bluuebunny/crossref_metadata_2025 huggingface dataset:
High-efficiency inverted metamorphic 1.7/1.1 eV GaInAsP/GaInAs dual-junction solar cells
Authors: Jain Nikhil , Schulte Kevin L. , Geisz John F. , Friedman Daniel J. , France Ryan M. , Perl Emmett E. , Norman Andrew G. , Guthrey Harvey L. , Steiner Myles A.
Published: February 2018

Photovoltaic conversion efficiencies of 32.6 ± 1.4% under the AM1.5 G173 global spectrum, and 35.5% ± 1.2% at 38-suns concentration under the direct spectrum, are demonstrated for a monolithic, dual-junction 1.7/1.1 eV solar cell. The tandem cell consists of a 1.7 eV GaInAsP top-junction grown lattice-matched to a GaAs substrate, followed by a metamorphic 1.1 eV GaInAs junction grown on a transparent, compositionally graded metamorphic AlGaInAs buffer. This bandgap combination is much closer to the dual-junction optimum and offers headroom for absolute 3% improvement in efficiency, in comparison to the incumbent lattice-matched GaInP/GaAs (∼1.86/1.41 eV) solar cells. The challenge of growing a high-quality 1.7 eV GaInAsP solar cell is the propensity for phase separation in the GaInAsP alloy. The challenge of lattice-mismatched GaInAs solar cell growth is that it requires minimizing the residual dislocation density during the growth of a transparent compositionally graded buffer to enable efficient metamorphic tandem cell integration. Transmission electron microscopy reveals relatively weak composition fluctuation present in the 1.7 eV GaInAsP alloy, attained through growth control. The threading dislocation density of the GaInAs junction is ∼1 × 106 cm−2, as determined from cathodoluminescence measurements, highlighting the quality of the graded buffer. These material advances have enabled the performance of both junctions to reach over 80% of their Shockley-Queisser limiting efficiencies, with both the subcells demonstrating a bandgap-voltage offset, WOC (=Eg/q-VOC), of ∼0.39 V.
Simple, low-noise piezo driver with feed-forward for broad tuning of external cavity diode lasers
Authors: Doret S. Charles
Published: February 2018

We present an inexpensive, low-noise (<260 μVrms, 0.1 Hz-100 kHz) design for a piezo driver suitable for frequency tuning of external-cavity diode lasers. This simple driver improves upon many commercially available drivers by incorporating circuitry to produce a “feed-forward” signal appropriate for making simultaneous adjustments to the piezo voltage and laser current, enabling dramatic improvements in a mode-hop-free laser frequency tuning range. We present the theory behind our driver’s operation, characterize its output noise, and demonstrate its use in absorption spectroscopy on the rubidium D1 line.
On the calculation of Lorenz numbers for complex thermoelectric materials
Authors: Wang Xufeng , Askarpour Vahid , Maassen Jesse , Lundstrom Mark
Published: February 2018

A first-principles informed approach to the calculation of Lorenz numbers for complex thermoelectric materials is presented and discussed. Example calculations illustrate the importance of using accurate band structures and energy-dependent scattering times. Results obtained by assuming that the scattering rate follows the density-of-states show that in the non-degenerate limit, Lorenz numbers below the commonly assumed lower limit of 2(kB/q)2 can occur. The physical cause of low Lorenz numbers is explained by the shape of the transport distribution. The numerical and physical issues that need to be addressed in order to produce accurate calculations of the Lorenz number are identified. The results of this study provide a general method that should contribute to the interpretation of measurements of total thermal conductivity and to the search for materials with low Lorenz numbers, which may provide improved thermoelectric figures of merit, zT.
Simulation study of the sub-terawatt laser wakefield acceleration operated in self-modulated regime
Authors: Hsieh C.-Y. , Lin M.-W. , Chen S.-H.
Published: February 2018

Laser wakefield acceleration (LWFA) can be accomplished by introducing a sub-terawatt (TW) laser pulse into a thin, high-density gas target. In this way, the self-focusing effect and the self-modulation that happened on the laser pulse produce a greatly enhanced laser peak intensity that can drive a nonlinear plasma wave to accelerate electrons. A particle-in-cell model is developed to study sub-TW LWFA when a 0.6-TW laser pulse interacts with a dense hydrogen plasma. Gas targets having a Gaussian density profile or a flat-top distribution are defined for investigating the properties of sub-TW LWFA when conducting with a gas jet or a gas cell. In addition to using 800-nm laser pulses, simulations are performed with 1030-nm laser pulses, as they represent a viable approach to realize the sub-TW LWFA driven by high-frequency, diode-pumped laser systems. The peak density which allows the laser peak power PL∼2Pcr of self-focusing critical power is favourable for conducting sub-TW LWFA. Otherwise, an excessively high peak density can induce an undesired filament effect which rapidly disintegrates the laser field envelope and violates the process of plasma wave excitation. The plateau region of a flat-top density distribution allows the self-focusing and the self-modulation of the laser pulse to develop, from which well-established plasma bubbles can be produced to accelerate electrons. The process of electron injection is complicated in such high-density plasma conditions; however, increasing the length of the plateau region represents a straightforward method to realize the injection and acceleration of electrons within the first bubble, such that an improved LWFA performance can be accomplished.
Phase-mixing of large amplitude electron oscillations in a cold inhomogeneous plasma
Authors: Karmakar Mithun , Maity Chandan , Chakrabarti Nikhil , Sengupta Sudip
Published: February 2018

