bluuebunny/crossref_metadata_2025 huggingface dataset:
Maize–lablab intercropping is promising in supporting the sustainable intensification of smallholder cropping systems under high climate risk in southern Africa
Authors: Rapholo Edith , Odhiambo Jude J. O. , Nelson William C. D. , Rötter Reimund P. , Ayisi Kingsley , Koch Marian , Hoffmann Munir P.
Published: July 2019

Identifying options for the sustainable intensification of cropping systems in southern Africa under prevailing high climate risk is needed. With this in mind, we tested an intercropping system that combined the staple crop maize with lablab, a local but underutilised legume. Grain and biomass productivity was determined for four variants (i) sole maize (sole-maize), (ii) sole lablab (sole-lablab), (iii) maize/lablab with both crops sown simultaneously (intercropped-SP) and (iv) maize/lablab with lablab sown 28 days after the maize crop (intercropped-DP). Soil water and weather data were monitored and evaluated. The trial was conducted for two seasons (2015/2016 and 2016/2017) at two sites in the Limpopo Province, South Africa: Univen (847 mm rainfall, 29.2 °C maximum and 18.9 °C minimum temperature average for the cropping season over the years 2008–2017) and Syferkuil (491 mm rainfall, with 27.0 °C maximum and 14.8 °C minimum temperature). Analysis revealed three key results: The treatment with intercropped-SP had significantly lower maize yields (2320 kg ha−1) compared with maize in intercropped-DP (2865 kg ha−1) or sole-maize (2623 kg ha−1). As expected, maize yields in the El Niño affected in season 2015/2016 were on average 1688 kg ha−1 lower than in 2016/2017. Maize yields were significantly lower (957 kg ha−1) at Univen, the warmer site with higher rainfall, than at Syferkuil. In 2015/2016, maximum temperature at Univen exceeded 40 °C around anthesis. Furthermore, soil water was close to the estimated permanent wilting point (PWP) for most of the cropping season, which indicates possible water limitations. In Syferkuil, the soil water was maintained well above PWP. Lablab yields were low, around 500 ha−1, but stable as they were not affected by treatment across season and site. Overall, the study demonstrated that intercropped-DP appears to use available soil water more efficiently than sole maize. Intercropped-DP could therefore be considered as an option for sustainable intensification under high climate risk and resource-limited conditions for smallholders in southern Africa.
Indonesian Islamic Socialism and its South Asian Roots
Authors: FOGG KEVIN W.
Published: July 2019

Islamic socialism was a major intellectual and political movement in Indonesia in the twentieth century, with ongoing influences until today. However, this movement did not follow the most common narratives of Indonesian intellectual history, which trace religious influences to the Middle East and political movements to anti-colonial reaction in terms framed by the Dutch. Rather, the first major Indonesian proponent of Islamic socialism, H. O. S. Tjokroaminoto, took his thinking on Islamic socialism directly from the English-language work of a South Asian itinerant scholar, Mushir Hosein Kidwai, in a process that most likely had the minority Ahmadiyyah community as intermediaries. Future Islamic socialist thought, much of it influenced by Tjokroaminoto, continued to echo through Indonesian secular nationalism, political Islam, and even Islamism. Studying the intellectual origins of Islamic socialism in Indonesia, then, shows not only the roots of an important strand of Southeast Asian politics in the last century, but also the importance of alternative currents of thought (South Asian, outside the mainstream, Anglophone) in Southeast Asian Islam.
Micro Aerial Vehicle Navigation with Visual-Inertial Integration Aided by Structured Light
Authors: Wang Yunshu , Liu Jianye , Wang Jinling , Zeng Qinghua , Shen Xuesong , Zhang Yueyuan
Published: July 2019

Considering that traditional visual navigation cannot be utilised in low illumination and sparse feature environments, a novel visual-inertial integrated navigation method using a Structured Light Visual (SLV) sensor for Micro Aerial Vehicles (MAVs) is proposed in this paper. First, the measurement model based on an SLV sensor is studied and built. Then, using the state model based on error equations of an Inertial Navigation System (INS), the measurement model based on the error of the relative motion measured by INS and SLV is built. Considering that the measurements in this paper are mainly related to the position and attitude information of the present moment, the state error accumulation in traditional visual-inertial navigation can be avoided. An Adaptive Sage-Husa Kalman Filter (ASHKF) based on multiple weighting factors is proposed and designed to make full use of the SLV measurements. The results of the simulation and the experiment based on real flight data indicate that high accuracy position and attitude estimations can be obtained with the help of the algorithm proposed in this paper.
Impact of a training program on the surveillance of Clostridioides difficile infection
Authors: Sopena N. , Freixas N. , Bella F. , Pérez J. , Hornero A. , Limon E. , Gudiol F. , Pujol M. ,   the VINCat Clostridioides difficile study group
Published: July 2019

