bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of sensory characteristic rice of Padi Gogo (dry land paddy) at Aceh Province
Authors: Jaya R , Ferayanti F , Idawanni  , Rahmah F F , Ardiansyah R , Rahmi C H , Yusriana
Published: February 2020

Agricultural vision Indonesia on 2045 is to become world food producers. In status, there has been reduction of paddy field at Aceh province caused by land use changes, furthermore, the reliable solution is optimizing a dry land use, locally estimated reach up to 200.000 ha. Several institutions have been developing dry land of paddy varieties (padi gogo), which suitable planted in dry land and rainfed area. The objectives of this research were to obtain rice character and rice grains shape which suites on Acehnese preference. Location of rice planting was at Tangse sub district, Pidie district, Aceh province, the varieties including Inpago 8, 9, 11, Unsoed, Limboto and Tuwoti. To find out the sensory characteristic of the rice, hedonic test was performed with the number of panelist were 31 (half-classified). In this research, we observed parameters were taste, aroma, color, and texture as well as rice grains shape. The analyzing of the data used kruskal-wallis test. Result of the study shows that the main parameters was significant different (asymp sig.000), on dry land paddy (padi gogo). Overall, the panelist more tends likes the Limboto variety.
The study of technology adoption on integrated crop management (ICM) of paddy rice in Aceh Province
Authors: Bakar B A , Azis A , Fitria E , Nazariah  , Rahmi C H , Ismail M , Bubu Y G , Fachruddin
Published: February 2020

The aim of these activities was to provide input/recommendations to policymakers about the issues and problems of agricultural development from the study of technology adoption on integrated crop management (ICM) of rice. The event was held from March - November 2015 in four districts namely Pidie, Aceh Utara, Aceh Barat, and Aceh Barat Daya. The activities implemented through field studies with respondents are farmers who received the SLICM program (purposive sampling). Each district was selected one district and each district will be selected two villages. In-depth interview respondents as much as 10-20 farmers per village. Respondents were selected randomly from members of rice SLICM. Data collected consists of primary data and secondary data and processed by descriptive analysis. The results showed that the level of technology adoption on integrated crop management (ICM) of rice in Pidie, Aceh Utara, Aceh Barat, and Aceh Barat Daya districts is not influenced by the characteristics of the respondent, such as; age, education, and experience of farmers in cropping rice. Technology adoption on integrated crop management (ICM) of rice is still limited to the use of the technology components of new varieties and seed labeled. The various components of the basic technology and the integrated crop management selection of paddy rice, which have not adopted by respondents include intermittent irrigation, organic fertilizer utilization, weeding with grok. While legowo cropping system is still limited. The adoption rate on integrated crop management (ICM) of rice is influenced by several factors, among others: the implemented technology is easy, uncomplicated. The technology is also cheap but in accordance with the conditions of society and new technologies can provide more benefit to them (increased yield).
The response of shallot (Allium ascalonicum L.) growth and yield to gibberelline concentration and the interval of NASA liquid organic fertilizer
Authors: Oktaviani Z , Hayati M , Kesumawati E
Published: February 2020

This study was aimed at determining the effect of gibberellin concentration and the interval of Natural Nusantara (NASA) liquid organic fertilizer, as well as their interactions to influence growth and yield of shallots. This study was conducted from April to July 2019 in Experimental Field and Horticulture Laboratory of the Faculty of Agriculture, Universitas Syiah Kuala. The experiment used a Randomized Block Design with a Factorial pattern of 4x3. Gibberellin concentrations were observed at 4 levels (control, 100, 150, and 200 ppm) and the interval of NASA liquid organic fertilizer was observed at 3 levels (controlled, every 7, and 14 days DAP). The results showed that the highest shallot plant was found of 14 DAP, and the largest number of bulbs was found at 100 ppm of gibberellins concentration. The highest of fresh biomass per clump and the largest bulb diameter were found at 150 ppm gibberellins concentration. The growth and yield of the highest shallots were found at the interval of control treatment of NASA liquid organic fertilizer. The highest number of bulbs was found in the combination of gibberellins control with the interval of NASA liquid organic fertilizer every 14 days.
Effect of planting densities and fertilization levels on the production and quality of Chicory (Cichorium intybus) in Yogyakarta, Indonesia
Authors: Umami N , Dewi M P , Suhartanto B , Suseno N , Agus A
Published: February 2020

