bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients
Authors: Zhou Bo , Sun Chaoyang , Huang Jia , Xia Meng , Guo Ensong , Li Na , Lu Hao , Shan Wanying , Wu Yifan , Li Yuan , Xu Xiaoyan , Weng Danhui , Meng Li , Hu Junbo , Gao Qinglei , Ma Ding , Chen Gang 
Published: February 2019

AbstractOvarian carcinoma is caused by multiple factors, but its etiology associated with microbes and infection is unknown. Using 16S rRNA high-throughput sequencing methods, the diversity and composition of the microbiota from ovarian cancer tissues (25 samples) and normal distal fallopian tube tissues (25 samples) were analyzed. High-throughput sequencing showed that the diversity and richness indexes were significantly decreased in ovarian cancer tissues compared to tissues from normal distal fallopian tubes. The ratio of the two phyla for Proteobacteria/Firmicutes was notably increased in ovarian cancer, which revealed that microbial composition change might be associated with the process of ovarian cancer development. In addition, transcriptome-sequencing (RNA-seq) analyses suggested that the transcriptional profiles were statistically different between ovarian carcinoma and normal distal fallopian tubes. Moreover, a set of genes including 84 different inflammation-associated or immune-associated genes, which had been named as the human antibacterial-response genes were also modulated expression. Therefore, we hypothesize that the microbial composition change, as a novel risk factor, may be involving the initiation and progression of ovarian cancer via influencing and regulating the local immune microenvironment of fallopian tubes except for regular pathways.
Plasmodium falciparum histidine-rich protein (PfHRP2 and 3) diversity in Western and Coastal Kenya
Authors: Nderu David , Kimani Francis , Thiong’o Kelvin , Karanja Evaline , Akinyi Maureen , Too Edwin , Chege William , Nambati Eva , Meyer Christian G. , Velavan Thirumalaisamy P. 
Published: February 2019

AbstractPlasmodium falciparum histidine-rich proteins 2 (PfHRP2) based RDTs are advocated in falciparum malaria-endemic regions, particularly when quality microscopy is not available. However, diversity and any deletion in the pfhrp2 and pfhrp3 genes can affect the performance of PfHRP2-based RDTs. A total of 400 samples collected from uncomplicated malaria cases from Kenya were investigated for the amino acid repeat profiles in exon 2 of pfhrp2 and pfhrp3 genes. In addition, PfHRP2 levels were measured in 96 individuals with uncomplicated malaria. We observed a unique distribution pattern of amino acid repeats both in the PfHRP2 and PfHRP3. 228 PfHRP2 and 124 PfHRP3 different amino acid sequences were identified. Of this, 214 (94%) PfHRP2 and 81 (65%) PfHRP3 amino acid sequences occurred only once. Thirty-nine new PfHRP2 and 20 new PfHRP3 amino acid repeat types were identified. PfHRP2 levels were not correlated with parasitemia or the number of PfHRP2 repeat types. This study shows the variability of PfHRP2, PfHRP3 and PfHRP2 concentration among uncomplicated malaria cases. These findings will be useful to understand the performance of PfHRP2-based RDTs in Kenya.
Gaze training supports self-organization of movement coordination in children with developmental coordination disorder
Authors: Słowiński Piotr , Baldemir Harun , Wood Greg , Alizadehkhaiyat Omid , Coyles Ginny , Vine Samuel , Williams Genevieve , Tsaneva-Atanasova Krasimira , Wilson Mark 
Published: February 2019

AbstractChildren with developmental coordination disorder (DCD) struggle with the acquisition of coordinated motor skills. This paper adopts a dynamical systems perspective to assess how individual coordination solutions might emerge following an intervention that trained accurate gaze control in a throw and catch task. Kinematic data were collected from six upper body sensors from twenty-one children with DCD, using a 3D motion analysis system, before and after a 4-week training intervention. Covariance matrices between kinematic measures were computed and distances between pairs of covariance matrices calculated using Riemannian geometry. Multidimensional scaling was then used to analyse differences between coordination patterns. The gaze trained group revealed significantly higher total coordination (sum of all the pairwise covariances) following training than a technique-trained control group. While the increase in total coordination also significantly predicted improvement in task performance, the distinct post-intervention coordination patterns for the gaze trained group were not consistent. Additionally, the gaze trained group revealed individual coordination patterns for successful catch attempts that were different from all the coordination patterns before training, whereas the control group did not. Taken together, the results of this interdisciplinary study illustrate how gaze training may encourage the emergence of coordination via self-organization in children with DCD.
Culturable endophytic fungal communities associated with plants in organic and conventional farming systems and their effects on plant growth
Authors: Xia Ye , Sahib Mohammad Radhi , Amna Amna , Opiyo Stephen Obol , Zhao Zhenzhen , Gao Yu Gary 
Published: February 2019