Phase-mixing of large amplitude non-relativistic electron oscillations around an inhomogeneous background of massive ions has been studied in a cold plasma. For our purpose, a space periodic but time independent ion density profile along with a perturbation in the electron density is considered. An exact space-time dependent solution is presented in the parametric form by using Lagrangian coordinates. An inhomogeneity in the ion density causes the characteristic plasma frequency to acquire spatial dependency, leading to phase-mixing and thus breaking of excited oscillations at arbitrary amplitudes. The effects of finite amplitude electron density perturbation on the process of phase-mixing have also been discussed.
Polarisation in spin-echo experiments: Multi-point and lock-in measurements
Authors: Tamtögl Anton , Davey Benjamin , Ward David J. , Jardine Andrew P. , Ellis John , Allison William
Published: February 2018

Spin-echo instruments are typically used to measure diffusive processes and the dynamics and motion in samples on ps and ns time scales. A key aspect of the spin-echo technique is to determine the polarisation of a particle beam. We present two methods for measuring the spin polarisation in spin-echo experiments. The current method in use is based on taking a number of discrete readings. The implementation of a new method involves continuously rotating the spin and measuring its polarisation after being scattered from the sample. A control system running on a microcontroller is used to perform the spin rotation and to calculate the polarisation of the scattered beam based on a lock-in amplifier. First experimental tests of the method on a helium spin-echo spectrometer show that it is clearly working and that it has advantages over the discrete approach, i.e., it can track changes of the beam properties throughout the experiment. Moreover, we show that real-time numerical simulations can perfectly describe a complex experiment and can be easily used to develop improved experimental methods prior to a first hardware implementation.
Communication: Time-dependent optimized coupled-cluster method for multielectron dynamics
Authors: Sato Takeshi , Pathak Himadri , Orimo Yuki , Ishikawa Kenichi L.
Published: February 2018

Time-dependent coupled-cluster method with time-varying orbital functions, called time-dependent optimized coupled-cluster (TD-OCC) method, is formulated for multielectron dynamics in an intense laser field. We have successfully derived the equations of motion for CC amplitudes and orthonormal orbital functions based on the real action functional, and implemented the method including double excitations (TD-OCCD) and double and triple excitations (TD-OCCDT) within the optimized active orbitals. The present method is size extensive and gauge invariant, a polynomial cost-scaling alternative to the time-dependent multiconfiguration self-consistent-field method. The first application of the TD-OCC method of intense-laser driven correlated electron dynamics in Ar atom is reported.
Poisson-Fermi modeling of ion activities in aqueous single and mixed electrolyte solutions at variable temperature
Authors: Liu Jinn-Liang , Eisenberg Bob
Published: February 2018

The combinatorial explosion of empirical parameters in tens of thousands presents a tremendous challenge for extended Debye-Hückel models to calculate activity coefficients of aqueous mixtures of the most important salts in chemistry. The explosion of parameters originates from the phenomenological extension of the Debye-Hückel theory that does not take steric and correlation effects of ions and water into account. By contrast, the Poisson-Fermi theory developed in recent years treats ions and water molecules as nonuniform hard spheres of any size with interstitial voids and includes ion-water and ion-ion correlations. We present a Poisson-Fermi model and numerical methods for calculating the individual or mean activity coefficient of electrolyte solutions with any arbitrary number of ionic species in a large range of salt concentrations and temperatures. For each activity-concentration curve, we show that the Poisson-Fermi model requires only three unchanging parameters at most to well fit the corresponding experimental data. The three parameters are associated with the Born radius of the solvation energy of an ion in electrolyte solution that changes with salt concentrations in a highly nonlinear manner.
Mast cells promote small bowel cancer in a tumor stage-specific and cytokine-dependent manner
Authors: Saadalla Abdulrahman M. , Osman Abu , Gurish Michael F. , Dennis Kristen L. , Blatner Nichole R. , Pezeshki Abdulmohammad , McNagny Kelly M. , Cheroutre Hilde , Gounari Fotini , Khazaie Khashayarsha
Published: February 2018

Significance

We show that distinct subsets of mast cells (MCs) expand with sequential oncogenic events in small bowel cancer. Mucosal mast cells (MMCs) previously detected early duringTrichinella spiralisinfection expand in adenomatous polyps in an IL-10–dependent manner. Connective tissue mast cells (CTMCs), earlier shown to expand during the resolution of inflammation following clearance ofT. spiralis,are independent of IL-10 and associate with the transition of polyps to adenocarcinoma. IL-33 upregulates the CTMC lineage-specific protease murine mast cell protease 6 (mMCP6). Ablation of mMCP6 attenuates tumor growth. Thus, tissue sentinel cells respond to oncogenic events and cellular transformation in effect to help promote cancer. Delineating the types of MCs present at various stages of disease offers actionable cellular targets for therapeutic intervention in disease progression.
Reconceptualizing crisis
Authors: De Rycker Antoon
Published: February 2018

