bluuebunny/crossref_metadata_2025 huggingface dataset:
Chlorophyll-a, and Sea Surface Temperature (SST) as proxies for Climate Changes: Case Study in Batu Ampar waters, Riau Islands
Authors: Antoni S , Bantan R A , Al-Dubai T A , Lubis M Z , Anurogo W , Silaban R D
Published: July 2019

The condition of Indonesian oceanography is largely determined by the development of the Monsoon Wind and the Indonesian Cross Flow (ARLINDO). The development of marine remote sensing technology that is so fast, able to make it easier to map the condition of waters in Indonesia in an actual way easily and cheaply. This can make it easier to obtain information about climate change approaches to the physical oceanography conditions in Indonesian waters. The purpose of this research is to study the changes of the physical oceanography parameters resulting from climate changes. Based on the results of the research that for the highest Sea Surface Temperature (SST) exist in 2013 (above 30,75 °C). It has increased from the previous year i.e. in 2012 with an increase of SST value of 30 o C. In 2013 SST is spread high on the Batu Ampar Permit - Harbor Bay ferry port. Analyzing the value of chlorophyll-a, sea surface temperature, and sea level to see global climate change in the waters of Batu Ampar. The analysis shows the highest sea level with an elevation of 3.1 meters, with sea surface temperature in the range of 29,5 °C - 29,75 °C, at the time of recording 00:05-02:55 (August 1, 2017 - September 1, 2017). The results of the analysis obtained from the oceanographic conditions in the waters of Batu Ampar did not experience a fluctuating change in global climate change in the waters. The annual SST interval spacing interval of 0.5-0.75 °C and the changing phase relationship could have an impact on subsequent climate change and sea level rise to be concrete evidence. Reduced levels of chlorophyll-a each year will have an impact on the heat of the sea level, thus rising sea levels and indicating a climate with hot temperatures (ice at the poles melt).
Geohazard Identification Using 2-D Resistivity Imaging For Seulawah Agam Volcano, Indonesia
Authors: Syukri Muhammad , Saad Rosli , Marwan  , Tri Anda Sabrian , Safitri R. , Fadhli Zul
Published: July 2019

Common parameter used for delineating geothermal system is resistivity. Hydrothermal alteration of primary minerals depends on temperature distribution and forms various clay minerals with conductivity properties. Clay minerals formed at high temperatures are more resistant than lower temperature. Most geothermal systems within active volcanic regions show low resistivity (1-5 Ohm.m) surrounding an inner core of higher resistivity. 2-D resistivity study conducted at Seulawah Agam active volcano and its vicinity (Aceh) with geothermal sources (Herzt, Ie Jue and Ie Seu’um) flowing from south-east to north-west. Two lines, L1 and L2 were conducted crossing the suspected geothermal flow using ABEM SAS4000 system with 10 m minimum electrode spacing and Pole-Dipole array. Resistivity results indicated two main zones; (i) top layer, <100 m depth with resistivity value of >60 Ohm.m and (ii) cap-rock, 30-100 m depth with resistivity value of 6-50 Ohm.m. Few fractures and low resistivity regions (<5 Ohm.m) were identified in the caprock. Hot water and hot mud have low resistivity value; hence the low resistivity regions were interpreted as geothermal flow and it is convincingly suspected to be a geohazard zone. New extension of Seulawah Agam geothermal flow was identified by 2-D resistivity method.
Tsunami and Earthquake Symbols and Signs on the Children’s Semiotic Understanding
Authors: Moriyanti  , Ismail N M , Yanti F , Rahma E A , Setyana R
Published: July 2019

This qualitative research aims at describing the coastal children’s knowledge and perspective about the Tsunami and earthquake’s symbols and signs. The use and purpose of the signs on the warning board is very important for children on the coastal area as an understanding of disaster preparedness. Consequently, the researchers chose 43 respondents with 8-13 years old who live at the coast of Kampung Jawa, Banda Aceh to respond questionnaire and interview. The questionnaire set contained the verbal and non-verbal symbols and signs about tsunami and earthquake which was formulated in the form open-ended questions. It was found that only 12 children who could answer 80% of the questions correctly from the questionnaire. This implies that their understanding and background knowledge about the tsunami and earthquake’s symbols and signs are very low level even though the symbols and signs are put on their enviroment. Moreover, during interview process, children had wrong interpretation about the signs and symbols and did not know the function because they never get information about the symbols, the way to evacuate and preparation before the disaster happened from their school and enviroment. Consequently, it is suggested that stakeholder should conduct practices for disaster education that can improve their disaster awareness.
Disaster Risk Communication Issues and Challenges: Lessons Learned From the Disaster Management Agency of Banda Aceh City
Authors: Adella Shylvana , Fauzan Nur Muhammad , Nisa Nazriatun , Tirtana Putra Arief , Rizki Ramadhana Fira , Maiyani Fitri , Munadi Khairul , Rahman Alfi
Published: July 2019