This study was aimed to determine the growth, production, and nutrient content of Cichorium intybus planted in different planting densities and fertilization levels in Yogyakarta, Indonesia. The study was arranged on factorial randomized design (3 x 3) with two factors: level of fertilization (0, 45, and 60 kg/ha) and planting density (2, 3, and 4 g of seeds/m2); with 6 replications – aggregating 54 plots. Chicory seeds were spread on 1 x 1.5 m2 plots with 20 cm of bedding height and 30 cm of distance between plots. NPK fertilizer was given when plants reached 15 days old. Plants were harvested at day-50 by cutting them 10 cm above the soil surface. The observation was performed on these following variables: growth (plant height, plant length, and leaf width), production (dry and organic matter production), and nutrient value (crude protein, dry and organic matter contents). All data were statistically evaluated using of the SPSS computer program. Significant treatments were subjected to Duncan’s new multiple range test (DMRT). The study shows that plants which received the greatest amount of fertilizer had the highest growth, production, and nutrient value (P-value <0.05). Higher planting density compensated the plant height, leaf width, number of leaves, dry and organic matter contents (P-value <0.05). However, it escalated the dry and organic matter production (P-value <0.05). The plant that received 60 kg/ha of fertilizer and planted in 3 g/m2 density demonstrated the most improved yield.
Analysis of value added agro industry arabica export coffee processing in Aceh Tengah case study at Oro Coffee Gayo
Authors: Baihaqi A , Hamid A H , Susanti E , Paga P E , Wardhana M Y , Marsudi E
Published: February 2020

This study aims to determine the value added of export Arabica coffee and the efficiency of export Arabica coffee marketing at Oro Coffee Gayo in Aceh Tengah Regency. Determination of the location of this study determined intentionally (purposive). The analytical method used in this research is the value-added analysis method of the Hayami model and the marketing efficiency analysis method. The analysis shows the value added of export Arabica coffee green bean grade 1 (special) on Oro Coffee Gayo is moderate, and green bean grade 2 (premium) is also moderate. Based on the value of marketing efficiency of green bean grade 1 and green bean grade 2 Oro Coffee Gayo marketing is assessed as efficient which is equal to (EP 0-50% efficient marketing).
The analysis of selection of upland rice variety in East Aceh District
Authors: Bakar B A , Azis A , Yusriani Y , Idawanni  , Andriani R , Bubu Y G , Rosa E , Fachruddin
Published: February 2020

The aim of this research was to determine important parameters based on farmers’ perceptions and the selection of the best alternative varieties for the development of upland rice in East Aceh. Data collected includes secondary data and primary data. Primary data collection is done by using questionnaire data in gathering information on farmers’ perceptions. Whereas the alternative selection combines elements of farmers’ perceptions and field observations of several varieties. The analytical method was carried out using observations in the field and processing data descriptively. The varieties used in the field study were Inpago 8, Inpago 9, Inpago 10, Inpago 11 and Situ Patenggang. The results of the study address important parameters in the cultivation of upland rice based on the results of the questionnaire with farmers are the age of fast harvesting plants and the average production with a very important category, then the weight of 1000 seeds in grams and the potential yield with important categories, then the productive tillers of each stem, the amount grain of each panicle (seeds) and tall plants in the Medium category. The choice of the best alternative varieties in East Aceh Regency based on the results of farmers’ perceptions and field studies were found in Inpago 9 varieties.
Physicochemical properties of sourdough bread made from local variety sweet potato and pineapple juice
Authors: Zaidiyah  , Lubis Y M , Putri C A R G , Rohaya S
Published: February 2020

A study was done to evaluate the characteristic of sweet potato sourdough bread made by pineapple juice. The bread was formulated using different variation of ratio of pineapple juice to starter as follows; 4:1, 3:2, and 2:3 and sweet potatoes differ in their flesh colour. Starter development was also daily observed for 10 days. The proximate composition of bread analysed were 5.60% protein, 1.63% crude fat, 44,19% moisture and 1,51% ash. The total available carbohydrate was 45, 91%. The breads pH and crude fibre were 3.73 and 1,15% Bread physical characteristic were also conducted in order to ensure the bread quality such porosity and loaf volume bread. The sourdough bread prepared by liquid starter from pineapple juice and white sweet potato with a ratio of 4:1 met the best performance.
Chemical characteristics of brownis substituted with sago starch and corn starch
Authors: Rasdiansyah  , Muzaifa M , Zaidiyah  , Monica R
Published: February 2020

Sago (Metroxylon sp) is a native plant to southeast Asia, and is one a food commodities that contain a lot of carbohydrated. Therefore, sago is used as a staple food for several regions in Indonesia such as Maluku and Irian Jaya. In the sago community, there is very little use of sago, even though sago can be used as raw material for making various products such as noodles, cakes, cookies, crackers and brownies. The study aimed to determine the effect of substitutions of sago starch and corn starch on the chemical properties of brownies. This study used factorial Completely Randomized Design which consisted of two factors. The first factor was the percentage of sago starch (S), which consisted of 3 levels, namely S1 = 50%, S2 = 75%, and S3 = 100%. The second factor was the concentration of corn starch (T) which consisted of 2 levels, namely T1 = 15% and T2 = 20%. The parameters observed werewater content, ash content, fiber content, fat content, protein content, and carbohydrate content. The best treatment for chemical test is on the T2S2 treatment with the results of water content of 23.62%, ash content 2.14%, fiber content 3.46%, fat content of 23.95%, protein content of 3.36%, and carbohydrates 50.15%.
Modelling ancient areas for date palms (Phoenixspecies: Arecaceae): Bayesian analysis of biological and cultural evidence
Authors: Rivera Diego , Abellán Javier , Palazón José Antonio , Obón Concepción , Alcaraz Francisco , Carreño Encarna , Laguna Emilio , Ruiz Alberto , Johnson Dennis
Published: February 2020