A high degree of vigilance and appropriate diagnostic methods are required to detect Clostridioides difficile infection (CDI). We studied the effectiveness of a multimodal training program for improving CDI surveillance and prevention. Between 2011 and 2016, this program was made available to healthcare staff of acute care hospitals in Catalonia. The program included an online course, two face-to-face workshops and dissemination of recommendations on prevention and diagnosis. Adherence to the recommendations was evaluated through surveys administered to the infection control teams at the 38 participating hospitals. The incidence of CDI increased from 2.20 cases/10 000 patient-days in 2011 to 3.41 in 2016 (P < 0.001). The number of hospitals that applied an optimal diagnostic algorithm rose from 32.0% to 71.1% (P = 0.002). Hospitals that applied an optimal diagnostic algorithm reported a higher overall incidence of CDI (3.62 vs. 1.92, P < 0.001), and hospitals that were more active in searching for cases reported higher rates of hospital-acquired CDI (1.76 vs. 0.84, P < 0.001). The results suggest that the application of a multimodal training strategy was associated with a significant rise in the reporting of CDI, as well as with an increase in the application of the optimal diagnostic algorithm.
Pubertal development mediates the association between family environment and brain structure and function in childhood
Authors: Thijssen Sandra , Collins Paul F. , Luciana Monica
Published: July 2019

Psychosocial acceleration theory suggests that pubertal maturation is accelerated in response to adversity. In addition, suboptimal caregiving accelerates development of the amygdala–medial prefrontal cortex circuit. These findings may be related. Here, we assess whether associations between family environment and measures of the amygdala–medial prefrontal cortex circuit are mediated by pubertal development in more than 2000 9- and 10-year-old children from the Adolescent Brain Cognitive Development Study (http://dx.doi.org/10.15154/1412097). Using structural equation modeling, demographic, child-reported, and parent-reported data on family dynamics were compiled into a higher level family environment latent variable. Magnetic resonance imaging preprocessing and compilations were performed by the Adolescent Brain Cognitive Development Study's data analysis core. Anterior cingulate cortex (ACC) thickness, area, white matter fractional anisotropy, amygdala volume, and cingulo-opercular network–amygdala resting-state functional connectivity were assessed. For ACC cortical thickness and ACC fractional anisotropy, significant indirect effects indicated that a stressful family environment relates to more advanced pubertal stage and more mature brain structure. For cingulo-opercular network–amygdala functional connectivity, results indicated a trend in the expected direction. For ACC area, evidence for quadratic mediation by pubertal stage was found. Sex-stratified analyses suggest stronger results for girls. Despite small effect sizes, structural measures of circuits important for emotional behavior are associated with family environment and show initial evidence of accelerated pubertal development.
PhD Abstracts
Authors: HUTTON GRAHAM
Published: July 2019

Many students complete PhDs in functional programming each year. As a service to the community, twice per year the Journal of Functional Programming publishes the abstracts from PhD dissertations completed during the previous year.
Psychometric Properties of the NIH Toolbox Cognition Battery in Healthy Older Adults: Reliability, Validity, and Agreement with Standard Neuropsychological Tests
Authors: Scott Emmi P. , Sorrell Anne , Benitez Andreana
Published: July 2019

Objective:

Few independent studies have examined the psychometric properties of the NIH Toolbox Cognition Battery (NIHTB-CB) in older adults, despite growing interest in its use for clinical purposes. In this paper we report the test–retest reliability and construct validity of the NIHTB-CB, as well as its agreement or concordance with traditional neuropsychological tests of the same construct to determine whether tests could be used interchangeably.

Methods:

Sixty-one cognitively healthy adults ages 60–80 completed “gold standard” (GS) neuropsychological tests, NIHTB-CB, and brain MRI. Test–retest reliability, convergent/discriminant validity, and agreement statistics were calculated using Pearson’s correlations, concordance correlation coefficients (CCC), and root mean square deviations.

Results:

Test–retest reliability was acceptable (CCC = .73 Fluid; CCC = .85 Crystallized). The NIHTB-CB Fluid Composite correlated significantly with cerebral volumes (r’s = |.35−.41|), and both composites correlated highly with their respective GS composites (r’s = .58−.84), although this was more variable for individual tests. Absolute agreement was generally lower (CCC = .55 Fluid; CCC = .70 Crystallized) due to lower precision in fluid scores and systematic overestimation of crystallized composite scores on the NIHTB-CB.

Conclusions:

These results support the reliability and validity of the NIHTB-CB in healthy older adults and suggest that the fluid composite tests are at least as sensitive as standard neuropsychological tests to medial temporal atrophy and ventricular expansion. However, the NIHTB-CB may generate different estimates of performance and should not be treated as interchangeable with established neuropsychological tests.
Visualizing Gendered Representations of Male and Female Teachers	Using a Reverse Correlation Paradigm
Authors: Degner Juliane , Mangels Jana , Zander Lysann
Published: July 2019

Abstract. Stereotypically, men are expected to outperform women in science, technology, engineering, and mathematics (STEM) domains, and women to outperform men in language. We conceptually replicated this association using reverse correlation tasks. Without available gender information, participants generated male images of physics teachers and female images of language teachers (Studies 1 and 3). Personal endorsement of respective ability stereotypes inconsistently predicted these effects (Studies 1 and 3). With unambiguous gender information (Study 2), participants generated feminized images of female language teachers and masculinized images of female physics teachers, whereas images of male teachers were unaffected by academic domain. Stereotype endorsement affected perceptions of female but not male teachers, suggesting that appearing feminine in STEM domains still signals professional mismatch.
Focal Mechanisms of Deep Low‐Frequency Earthquakes Beneath Zao Volcano, Northeast Japan, and Relationship to the 2011 Tohoku Earthquake
Authors: Oikawa Genki , Aso Naofumi , Nakajima Junichi
Published: July 2019