As a major socially significant phenomenon, crisis has been variously understood as an event, a moment of history, a turning point, a problem, a set of challenges, a paradox and so on. Drawing on third-generation practice theory and a range of case studies, the present study explores the possibility of reconceptualizing crisis as a social practice, i.e. as ‘doing crisis’. In addition, it considers whether a social practice approach can inform the analysis of crisis-related media practices and discourses. It is argued that a crisis-as-practice perspective is possible and also directly relevant to media discourse analysis, and that it can offer new and fresh insights.
Language-specificity in motion expression
Authors: Choi Soonja
Published: February 2018

This chapter examines the development of motion expression in two Korean children (1;11 to 4;2), compared to children acquiring French and English (from Hickmann et al. 2009). Korean is a verb-framed language (like French but unlike English which is satellite-framed; cf. Talmy 1985, 2000), and offers the following devices for motion expression: Serial verb constructions (SVC) in which Manner and Path verbs can co-occur within a single clause, and Manner adverbs including mimetics. Analyses show that from two years on, Korean children use SVCs and start producing Manner adverbs (particularly mimetics). As a result, they express more motion information and their motion expression is therefore semantically denser than in French (but less dense than in English). These findings support the view that language-specific features influence children’s motion expression from an early stage.
Development of discourse competence
Authors: Watorek Marzena
Published: February 2018

This paper examines the development of discourse competence through the oral production of two text types: spatial descriptions and film retellings, collected from French children (aged 4, 7, and 10) and a control group of adult French speakers. Results suggest that for young children the construction of a static spatial description is intrinsically more complex and poses more difficulties compared to the production of narratives. The construction of a description of a multidimensional configuration implies a heavier cognitive load than the construction of a narrative based on a chronological – inherently linear – event structure. Based on the analysis of reference to entities, we identify phenomena reflecting specific difficulties for children when performing a descriptive vs. a narrative task.
The blossoming of negation in gesture, sign and oral productions
Authors: Morgenstern Aliyah , Blondel Marion , Beaupoil-Hourdel Pauline , Benazzo Sandra , Boutet Dominique , Kochan Angelika , Limousin Fanny
Published: February 2018

Negation constructions in longitudinal adult-child data are an excellent source for the study of multimodality in language acquisition. First negative constructions seem to take over from early forms of rejection and avoidance, but tracing the transitions between actions and gestures, and between gestures and signed or spoken expressions in young children is quite complex. We focus on multimodal analysis of negation in the productions of five children between the ages of 0;10 and 3;6 interacting with their parents in various linguistic environments (monolingual French, monolingual English, monolingual LSF, bilingual French/LSF, bilingual French/Italian). We present the individual multimodal path of each child, illustrate the continuum between actions, gestures and signed/spoken constructions and analyze the common trend that leads children into symbolic communication through multi-semiotic means of expression.
Early predictors of language development in Autism Spectrum Disorder
Authors: Tager-Flusberg Helen
Published: February 2018

Although deficits in language are no longer considered diagnostic of Autism Spectrum Disorder (ASD), delays in language are among the earliest concerns noted by parents. By the time children with ASD enter school, their language skills vary widely from intact linguistic ability to no spoken language, though in all cases, communication is impaired and atypical. This chapter first reviews the research on the earliest behavioral and neural predictors of language in ASD based on studies that have prospectively followed infants who are at familial risk for ASD because they have an older sibling with the disorders. In the second part of the chapter research on behavioral predictors of language development in toddlers and preschoolers with ASD is presented. The gaps in the current literature and the clinical implications are discussed in the final sections.
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
Authors: Urrutia Eugene , Chen Hao , Zhou Zilu , Zhang Nancy R , Jiang Yuchao
Published: February 2018

Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies.

Availability and implementation

MARATHON is publicly available at https://github.com/yuchaojiang/MARATHON.

Supplementary information

Supplementary data are available at Bioinformatics online.
Health and Housework in Later Life: A Longitudinal Study of Retired Couples
Authors: Leopold Thomas , Schulz Florian
Published: February 2018

Objectives

To examine how changes in wives’ and husbands’ health influenced housework time and domestic outsourcing in retired couples.

Method

We estimated fixed-effects models to test hypotheses about the gendered influence of health declines on absolute and relative measures of time spent on routine and nonroutine housework as well as the probability of outsourcing housework. The data were obtained from 23 waves of the German Socio-Economic Panel Study, comprising N = 25,119 annual observations of N = 3,889 retired couples aged 60–85 years.

Results

Wives’ and husbands’ housework time declined with health status, but these effects were large only for serious health problems. We found evidence for within-couple compensation of spouses’ health declines, a mechanism that was limited to indispensable tasks of routine housework. The probability of getting paid help from outside the household increased with declining health, and this increase was more strongly tied to wives’ health declines than to husbands’ health declines.