AbstractAs compared to organic farming system, conventional farming system relies on higher inputs of synthetic agrochemicals, which may reduce the abundance, diversity, and beneficial effects of plant endophytic fungal communities. This study compares the diversity and abundance of culturable endophytic fungal communities associated with four plant species –corn, tomato, pepper, and watermelon grown in separate organic and conventional fields. In all, 740 fungal isolates were identified, of which 550 were from the organic fields and 190 from the conventional ones. These fungal isolates were grouped into eight orders and 22 species, with the two most abundant species being Trichoderma sp. and Pichia guilliermondi. The fungal species diversity and abundance were both significantly higher in the organic than in the conventional fields. All the isolated endophytic fungi improved tomato plants’ shoot growth and biomass significantly, as compared with the water control. Six fungal isolates also exhibited activity that enhanced tomato fruit yields. These results suggest that these endophytic fungi might be a considerable boost to sustainable agricultural production, while also reducing the agricultural application of chemicals and thus benefiting the environment and human health.
Extreme sediment fluxes in a dryland flash flood
Authors: Hooke J. M. 
Published: February 2019

AbstractA flash flood on 28th September, 2012, rose to a peak discharge of 2357 m3 s−1 from zero within one hour in the ephemeral Nogalte channel in SE Spain. Channel morphology and sediment sizes were measured at existing monitored sites before and after the flood and peak flow hydraulics calculated from surveyed floodmarks and cross-sections. Maximum peak sediment fluxes were calculated as ~600 kg s−1 m−1, exceeding maximum published, measured dryland channel values by 10 times and common perennial stream fluxes by 100 times. These high fluxes fit the established simple bedload flux - shear stress relations for dryland channels very well, but now extended over a much wider data range. The high sediment fluxes are corroborated by deposits at >1 m height in a channel-side tank, with 90 mm diameter sediment carried in suspension, by transport of large blocks and by massive net aggradation as extensive, structureless channel bars. Very high sediment supply and rapid hydrograph rise and recession produced the conditions for these exceptional sediment dynamics. The results demonstrate the extreme sediment loads that may occur in dryland flash floods and have major implications for catchment and channel management.
Local agro-pastoralists’ perspectives on forage species diversity, habitat distributions, abundance trends and ecological drivers for sustainable livestock production in West Africa
Authors: Naah John-Baptist S. N. , Braun Boris 
Published: February 2019

AbstractDespite the importance of local ecological knowledge of forage plants, there has been little discussion on how local agro-pastoralists perceive forage species diversity, abundance trends, habitat distributions and ecological drivers influencing changing abundance trends over time in rural West Africa’s savannas. In estimating, assessing and investigating the ecological variables, we performed elaborate ethnobotanical surveys in seven villages in northern Ghana and nine villages in southern-central Burkina Faso. Data were analyzed using descriptive statistics, bivariate correlation analysis and cognitive salience index calculations to disentangle the dynamics of local responses to ecological variables considered in this study. Our results revealed that agro-pastoralists exhibited extensive knowledge on forage species diversity, habitat types, abundance trends and ecological drivers. According to agro-pastoralists interviewed, about 82 percent of all forage species known to them were commonly available in local landscapes, while a majority of our interviewees indicated that available forage resources have shown a gradually increasing trend over the past few years. Rainfall variability, tree cutting and drought were the topmost perceived threats causing changes in the trends of forage species abundance. Given our findings, local perceptions of agro-pastoralists could have substantial practical implications in favor of forage-related biodiversity conservation and sustainable livestock production.
The effects of dietary selenomethionine on tissue-specific accumulation and toxicity of dietary arsenite in rainbow trout (Oncorhynchus mykiss) during chronic exposure
Authors: Jamwal Ankur , Saibu Yusuf , MacDonald Tracy C , George Graham N , Niyogi Som 
Published: February 2019