Small, deep low‐frequency earthquakes (LFEs) with dominant frequencies of 2–8 Hz occur at depths of 20–40 km and are thought to be related to movement of magma or crustal fluid, but their physical source processes remain largely unknown. Therefore, we determine the focal mechanisms of LFEs beneath Zao volcano, Northeast Japan, using the S/P amplitude ratio. Most focal mechanisms are classified into five groups: three types of double couples, a compensated linear vector dipole group, and a single force group. Double couples in 2007–2012 are consistent with those expected for the regional stress field, but no such events have been observed since 2013. This transition in focal mechanisms was simultaneous with a rapid increase in LFE activity beneath Zao. Our results suggest that LFEs beneath Zao were controlled mainly by the local stress field, but the stress field changed about two years after the 2011 Tohoku earthquake.
Spray Generation by a Plunging Breaker
Authors: Erinin M. A. , Wang S. D. , Liu R. , Towle D. , Liu X. , Duncan J. H.
Published: July 2019

An experimental investigation of droplet generation by a plunging breaking wave is presented. In this work, simultaneous measurements of the wave crest profile evolution and of droplets ranging in radius down to 50 μm for a mechanically generated plunging breaker during many repeated breaking events in freshwater are performed. We find three distinct time zones of droplet production, first when the jet impacts the free surface upstream of the wave crest, second when the large air bubbles entrapped by the plunging jet impact reach the free surface and burst, and third when smaller bubbles burst upon reaching the free surface later in the breaking process. These subprocesses account for 22%, 44%, and 34%, respectively, of the average of 653 droplets produced per breaking event. The probability distributions of the ranges of large and small droplet radii are well represented by power law functions that intersect at a radius of 418 μm.
Two Typical Ionospheric Irregularities Associated With the Tropical Cyclones Tembin (2012) and Hagibis (2014)
Authors: Lou Yidong , Luo Xiaomin , Gu Shengfeng , Xiong Chao , Song Qian , Chen Biyan , Xiao Qinqin , Chen Dezhong , Zhang Zheng , Zheng Gang
Published: July 2019

Two remarkable ionospheric irregularities named equatorial plasma bubble (EPB) and medium‐scale traveling ionospheric disturbance (MSTID) are verified by using multi‐instrumental observations, for example, the ground‐based GPS networks, ionosonde stations, and Swarm satellites, when the tropical cyclones Tembin and Hagibis approached Hong Kong on 26 August 2012 and 15 June 2014, respectively. The low‐latitude plasma bubble over an area of 105–120 °E in longitude was observed during 12:30–17:00 universal time (UT) on 26 August 2012. GPS observations from magnetically conjugate locations indicate that the nighttime bubble during 20:30–01:00 local time (LT = UT + 8h) on 26 August should be formed from the magnetically equatorial region rather than drifted from the west (eastward drift) or generated locally. Different from the EPB, during another cyclone on 15 June 2014, the northwest‐southeast aligned nighttime MSTID was verified in midlatitude regions at a mean horizontal velocity of 156 m/s southwestward propagation during 12:30–17:30 UT when Hagibis was near the mainland coast. By comparing the ionospheric observations during the two cyclones, differences are identified: small‐scale irregularities associated with plasma bubble cause obvious perturbations of the rate of total electron content index with the value of ~3.0 TECU/min; while the MSTID in midlatitude only cause relatively slight rate of total electron content index disturbances with the value of ~1.5 TECU/min. In addition, the magnetic conjugacy of EPB and MSTID in two hemispheres during the passage of tropical cyclones has been also discussed in this study.
Climate Change and Regional Ocean Water Mass Disappearance: Case of the Black Sea
Authors: Stanev Emil V. , Peneva Elisaveta , Chtirkova Boriana
Published: July 2019

Data from profiling floats reveal that climate change in the Black Sea leads to the disappearance of specific water masses. The observed thermohaline change is possibly an amplified precursor of the changes to expect in the greater oceans. The warming trend in the cold intermediate layer (CIL) of ~0.05 °C/year was more than double the trend in previous decades, and its temperature approached that of the waters in the deeper layers (~9 °C), which signified its disappearance. This evolution was due to the warmer winters over the last 14 years. Intermittent major cold water formation events (only three during this period) could not sufficiently refill the CIL. A “density constriction” (minimum spread of density) was found at ~14.25 σt, and it separated two thermohaline regimes: temperature‐dominated above and salinity‐dominated beneath. Below this depth, the CIL is seen as a “corner” in the T‐S diagram at ~18 salinity and ~9 °C, where the profiles make a curve. The variability in the T‐S relationships at given σt levels in the CIL revealed trends dominated by diapycnic mixing with deeper layers (the high‐salinity pool acts as a source of salt for the upper ocean). After 2010, salinity anomalies started to occur rhythmically with increasing amplitudes at the depths of the CIL. In the absence of a pronounced CIL in recent years, the relative role of salinity variability in the thermohaline state of the upper layers increased. Further trends and the plausibility of similar events in other similar environments are also addressed.
The Impact of Biological Bedforms on Near‐Bed and Subsurface Flow: A Laboratory‐Evaluated Numerical Study of Flow in the Vicinity of Pits and Mounds
Authors: Han X. , Fang H. W. , Johnson M. F. , Rice S. P.
Published: July 2019