Discussion

The results demonstrate the relevance of health status for the performance of housework in retired couples. The evidence attests to the resilience of couples during later-life stages in which health issues may severely inhibit domestic productivity.
Age of Migration and the Incidence of Cognitive Impairment: A Cohort Study of Elder Mexican-Americans
Authors: Garcia Marc A , Reyes Adriana M , Downer Brian , Saenz Joseph L , Samper-Ternent Rafael A , Raji Mukaila
Published: February 2018

Background and Objectives

To explore nativity and age of migration differentials in the incidence of cognitive impairment among older Mexican-Americans.

Research Design and Methods

We employ maximum-likelihood discrete time hazard models to estimate risk ratios of cognitive impairment in a sample of 2,708 Mexican-Americans 65 and older who were cognitively healthy at baseline over a follow-up period of up to 20 years.

Results

Late-life immigrant women have a 46% higher risk of cognitive impairment compared to U.S.-born Mexican-American women. Conversely, midlife immigrant men have a 29% lower risk of cognitive impairment compared to U.S.-born Mexican-American men. The incidence of cognitive impairment did not differ for early-life and midlife immigrant women relative to U.S.-born women or for early- and late-life immigrant men compared to U.S.-born men.

Discussion and Implications

Differences in cognitive impairment risk between U.S.-born and foreign-born Mexican-American subgroups may be partly due to health selectivity. Cognitive impairment is more prevalent among immigrant groups which may result in a higher burden on family members and/or high dependency on public resources. Programs are needed that can detect decline at earlier stages and reduce the risk for cognitive impairment among older immigrants entering their last decades of life.
Movement and Motion of Soybean Cyst Nematode Heterodera glycines Populations and Individuals in Response to Abamectin
Authors: Jensen Jared P. , Beeman Augustine Q. , Njus Zach L. , Kalwa Upender , Pandey Santosh , Tylka Gregory L.
Published: February 2018

Two new in vitro methods were developed to analyze plant-parasitic nematode behavior, at the population and the individual organism levels, through time-lapse image analysis. The first method employed a high-resolution flatbed scanner to monitor the movement of a population of nematodes over a 24-h period at 25°C. The second method tracked multiple motion parameters of individual nematodes on a microscopic scale, using a high-speed camera. Changes in movement and motion of second-stage juveniles (J2) of the soybean cyst nematode Heterodera glycines Ichinohe were measured after exposure to a serial dilution of abamectin (0.1 to 100 μg/ml). Movement and motion of H. glycines were significantly reduced as the concentration of abamectin increased. The effective range of abamectin to inhibit movement and motion of H. glycines J2 was between 1.0 and 10 μg/ml. Proof-of-concept experiments for both methods produced one of the first in vitro sensitivity studies of H. glycines to abamectin. The two methods developed allow for higher-throughput analysis of nematode movement and motion and provide objective and data-rich measurements that are difficult to achieve from conventional microscopic laboratory methods.
Provider-performed microscopy empowers PAs at the point of care
Authors: Brown Gina R. , Wigdahl Joshua B. , Stebens Tiana M.
Published: February 2018

Provider-performed microscopy (PPM) is a diagnostic tool recommended when patients present with several types of gynecologic infections or fungal infections of skin or nails. PPM allows for immediate and accurate treatment, and can strengthen the relationship between clinician and patient. This article reviews two microscopy techniques, the saline wet mount and the potassium hydroxide (KOH) preparation, and discusses their indications for use.
End-of-Life Communication
Authors: Isaacson Mary J. , Minton Mary E.
Published: February 2018

Communication is imperative for end-of-life decision-making; however, descriptions of key strategies used by nurses are missing. A phenomenological approach was used to interpret interviews from 10 hospice/palliative nurses. The overarching pattern is the closing composition. Key communication strategies/patterns include establishing context, acknowledging through attentive listening, making it safe for them to die, planning goals of care, and being honest. Essential is the awareness that nurse, patient, and family all hold expertise in the subject matter. It is imperative that pre-/postnursing licensure curriculum be expanded to include training in mutual influence communication practices and mentoring in the skill of orchestration.
Safe Zone Quantification of the Third Sacral Segment in Normal and Dysmorphic Sacra
Authors: Hwang John S. , Reilly Mark C. , Shaath Mohammad K. , Changoor Stuart , Eastman Jonathan , Routt Milton Lee (Chip) , Sirkin Michael S. , Adams Mark R.
Published: February 2018

Objective:

To quantify the osseous anatomy of the dysmorphic third sacral segment and assess its ability to accommodate internal fixation.

Design:

Retrospective chart review of a trauma database.

Setting:

University Level 1 Trauma Center.

Patients:

Fifty-nine patients over the age of 18 with computed tomography scans of the pelvis separated into 2 groups: a group with normal pelvic anatomy and a group with sacral dysmorphism.

Main Outcome Measurements:

The sacral osseous area was measured on computed tomography scans in the axial, coronal, and sagittal planes in normal and dysmorphic pelves. These measurements were used to determine the possibility of accommodating a transiliac transsacral screw in the third sacral segment.

