohan , Ding Yongkun
Published: July 2019

Optical Thomson scattering (OTS) diagnostics have been continuously developed on a series of large laser facilities for inertial confinement fusion (ICF) research in China. We review recent progress in the use of OTS diagnostics to study the internal plasma conditions of ICF gas-filled hohlraums. We establish the predictive capability for experiments by calculating the time-resolved Thomson scattering spectra based on the 2D radiation-hydrodynamic code LARED, and we explore the fitting method for the measured spectra. A typical experiment with a simplified cylindrical hohlraum is conducted on a 10 kJ-level laser facility, and the plasma evolution around the laser entrance hole is analyzed. The dynamic effects of the blast wave from the covering membrane and the convergence of shocks on the hohlraum axis are observed, and the experimental results agree well with those of simulations. Another typical experiment with an octahedral spherical hohlraum is conducted on a 100 kJ-level laser facility, and the plasma evolution at the hohlraum center is analyzed. A discrepancy appears between experiment and simulation as the electron temperature rises, indicating the occurrence of nonlocal thermal conduction.
An experimental investigation of blob behaviors in lower hybrid wave dominant heating scenarios on EAST
Authors: Wang Q. , Hu G. H. , Sheng Z. M. , Yan N. , Wang H. Q. , Xu G. S. , Chen R. , Yang Q. Q. , Wang Y. F.
Published: July 2019

Systematic measurements on scrape-off layer (SOL) blob behaviors have been performed by lithium beam emission spectroscopy on EAST in lower hybrid wave (LHW) heating dominant low confinement (L-mode) discharges. With the application of LHW, blob fluctuation amplitude and associated blob radial transport flux are profoundly suppressed. The reductions of the blob amplitude and transport flux are concomitant with the increase of SOL poloidal velocity and Er×B flow shear. Meanwhile, the blob eddy is strongly tilted and the radial correlation length is reduced. All the measurements point toward the important influences of the LHW induced Doppler shift effect and Er×B flow shear on the suppression of blobs and low frequency turbulence.
Amplification of mid-infrared lasers via backscattering in magnetized plasmas
Authors: Shi Yuan , Fisch Nathaniel J.
Published: July 2019

Plasmas may be used as gain media for amplifying intense lasers, and external magnetic fields may be applied to improve the performance. For midinfrared lasers, the requisite magnetic field is on the megagauss scale, which can already be provided by current technologies. Designing the laser amplifier requires knowing the magnetized three-wave coupling coefficient, which is mapped out systematically in this paper. By numerically evaluating its formula, we demonstrate how the coupling coefficient depends on the angle of wave propagation, laser polarization, magnetic field strength, plasma temperature, and plasma density in the backscattering geometry. Since the mediation is now provided by magnetized plasma waves, the coupling can differ significantly from unmagnetized Raman and Brillouin scatterings.
Strong-field coherence breaking as a tool for identifying methyl rotor states in microwave spectra: 2-hexanone
Authors: Fritz Sean M. , Mishra Piyush , Zwier Timothy S.
Published: July 2019

The rotational spectrum of 2-hexanone was recorded over the 8–18 GHz region using a chirped pulse Fourier transform microwave spectrometer. Strong field coherence breaking (SFCB) was utilized to selectively modulate the intensities of rotational transitions belonging to the two lowest energy conformers of 2-hexanone, aiding the assignment. In addition, the SFCB method was applied for the first time to selectively identify rotational transitions built off the two lowest energy hindered methyl rotor states of each conformer, 0a1 and 1e. Since these two states have rotational energy levels with different nuclear spin symmetries, their intensities could be selectively modulated by the resonant monochromatic pulses used in the SFCB method. The difference spectra, final fit, and structural parameters are discussed for the three assigned conformers of 2-hexanone.
Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size
Authors: Schwinn Karno , Ferré Nicolas , Huix-Rotllant Miquel
Published: July 2019

In electrostatic embedding mixed quantum and molecular mechanics (QM/MM) approaches, the QM charge distribution is polarized by the electrostatic interaction with the MM environment. Analytic derivatives of expectation values of operators are required to extract properties such as vibrational spectra. These derivatives usually require solving a set of coupled perturbed equations for each nucleus/atom in the system, thus becoming prohibitive when the MM subsystem contains thousands of atoms. In the context of Electrostatic Potential Fitting (ESPF) QM/MM, we can easily overcome this bottleneck by defining a set of auxiliary coupled perturbed equations called the Q-vector equations. The Q-vector method scales only with the size of the QM subsystem, producing an effective charge tensor that leads to the atomic charge derivative after contraction with the MM electrostatic potential gradient. As an example, we use the charge derivatives as an analysis tool to identify the most important chromophore-polarizing amino-acids in plant cryptochrome. This finding opens up the route of defining polarizable force fields and simulating vibrational spectroscopy using ESPF QM/MM electrostatic embedding at an affordable computational cost.
Human smell perception is governed by quantum spin-residual information
Authors: Bandari Anashe
Published: July 2019