Our aim in this study is to build a model for the expansion of date palms (Phoenix spp., Arecaceae) that can be linked to domestication processes. Palaeontological and archaeobotanical evidence concerning date palm is extremely diversified around the Mediterranean Basin and in West Asia, mainly consisting of date fruit remains, but also including leaf fragments and other plant remains. This biological evidence is further compared with cultural evidence (coins, pottery, ancient texts) and the present distribution of Phoenix spp. in the area. Bayesian methods working with likelihood and conditional probabilities are successfully applied to generate a model for displaying in maps the ancient distribution of palm groves in terms of probabilities. The model suggests that the domestication of Phoenix dactylifera occurred mainly east of 30°E, probably in the Jordan Valley area, starting before 7 kya and, in a westward shift, that this was gradually superposed onto pre-existing local western populations of the same genus, especially in the Nile valley. It appears that this mainly affected the P. dactylifera western cluster (P. excelsior, P. atlantica, P. iberica). However, other taxa persisted as independent species (P. theophrasti, P. canariensis).
Adaptive Filter with Type-2 Fuzzy System and Optimization-Based Kernel Interpolation for Satellite Image Denoising
Authors: Mahalakshmi T , Sreenivas Alluri
Published: February 2020

Satellite image denoising is a recent trend in image processing, but faces many challenges due to the environmental factors. Previous works have developed many filters for denoising the hyperspectral satellite images. Accordingly, this work utilizes an adaptive filter with the type 2 fuzzy system and the optimization-based kernel interpolation for the satellite image denoising. Here, the image denoising has been done through three steps, namely noise identification, noise correction and image enhancement. Initially, the type 2 fuzzy system identifies the noisy pixels in the satellite image and converts the image into a binary image, which is passed through the adaptive nonlocal mean filter (ANLMF) for the noise correction. Finally, the kernel-based interpolation scheme carries out the image enhancement, which is done through the proposed chronological Jaya optimization algorithm (chronological JOA) that is developed by modifying Jaya optimization algorithm (JOA) with the chronological idea. The performance of the proposed denoising scheme is analyzed by considering the satellite images from two standard databases, namely Indian pines database and NRSC/ISRO satellite database. Also, the comparative analysis is performed with the state-of-the-art denoising methods using the evaluation metrics, peak signal to noise ratio (PSNR), structural similarity index (SSIM) and second derivative-like measure of enhancement (SDME). From the results, it is exposed that the proposed adaptive filter with the chronological JOA has the improved performance with the PSNR of 22.0408 dB, SDME of 244.133 dB and SSIM of 0.872.
PBP1a glycosyltransferase and transpeptidase activities are both required for maintaining cell morphology and envelope integrity inShewanella oneidensis
Authors: Yin Jianhua , Zhang Ting , Cai Jingxiao , Lou Jie , Cheng Dan , Zhou Weifeng , Xu Chaoyi , Liu Yanqiu , Gao Haichun , Yu Zhiliang
Published: February 2020

In rod-shaped Gram-negative bacteria, penicillin binding protein 1a (PBP1a) and 1b (PBP1b) form peptidoglycan-synthesizing complexes with the outer membrane lipoprotein LpoA and LpoB, respectively. Escherichia coli mutants lacking PBP1b/LpoB are sicker than those lacking PBP1a/LpoA. However, we previously found that mutants lacking PBP1a/LpoA but not PBP1b/LpoB are deleterious in Shewanella oneidensis. Here, we show that S. oneidensis PBP1a (SoPBP1a) contains conserved signature motifs with its E. coli counterpart, EcPBP1a. Although EcPBP1a play a less prominent role in E. coli, it is capable of substituting for the SoPBP1a in a manner dependent on SoLpoA. In S. oneidensis, expression of PBP1b is lower than PBP1a, and therefore the additional expression of SoPBP1b at low levels can functionally compensate for the absence of SoPBP1a. Importantly, S. oneidensis PBP1a variants lacking either glycosyltransferase (GTase) or transpeptidase (TPase) activity fail to maintain normal morphology and cell envelope integrity. Similarly, SoPBP1b variants also fail to compensate for the loss of SoPBP1a. Furthermore, overproduction of variants of SoPBP1a, but not SoPBP1b, has detrimental effects on cell morphology in S. oneidensis wild type cells. Overall, our results indicate that the combined enzymatic activities of SoPBP1a are essential for cell wall homeostasis.
Local multipliers at work
Authors: Cerqua Augusto , Pellegrini Guido
Published: February 2020

We propose a novel evaluation strategy to estimate local multipliers in Italy during 1996–2006. We find the presence of positive multipliers: 0.26–0.33 for the tradable sector (manufacturing) and 0.88–1.13 for the non-tradable sector (construction and services). They are lower than what was previously found for the United States but much higher than those identified for European and Asian countries. The reasons for this finding lie in the higher accuracy of the data, in the relevance of the instrument used, and in the widespread underutilization of production factors.
Factors associated with tenofovir diphosphate concentrations in dried blood spots in persons living with HIV
Authors: Coyle Ryan P , Morrow Mary , Coleman Stacey S , Gardner Edward M , Zheng Jia-Hua , Ellison Lucas , Bushman Lane R , Kiser Jennifer J , MaWhinney Samantha , Anderson Peter L , Castillo-Mancilla Jose R
Published: February 2020

Objectives

To determine factors associated with interindividual variability in tenofovir diphosphate (TFV-DP) concentrations in dried blood spots (DBSs) among persons living with HIV (PLWH).