The Badan Penanggulan Bencana Daerah (BPBD or Disaster Management Agency) of Banda Aceh City was established through Banda Aceh bylaw (or Qanun) No. 3 of 2011 following the significant 2004 Indian Ocean tsunami. Meanwhile, as Banda Aceh’s population has grown, an increasing number of people have moved to and decided to stay in areas once affected by the tsunami. Given this background, disaster risk communication is indispensable. It is important for the BPBD of Banda Aceh City to disseminate risk messages throughout the community. Disaster risk communication is informed by the communication targets set by the BPBD of Banda Aceh City. The purpose of this study is to explore the issues and challenges in implementing disaster risk communication in the Banda Aceh community and across various sectors. A qualitative research design is applied to gain an insight into the disaster risk communication of the BPBD of Banda Aceh City. Data were collected through interviews and document analysis. The results of this study show that the BPBD of Banda Aceh City has carried out disaster risk communication in accordance with its primary mandated tasks and functions. However, there have been several challenges and issues, namely limited funding and a lack of technology and disaster knowledge. Consequently, the BPBD of Banda Aceh City has been unable to efficiently realize its disaster risk communication goals.
WEBGIS Application for Planning the Tsunami Evacuation Route
Authors: Nizamuddin  , Aldika W A , Ardiansyah  , Hizir  , Muzailin
Published: July 2019

The tsunami that occurred on December 26, 2004 has resulted in massive casualties in Banda Aceh City. As one of the steps to avoid the huge casualty if the tsunami repeats itself, a number of Escape Buildings have been built in the city. In spite of the availability of the Tsunami Escape Buildings, the number of casualties can be reduced only if everyone in the tsunami-prone areas knows the nearest Escape Building from his or her position and the best route to reach the building. The purpose of this research was to build a GIS web application that can help determine the nearest Escape Building from a user-selected location and the best route to reach it. This application utilizes a web service that implements the Dijkstra algorithm to find the closest facility and the best route to the facility. The web GIS application was built using the open source API. The web GIS application developed in this research helps users find the nearest Escape Building and the best route to reach it without the need of any GIS software. The application is easy to use because it provides a user-friendly interface via a web browser.
Post-Disaster Recovery and A New Economic Growth Path: A Comparative Study of Three Provinces in Indonesia
Authors: Nazamuddin B S , Nugroho Agus
Published: July 2019

The purpose of this study is to examine whether there exists a new regional output growth path in post-disaster situation in three provinces of Indonesia affected by relatively large-scale natural disasters, i.e. Aceh, West Sumatera (Sumbar), and Yogyakarta. By using real Gross Regional Domestic Product time series for the period 2001-2017 obtained from the Central Agency of Statistics, a comparative analysis was made from the differences in the effects across those provinces between pre-disaster and post-disaster periods. This study used a simple model with deterministic trend, post-disaster recovery dummy and autoregressive component to estimate changes in the coefficients of trends for each province’s output growth path. The results show that there is no significant difference in the overall effects of trend changes across provinces, while the effects of trend changes between pre-and post-disaster periods vary across provinces and in general post-disaster interventions do not move upward the long-term effects on regional output trends.
Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
Authors: Huang Xiao-Chen , German Dmitry A , Koch Marcus A
Published: July 2019

Background and Aims

Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution.

Methods

We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness.

Key Results

Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes.

Conclusions

The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant ‘pump’ for continuous and high species diversification.
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
Authors: Zeng Wanwen , Wang Yong , Jiang Rui
Published: July 2019

Motivation

Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them neglect long-range enhancer–promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, HiChIP, a novel high-throughput experimental approach, has generated comprehensive data on high-resolution interactions between promoters and distal enhancers. Moreover, plenty of studies suggest that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer–promoter interactions to accurately predict gene expression.

Results

We propose DeepExpression, a densely connected convolutional neural network, to predict gene expression using both promoter sequences and enhancer–promoter interactions. We demonstrate that our model consistently outperforms baseline methods, not only in the classification of binary gene expression status but also in regression of continuous gene expression levels, in both cross-validation experiments and cross-cell line predictions. We show that the sequential promoter information is more informative than the experimental enhancer information; meanwhile, the enhancer–promoter interactions within ±100 kbp around the TSS of a gene are most beneficial. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures with known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation.