Abstract
The interactive effects of different doses of dietary selenium [as selenomethionine; 1.8 μg g−1 (control), 10 μg g−1 and 40 μg g−1 diet] on the toxicity of dietary arsenic [as arsenite (As3+); 80 μg As per g diet] were investigated in rainbow trout over an exposure period of 30 days. Fish fed with As3+ alone showed an increased hepatic lipid peroxidation (LPO) and a concomitant decline in cellular redox potential (determined as GSH:GSSG) in the liver tissue relative to the control fish. Interestingly, fish fed with low (10 μg g−1) or high (40 μg g−1) concentration of dietary selenomethionine in combination with As3+ showed an even higher degree of hepatic LPO and a further decrease in GSH : GSSG molar ratio relative to the fish treated with As3+ alone. Our study also revealed that exposure to dietary selenomethionine (both at low and high levels) resulted in significantly higher levels of arsenic in target tissues (liver, kidney, and muscle) relative to fish treated with As3+ alone. Similarly, the synchrotron-based X-ray fluorescence imaging analysis also suggested a dose-dependent increase in the co-localization of arsenic and selenium in the brain of fish co-treated with dietary As3+ and selenomethionine. These observations suggested that selenomethionine facilitated arsenic deposition in the brain and likely in other tissues, possibly via bio-complexation. Overall, our findings indicated that elevated dietary selenomethionine can increase the tissue-specific accumulation and toxicity of As3+ in fish during chronic dietary exposure.
The first identified heterozygous nonsense mutations in podocalyxin offer new perspectives on the biology of podocytopathies
Authors: Refaeli Ido , Hughes Michael R. , McNagny Kelly M. 
Published: February 2019

Abstract
In the last two decades, our understanding of the genetic underpinnings of inherited podocytopathies has advanced immensely. By sequencing the genomes of a large pool of families affected by focal segmental glomerulosclerosis (FSGS), researchers have identified a common theme: familial podocytopathies are frequently caused by genes selectively expressed in podocytes. Podocalyxin is a podocyte-specific surface sialomucin that has long been known to play important roles in podocyte morphogenesis and function. Few studies, however, have shown a conclusive link between mutations in the gene and FSGS complemented by functional evidence. In a fascinating new paper published in Clinical Science, Lin et al. identify two unrelated pedigrees in which dominant loss-of-function mutations in PODXL lead to adult-onset FSGS. Nonsense-mediated decay of the mutated PODXL transcripts leads to protein insufficiency, which in turn cause podocyte dysfunction through defects in motility and cytoskeletal organization. This is the first study to date that demonstrates, mechanistically, how autosomal dominant mutations in podocalyxin can lead to FSGS and renal insufficiency. Here, we summarize the experimental findings of this manuscript and propose, perhaps, a more controversial hypothesis: down-regulation of podocalyxin protein expression from podocytes is a critical turning point in the progression of most podocytopathies and may be mechanistically relevant to glomerulopathies in which podocyte damage is not necessarily induced by genetic lesions.
Eliciting Naturalistic Conversations: A Method for Assessing Communication Ability, Subjective Experience, and the Impacts of Noise and Hearing Impairment
Authors: Beechey Timothy , Buchholz Jörg M. , Keidser Gitte 
Published: February 2019

PurposeThe purpose of this study was to introduce a method of eliciting conversational behavior with many aspects of realism, which may be used to study the impacts of hearing impairment and noise on verbal communication; to describe the characteristics of speech and language participants produced during the task; and to assess participants' engagement and motivation while completing the task.MethodTwenty young adults with normal hearing and 20 older adults with hearing impairment took part in face-to-face conversations while completing a referential communication puzzle task designed to elicit natural conversational speech production and language with a number of realistic characteristics. Participants rated the difficulty and relevance of acoustic scenes for communication and their engagement in conversations.ResultsThe communication task elicited speech production in a natural conversational register and language with many realistic characteristics, including complex linguistic constructions and typical disfluencies found in everyday speech, and approximately balanced contributions within dyads. Subjective ratings suggest that the task is robust to learning and fatigue effects and that participants remained highly engaged throughout the experiment. All participants were able to maintain successful communication regardless of background noise level and degree of hearing impairment.ConclusionsThe communication task described here may be used as part of a functional assessment of the ability to communicate in the presence of noise and hearing impairment. Although existing speech assessments have many strengths, they do not take into account the inherently interactive nature of spoken communication or the effects of motivation and engagement.
Knowledge Is Power: Improving Outcomes for Patients, Partners, and Professionals in the Digital Age
Authors: Ferguson Melanie , Maidment David , Henshaw Helen , Gomez Rachel 
Published: February 2019