A new method of testing human smell shows molecular bonding vibrations in an odor molecule affect the perceived olfactory intensity.
OsMTOPVIB is required for meiotic bipolar spindle assembly
Authors: Xue Zhihui , Liu Changzhen , Shi Wenqing , Miao Yongjie , Shen Yi , Tang Ding , Li Yafei , You Aiqing , Xu Yunyuan , Chong Kang , Cheng Zhukuan
Published: July 2019

Significance

The organization of microtubules into a bipolar spindle is essential for chromosome segregation. Both centrosome and chromatin-dependent spindle assembly mechanisms are well studied in animals; however, the mechanism of bipolar spindle assembly in plant meiosis remains unclear. We found the key step of plant bipolar spindle assembly is the correction of multipolar spindles into bipolar spindles at metaphase I. The multipolar spindles failed to transition into bipolar spindles in
OsmtopVIB
. However, the absence of cohesion subunit OsREC8 resulted in bipolar spindles in the background of
OsmtopVIB
. Thus, OsMTOPVIB plays a crucial role in meiotic spindle assembly. Biorientation of sister kinetochores in a univalent is essential for bipolar spindle formation when homologous recombination is absent.
Medidas de longitud en la investigación empírica de
ASL
Authors: Mavrou Irini , Ainciburu María Cecilia
Published: July 2019

El objetivo del presente estudio fue analizar el controvertido
estatus de tres medidas lingüísticas ampliamente utilizadas en la investigación
empírica de Adquisición de Segundas Lenguas, como son la longitud promedio de la
unidad terminal, la longitud promedio de la cláusula y la longitud promedio de
la oración. Sesenta y cinco aprendientes griegos de español como lengua
extranjera realizaron dos tareas escritas y su actuación se evaluó con base en
un total de 24 medidas de precisión, fluidez y complejidad sintáctica y léxica.
Mediante la aplicación del Análisis Factorial Común se pudo constatar que las
medidas de longitud (longitud promedio de la unidad terminal y de la cláusula) y
de subordinación cargan en factores diferentes y, más que fluidez, dichas
medidas evalúan diferentes facetas del constructo de complejidad sintáctica. En
cuanto a la longitud promedio de la oración, los resultados sugieren que esta
medida se ve influenciada por factores relacionados con su cómputo, con la
extensión de los textos analizados, así como por las convenciones lingüísticas
que rigen la lengua materna o extranjera.
Metáforas de la esquizofrenia
Authors: Coll-Florit Marta , Miranda Xavier , Climent Salvador
Published: July 2019

Este estudio presenta el análisis de las metáforas conceptuales producidas en el discurso de afectados de esquizofrenia y profesionales relacionados con dicho trastorno mental. La investigación permite distinguir y comparar subgrupos coherentes de estos colectivos en el corpus de trabajo e interpretar modelos subyacentes de conceptualización de la enfermedad. El corpus analizado consiste en tres documentales que recogen relatos en primera persona. Se han clasificado cuantitativa y cualitativamente las expresiones metafóricas de los intervinientes y se han inferido conjuntos de ideas y creencias a la luz de la teoría de la metáfora conceptual, un marco teórico bien establecido en la lingüística cognitiva. Las conclusiones muestran los principales patrones de conceptualización de la enfermedad por parte de afectados vinculados a programas de rehabilitación social, afectados no vinculados a ellos, psiquiatras, y otros profesionales relacionados con la salud mental, así como similitudes y diferencias relevantes entre dichos grupos.
Dialect and identity
Authors: George Angela , Hoffman-González Anne
Published: July 2019

Heritage language learners of Spanish are studying abroad in Spanish-speaking countries yet their linguistic evolution in Spanish is not addressed sufficiently in existing published scholarship. The current study consists of four case studies of US heritage speakers of Spanish studying abroad in Spanish-speaking countries different from their ancestors. Previous research on heritage speakers abroad has not addressed linguistic development. The current study attempts to fill this gap by using a variety of tasks to elicit the use of regional features to compare these heritage learners to second language learners and also first language learners who develop second dialects as a result of living abroad. The findings reveal changes in the production of regional features throughout the semester by three of the four learners of Spanish. These changes are attributed to shifts in identity coupled with proficiency level and contact with locals.
Lexical chunks in English and Spanish sales contracts
Authors: López Arroyo Belén , Pérez Leticia Moreno
Published: July 2019