Methods

PLWH who were at least 18 years old and taking tenofovir disoproxil fumarate-containing ART were prospectively recruited and enrolled from a clinical cohort and followed longitudinally (up to three visits over 48 weeks). With log-transformed TFV-DP concentrations in DBSs as the outcome, mixed-model regression analyses were used to assess associations between self-reported 3 month ART adherence, race and other clinical covariates (gender, age, BMI, CD4+ T cell count, estimated glomerular filtration rate, haematocrit, duration on current ART and anchor drug class) on TFV-DP in DBSs.

Results

Five hundred and twenty-seven participants (1150 person-visits) were analysed. Adjusting for race and other clinical covariates, every 10% increase in self-reported 3 month ART adherence was associated with an average TFV-DP concentration increase in DBSs of 28% (95% CI: 24%–32%; P < 0.0001). In the same model, female participants had 20% (95% CI: 3%–40%; P = 0.02) higher TFV-DP concentrations in DBSs, compared with male participants, and every 1 kg/m2 increase in BMI was associated with a decrease in TFV-DP concentration in DBSs by 2% (95% CI: −3% to −1%; P < 0.0001).

Conclusions

Individual patient characteristics were predictive of TFV-DP concentration in DBSs in PLWH receiving tenofovir disoproxil fumarate-based ART. Future research to incorporate these predictors into the interpretation of this ART adherence biomarker, and to establish whether these associations extend to PLWH taking tenofovir alafenamide-containing ART, is needed.
Impact of increasing weaning age on pig performance and belly nosing prevalence in a commercial multisite production system
Authors: Faccin Jamil E G , Laskoski Fernanda , Hernig Luciana F , Kummer Rafael , Lima Gustavo F R , Orlando Uislei A D , Gonçalves Márcio A D , Mellagi Ana Paula G , Ulguim Rafael R , Bortolozzo Fernando P
Published: February 2020

The effects of increasing weaning age in a commercial production system on nursery and finishing performance were evaluated. A total of 1,176 pigs (PIC 337 × Camborough) were used in a 136-d growth trial with 14 and 10 replications/weaning age on the nursery and finishing phases, respectively. Treatments included weaning litters at 19, 22, 25, or 28 d of age. In the nursery, as weaning age increased, initial (5.04, 5.70, 6.52, and 7.26 kg) and final body weight (BW) (18.2, 19.8, 23.0, and 25.1 kg) increased (linear, P < 0.001). Increasing the weaning age reduced (linear, P < 0.001) the prevalence of pigs exhibiting belly nosing (27.6%, 15.0%, 6.5%, and 1.4%) during the first 3 wk. The percentage of pigs losing weight during the first week after weaning (35.1%, 28.7%, 12.4%, and 9.2%) decreased (linear, P < 0.001) as weaning age increased. Average daily gain (ADG; 295, 320, 374, 406 g/d) and average daily feed intake (493, 534, 619, 661 g/d) increased (linear, P < 0.001), while feed efficiency (G:F) (596, 599, 604, and 615) tended to increase (linear, P = 0.081) with weaning age. Removal rate (8.01%, 3.79%, 2.29%, and 1.65%) declined (linear, P = 0.001) as weaning age increased, while there was no evidence of difference (P = 0.463) in mortality rate (0.71%, 0.36%, 0.96%, 1.04%). In the finishing period, BW at 136 d post-weaning (114.9, 117.8, 124.7, and 126.5 kg) and ADG (1.02, 1.04, 1.08, and 1.07 kg/d) improved (linear, P < 0.001). There was no evidence of differences (P > 0.24) in removal (1.5%, 2.4%, 1.0%, and 0.0%) or mortality rates (0.9%, 1.0%, 1.0%, and 1.4%) with changes in weaning age. When performance was analyzed at a common day of life (164 d of age), no effects of weaning age (P > 0.25) were found for BW (125.2, 124.4, 128.0, and 126.5 kg) and lifetime ADG (growth rate from birth to market) (754, 751, 774, and 762 g/d). The BW sold per pig weaned increased (linear, P < 0.001) with weaning age. Even though the slope indicated a linear response, the magnitude of improvement was high until 25 d, before exhibiting diminishing returns from 25 to 28 d. Thus, the study suggests that increasing the weaning age can be an effective strategy to improve the overall performance in a commercial system. Although lifetime performance was not affected by the weaning age range studied, the consistent effect in the nursery and the increment in the number of pigs reaching the market facilitated by the improvement in the removal rate in the nursery phase imply that 25 d is the optimal weaning age.
Factors Influencing Cold Hardiness during Overwintering of Streltzoviella insularis (Lepidoptera: Cossidae)
Authors: Pei Jiahe , Li Chengcheng , Ren Lili , Zong Shixiang
Published: February 2020

Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) is a woodboring pest that severely damages urban and plain afforestation trees in northern China. Cold hardiness is an important strategy for the insect to survived during low winter temperatures. Understanding the strategy of S. insularis might provide insights for pest management approaches. To assess the key factors affecting cold hardiness, we measured the supercooling point, freezing point, total water content, total fat content, glycogen content, and total protein content of overwintering larvae. The relationships between supercooling points, temperature, body size, and nutrients were analyzed. The results showed that the supercooling point and freezing point of the larvae decreased first, reached the lowest point in January, and then increased during the rest of the overwintering period. The supercooling point positively correlated with the daily average temperature and the daily minimum temperature. Total lipid content negatively correlated with the supercooling point, while glycogen content had a significant positive correlation with the supercooling point. The temperature may have a major impact on cold hardiness, whereas individual body size may have no significant influence over cold tolerance. During the overwintering process, glycogen and total lipid contents may directly affect cold hardiness. Therefore, the lipid and carbohydrate metabolism may play a role in the cold tolerance of S. insularis larvae. This study provides a physiological and biochemical basis for future metabolic studies on S. insularis larva and the research of overwintering strategies.
Observational signatures of gamma-rays from bright blazars and wakefield theory
Authors: Canac N E , Abazajian K N , Tajima T , Ebisuzaki T , Horiuchi S
Published: February 2020

Gamma-ray observations have revealed strong variability in blazar luminosities in the gamma-ray band over time-scales as short as minutes. We show, for the first time, that the correlation of the spectrum with intensity is consistent with the behaviour of the luminosity variation of blazar spectral energy distributions (SEDs) along a blazar sequence for low synchrotron peak blazars. We show that the observational signatures of variability with flux are consistent with wakefield acceleration of electrons initiated by instabilities in the blazar accretion disc. This mechanism reproduces the observed time variations as short as 100 s. The wakefield mechanism also predicts a reduction of the electron spectral index with increased gamma-ray luminosity, which could be detected in higher energy observations well above the inverse Compton peak.
Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting
Authors: Hong Nguyen Thi Thu , Anh Nguyen To , Mai Nguyen Thi Hoang , Nghia Ho Dang Trung , Nhu Le Nguyen Truc , Thanh Tran Tan , Phu Nguyen Hoan , Deng Xutao , van Doorn H Rogier , Chau Nguyen Van Vinh , Delwart Eric , Thwaites Guy , Tan Le Van
Published: February 2020

Background

Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious diseases diagnosis, but few studies have been conducted in resource-limited settings.

Methods

We assessed the performance of mNGS in the cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral-specific polymerase chain reaction (PCR). As a complementary analysis, 6 viral PCR-positive samples were analyzed using MinION-based metagenomics.

Results

Routine diagnosis could identify a virus in 15 (22.7%) patients, including herpes simplex virus (HSV; n = 7) and varicella zoster virus (VZV; n = 1) by PCR, and mumps virus (n = 4), dengue virus (DENV; n = 2), and Japanese encephalitis virus (JEV; n = 1) by serological diagnosis. mNGS detected HSV, VZV, and mumps virus in 5/7, 1/1, and 1/4 of the CSF positive by routine assays, respectively, but it detected DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in 7 patients of unknown cause. Metagenomic MinION-Nanopore sequencing could detect a virus in 5/6 PCR-positive CSF samples, including HSV in 1 CSF sample that was negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR.

Conclusions

In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in the CSF of meningoencephalitis patients. Further studies are needed to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.
Carbon–Strontium Isotope Decoupling in Carbonatites from Caotan (Qinling, China): Implications for the Origin of Calcite Carbonatite in Orogenic Settings
Authors: Wei Chun-Wan , Xu Cheng , Chakhmouradian Anton R , Brenna Marco , Kynicky Jindrich , Song Wen-Lei
Published: February 2020