The complex surface topography of river substrates controls near‐bed hydraulics and drives the exchange of subsurface and surface flow. In rivers, the topographic structures that are studied are usually formed by the flow, but it is known that many animals also create biogenic bedforms, such as pits and mounds. Here, a large‐eddy simulation model of flow over a pit and a mound is evaluated with flume experiments. The model includes actual bedform topography, and the topographic complexity of the surrounding bed surface. Subsurface grains are organized in a body‐centered cubic packing arrangement. Model evaluation showed strong agreement between experimental and modeling results for velocity (R2 > 0.8) and good agreement for Reynolds stresses (R2 > 0.7), which is comparable to other similar studies. Simulation of the pit shows that the length of the downwelling region is smaller than the upwelling region and that the velocity magnitude is higher in the downwelling region. Simulation of the mound reveals that the flow is forced into the bed upstream of the mound and reemerges near the top of the mound. The recirculation zone is limited at the leeside of the mound. With increasing Reynolds number, the depth of the upwelling region at the leeside of the mound increases. The analysis of shear stress indicates that sediments on the upstream edge of the pit and on the downstream face of the mound are relatively unstable. These results demonstrate the effect of biogenic structures on the near‐bed flow field, hyporheic exchange, and sediment stability.
Quantifying the Performance of Geomagnetically Induced Current Models
Authors: Marsal S. , Torta J.M.
Published: July 2019

We describe a metric that has been repeatedly applied to assess the performance of models aimed at predicting geomagnetically induced currents from Space Weather events. The used parameterization, based on the well‐known root‐mean‐square error between model and observations, is simple and intuitive. Its use is exemplified, and its advantages and disadvantages are discussed, as well as its relationship with the widely extended correlation coefficient, r. Although the use of r alone is inappropriate for purposes of evaluating the agreement between model and observations, its use is recommended to complement the described performance parameter.
Customizing droplet contents and dynamic ranges via integrated programmable picodroplet assembler
Authors: Zhang Pengfei , Kaushik Aniruddha , Hsieh Kuangwen , Wang Tza-Huei
Published: July 2019

Droplet microfluidic technology is becoming increasingly useful for high-throughput and high-sensitivity detection of biological and biochemical reactions. Most current droplet devices function by passively discretizing a single sample subject to a homogeneous or random reagent/reaction condition into tens of thousands of picoliter-volume droplets for analysis. Despite their apparent advantages in speed and throughput, these droplet devices inherently lack the capability to customize the contents of droplets in order to test a single sample against multiple reagent conditions or multiple samples against multiple reagents. In order to incorporate such combinatorial capability into droplet platforms, we have developed the fully Integrated Programmable Picodroplet Assembler. Our platform is capable of generating customized picoliter-volume droplet groups from nanoliter-volume plugs which are assembled in situ on demand. By employing a combination of microvalves and flow-focusing-based discretization, our platform can be used to precisely control the content and volume of generated nanoliter-volume plugs, and thereafter the content and the effective dynamic range of picoliter-volume droplets. Furthermore, we can use a single integrated device for continuously generating, incubating, and detecting multiple distinct droplet groups. The device successfully marries the precise control and on-demand capability of microvalve-based platforms with the sensitivity and throughput of picoliter droplet platforms in a fully automated monolithic device. The device ultimately will find important applications in single-cell and single-molecule analyses.
Rapid two-dimensional characterisation of proteins in solution
Authors: Saar Kadi L. , Peter Quentin , Müller Thomas , Challa Pavan K. , Herling Therese W. , Knowles Tuomas P. J.
Published: July 2019

Microfluidic platforms provide an excellent basis for working with heterogeneous samples and separating biomolecular components at high throughput, with high recovery rates and by using only very small sample volumes. To date, several micron scale platforms with preparative capabilities have been demonstrated. Here we describe and demonstrate a microfluidic device that brings preparative and analytical operations together onto a single chip and thereby allows the acquisition of multidimensional information. We achieve this objective by using a free-flow electrophoretic separation approach that directs fractions of sample into an on-chip analysis unit, where the fractions are characterised through a microfluidic diffusional sizing process. This combined approach therefore allows simultaneously quantifying the sizes and the charges of components in heterogenous mixtures. We illustrate the power of the platform by describing the size distribution of a mixture comprising components which are close in size and cannot be identified as individual components using state-of-the-art solution sizing techniques on their own. Furthermore, we show that the platform can be used for two-dimensional fingerprinting of heterogeneous protein mixtures within tens of seconds, opening up a possibility to obtain multiparameter data on biomolecular systems on a minute timescale.
Low voltage control of exchange coupling in a ferromagnet-semiconductor quantum well hybrid structure
Authors: Korenev V. L. , Kalitukha I. V. , Akimov I. A. , Sapega V. F. , Zhukov E. A. , Kirstein E. , Ken O. S. , Kudlacik D. , Karczewski G. , Wiater M. , Wojtowicz T. , Ilyinskaya N. D. , Lebedeva N. M. , Komissarova T. A. , Kusrayev Yu. G. , Yakovlev D. R. , Bayer M.
Published: July 2019