Results:

In the normal group, the S3 coronal transverse width averaged 7.71 mm and the S3 axial transverse width averaged 7.12 mm. The mean S3 cross-sectional area of the normal group was 55.8 mm. The dysmorphic group was found to have a mean S3 coronal transverse width of 9.49 mm, an average S3 axial transverse width of 9.14 mm, and an S3 cross-sectional area of 77.9 mm.

Conclusions:

The third sacral segment of dysmorphic sacra has a larger osseous pathway available to safely accommodate a transiliac transsacral screw when compared with normal sacra. The S3 segment of dysmorphic sacra can serve as an additional site for screw placement when treating unstable posterior pelvic ring fractures.
The Utility of ICU Readmission as a Quality Indicator and the Effect of Selection*
Authors: Maharaj Ritesh , Terblanche Marius , Vlachos Savvas
Published: February 2018

Objectives:

Intensive care readmission rates are used to signal quality, yet it is unclear whether they represent poor quality in the transition of care from the ICU to the ward, patient factors, or differences in survival of the initial admission. This study aims to measure the selection effect of surviving the initial ICU admission on readmission rates.

Design:

Retrospective cohort study of adult patients admitted to ICUs participating in the Case Mix Program database from the Intensive Care National Audit Research Centre.

Settings:

The study includes 262 ICUs in the United Kingdom.

Patients:

The study includes 682,975 patients admitted to ICUs between 2010 and 2014.

Interventions:

None.

Measurements and Main Results:

The study includes 682,975 patients admitted to ICUs in the United Kingdom. There were 591,710 patients discharged alive, of which 9,093 (1.53%) were readmitted within the first 2 days of ICU discharge. Post-ICU admission hospital mortality and ICU readmission were poorly correlated (r = 0.130). The addition of a selection model resulted in a weaker correlation (r = 0.082).

Conclusions:

ICU readmission performed poorly as a performance metric. The selection process by which only patients who survive their index admission are eligible for readmission has a significant effect on ICU readmission rankings, particularly the higher ranked ICUs. Failure to consider this selection bias gives misleading signals about ICU performance and leads to faulty design of incentive schemes.
Differences in Optic Nerve Head, Retinal Nerve Fiber Layer, and Ganglion Cell Complex Parameters Between Caucasian and Chinese Subjects
Authors: Chansangpetch Sunee , Huang Guofu , Coh Paul , Oldenburg Catherine , Amoozgar Behzad , He Mingguang , Lin Shan C.
Published: February 2018

Purpose:

To compare optic nerve head, peripapillary retinal nerve fiber layer (pRNFL), and ganglion cell complex (GCC) parameters between Caucasian and ethnic Chinese.

Materials and Methods:

Normal subjects above 40 years old and self-identified as being Caucasian and Chinese were recruited. They were evaluated with spectral-domain optical coherence tomography (RTVue-100). Parameters related to the optic nerve head, pRNFL, and GCC analysis protocols were acquired. Multivariable linear regression was performed adjusting for potential confounders.

Results:

Data from 116 Caucasian and 130 Chinese subjects were available for analysis. Mean age of all participants was 66.72 (SD 10.82) years. There were statistically significant differences for disc area (DA), area cup-to-disc, vertical cup-to-disc, and cup volume (P=0.02, 0.004, 0.02, and 0.03, respectively), greater in Chinese. After adjusting for age, sex, axial length (AL), intraocular pressure (IOP), DA, and GCC thickness, Chinese subjects had significantly greater thickness in all pRNFL parameters (mean differences ranged between 4.29 and 9.93 μm; all P<0.001) except the nasal quadrant. GCC outcomes were also adjusted for DA and pRNFL; Caucasians had significantly higher average GCC and inferior GCC (mean difference 2.97 and 3.45 μm, respectively; P<0.01), whereas the Chinese group had significantly higher ganglion cell global loss volume (mean difference 2.47 %, P<0.001).

Conclusions:

This study suggests there is significantly greater pRNFL thickness in Chinese, which were independent of age, AL, IOP, and DA, and possibly greater GCC in Caucasians after adjustment for age, AL, IOP, DA, and pRNFL thickness.
Sexually Transmitted Infection Positivity Rate and Treatment Uptake Among Female and Male Sexual Assault Victims Attending The Amsterdam STI Clinic Between 2005 and 2016
Authors: van Rooijen Martijn S. , Schim van der Loeff Maarten F. , van Kempen Loes , de Vries Henry J.C.
Published: February 2018

Background

Victims could become infected with sexually transmitted infections (STIs) during a sexual assault. Several guidelines recommend presumptive antimicrobial therapy for sexual assault victims (SAVs). We assessed the STI positivity rate and treatment uptake of female and male SAVs at the Amsterdam STI clinic.