This paper focuses on the study of word combinations “of common usage” which are “lexicalized”, have “syntactic and semantic stability, may be idiomatized and carry connotations, and have an emphatic or intensifying function.” (Gläser 1994/1995, 45). Following previous research on Languages for Specific Purposes (LSP) and legal phraseology, we will define, identify and classify these units in English and Spanish according to their form and meaning, using a comparable corpus of sales contracts. To carry out our study, we will focus on a number of descriptors that are commonly used within these units on the basis of the headwords they collocate with, in order to determine how specific or general they are in their form, use and meaning since this issue poses translation problems. As genres determine matters such as or terminology and phraseology, the results will be useful for specialized translators and legal drafters.
Attacking a high-dimensional quantum key distribution system with wavelength-dependent beam splitter*
Authors: Du Ge-Hai , Li Hong-Wei , Wang Yang , Bao Wan-Su
Published: July 2019

The unconditional security of quantum key distribution (QKD) can be guaranteed by the nature of quantum physics. Compared with the traditional two-dimensional BB84 QKD protocol, high-dimensional quantum key distribution (HD-QKD) can be applied to generate much more secret key. Nonetheless, practical imperfections in realistic systems can be exploited by the third party to eavesdrop the secret key. The practical beam splitter has a correlation with wavelength, where different wavelengths have different coupling ratios. Using this property, we propose a wavelength-dependent attack towards time-bin high-dimensional QKD system. What is more, we demonstrate that this attacking protocol can be applied to arbitrary d-dimensional QKD system, and higher-dimensional QKD system is more vulnerable to this attacking strategy.
Relativistic electron scattering from freely movable proton/

μ

+

in the presence of strong laser field*
Authors: Wang Ningyue , Jiao Liguang , Liu Aihua
Published: July 2019

We have investigated the electron scattering from the freely movable spin-1/2 particle in the presence of a linearly polarized laser field in the first Born approximation. The laser-dressed state of electrons is described by a time-dependent wave function which is derived from a perturbation treatment. With the aids of numerical simulations, we explore the dependencies of the differential cross section on the laser field intensity as well as the electron-impact energy. Due to the mobility of the target, the differential cross section of this process is smaller than that of Mott scattering.
Performance improvement of 4H-SiC PIN ultraviolet avalanche photodiodes with different intrinsic layer thicknesses*
Authors: Cai Xiaolong , Zhou Dong , Cheng Liang , Ren Fangfang , Zhong Hong , Zhang Rong , Zheng Youdou , Lu Hai
Published: July 2019

Four 4H-SiC p–i–n ultraviolet (UV) avalanche photodiode (APD) samples PIN-0.1, PIN-0.35, PIN-0.5, and PIN-1.0 with different intrinsic layer thicknesses (

0.1

μ
m

,

0.35

μ
m

,

0.5

μ
m

, and

1.0

μ
m

, respectively) are designed and fabricated. Single photon detection efficiency (SPDE) performance becomes better as the intrinsic layer thickness increases, which is attributed to the inhibitation of tunneling. Dark count origin is also investigated, an activation energy as small as 0.22 eV of the dark count rate (DCR) confirms that the trap-assisted tunneling (TAT) process is the main source of DCR. The temperature coefficient ranges from −2.6 mV/°C to 18.3 mV/°C, demonstrating that the TAT process is dominant in APDs with thinner intrinsic layers. Additionally, the room temperature maximum quantum efficiency at 280 nm differs from 48% to 65% for PIN-0.35, PIN-0.5, and PIN-1.0 under 0 V bias, and UV/visible rejection ratios higher than 104 are obtained.
Efficient molecular model for squeeze-film damping in rarefied air*
Authors: Lu Cun-Hao , Li Pu , Fang Yu-Ming
Published: July 2019

Based on the energy transfer model (ETM) proposed by Bao et al. and the Monte Carlo (MC) model proposed by Hutcherson and Ye, this paper proposes an efficient molecular model (MC-S) for squeeze-film damping (SQFD) in rarefied air by releasing the assumption of constant molecular velocity in the gap. Compared with the experiment data, the MC-S model is more efficient than the MC model and more accurate than ETM. Besides, by using the MC-S model, the feasibility of the empirical model proposed by Sumali for SQFD of different plate sizes is discussed. It is proved that, for various plate sizes, the accuracy of the empirical model is relatively high. At last, the SQFD of various vibration frequencies is discussed, and it shows that, for low vibration frequency, the MC-S model is reduced to ETM.
Quasi-periodic events on structured earthquake models*
Authors: Li Bin-Quan , Wu Zhi-Xi , Wang Sheng-Jun
Published: July 2019

There has been much interest in studying quasi-periodic events on earthquake models. Here we investigate quasi-periodic events in the avalanche time series on structured earthquake models by the analysis of the autocorrelation function and the fast Fourier transform. For random spatial earthquake models, quasi-periodic events are robust and we obtain a simple rule for a period that is proportional to the choice of unit time and the dissipation of the system. Moreover, computer simulations validate this rule for two-dimensional lattice models and cycle graphs, but our simulation results also show that small-world models, scale-free models, and random rule graphs do not have periodic phenomena. Although the periodicity of avalanche does not depend on the criticality of the system or the average degree of the system or the size of the system, there is evidence that it depends on the time series of the average force of the system.
Detection of Nonhematologic Neoplasms by Routine Flow Cytometry Analysis
Authors: Annunziata Joseph , Miller Michael L , Park David C , Vlad George , Bhagat Govind , Alobeid Bachir
Published: July 2019

Objectives

We investigated the ability of routine flow cytometry (FC) to detect nonhematologic neoplasms (non-HN) using antibody panels routinely used for the diagnosis of hematologic neoplasms.