Voltage control of ferromagnetism on the nanometer scale is highly appealing for the development of novel electronic devices with low power consumption, high operation speed, reliable reversibility and compatibility with semiconductor technology. Hybrid structures based on the assembly of ferromagnetic and semiconducting building blocks are expected to show magnetic order as a ferromagnet and to be electrically tunable as a semiconductor. Here, we demonstrate the electrical control of the exchange coupling in a hybrid consisting of a ferromagnetic Co layer and a semiconductor CdTe quantum well, separated by a thin non-magnetic (Cd,Mg)Te barrier. The electric field controls the phononic ac Stark effect—the indirect exchange mechanism that is mediated by elliptically polarized phonons emitted from the ferromagnet. The effective magnetic field of the exchange interaction reaches up to 2.5 Tesla and can be turned on and off by application of 1V bias across the heterostructure.
Identification and structural analysis of the tripartite α-pore forming toxin of
Aeromonas hydrophila
Authors: Wilson Jason S. , Churchill-Angus Alicia M. , Davies Simon P. , Sedelnikova Svetlana E. , Tzokov Svetomir B. , Rafferty John B. , Bullough Per A. , Bisson Claudine , Baker Patrick J.
Published: July 2019

Abstract

The alpha helical CytolysinA family of pore forming toxins (α-PFT) contains single, two, and three component members. Structures of the single component Eschericia coli ClyA and the two component Yersinia enterolytica YaxAB show both undergo conformational changes from soluble to pore forms, and oligomerization to produce the active pore. Here we identify tripartite α-PFTs in pathogenic Gram negative bacteria, including Aeromonas hydrophila (AhlABC). We show that the AhlABC toxin requires all three components for maximal cell lysis. We present structures of pore components which describe a bi-fold hinge mechanism for soluble to pore transition in AhlB and a contrasting tetrameric assembly employed by soluble AhlC to hide their hydrophobic membrane associated residues. We propose a model of pore assembly where the AhlC tetramer dissociates, binds a single membrane leaflet, recruits AhlB promoting soluble to pore transition, prior to AhlA binding to form the active hydrophilic lined pore.
Proprioceptive Sonomyographic Control: A novel method for intuitive and proportional control of multiple degrees-of-freedom for individuals with upper extremity limb loss
Authors: Dhawan Ananya S. , Mukherjee Biswarup , Patwardhan Shriniwas , Akhlaghi Nima , Diao Guoqing , Levay Gyorgy , Holley Rahsaan , Joiner Wilsaan M. , Harris-Love Michelle , Sikdar Siddhartha
Published: July 2019

Technological advances in multi-articulated prosthetic hands have outpaced the development of methods to intuitively control these devices. In fact, prosthetic users often cite "difficulty of use" as a key contributing factor for abandoning their prostheses. To overcome the limitations of the currently pervasive myoelectric control strategies, namely unintuitive proportional control of multiple degrees-of-freedom, we propose a novel approach: proprioceptive sonomyographiccontrol. Unlike myoelectric control strategies which measure electrical activation of muscles and use the extracted signals to determine the velocity of an end-effector; our sonomyography-based strategy measures mechanical muscle deformation directly with ultrasound and uses the extracted signals to proportionally control the position of an end-effector. Therefore, our sonomyography-based control is congruent with a prosthetic user’s innate proprioception of muscle deformation in the residual limb. In this work, we evaluated proprioceptive sonomyographic control with 5 prosthetic users and 5 able-bodied participants in a virtual target achievement and holding task for 5 different hand motions. We observed that with limited training, the performance of prosthetic users was comparable to that of able-bodied participants and thus conclude that proprioceptive sonomyographic control is a robust and intuitive prosthetic control strategy.
Major changes in chromosomal somy, gene expression and gene dosage driven by SbIII in Leishmania braziliensis and Leishmania panamensis
Authors: Patino Luz H. , Imamura Hideo , Cruz-Saavedra Lissa , Pavia Paula , Muskus Carlos , Méndez Claudia , Dujardin Jean Claude , Ramírez Juan David
Published: July 2019

Leishmania braziliensis and Leishmania panamensis are two species clinically and epidemiologically important, among others because of their relative resistance to first-line drugs (antimonials). The precise mechanism underlying the ability of these species to survive antimony treatment remains unknown. Therefore, elucidating the pathways mediating drug resistance is essential. We herein experimentally selected resistance to trivalent antimony (SbIII) in the reference strains of L. braziliensis (MHOM/BR75/M2904) and L. panamensis (MHOM/COL/81L13) and compared whole genome and transcriptome alterations in the culture promastigote stage. The results allowed us to identify differences in somy, copy number variations in some genes related to antimony resistance and large-scale copy number variations (deletions and duplications) in chromosomes with no somy changes. We found mainly in L. braziliensis, a direct relation between the chromosomal/local copy number variation and the gene expression. We identified differentially expressed genes in the resistant lines that are involved in antimony resistance, virulence, and vital biological processes in parasites. The results of this study may be useful for characterizing the genetic mechanisms of these Leishmania species under antimonial pressure, and for clarifying why the parasites are resistant to first-line drug treatments.
Deciphering the genetic basis for vitamin E accumulation in leaves and grains of different barley accessions
Authors: Schuy Christian , Groth Jennifer , Ammon Alexandra , Eydam Julia , Baier Steffen , Schweizer Günther , Hanemann Anja , Herz Markus , Voll Lars M. , Sonnewald Uwe
Published: July 2019