Methods

Sexual assault victims answered assault-related questions and were tested for bacterial STI (chlamydia, gonorrhea, and syphilis), hepatitis B, and HIV during their initial visits. Sexual assault victim characteristics were compared with non-SAV clients. Backward multivariable logistic regression analysis was conducted to assess whether being an SAV was associated with a bacterial STI. The proportion of those returning for treatment was calculated.

Results

From January 2005 to September 2016, 1066 (0.6%) of 168,915 and 135 (0.07%) of 196,184 consultations involved female and male SAVs, respectively. Among female SAVs, the STI positivity rate was 11.2% versus 11.6% among non-SAVs (P = 0.65). Among male SAVs, the STI positivity rate was 12.6% versus 17.7% among non-SAVs (P = 0.12). In multivariable analysis, female SAVs did not have increased odds for an STI (odds ratio 0.94; 95% confidence interval, 0.77–1.13), and male SAVs had significantly lower odds for an STI (odds ratio, 0.60; 95% confidence interval, 0.36–0.98). Of SAVs requiring treatment, 89.0% (female) and 92.0% (male) returned.

Conclusions

The STI positivity rate among female SAVs was comparable with female non-SAVs, but male SAVs had lower odds for having a bacterial STI than did male non-SAVs, when adjusting for confounders. The return rate of SAV for treatment was high and therefore does not support the recommendations for presumptive therapy.
Psychological Stress and Mitochondria: A Systematic Review
Authors: Picard Martin , McEwen Bruce S.
Published: February 2018

Objective

Mitochondria are multifunctional life-sustaining organelles that represent a potential intersection point between psychosocial experiences and biological stress responses. This article provides a systematic review of the effects of psychological stress on mitochondrial structure and function.

Methods

A systematic review of the literature investigating the effects of psychological stress on mitochondrial function was conducted. The review focused on experimentally controlled studies allowing us to draw causal inference about the effect of induced psychological stress on mitochondria.

Results

A total of 23 studies met the inclusion criteria. All studies involved male laboratory animals, and most demonstrated that acute and chronic stressors influenced specific facets of mitochondrial function, particularly within the brain. Nineteen studies showed significant adverse effects of psychological stress on mitochondria and four found increases in function or size after stress. In humans, only six observational studies were available, none with experimental designs, and most only measured biological markers that do not directly reflect mitochondrial function, such as mitochondrial DNA copy number.

Conclusons

Overall, evidence supports the notion that acute and chronic stressors influence various aspects of mitochondrial biology, and that chronic stress exposure can lead to molecular and functional recalibrations among mitochondria. Limitations of current animal and human studies are discussed. Maladaptive mitochondrial changes that characterize this subcellular state of stress are termed mitochondrial allostatic load. Prospective studies with sensitive measures of specific mitochondrial outcomes will be needed to establish the link between psychosocial stressors, emotional states, the resulting neuroendocrine and immune processes, and mitochondrial energetics relevant to mind-body research in humans.
Urinary Management With an External Female Collection Device
Authors: Beeson Terrie , Davis Carmen
Published: February 2018

BACKGROUND:

Strategies to decrease use of female indwelling urinary catheters and catheter-associated urinary tract infections are challenging due to the limited availability of proper fitting external collection devices. Female urinary incontinence predisposes the skin to potential pain, itching, burning, infection, or pressure injuries.

CASE STUDIES:

This article discusses 3 patients' trajectory of care with use of an external female urinary collection device. All of these females were incontinent of urine after the indwelling urinary catheter was removed and managed with an external female urinary collection device.

CONCLUSIONS:

The use of an external female urinary collection device is a feasible alternative to an indwelling urinary catheter as well as managing urinary incontinence.
Adventure tourism and schistosomiasis: serology and clinical findings in a group of Danish students after white-water rafting in Uganda
Authors: Röser Dennis , Bjerrum Stephanie , Helleberg Marie , Nielsen Henrik Vedel , David Kim Peter , Thybo Søren , Stensvold Christen Rune
Published: February 2018

Introduction. Diagnosis of schistosomiasis in travellers is a clinical challenge, since cases may present with no symptoms or a few non-specific symptoms. Here, we report on the laboratory and clinical findings in Danish travellers exposed to Schistosoma-infested water during white-water rafting on the Ugandan part of the upper Nile River in July 2009.

Case presentation. Forty travellers were offered screening for Schistosoma-specific antibodies. Serological tests were performed 6–65 weeks after exposure. A self-reporting questionnaire was used to collect information on travel activity and health history, fresh water exposure, and symptoms. Seropositive cases were referred to hospitals where clinical and biochemical data were collected. Schistosoma-specific antibodies were detected in 13/35 (37 %) exposed participants, with 4/13 (31 %) seroconverting later than 2 months following exposure. Four of thirteen (31 %) cases reported ≥3 symptoms compatible with schistosomiasis, with a mean onset of 41 days following exposure. No Schistosoma eggs were detected in stool or urine in any of the cases. Peripheral eosinophilia (>0.45×109 cells l−1) was seen in 4/13 cases, while IgE levels were normal in all cases.