Methods

FC analyses of 4,000 various diagnostic samples were retrospectively reviewed to identify cases in which an aberrant, viable CD45-negative, nonhematologic neoplastic population was detected by FC panels designed to evaluate hematologic neoplasms.

Results

A total of 57 (1.4%) diverse non-HNs were identified, representing neuroendocrine tumors (33/57) and carcinomas (9/57), as well as other malignancies (15/57) such as sarcoma and melanoma. The majority of neoplasms were positive for at least one antibody, typically CD56 (43/51, 84.3%), followed by CD117 (15/34, 44.1%) and CD138 (6/33, 18.2%).

Conclusions

Our findings highlight the importance of carefully inspecting CD45-negative events to identify non-HNs by routine FC analysis. This can help expedite further downstream immunophenotypic analysis of specimens and triage samples for appropriate genetic and molecular studies.
Erythrocyte Sedimentation Rate and C-Reactive Protein in Acute Inflammation
Authors: Lapić Ivana , Padoan Andrea , Bozzato Dania , Plebani Mario
Published: July 2019

Objectives

To assess the diagnostic accuracy of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) in acute inflammation.

Methods

PubMed and Scopus were searched and eligible articles were screened for methodologic quality using the Quality Assessment of the Diagnostic Accuracy Studies–Revised. Meta-analysis with calculation of pooled sensitivity (Se), specificity (Sp), and summary area under the curve (SAUC) was performed.

Results

Twenty-nine studies were eligible. Se and Sp were 0.78 and 0.68 (SAUC = 0.80) for ESR in orthopedic infections and 0.79 and 0.70 (SAUC = 0.81) for CRP. For the diagnosis of other various inflammatory conditions, CRP had a superior diagnostic accuracy, with a Se of 0.86, Sp of 0.67, and SAUC of 0.86 compared with a Se of 0.77, Sp of 0.59, and SAUC of 0.75 for ESR. Heterogeneity among studies was elevated. Combined use of ESR and CRP yielded higher diagnostic accuracy.

Conclusions

Despite observed heterogeneity among studies, ESR and CRP have a similar diagnostic accuracy in assessment of inflammation, especially in orthopedic conditions.
Venous Blood-Based Biomarkers in the China Health and Retirement Longitudinal Study: Rationale, Design, and Results From the 2015 Wave
Authors: Chen Xinxin , Crimmins Eileen , Hu Peifeng (Perry) , Kim Jung Ki , Meng Qinqin , Strauss John , Wang Yafeng , Zeng Junxia , Zhang Yuan , Zhao Yaohui
Published: July 2019

Blood biomarkers provide critical information about the health of older populations, especially in large developing countries where self-reports of health are often inaccurate due to lack of access to health care. However, it is very difficult to collect blood samples in representative population surveys in such countries. The China Health and Retirement Longitudinal Study (CHARLS), a nationally representative study of middle-aged and older Chinese, represents one of the first efforts to include blood biomarkers in a nationally representative survey of China. In the 2015 wave of CHARLS, 13,013 respondents located in 150 counties around China donated whole blood, which was assayed on a range of indicators. Here we describe the process of the sample collection, transportation, storage, and analysis and present basic statistics.
Endothelial Microvesicles Circulating in Peripheral and Coronary Circulation Are Associated With Central Blood Pressure in Coronary Artery Disease
Authors: Gkaliagkousi Eugenia , Gavriilaki Eleni , Vasileiadis Ioannis , Nikolaidou Barbara , Yiannaki Efthalia , Lazaridis Antonios , Triantafyllou Areti , Anyfanti Panagiota , Markala Dimitra , Zarifis Ioannis , Douma Stella
Published: July 2019

BACKGROUND

Endothelial microvesicles (EMVs) have emerged as markers of endothelial injury. However, little is known about their levels in the coronary circulation of acute coronary syndrome (ACS) and stable coronary artery disease (CAD). We hypothesized that ACS patients exhibit a more pronounced increase of EMVs both in the peripheral and coronary circulation when compared with CAD. We also investigated possible associations of EMVs with markers preclinical target organ damage.

METHODS

We enrolled consecutive eligible patients undergoing coronary angiography. Blood samples were collected from the stem of the left coronary artery and the femoral artery. ΕMVs were measured by a standardized flow cytometry protocol. Central systolic blood pressure (cSBP) was measured invasively and patients’ history was recorded.