Mantle-derived carbonatites emplaced in orogenic belts and some extensional settings are hypothesized to contain recycled crustal material. However, these carbonatites are typically composed of calcite showing a typical mantle range of C–O isotopic values devoid of recognizable sedimentary fingerprints. Here, we report the first known instance of C–Sr isotope decoupling between intimately associated dolomite carbonatites and magnetite–forsterite–calcite carbonatites from the northern Qinling orogen, central China. The calcite-dominant variety is developed at the contact between the dolomite carbonatite and metasomatized wall-rock gneiss. The two types of carbonatites have similar δ18OVSMOW (6·98‰ to 9·96‰), εNd(i) (-3·01 to -6·47) and Pb (206Pb/204Pb(i) = 17·369–17·584, 207Pb/204Pb(i) = 15·443–15·466) isotopic compositions, but significantly different C and Sr isotopic signatures (δ13CVPDB = -3·09 to -3·58‰ and -6·11 to -7·19‰; 87Sr/86Sr(i) = 0·70373 to 0·70565 vs 0·70565 to 0·70624 for the dolomite and calcite rocks, respectively). The relative enrichment of the early-crystallizing dolomite carbonatite in 13C and its depletion in 87Sr are primary isotopic characteristics inherited from its mantle source. The observed field relations, petrographic and geochemical characteristics of the Caotan dolomite and calcite carbonatites imply that the strong C–Sr isotopic decoupling between them could not result from mixing of different mantle reservoirs (e.g. HIMU and EM1), or from magma fractionation processes. We propose that the calcite carbonatites were a by-product of metasomatic reactions between primary dolomitic melts and felsic wall-rock. These reactions involved the loss of Mg and CO2 from the magma, leading to depletion of the evolved calcite-saturated liquid in 13C and its enrichment in radiogenic Sr. We conclude that calcite carbonatites in plate-collision zones may not represent primary melts even if their isotopic signature is recognizably ‘mantle-like’.
Acoustic closed-loop stimulation during sleep improves consolidation of reward-related memory information in healthy children but not in children with attention-deficit hyperactivity disorder
Authors: Prehn-Kristensen Alexander , Ngo Hong-Viet V , Lentfer Luisa , Berghäuser Julia , Brandes Lena , Schulze Larissa , Göder Robert , Mölle Matthias , Baving Lioba
Published: February 2020

Study Objectives

Slow oscillations (SO) during slow-wave sleep foster the consolidation of declarative memory. Children with attention-deficit hyperactivity disorder (ADHD) display deficits in the sleep-associated consolidation of declarative memory, possibly due to an altered function of SO. The present study aimed at enhancing SO activity using closed-looped acoustic stimulation during slow-wave sleep in children with ADHD.

Methods

A total of 29 male children (14 with ADHD; aged 8–12 years) participated in a double-blind, placebo-controlled study trial. Children spent two experimental nights in a sleep lab, one stimulation night and one sham night. A declarative learning task (word-pair learning) with a reward condition was used as a primary outcome. Secondary outcome variables were a procedural memory (serial reaction time) and working memory (WM; n-back) task. Encoding of declarative and procedural memory took place in the evening before sleep. After sleep, the retrieval took place followed by the n-back task.

Results

The stimulation successfully induced SO activity during sleep in children with and without ADHD. After stimulation, only healthy children performed better on high-rewarded memory items (primary outcome). In contrast, there were indications that only children with ADHD benefitted from the stimulation with respect to procedural as well as WM performance (secondary outcome).

Conclusions

We were able to show that the acoustic closed-loop stimulation can be applied to enhance SO activity in children with and without ADHD. Our data indicate that SO activity during sleep interacts with subsequent memory performance (primary outcome: rewarded declarative memory; secondary outcome: procedural and WM) in children with and without ADHD.
Relationship between heifer carcass maturity and beef quality characteristics
Authors: Hoffman Kacie C , Colle Michael J , Nasados James A , Gray Sara J , Rogers Jakobie , Van Buren Jessie B , Puga Kendelle J , Murdoch Gordon K , Richard Ronald P , Doumit Matthew E
Published: February 2020

Our objective was to determine the relationship between heifer carcass maturity and beef palatability of the longissimus lumborum (LM) and biceps femoris (BF). Left sides of A (n = 30), B (n = 30), and C (n = 30) maturity heifer carcasses under 30 mo of age by dentition were used. Carcasses were selected to ensure similar marbling scores across maturity groups (Small to Modest). Beef strip loins (LM) and outside rounds (BF) were obtained from these carcasses. Steaks were used to measure color stability, lipid oxidation (thiobarbituric acid reactive substances; TBARS), Warner-Bratzler shear force (WBSF), soluble and insoluble collagen, and consumer sensory perceptions. Heifer carcass maturity did not affect pH, fluid loss, WBSF, or collagen content of LM or BF steaks (P > 0.29). In LM and BF steaks, a maturity × day of retail display interaction occurred for TBARS, in which B maturity steaks had lower levels of lipid oxidation compared with A and C maturity steaks from the fourth day to the end of the retail display (P < 0.01). Nevertheless, LM steaks from B maturity carcasses tended to have lower overall acceptability (P = 0.08) and juiciness (P = 0.09) than steaks from C maturity carcasses, but steaks from B and C maturity carcasses did not differ from LM steaks obtained from A maturity carcasses. No differences in tenderness or flavor were observed due to maturity (P > 0.24). Similarly, maturity had no effect on sensory characteristics of BF steaks (P > 0.30). In conclusion, our results indicate that advanced physiological maturity does not decrease palatability of strip loin or outside round steaks from carcasses of heifers under 30 mo of age.
Pharmaceutic application of vitamin D3 on particle-induced fibrotic effects through induction of Nrf2 signals
Authors: Zhang Hong , Deng Wuquan , Yang Youjing , Wei Shuhui , Xue Lian , Tao Shasha
Published: February 2020