Tocopherols and tocotrienols, commonly referred to as vitamin E, are essential compounds in food and feed. Due to their lipophilic nature they protect biomembranes by preventing the propagation of lipid-peroxidation especially during oxidative stress. Since their synthesis is restricted to photosynthetic organisms, plant-derived products are the major source of natural vitamin E. In the present study the genetic basis for high vitamin E accumulation in leaves and grains of different barley (Hordeum vulgare L.) accessions was uncovered. A genome wide association study (GWAS) allowed the identification of two genes located on chromosome 7H, homogentisate phytyltransferase (HPT-7H) and homogentisate geranylgeranyltransferase (HGGT) that code for key enzymes controlling the accumulation of tocopherols in leaves and tocotrienols in grains, respectively. Transcript profiling showed a correlation between HPT-7H expression and vitamin E content in leaves. Allele sequencing allowed to decipher the allelic variation of HPT-7H and HGGT genes corresponding to high and low vitamin E contents in the respective tissues. Using the obtained sequence information molecular markers have been developed which can be used to assist smart breeding of high vitamin E barley varieties. This will facilitate the selection of genotypes more tolerant to oxidative stress and producing high-quality grains.
HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells
Authors: Klinge Carolyn M. , Piell Kellianne M. , Tooley Christine Schaner , Rouchka Eric C.
Published: July 2019

MicroRNAs are dysregulated in breast cancer. Heterogeneous Nuclear Ribonucleoprotein A2/B1 (HNRNPA2/B1) is a reader of the N(6)-methyladenosine (m6A) mark in primary-miRNAs (pri-miRNAs) and promotes DROSHA processing to precursor-miRNAs (pre-miRNAs). We examined the expression of writers, readers, and erasers of m6A and report that HNRNPA2/B1 expression is higher in tamoxifen-resistant LCC9 breast cancer cells as compared to parental, tamoxifen-sensitive MCF-7 cells. To examine how increased expression of HNRNPA2/B1 affects miRNA expression, HNRNPA2/B1 was transiently overexpressed (~5.4-fold) in MCF-7 cells for whole genome miRNA profiling (miRNA-seq). 148 and 88 miRNAs were up- and down-regulated, respectively, 48 h after transfection and 177 and 172 up- and down-regulated, respectively, 72 h after transfection. MetaCore Enrichment analysis identified progesterone receptor action and transforming growth factor β (TGFβ) signaling via miRNA in breast cancer as pathways downstream of the upregulated miRNAs and TGFβ signaling via SMADs and Notch signaling as pathways of the downregulated miRNAs. GO biological processes for mRNA targets of HNRNPA2/B1-regulated miRNAs included response to estradiol and cell-substrate adhesion. qPCR confirmed HNRNPA2B1 downregulation of miR-29a-3p, miR-29b-3p, and miR-222 and upregulation of miR-1266-5p, miR-1268a, miR-671-3p. Transient overexpression of HNRNPA2/B1 reduced MCF-7 sensitivity to 4-hydroxytamoxifen and fulvestrant, suggesting a role for HNRNPA2/B1 in endocrine-resistance.
Smoking is associated with ulnar nerve entrapment: a birth cohort study
Authors: Hulkkonen Sina , Auvinen Juha , Miettunen Jouko , Karppinen Jaro , Ryhänen Jorma
Published: July 2019

Ulnar nerve entrapment is the second most common compression neuropathy of the upper extremity. It has been associated with smoking in cross-sectional studies. Our aim was to study whether smoking is associated with ulnar nerve entrapment. The study population consisted of the Northern Finland Birth Cohort 1966 participants, who attended the 31-year follow-up in 1997 (N = 8,716). Information on smoking, body mass index (BMI), long-term illnesses, and socio-economic status were recorded at baseline in 1997. Data on hospitalizations due to ulnar nerve entrapment neuropathies was obtained from the Care Register for Health Care, 1997–2016. Hazard ratios (HR) with 95% confidence intervals (CI) and population attributable risk (PAR) were calculated adjusted for gender, BMI and socio-economic status. 66 patients were diagnosed with ulnar nerve entrapment in the follow-up 1997–2016. Before the age of 31 years, smoking ≤10 pack years associated with more than doubled (HR = 2.57, 95% CI = 1.29–5.15) and smoking >10 pack years with more than five-folded (HR = 5.61, 95% CI = 2.80–11.23) risk for ulnar nerve entrapment compared to non-smokers in the adjusted analyses. Adjusted PAR for smoking (reference of no smoking) was 53.6%. In our study, smoking associated with increased risk for ulnar nerve entrapment, accounting for considerable proportion of increased risk.
Reaching measures and feedback effects in auditory peripersonal space
Authors: Hüg Mercedes X. , Vergara Ramiro O. , Tommasini Fabián C. , Etchemendy Pablo E. , Bermejo Fernando , Fernandez Laura G.
Published: July 2019

We analyse the effects of exploration feedback on reaching measures of perceived auditory peripersonal space (APS) boundary and the auditory distance perception (ADP) of sound sources located within it. We conducted an experiment in which the participants had to estimate if a sound source was (or not) reachable and to estimate its distance (40 to 150 cm in 5-cm steps) by reaching to a small loudspeaker. The stimulus consisted of a train of three bursts of Gaussian broadband noise. Participants were randomly assigned to two groups: Experimental (EG) and Control (CG). There were three phases in the following order: Pretest–Test–Posttest. For all phases, the listeners performed the same task except for the EG-Test phase where the participants reach in order to touch the sound source. We applied models to characterise the participants’ responses and provide evidence that feedback significantly reduces the response bias of both the perceived boundary of the APS and the ADP of sound sources located within reach. In the CG, the repetition of the task did not affect APS and ADP accuracy, but it improved the performance consistency: the reachable uncertainty zone in APS was reduced and there was a tendency to decrease variability in ADP.
High Power UV-Light Irradiation as a New Method for Defect Passivation in Degraded Perovskite Solar Cells to Recover and Enhance the Performance
Authors: Arabpour Roghabadi Farzaneh , Mansour Rezaei Fumani Nasibeh , Alidaei Maryam , Ahmadi Vahid , Sadrameli Seyed Mojtaba
Published: July 2019