PurposeThe aim of this research was to develop and evaluate methods to address poor knowledge of hearing aids, hearing loss, and communication in patients, partners, and nonaudiologic health and social care professionals.MethodAn interactive multimedia educational program (C2Hear) has been co-produced with hearing aid users and audiologists to provide high-quality information and demonstrate complex concepts relating to hearing aids and communication.ResultsA randomized controlled trial showed numerous benefits for first-time hearing aid users that included better knowledge and skill, and increased hearing aid use and satisfaction. Patients reported that C2Hear was highly useful, enjoyable, and preferable to written information. C2Hear Online is now freely available on YouTube and has global reach, well in excess of 150,000 views. Further developments include a version for communication partners, which showed that joint-working between hearing aid users and their communication partners resulted in joint responsibility for communication that facilitated communication behaviors. In addition, a behavior theory-driven version for use with mobile technologies (m2Hear) has been designed to be tailored to the needs of individual hearing aid users. m2Hear includes more activities/interaction to maximize user engagement and learning. Finally, C2Hear has been used to improve hearing-related knowledge in other health and social care professionals, such as carehome assistants.ConclusionThis range of educational programs and tools aims to improve knowledge and skills, leading to better outcomes for patients, partners, and health care professionals.
So close, so different: characterization of the K2-36 planetary system with HARPS-N
Authors: Damasso M. , Zeng L. , Malavolta L. , Mayo A. , Sozzetti A. , Mortier A. , Buchhave L. A. , Vanderburg A. , Lopez-Morales M. , Bonomo A. S. , Cameron A. C. , Coffinet A. , Figueira P. , Latham D. W. , Mayor M. , Molinari E. , Pepe F. , Phillips D. F. , Poretti E. , Rice K. , Udry S. , Watson C. A. 
Published: February 2019

Context. K2-36 is a K dwarf orbited by two small (Rb = 1.43 ± 0.08 R⊕ and Rc = 3.2 ± 0.3 R⊕), close-in (ab = 0.022 au and ac = 0.054 au) transiting planets discovered by the Kepler/K2 space observatory. They are representatives of two distinct families of small planets (Rp < 4 R⊕) recently emerged from the analysis of Kepler data, with likely a different structure, composition and evolutionary pathways.
Aims. We revise the fundamental stellar parameters and the sizes of the planets, and provide the first measurement of their masses and bulk densities, which we use to infer their structure and composition.
Methods. We observed K2-36 with the HARPS-N spectrograph over ~3.5 yr, collecting 81 useful radial velocity measurements. The star is active, with evidence for increasing levels of magnetic activity during the observing time span. The radial velocity scatter is ~17 m s−1 due to the stellar activity contribution, which is much larger that the semi-amplitudes of the planetary signals. We tested different methods for mitigating the stellar activity contribution to the radial velocity time variations and measuring the planet masses with good precision.
Results. We find that K2-36 is likely a ~1 Gyr old system, and by treating the stellar activity through a Gaussian process regression, we measured the planet masses mb = 3.9 ± 1.1 M⊕ and mc = 7.8 ± 2.3 M⊕. The derived planet bulk densities ρb = 7.2−2.1+2.5 g cm−3 and ρc = 1.3−0.5+0.7 g cm−3 point out that K2-36 b has a rocky, Earth-like composition, and K2-36 c is a low-density sub-Neptune.
Conclusions. Composed of two planets with similar orbital separations but different densities, K2-36 represents an optimal laboratory for testing the role of the atmospheric escape in driving the evolution of close-in, low-mass planets after ~1 Gyr from their formation. Due to their similarities, we performed a preliminary comparative analysis between the systems K2-36 and Kepler-36, which we deem worthy of a more detailed investigation.
Analytical ray-tracing in planetary atmospheres
Authors: Bourgoin A. , Zannoni M. , Tortora P. 
Published: February 2019

Context. Ground-based astro-geodetic observations and atmospheric radio occultations are two examples of observational techniques requiring a scrutiny analysis of atmospheric refraction. In both cases, the measured changes of the observables are geometrically related to changes in the photon path through the refractive profile of the crossed medium. Therefore, having a clear knowledge of how the refractivity governs the photon path evolution is of prime importance to clearly understand observational features.
Aims. We analytically performed the integration of the photon path and the light time of rays traveling across a non-spherically symmetric planetary atmosphere.
Methods. Assuming that the atmospheric refraction evolves linearly with the Newtonian potential, we derived an exact solution to the equations of geometrical optics. By varying the solution’s arbitrary constants of integration, we reformulated the equation of geometrical optics into a new set of osculating equations describing the constants’ evolution following any changes in the refractive profile. We have highlighted the capabilities of the formalism, carrying out five realistic applications in which we derived analytical expressions. Finally, we assessed the accuracy by comparing the solution to results from a numerical integration of the equations of geometrical optics in the presence of a quadrupolar moment (J2).
Results. Analytical expressions for the light time and the refractive bending are given with relative errors at the level of one part in 108 and one part in 105, for typical values of the refractivity and J2 at levels of 10−4 and 10−2, respectively.
Conclusions. The establishment of the osculating equations for the ray propagation has two main advantages. Firstly, it provides an easy and comprehensive geometrical picture for interpreting the photon path. Secondly, it allows the analytical solving of the ray propagation in the presence of non-radial dependencies in the refractive profile.