Fine particulate matter, a major air pollutant across the world, causes a series of pulmonary diseases. Vitamin D is a typical vitamin with emerging roles in inflammation and fibrosis. Different situations and diseases need different doses and modes of vitamin D administration, which challenges the existing vitamin D supplementary rules. Thus, studies of vitamin D applications and their mechanisms in various diseases are important for its future therapeutic applications. In this study, the therapeutic application of vitamin D3 in chronic particle-exposure-associated lung fibrosis and tissue remodeling was investigated. In vivo studies showed that vitamin D3 significantly attenuated fibrosis effects by decreasing α-smooth muscle actin-regulated extracellular matrix deposition and restoring expressions of E-cadherin and N-cadherin. With the importance of activated macrophage in the regulation of local epithelium and fibroblast in the process of tissue fibrosis, two separate in vitro systems of co-culture of macrophages with lung epithelium or fibroblast were built. The results confirmed that vitamin D3 promoted the proliferation of lung epithelium and depressed the fibrosis effects of fibroblasts as well. In addition, our results indicated that the therapeutic effects of vitamin D3 were through Nrf2 signals. Our work provides convincing experimental evidence for vitamin D therapeutic application to promote tissue repair and improve particle-associated lung fibrosis.
Incorporating phylogenetic information in microbiome abundance studies has no effect on detection power and FDR control
Authors: Bichat Antoine , Plassais Jonathan , Ambroise Christophe , Mariadassou Mahendra
Published: February 2020

We consider the problem of incorporating evolutionary information (e.g. taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierachical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non hierachical, Benjamini-Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierachical structure with profit but do not control the False Discovery Rate (FDR)a prioriand remain inferior to a classical Benjamini-Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Although intuition advocates the use of a hierachical structure, be it the phylogeny or the correlation tree, to increase the detection rate in microbiome studies, current hierachical procedures are still inferior to non hierachical ones and effective procedures remain to be invented.
Clinically Applicable Deep Learning Strategy for Pulmonary Nodule Risk Prediction: Insights into HONORS
Authors: Lv Wenhui , Wang Yang , Zhou Changsheng , Huang Sheng , Fang Xiangming , Xu Qiuzhen , Zhang Qirui , Huang Chuxi , Li Xinyu , Zhou Zhen , Yu Yizhou , Wang Yizhou , Lu Mengjie , Xu Qiang , Li Xiuli , Lin Haoliang , Lu Xiaofan , Xu Qinmei , Sun Jing , Tang Yuxia , Song Yong , Yan Fangrong , Zhang Bing , Cheng Zhen , Zhang Longjiang , Lu Guangming
Published: February 2020

Background and Purpose

Limited optimization was clinically applicable for reducing missed diagnosis, misdiagnosis and inter-reader variability in pulmonary nodule diagnosis. We aimed to propose a deep learning-based algorithm and a practical strategy to better stratify the risk of pulmonary nodules, thus reducing medical errors and optimizing the clinical workflow.

Materials and Methods

A total of 2,348 pulmonary nodules (1,215 with lung cancer) containing screened nodules from National Lung Cancer Screening Trial (NLST) and incidentally detected nodules from Jinling Hospital (JLH) were used to train and evaluate a deep learning algorithm, Filter-guided pyramid network (FGP-NET). Internal and external test of FGP-NET were performed on two independent datasets (n=542). The performance of FGP-NET at Youden point which maximizing the Youden index was compared with 126 board-certificated radiologists. We further proposed Hierarchical Ordered Network ORiented Strategy (HONORS), which manipulates the emphasis either on sensitivity or specificity to target risk-stratified clinical scenarios, directly making decisions for some patients.

Results

FGP-NET achieved a high area under the curve (AUC) of 0.969 and 0.855 for internal and external testing, and was comparable or even outperformed the radiologists when considering sensitivity. HONORS-guided FGP-NET identified benign nodules with a high sensitivity (95.5%) in the screening scenario, and demonstrated satisfactory performance for the rest ambiguous nodules with 0.945 of AUC by the Youden point. FGP-NET also detected lung cancer with a high specificity of 94.5% in routine diagnostic scenario; an AUC of 0.809 was achieved for the rest nodules.

Conclusion

The combination of HONORS and FGP-NET provides well-organized stratification for pulmonary nodules and also offers the potential for reducing medical errors.

Highlights

Pulmonary nodules were managed for both screening and diagnostic scenarios

Proposal of a hierarchical strategy for targeting risk-stratified clinical scenarios

A large scale Human-deep learning contest for reliable performance evaluation
Hippocampal volume in Provisional Tic Disorder predicts tic severity at 12-month follow-up
Authors: Kim Soyoung , Greene Deanna J. , D’Andrea Carolina Badke , Bihun Emily C. , Koller Jonathan M. , O’Reilly Bridget , Schlaggar Bradley L. , Black Kevin J.
Published: February 2020

Background

Previous studies have investigated differences in the volumes of subcortical structures (e.g., caudate nucleus, putamen, thalamus, amygdala, hippocampus) between individuals with and without Tourette syndrome (TS), as well as the relationships between these volumes and tic symptom severity. These volumes may also predict clinical outcome in Provisional Tic Disorder (PTD), but that hypothesis has never been tested.