Although the power conversion efficiency (PCE) of perovskite solar cells (PSCs) reached up to 23%, their short lifetime and fast degradation still remain as the main challenges. In this work, a new facile optical method based on the high power UV-irradiation is presented for the recovery of the degraded PSCs. Addition to the full recovery of the performance, about 20% PCE enhancement and hystersis reduction are also achieved by UV-irradiation. UV-treatment causes modifications in both the bulk properties of the perovskite layer and the energy equilibrium at the interfaces. It is shown that UV-treatment effectively passivates the surface and grain boundaries defects in different types of the devices comprising normal and inverted configurations that is confirmed by the reduction of the density of defect states (DOS). It is proposed that UV-light passivates the shallow and deep defects by dissociation of adsorbed hydroxyl groups and water molecules during the device storage.
Repeatability of Multiparametric Prostate MRI Radiomics Features
Authors: Schwier Michael , van Griethuysen Joost , Vangel Mark G. , Pieper Steve , Peled Sharon , Tempany Clare , Aerts Hugo J. W. L. , Kikinis Ron , Fennessy Fiona M. , Fedorov Andriy
Published: July 2019

In this study we assessed the repeatability of radiomics features on small prostate tumors using test-retest Multiparametric Magnetic Resonance Imaging (mpMRI). The premise of radiomics is that quantitative image-based features can serve as biomarkers for detecting and characterizing disease. For such biomarkers to be useful, repeatability is a basic requirement, meaning its value must remain stable between two scans, if the conditions remain stable. We investigated repeatability of radiomics features under various preprocessing and extraction configurations including various image normalization schemes, different image pre-filtering, and different bin widths for image discretization. Although we found many radiomics features and preprocessing combinations with high repeatability (Intraclass Correlation Coefficient > 0.85), our results indicate that overall the repeatability is highly sensitive to the processing parameters. Neither image normalization, using a variety of approaches, nor the use of pre-filtering options resulted in consistent improvements in repeatability. We urge caution when interpreting radiomics features and advise paying close attention to the processing configuration details of reported results. Furthermore, we advocate reporting all processing details in radiomics studies and strongly recommend the use of open source implementations.
Functional characterization of SMN evolution in mouse models of SMA
Authors: Osman Erkan Y. , Bolding Madeline R. , Villalón Eric , Kaifer Kevin A. , Lorson Zachary C. , Tisdale Sarah , Hao Yue , Conant Gavin C. , Pires J. Chris , Pellizzoni Livio , Lorson Christian L.
Published: July 2019

Spinal Muscular Atrophy (SMA) is a monogenic neurodegenerative disorder and the leading genetic cause of infantile mortality. While several functions have been ascribed to the SMN (survival motor neuron) protein, their specific contribution to the disease has yet to be fully elucidated. We hypothesized that some, but not all, SMN homologues would rescue the SMA phenotype in mouse models, thereby identifying disease-relevant domains. Using AAV9 to deliver Smn homologs to SMA mice, we identified a conservation threshold that marks the boundary at which homologs can rescue the SMA phenotype. Smn from Danio rerio and Xenopus laevis significantly prevent disease, whereas Smn from Drosophila melanogaster, Caenorhabditis elegans, and Schizosaccharomyces pombe was significantly less efficacious. This phenotypic rescue correlated with correction of RNA processing defects induced by SMN deficiency and neuromuscular junction pathology. Based upon the sequence conservation in the rescuing homologs, a minimal SMN construct was designed consisting of exons 2, 3, and 6, which showed a partial rescue of the SMA phenotype. While a significant extension in survival was observed, the absence of a complete rescue suggests that while the core conserved region is essential, additional sequences contribute to the overall ability of the SMN protein to rescue disease pathology.
Arsenic accumulation in lentil (Lens culinaris) genotypes and risk associated with the consumption of grains
Authors: Alam Mohammad Zahangeer , Hoque Md. Anamul , Ahammed Golam Jalal , McGee Rebecca , Carpenter-Boggs Lynne
Published: July 2019

Arsenic (As) is a toxic metalloid. As phyto-toxicity is manifested by its accumulation in different tissue types and subsequent growth inhibition in plants. Despite the vital role of leguminous crops in providing proteins to human diets, a little is known about the As accumulation in lentil. In this study, the rate of As uptake and transport from soil to root, shoot and grain of lentil as well as associated risks with the consumption of As contaminated food were examined. Biomass accumulation of lentil genotypes pardina, red chief and precoz drastically decreased when treated with As at 6 mg kg−1 concentration in comparison to 0 and 3 mg kg−1 As. Quantification of As concentrations following different treatment periods showed that As accumulation in roots and shoots of 0, 3 and 6 mg kg−1 As-treated lentil genotypes was statistically different. Arsenic content in grains of red chief genotype was found significantly lower than pardina and precoz. Moreover, As transport significantly increased in roots and shoots compared to the grains. Due to the high concentrations of As in biomass of lentil genotypes, animal as well as human health risk might be associated with the consumption of the As contaminated legume crops.
Neighborhood environments influence emotion and physiological reactivity
Authors: Hackman Daniel A. , Robert Stephanie A. , Grübel Jascha , Weibel Raphael P. , Anagnostou Eirini , Hölscher Christoph , Schinazi Victor R.
Published: July 2019