RESULTS

CAD patients exhibited increased levels of EMVs compared with controls. When patients with ACS and stable CAD were compared, the former had significantly increased EMVs in both coronary and peripheral circulation. Importantly, both ACS and CAD patients exhibited increased levels of EMVs in the coronary circulation compared with periphery. In addition, EMVs were associated with cSBP.

CONCLUSIONS

EMVs emerge as novel markers of ongoing underlying vascular damage, further augmenting the vicious cycle of inflammation and thrombosis mainly in ACS but also in stable CAD.
Circulating Plasma Metabolomic Profiles Differentiate Rodent Models of Pulmonary Hypertension and Idiopathic Pulmonary Arterial Hypertension Patients
Authors: Zhao Jun-Han , He Yang-Yang , Guo Shan-Shan , Yan Yi , Wang Zhe , Ye Jue , Zhang Jin-Lan , Wang Yong , Pang Xiao-Bin , Xie Xin-Mei , Lin Jian-Hui , Jing Zhi-Cheng , Han Zhi-Yan
Published: July 2019

BACKGROUND

Pulmonary arterial hypertension (PAH) is a severe progressive disease with systemic metabolic dysregulation. Monocrotaline (MCT)-induced and hypoxia-induced pulmonary hypertension (PH) rodent models are the most widely used preclinical models, however, whether or not these preclinical models recapitulate metabolomic profiles of PAH patients remain unclear.

METHODS

In this study, a targeted metabolomics panel of 126 small molecule metabolites was conducted. We applied it to the plasma of the 2 preclinical rodent models of PH and 30 idiopathic pulmonary arterial hypertension (IPAH) patients as well as 30 healthy controls to comparatively assess the metabolomic profiles of PAH patients and rodent models.

RESULTS

Significantly different metabolomics profiling and pathways were shown among the 2 classical rodent models and IPAH patients. Pathway analysis demonstrated that methionine metabolism and urea cycle metabolism were the most significant pathway involved in the pathogenesis of hypoxia-induced PH model and MCT-induced model, respectively, and both of them were also observed in the dysregulated pathways in IPAH patients.

CONCLUSIONS

These 2 models may develop PAH through different metabolomic pathways and each of the 2 classical PH model resembles IPAH patients in certain aspects.
Semiconductor Work and Adverse Pregnancy Outcomes Associated with Male Workers: A Retrospective Cohort Study
Authors: Choi Kyung-Hwa , Kim Hyunjoo , Kim Myoung-Hee , Kwon Ho-Jang
Published: July 2019

Objectives

A hazardous work environment in semiconductor factories is a threat to the workers’ health. Semiconductor manufacturing characteristically requires young workers, and reproductive toxicity is an important issue. Studies investigating reproductive toxicity among individuals working in the semiconductor manufacturing industry have primarily focused on outcomes in women. Information on the reproductive health of male semiconductor factory workers is limited. This study aimed to evaluate the association between workplace exposures among male workers in a Korean semiconductor company and adverse pregnancy outcomes.

Methods

Based on the data from the 2015 Semiconductor Health Survey (SHS), which evaluated the workplace exposures, pregnancy outcomes, and general health of 21 969 employees of the semiconductor industry in South Korea, we included 3868 male workers with 7504 pregnancy outcomes identified by self-reports for this retrospective cohort study. Data regarding the pregnancy outcomes, order of pregnancy, and the years of the outcomes were collected via the SHS questionnaire. Adverse pregnancy outcomes were defined as preterm labor, spontaneous abortion, and stillbirth. Workplace exposures were classified as fabrication, assembly, others, lab, and office work (reference group). A generalized estimating equations model including repeated events of individuals and producing relative risk (RR) and 95% confidence interval (CI) was used to estimate the association between workplace exposure and adverse pregnancy outcomes. Analyses were adjusted for work location, spouse’s employment in semiconductor production work, educational level, marital status, risky alcohol drinking, smoking status, body mass index, order of pregnancy, and age and year of pregnancy outcome, which were based on a priori decisions.

Results

The adjusted risk for adverse outcomes was higher [RR (95% CI): 1.47 (1.04, 2.07)] among assembly process workers compared with the office workers. Adjusted risks for adverse outcomes among workers in assembly and fabrication, whose spouses also worked in semiconductor production, were 1.60 (95% CI: 1.04, 2.46) and 1.74 (95% CI: 1.18, 2.57) times higher, respectively, compared with the office workers with spouses not working in semiconductor production.