Conclusion. Schistosomiasis in travellers is not necessarily associated with specific signs or symptoms, eosinophilia, raised IgE levels, or detection of eggs. The only prognostic factor for infection was exposure to freshwater in a Schistosoma-endemic area. Seroconversion may occur later than 2 months after exposure and therefore – in the absence of other diagnostic evidence – serology testing should be performed up to at least 2–3 months following exposure to be able to rule out schistosomiasis.
Dopamine signaling modulates the stability and integration of intrinsic brain networks
Authors: Shafiei Golia , Zeighami Yashar , Clark Crystal A. , Coull Jennifer T. , Nagano-Saito Atsuko , Leyton Marco , Dagher Alain , Mišić Bratislav
Published: February 2018

Dopaminergic projections are hypothesized to stabilize neural signaling and neural representations, but how they shape regional information processing and large-scale network interactions remains unclear. Here we investigated effects of lowered dopamine levels on within-region temporal signal variability (measured by sample entropy) and between-region functional connectivity (measured by pairwise temporal correlations) in the healthy brain at rest. The acute phenylalanine and tyrosine depletion (APTD) method was used to decrease dopamine synthesis in 51 healthy participants who underwent resting-state functional MRI (fMRI) scanning. Functional connectivity and regional signal variability were estimated for each participant. Multivariate partial least squares (PLS) analysis was used to statistically assess changes in signal variability following APTD as compared to the balanced control treatment. The analysis captured a pattern of increased regional signal variability following dopamine depletion. Changes in hemodynamic signal variability were concomitant with changes in functional connectivity, such that nodes with greatest increase in signal variability following dopamine depletion also experienced greatest decrease in functional connectivity. Our results suggest that dopamine may act to stabilize neural signaling, particularly in networks related to motor function and orienting attention towards behaviorally-relevant stimuli. Moreover, dopaminedependent signal variability is critically associated with functional embedding of individual areas in large-scale networks.
Machine learning algorithms for systematic review: reducing workload in a preclinical review of animal studies and reducing human screening error
Authors: Bannach-Brown Alexandra , Przybyła Piotr , Thomas James , Rice Andrew S.C. , Ananiadou Sophia , Liao Jing , Macleod Malcolm Robert
Published: February 2018

Background

Here we outline a method of applying existing machine learning (ML) approaches to aid citation screening in an on-going broad and shallow systematic review of preclinical animal studies, with the aim of achieving a high performing algorithm comparable to human screening.

Methods

We applied ML approaches to a broad systematic review of animal models of depression at the citation screening stage. We tested two independently developed ML approaches which used different classification models and feature sets. We recorded the performance of the ML approaches on an unseen validation set of papers using sensitivity, specificity and accuracy. We aimed to achieve 95% sensitivity and to maximise specificity. The classification model providing the most accurate predictions was applied to the remaining unseen records in the dataset and will be used in the next stage of the preclinical biomedical sciences systematic review. We used a cross validation technique to assign ML inclusion likelihood scores to the human screened records, to identify potential errors made during the human screening process (error analysis).

Results

ML approaches reached 98.7% sensitivity based on learning from a training set of 5749 records, with an inclusion prevalence of 13.2%. The highest level of specificity reached was 86%. Performance was assessed on an independent validation dataset. Human errors in the training and validation sets were successfully identified using assigned the inclusion likelihood from the ML model to highlight discrepancies. Training the ML algorithm on the corrected dataset improved the specificity of the algorithm without compromising sensitivity. Error analysis correction leads to a 3% improvement in sensitivity and specificity, which increases precision and accuracy of the ML algorithm.

Conclusions

This work has confirmed the performance and application of ML algorithms for screening in systematic reviews of preclinical animal studies. It has highlighted the novel use of ML algorithms to identify human error. This needs to be confirmed in other reviews, , but represents a promising approach to integrating human decisions and automation in systematic review methodology.
Pleiotropic Mapping and Annotation Selection in Genome-wide Association Studies with Penalized Gaussian Mixture Models
Authors: Zeng Ping , Hao Xinjie , Zhou Xiang
Published: February 2018

Motivation

Genome-wide association studies (GWASs) have identified many genetic loci associated with complex traits. A substantial fraction of these identified loci are associated with multiple traits – a phenomena known as pleiotropy. Identification of pleiotropic associations can help characterize the genetic relationship among complex traits and can facilitate our understanding of disease etiology. Effective pleiotropic association mapping requires the development of statistical methods that can jointly model multiple traits with genome-wide SNPs together.