Objective

This study aimed to examine whether the volumes of subcortical structures measured shortly after tic onset can predict tic symptom severity at one year post tic onset, when TS can first be diagnosed.

Methods

We obtained T1-weighted structural MRI scans from 41 children with PTD (25 with prospective motion correction [vNavs]) whose tics had begun less than 9 months (median 3.7 months) prior to the first study visit (baseline). We re-examined them at the 12-month anniversary of their first tic (follow-up), assessing tic severity using the Yale Global Tic Severity Scale. We quantified the volumes of subcortical structures using volBrain software.

Results

Baseline hippocampal volume was correlated with tic severity at the 12-month follow-up, with a larger hippocampus at baseline predicting worse tic severity at follow-up. This result was confirmed in the subgroup scanned with prospective motion correction. The volumes of other subcortical structures did not significantly predict tic severity at follow-up.

Conclusion

These findings suggest that hippocampal volume may be an important marker in predicting prognosis in Provisional Tic Disorder.
External error attribution dampens efferent-based predictions but not proprioceptive changes in hand localization
Authors: Gastrock Raphael Q. , Modchalingam Shanaathanan , ’t Hart Bernard Marius , Henriques Denise Y. P.
Published: February 2020

In learning and adapting movements in changing conditions, people attribute the errors they experience to a combined weighting of internal or external sources. As such, error attribution that places more weight on external sources should lead to decreased updates in our internal models for movement of the limb or estimating the position of the effector, i.e. there should be reduced implicit learning. However, measures of implicit learning are the same whether or not we induce explicit adaptation with instructions about the nature of the perturbation. Here we evoke clearly external errors by either demonstrating the rotation on every trial, or showing the hand itself throughout training. Implicit reach aftereffects persist, but are reduced in both groups. Only for the group viewing the hand, changes in hand position estimates suggest that predicted sensory consequences are not updated, but only rely on recalibrated proprioception. Our results show that estimating the position of the hand incorporates source attribution during motor learning, but recalibrated proprioception is an implicit process unaffected by external error attribution.
Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity
Authors: Deng Lei , Cai Yideng , Zhang Wenhao , Yang Wenyi , Gao Bo , Liu Hui
Published: February 2020

Motivation

To efficiently save cost and reduce risk in drug research and development, there is a pressing demand to developin-silicomethods to predict drug sensitivity to cancer cells. With the exponentially increasing number of multi-omics data derived from high-throughput techniques, machine learning-based methods have been applied to the prediction of drug sensitivities. However, these methods have drawbacks either in the interpretability of mechanism of drug action or limited performance in modeling drug sensitivity.

Results

In this paper, we presented a pathway-guided deep neural network model, referred to as pathDNN, to predict the drug sensitivity to cancer cells. Biological pathways describe a group of molecules in a cell that collaborates to control various biological functions like cell proliferation and death, thereby abnormal function of pathways can result in disease. To make advantage of both the excellent predictive ability of deep neural network and the biological knowledge of pathways, we reshape the canonical DNN structure by incorporating a layer of pathway nodes and their connections to input gene nodes, which makes the DNN model more interpretable and predictive compared to canonical DNN. We have conducted extensive performance evaluations on multiple independent drug sensitivity data sets, and demonstrate that pathDNN significantly outperformed canonical DNN model and seven other classical regression models. Most importantly, we observed remarkable activity decreases of disease-related pathway nodes during forward propagation upon inputs of drug targets, which implicitly corresponds to the inhibition effect of disease-related pathways induced by drug treatment on cancer cells. Our empirical experiments show that pathDNN achieves pharmacological interpretability and predictive ability in modeling drug sensitivity to cancer cells.

Availability

The web server, as well as the processed data sets and source codes for reproducing our work, is available athttp://pathdnn.denglab.org
Comparing Community Detection Methods in Brain Functional Connectivity Networks
Authors: Vangimalla Reddy Rani , Sreevalsan-Nair Jaya
Published: February 2020

Brain functional networks are essential for understanding functional connectome. Computing the temporal dependencies between the regions of brain activities of functional magnetic resonance imaging (fMRI) gives us the functional connectivity between the regions. The pairwise connectivities in matrix form correspond to the functional network (fNet), also referred to as a functional connectivity network (FCN). We start with analyzing a correlation matrix, which is an adjacency matrix of the FCN. In this work, we perform a case study of comparison of different analytical approaches in finding node-communities of the brain network. We use five different methods of community detection, out of which two methods are implemented on the network after filtering out the edges with weight below a predetermined threshold. We additionally compute and observe the following characteristics of the outcomes: (i)modularityof the communities, (ii) symmetrical node-partition between the left and right hemispheres of the brain, i.e.,hemispheric symmetry, and (iii)hierarchical modular organization. Our contribution is in identifying an appropriate test-bed for comparison of outcomes of approaches using different semantics, such as network science, information theory, multivariate analysis, and data mining.