Conclusions

Based on these findings, semiconductor work might be considered a risk factor for reproductive toxicity among male workers, especially for those whose spouses have the same job.
Estimation of Source-Specific Occupational Benzene Exposure in a Population-Based Case–Control Study of Non-Hodgkin Lymphoma
Authors: Dopart Pamela J , Locke Sarah J , Cocco Pierluigi , Bassig Bryan A , Josse Pabitra R , Stewart Patricia A , Purdue Mark P , Lan Qing , Rothman Nathaniel , Friesen Melissa C
Published: July 2019

Objectives

Occupational exposures in population-based case–control studies are increasingly being assessed using decision rules that link participants’ responses to occupational questionnaires to exposure estimates. We used a hierarchical process that incorporated decision rules and job-by-job expert review to assign occupational benzene exposure estimates in a US population-based case–control study of non-Hodgkin lymphoma.

Methods

We conducted a literature review to identify scenarios in which occupational benzene exposure has occurred, which we grouped into 12 categories of benzene exposure sources. For each source category, we then developed decision rules for assessing probability (ordinal scale based on the likelihood of exposure > 0.02 ppm), frequency (proportion of work time exposed), and intensity of exposure (in ppm). The rules used the participants’ occupational history responses and, for a subset of jobs, responses to job- and industry-specific modules. For probability and frequency, we used a hierarchical assignment procedure that prioritized subject-specific module information when available. Next, we derived job-group medians from the module responses to assign estimates to jobs with only occupational history responses. Last, we used job-by-job expert review to assign estimates when job-group medians were not available or when the decision rules identified possible heterogeneous or rare exposure scenarios. For intensity, we developed separate estimates for each benzene source category that were based on published measurement data whenever possible. Frequency and intensity annual source-specific estimates were assigned only for those jobs assigned ≥75% probability of exposure. Annual source-specific concentrations (intensity × frequency) were summed to obtain a total annual benzene concentration for each job.

Results

Of the 8827 jobs reported by participants, 8% required expert review for one or more source categories. Overall, 287 (3.3%) jobs were assigned ≥75% probability of exposure from any benzene source category. The source categories most commonly assigned ≥75% probability of exposure were gasoline and degreasing. The median total annual benzene concentration among jobs assigned ≥75% probability was 0.11 ppm (interquartile range: 0.06–0.55). The highest source-specific median annual concentrations were observed for ink and printing (2.3 and 1.2 ppm, respectively).

Conclusions

The applied framework captures some subject-specific variability in work tasks, provides transparency to the exposure decision process, and facilitates future sensitivity analyses. The developed decision rules can be used as a starting point by other researchers to assess occupational benzene exposure in future population-based studies.
Kelp beds as coastal protection: wave attenuation of Ecklonia radiata in a shallow coastal bay
Authors: Morris Rebecca L , Graham Tristan D J , Kelvin Jaya , Ghisalberti Marco , Swearer Stephen E
Published: July 2019

Background and Aims

Coastal protection from erosion and flooding is a significant ecosystem service provided by vegetated marine systems. Kelp beds are a dominant habitat-forming species on temperate reefs worldwide. While they are valued as hotspots of biodiversity, there is a paucity of information that supports their use in nature-based coastal defence. This includes the effectiveness of kelp beds in attenuating waves approaching the shore and how this influences sediment transport.

Methods

Wave loggers were deployed at paired kelp bed and control (urchin barren) treatments at four sites in Port Phillip Bay, Australia. The significant wave height offshore (exposed side) to onshore (sheltered side) of the treatment were compared to determine wave attenuation.

Key Results

At three sites, the wave attenuation of kelp beds was significantly less than the control. This result was consistent across the environmental conditions recorded in this study. At the fourth site, on average there was no significant difference in wave transmission between kelp and control. However, wave attenuation at kelp beds was 10% greater than the control during periods of northerly winds. We highlight the importance of disentangling the effects of the reef substratum and kelp when evaluating the efficacy of kelp at providing coastal protection.

Conclusions

We have highlighted a significant gap in the research on ecosystem services provided by kelp beds. A greater understanding is needed on which kelp species are able to provide coastal protection, and under what conditions. Such future research is essential for providing managers and policy makers with actionable information on sustainable and cost-effective solutions for coastal defence when faced with a changing climate.
Technology Use in Everyday Financial Activities: Evidence from Online and Offline Survey Data
Authors: Sunderaraman Preeti , Ho Sarah , Chapman Silvia , Joyce Jillian L , Colvin Leigh , Omollo Shalom , Pleshkevich Maria , Cosentino Stephanie
Published: July 2019

Objective

Internet use and mobile devices permeate every aspect of our lives and are changing our financial habits. Assessment of financial decision-making (FDM) has not yet caught up to apparent changes in financial behavior. To modernize assessment methods and create current and comprehensive FDM frameworks, we first need to establish the most commonly used and most preferred methods of performing specific financial activities.

Method

Cross-sectional survey data were collected using an online platform and offline approaches (in person and by mail) (N = 234). The frequency of using technological (e.g., laptop) and non-technological (e.g., in-person banking) means of completing seven financial activities was assessed first, including Depositing checks, Reviewing bank statements, Keeping track of money spent, Transferring funds, Withdrawing cash, Paying bills, and Purchasing products online. Second, preference for technological versus non-technological methods was assessed. Finally, linear regression models examined associations between demographics and preference for technological methods for each financial activity.