Results

We develop a joint modeling method, which we refer to as the integrative MApping of Pleiotropic association (iMAP). iMAP models summary statistics from GWASs, uses a multivariate Gaussian distribution to account for phenotypic correlation, simultaneously infers genome-wide SNP association pattern using mixture modeling, and has the potential to reveal causal relationship between traits. Importantly, iMAP integrates a large number of SNP functional annotations to substantially improve association mapping power, and, with a sparsity-inducing penalty, is capable of selecting informative annotations from a large, potentially noninformative set. To enable scalable inference of iMAP to association studies with hundreds of thousands of individuals and millions of SNPs, we develop an efficient expectation maximization algorithm based on an approximate penalized regression algorithm. With simulations and comparisons to existing methods, we illustrate the benefits of iMAP both in terms of high association mapping power and in terms of accurate estimation of genome-wide SNP association patterns. Finally, we apply iMAP to perform a joint analysis of 48 traits from 31 GWAS consortia together with 40 tissue-specific SNP annotations generated from the Roadmap Project. iMAP is freely available atwww.xzlab.org/software.html.
Multiple prebiotic metals mediate translation
Authors: Bray Marcus S. , Lenz Timothy K. , Haynes Jay William , Bowman Jessica C. , Petrov Anton S. , Reddi Amit R. , Hud Nicholas V. , Williams Loren Dean , Glass Jennifer B.
Published: February 2018

Today, Mg2+is an essential cofactor with diverse structural and functional roles in life’s oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (Selective 2’HydroxylAcylation analyzed byPrimerExtension) was used to compare the effect of Mg2+, Fe2+, and Mn2+on the tertiary structure of rRNA. Then, we usedin vitrotranslation reactions to test whether Fe2+or Mn2+could mediate protein production, and quantified ribosomal metal content. We found that: (i) Mg2+, Fe2+, and Mn2+had strikingly similar effects on rRNA folding; (ii) Fe2+and Mn2+can replace Mg2+as the dominant divalent cation during translation of mRNA to functional protein; (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+and Mn2+were abundant, these findings suggest that Fe2+and Mn2+played a role in early ribosomal evolution.

SIGNIFICANCE

Ribosomes are found in every living organism where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ~4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions (low O2, high Fe2+, high Mn2+). Our results expand the roles of Fe2+and Mn2+in ancient and extant biochemistry as cofactors for ribosomal structure and function.
The neurobiology of BRD1 implicates sex-biased dysregulation of nuclear receptor signaling in mental disorders
Authors: Rajkumar Anto P. , Qvist Per , Larsen Sanne H. , Lazarus Ross , Pallesen Jonatan , Nava Nicoletta , Winther Gudrun , Liebenberg Nico , Paternoster Veerle , Fryland Tue , Palmfeldt Johan , Fejgin Kim , Mørk Arne , Nyegaard Mette , Pakkenberg Bente , Didriksen Michael , Nyengaard Jens R. , Wegener Gregers , Mors Ole , Christensen Jane H. , Børglum Anders D.
Published: February 2018

The schizophrenia and bipolar disorder associated gene, BRD1, encodes a scaffold protein that in complex with epigenetic modifiers regulate gene sets enriched for psychiatric disorder risk. Preclinical evidence from male Brd1+/− mice has previously implicated BRD1 with phenotypes of translational relevance to schizophrenia. Here we describe the phenotype of female Brd1+/− mice and report attenuated dendritic architecture and monoaminergic dysregulation accompanied by sex-specific changes in affective behaviors. In accordance, global gene expression profiling reveals regional dysregulation of gene sets enriched with major depressive disorder and schizophrenia risk in female and male Brd1+/− mice, respectively. Independent of sex, however, differentially expressed genes cluster in common functional pathways associated with psychiatric disorders, including mitochondrial dysfunction and oxidative phosphorylation as well as G-protein coupled-, and nuclear receptor mediated signaling. Accordingly, we provide in vitro evidence that BRD1 modulates the transcriptional drive of a subset of nuclear receptors (e.g. the vitamin D and glucocorticoid receptors). Moreover, we demonstrate enrichment of psychiatric disorder risk in the target genes of nuclear receptors, sex-biased expression of several nuclear receptor genes in the adult brain of Brd1+/− mice, and that sex-biased genes in general are enriched with nuclear receptor genes particularly at the earliest developmental stage of the human brain. Overall, our data suggests that the spatio-temporal interaction between BRD1 and subsets of nuclear receptors in the brain is sex-biased and that hampered BRD1 mediated regulation of target genes governed by certain nuclear receptors may significantly contribute to sex differences in psychopathology.
A bacterial growth law out of steady-state
Authors: Kohanim Yael Korem , Levi Dikla , Jona Ghil , Bren Anat , Alon Uri
Published: February 2018

Bacterial growth depends on numerous reactions, and yet follows surprisingly simple laws that inspired biologists for decades. Growth laws until now primarily dealt with steady-state exponential growth in constant conditions. However, bacteria in nature often face fluctuating environments, with nutritional upshifts and downshifts. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for strong upshifts using an optimal resource-allocation model that was previously calibrated at steady-state growth: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and robotic batch culture experiments, as well as previous data from several species, and find good agreement with the model predictions. The increase in growth rate after an upshift indicates that ribosomes have spare capacity. We demonstrate theoretically that spare ribosomal capacity has the cost of slow steady-state growth, but is beneficial in fluctuating environments because it prevents large overshoots in intracellular metabolites after an upshift and allows rapid response to change. We also provide predictions for downshifts for future experimental tests. Spare capacity appears in diverse biological systems, and the present study quantifies the optimal degree of spare capacity, which rises the slower the growth rate, and suggests that it can be precisely regulated.