Living in a disadvantaged neighborhood is associated with worse health and early mortality. Although many mechanisms may partially account for this effect, disadvantaged neighborhood environments are hypothesized to elicit stress and emotional responses that accumulate over time and influence physical and mental health. However, evidence for neighborhood effects on stress and emotion is limited due to methodological challenges. In order to address this question, we developed a virtual reality experimental model of neighborhood disadvantage and affluence and examined the effects of simulated neighborhoods on immediate stress and emotion. Exposure to neighborhood disadvantage resulted in greater negative emotion, less positive emotion, and more compassion, compared to exposure to affluence. However, the effect of virtual neighborhood environments on blood pressure and electrodermal reactivity depended on parental education. Participants from families with lower education exhibited greater reactivity to the disadvantaged neighborhood, while those from families with higher education exhibited greater reactivity to the affluent neighborhood. These results demonstrate that simulated neighborhood environments can elicit immediate stress reactivity and emotion, but the nature of physiological effects depends on sensitization to prior experience.
Short-period scattering-assisted terahertz quantum cascade lasers operating at high temperatures
Authors: Wang Li , Lin Tsung-Tse , Wang Ke , Grange Thomas , Birner Stefan , Hirayama Hideki
Published: July 2019

Operating at high temperatures in the range of thermoelectric coolers is essential for terahertz quantum cascade lasers to real applications. The use of scattering-assisted injection scheme enables an increase in operating temperature. This concept, however, has not been implemented in a short-period structure consisting of two quantum wells. In this work, based on non-equilibrium Green’s function calculations, it emphasizes on the current leakage and parasitic absorption via high-energy states as fundamental limitations in this scheme with short-period. A new design concept employing asymmetric wells composition is proposed to suppress these limitations. A peak gain of 40 cm−1 at 230 K is predicted in the GaAs/AlGaAs semiconductor material system with an emission frequency of 3.5 THz.
Retinoic acid and arsenic trioxide induce lasting differentiation and demethylation of target genes in APL cells
Authors: Huynh Thomas T. , Sultan Mohammad , Vidovic Dejan , Dean Cheryl A. , Cruickshank Brianne M. , Lee Kristen , Loung Chao-Yu , Holloway Ryan W. , Hoskin David W. , Waisman David M. , Weaver Ian C. G. , Marcato Paola
Published: July 2019

Acute promyelocytic leukemia (APL) is characterized by arrested differentiation of promyelocytes. Patients treated with all-trans retinoic acid (ATRA) alone experience relapse, while patients treated with ATRA and arsenic trioxide (ATO) are often relapse-free. This suggests sustained changes have been elicited by the combination therapy. To understand the lasting effects of the combination therapy, we compared the effects of ATRA and ATO on NB4 and ATRA-resistant NB4-MR2 APL cells during treatment versus post treatment termination. After treatment termination, NB4 cells treated with ATRA or ATO reverted to non-differentiated cells, while combination-treated cells remained terminally differentiated. This effect was diminished in NB4-MR2 cells. This suggests combination treatment induced more permanent changes. Combination treatment induced higher expression of target genes (e.g., transglutaminase 2 and retinoic acid receptor beta), which in NB4 cells was sustained post treatment termination. To determine whether sustained epigenetic changes were responsible, we quantified the enrichment of histone modifications by chromatin immunoprecipitation, and CpG methylation by bisulfite-pyrosequencing. While ATRA and combination treatment induced similar histone acetylation enrichment, combination treatment induced greater demethylation of target genes, which was sustained. Therefore, sustained demethylation of target genes by ATRA and ATO combination treatment is associated with lasting differentiation and gene expression changes.
Bioaccumulation of metals in calanoid copepods by oral intake
Authors: Kadiene Esther U. , Ouddane Baghdad , Hwang Jiang-Shiou , Souissi Sami
Published: July 2019

We demonstrated that oral intake of water by two calanoid copepods, Pseudodiaptomus annandalei and Eurytemora affinis takes place and has implications for their ecotoxicology. In the first experiment, copepods were exposed to a dyed medium, which allowed us to visually examine the possibility of water uptake by the copepod. We observed that both copepod species were taking in water orally and evacuated dye at different speeds. This exposure left concentrated dye in the guts of the copepods indicating adsorption into the gut epithelium. This was further demonstrated by exposing both copepod species independently to dissolved metals (Cd,17 µg/L; Cu,13.8 µg/L; Ni, 29.3 µg/L) and to dietary metals (Cd,18.8 µg/g; Cu, 35.3 µg/g; Ni, 32.5 µg/g). The results showed that although the concentration of dissolved metals they were exposed to were lower than those of the dietary metals, nevertheless, uptake of metals by both copepod species from the dissolved phase alone was substantially higher than from dietary exposure. This provides clear evidence to support our hypothesis that higher metal body burden observed in copepods exposed to dissolved metals than in those exposed to dietary metals is an implication of oral intake of water. P. annandalei showed higher excretion rate of metals when exposed to dissolved metals than E. affinis. However, the excretion rate of metals from both copepod species exposed to dietary metal was similar. We conclude here that both copepod species take in water orally. Our study further showed that metal uptake depends on the exposure routes and the uptake and excretion rates are dependent on the type of metals, amounts and the species.