Results

The majority of respondents (77% online, 74% offline) used technology to perform various financial activities and preferred technological to non-technological methods for completing five out of the six financial activities. Increased preference for technological methods was associated with younger age for all the financial activities, and higher education was associated with reviewing bank statement and transferring funds.

Conclusions

Our survey findings provide empirical evidence for the changing nature of our financial habits. We discuss the implications of this change for researchers, clinicians, and the individuals themselves and emphasize the importance of modernizing FDM tools.
XIV—Sexual Orientation: What Is It?
Authors: Stock Kathleen
Published: July 2019

I defend an account of sexual orientation, understood as a reflexive disposition to be sexually attracted to people of a particular biological Sex or Sexes. An orientation is identified in terms of two aspects: the Sex of the subject who has the disposition, and whether that Sex is the same as, or different to, the Sex to which the subject is disposed to be attracted. I explore this account in some detail and defend it from several challenges. In doing so, I provide a theoretical framework that justifies our continued reference to Sex-directed sexual orientation as an important means of classifying human subjects.
Reproduction and maternal care increase oxidative stress in a mouthbrooding cichlid fish
Authors: Sawecki Jacob , Miros Emily , Border Shana E , Dijkstra Peter D
Published: July 2019

Investment in reproduction and postzygotic parental care is an energetically costly yet fundamental aspect of the life-history strategies in many species. Recently, oxidative stress has received attention as a potential mediator in the trade-off between reproduction, growth, and survival. During activities that increase metabolic activity, such as providing offspring care, an overproduction of reactive oxygen species can occur that cannot be counteracted by antioxidants, leading to oxidative stress and tissue damage. Here, we investigated the oxidative costs of reproduction and maternal care over the course of the reproductive cycle in a mouthbrooding cichlid fish within socially stable and unstable environments. We manipulated social stability by disrupting the habitat in socially unstable tanks. We expected to see an increase in the burden of maternal care within unstable environments due to increased male harassment of females as a byproduct of increased male–male aggression. We found that brooding females have higher levels of oxidative stress than nonbrooding females and oxidative stress fluctuates throughout the reproductive cycle. These fluctuations were driven by a spike in reactive oxygen metabolites at the beginning of brood care followed by an increase in antioxidant defense. Surprisingly, the link between reproduction and oxidative stress was not different between females from stable or unstable environments. Our study illustrates a more complete picture of the physiological costs of reproduction and parental care throughout different stages of care rather than a simplistic end-point observation of how reproduction and parental care affect an individual.
Evidence for differing trajectories of songs in urban and rural populations
Authors: Moseley Dana L , Phillips Jennifer N , Derryberry Elizabeth P , Luther David A
Published: July 2019

Learned traits, such as foraging strategies and communication signals, can change over time via cultural evolution. Using historical recordings, we investigate the cultural evolution of birdsong over nearly a 50-year period. Specifically, we examine the parts of white-crowned sparrow (Zonotrichia leucophrys nuttalli) songs used for mate attraction and territorial defense. We compared historical (early 1970s) recordings with contemporary (mid-2010s) recordings from populations within and near San Francisco, CA and assessed the vocal performance of these songs. Because birds exposed to anthropogenic noise tend to sing at higher minimum frequencies with narrower frequency bandwidths, potentially reducing one measure of song performance, we hypothesized that other song features, such as syllable complexity, might be exaggerated, as an alternative means to display performance capabilities. We found that vocal performance increased between historical and contemporary songs, with a larger effect size for urban songs, and that syllable complexity, measured as the number of frequency modulations per syllable, was historically low for urban males but increased significantly in urban songs. We interpret these results as evidence for males increasing song complexity and trilled performance over time in urban habitats, despite performance constraints from urban noise, and suggest a new line of inquiry into how environments alter vocal performance over time.
Reproductive conflict resolution in cooperative breeders
Authors: Cram Dominic L , Jungwirth Arne , Spence-Jones Helen , Clutton-Brock Tim
Published: July 2019

Female infanticide is common in animal societies where groups comprise multiple co-breeding females. To reduce the risk that their offspring are killed, mothers can synchronize breeding and pool offspring, making it hard for females to avoid killing their own young. However, female reproductive conflict does not invariably result in reproductive synchrony, and we lack a general hypothesis explaining the variation in conflict resolution strategies seen across species. Here, we investigate the fitness consequences of birth timing relative to other females and the prevalence of birth synchrony in cooperatively breeding Kalahari meerkats (Suricata suricatta). We show that, although there would be substantial benefits to females in synchronizing births and reducing their risk of infanticide, birth synchrony is rare. Since precise breeding synchrony has evolved in a related species with similar infanticidal female reproductive conflict, its absence in meerkats requires an evolutionary explanation. We therefore explore the costs and benefits of synchronizing breeding in two theoretical models, each of which contrasts synchrony with an alternative reproductive strategy: (i) breeding opportunistically and accepting fitness losses to infanticide or (ii) suppressing the reproduction of others to prevent infanticide. Our models show that the costs of synchrony constrain its development if subordinates breed infrequently, and that selection instead favors the suppression of subordinate reproduction by the dominant and opportunistic reproduction by subordinates. Together, our results suggest that the resolution of reproductive conflict in animal societies is shaped by differential breeding propensities among female group members, leading to divergent conflict resolution strategies even in closely related species.
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data
Authors: Xue Albert Y , Yu Angela M , Lucks Julius B , Bagheri Neda
Published: July 2019

Motivation

RNA molecules can undergo complex structural dynamics, especially during transcription, which influence their biological functions. Recently developed high-throughput chemical probing experiments that study RNA cotranscriptional folding generate nucleotide-resolution ‘reactivities’ for each length of a growing nascent RNA that reflect structural dynamics. However, the manual annotation and qualitative interpretation of reactivity across these large datasets can be nuanced, laborious, and difficult for new practitioners. We developed a quantitative and systematic approach to automatically detect RNA folding events from these datasets to reduce human bias/error, standardize event discovery and generate hypotheses about RNA folding trajectories for further analysis and experimental validation.

Results

Detection of Unknown Events with Tunable Thresholds (DUETT) identifies RNA structural transitions in cotranscriptional RNA chemical probing datasets. DUETT employs a feedback control-inspired method and a linear regression approach and relies on interpretable and independently tunable parameter thresholds to match qualitative user expectations with quantitatively identified folding events. We validate the approach by identifying known RNA structural transitions within the cotranscriptional folding pathways of the Escherichia coli signal recognition particle RNA and the Bacillus cereus crcB fluoride riboswitch. We identify previously overlooked features of these datasets such as heightened reactivity patterns in the signal recognition particle RNA about 12 nt lengths before base-pair rearrangement. We then apply a sensitivity analysis to identify tradeoffs when choosing parameter thresholds. Finally, we show that DUETT is tunable across a wide range of contexts, enabling flexible application to study broad classes of RNA folding mechanisms.

Availability and implementation

https://github.com/BagheriLab/DUETT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model
Authors: Zhang Le , Liu Guangdi , Kong Meijing , Li Tingting , Wu Dan , Zhou Xiaobo , Yang Chuanwei , Xia Lei , Yang Zhenzhou , Chen Luonan
Published: July 2019

Motivation

The growth and survival of myeloma cells are greatly affected by their surrounding microenvironment. To understand the molecular mechanism and the impact of stiffness on the fate of myeloma-initiating cells (MICs), we develop a systems biological model to reveal the dynamic regulations by integrating reverse-phase protein array data and the stiffness-associated pathway.

Results

We not only develop a stiffness-associated signaling pathway to describe the dynamic regulations of the MICs, but also clearly identify three critical proteins governing the MIC proliferation and death, including FAK, mTORC1 and NFκB, which are validated to be related with multiple myeloma by our immunohistochemistry experiment, computation and manually reviewed evidences. Moreover, we demonstrate that the systematic model performs better than widely used parameter estimation algorithms for the complicated signaling pathway.

Availability and implementation

We can not only use the systems biological model to infer the stiffness-associated genetic signaling pathway and locate the critical proteins, but also investigate the important pathways, proteins or genes for other type of the cancer. Thus, it holds universal scientific significance.

Supplementary information

Supplementary data are available at Bioinformatics online
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics
Authors: Shi Ning , Zhu Zexuan , Tang Ke , Parker David , He Shan
Published: July 2019

Motivation

Inferring gene regulatory networks from gene expression time series data is important for gaining insights into the complex processes of cell life. A popular approach is to infer Boolean networks. However, it is still a pressing open problem to infer accurate Boolean networks from experimental data that are typically short and noisy.

Results

To address the problem, we propose a Boolean network inference algorithm which is able to infer accurate Boolean network topology and dynamics from short and noisy time series data. The main idea is that, for each target gene, we use an And/Or tree ensemble algorithm to select prime implicants of which each is a conjunction of a set of input genes. The selected prime implicants are important features for predicting the states of the target gene. Using these important features we then infer the Boolean function of the target gene. Finally, the Boolean functions of all target genes are combined as a Boolean network. Using the data generated from artificial and real-world gene regulatory networks, we show that our algorithm can infer more accurate Boolean network topology and dynamics from short and noisy time series data than other algorithms. Our algorithm enables us to gain better insights into complex regulatory mechanisms of cell life.

Availability and implementation

Package ATEN is freely available at https://github.com/ningshi/ATEN.

Supplementary information

Supplementary data are available at Bioinformatics online.