Availability and implementation

DeepExpression is freely available at https://github.com/wanwenzeng/DeepExpression.

Supplementary information

Supplementary data are available at Bioinformatics online.
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
Authors: Berselli Michele , Lavezzo Enrico , Toppo Stefano
Published: July 2019

Motivation

G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE.

Results

QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT.

Availability and implementation

QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse

Supplementary information

Supplementary data are available at Bioinformatics online.
Extended studies of interspecific relationships in Daucus (Apiaceae) using DNA sequences from ten nuclear orthologues
Authors: Martínez-Flores Fernando , Crespo Manuel B , Geoffriau Emmanuel , Allender Charlotte , Ruess Holly , Arbizu Carlos I , Simon Philipp , Spooner David M
Published: July 2019

Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated.
Study on the performance of titanium film as a diffusion barrier layer for CIGS solar-cell application on stainless-steel substrates
Authors: Jiang Xinxian , Li Boyan , Song Binbin , Zhang Shuwang , Qiu Yang , Zhao Ying , Zhong Dalong
Published: July 2019

In this paper, pure titanium (Ti) thin films deposited by radio frequency sputtering were used as a diffusion barrier layer in a flexible copper indium gallium selenium (CIGS) solar cell on a stainless-steel foil and characterized by X-ray diffraction, scanning electron microscopy and second ion mass spectroscopy measurement methods. The influences of the magnetron sputtering pressure on the surface morphology and preferred crystal orientation of Ti films are discussed. It was found that the Ti film showed a (001) preferred orientation and smooth surface topography at lower deposition pressure, while (002) preferred orientation and relatively rough surface topography at higher deposition pressure. In addition, Ti films made with different process pressures were deposited as the barriers and the second ion mass spectroscopy results indicated that a Ti film with the thickness of 200 nm was able to effectively block Fe and Cr diffusion from the stainless-steel foil into the CIGS absorber across the molybdenum back contact. The Ti barrier significantly improved the conversion efficiency of the CIGS solar cell.
Separation of Unprecedented Degradants of Domperidone by Ultra-Performance Convergence Chromatography and Their Structure Elucidation
Authors: Mutha V V S R N Anji Karun , Chandra Chakravarthy , Vijayabhaskar B , Achanta Prabhakar S , Narkedimilli Jagadeesh , Kaliyaperumal Muralidharan , Korupolu Raghu Babu , Gajbhiye Susheela Bai , Rumalla Chidananda Swamy
Published: July 2019

Domperidone, a gastroprokinetic agent, is a common drug to treat emesis. It was subjected to acid, base-mediated hydrolysis, peroxide-mediated oxidation, photolysis and thermal degradation according to ICH guidelines to observe stability of the selected drug under the stress conditions. Although the drug is resistant to base hydrolysis, photolysis and thermal stressors, two degradants (DP-ISO1 and DP-ISO2) were formed in acid mediated hydrolysis. Oxidation with hydrogen peroxide also resulted in one product (DP-OX). All three degradants were isolated from the crude reaction mixture by preparative high-performance liquid chromatography and supercritical fluid chromatography. Structures of isolated compounds were unambiguously characterized as 5-chloro-1-(1-(3-(6-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidin-4-yl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO1), 5-chloro-1-(3-(4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)piperidin-1-yl)propyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO2), 4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)-1-(3-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidine 1-oxide (DP-OX) by analysis of mass spectrometry, 1D and 2D nuclear magnetic resonance spectra. To the best of our knowledge, DP-ISO1 and DP-ISO2 are new and DP-OX was previously reported as domperidone impurity.
Optimizing Contact Precautions to Curb the Spread of Antibiotic-resistant Bacteria in Hospitals: A Multicenter Cohort Study to Identify Patient Characteristics and Healthcare Personnel Interactions Associated With Transmission of Methicillin-resistant Staphylococcus aureus
Authors: O’Hara Lyndsay M , Calfee David P , Miller Loren G , Pineles Lisa , Magder Laurence S , Johnson J Kristie , Morgan Daniel J , Harris Anthony D
Published: July 2019

Background

Healthcare personnel (HCP) acquire antibiotic-resistant bacteria on their gloves and gowns when caring for intensive care unit (ICU) patients. Yet, contact precautions for patients with methicillin-resistant Staphylococcus aureus (MRSA) remains controversial despite existing guidelines. We sought to understand which patients are more likely to transfer MRSA to HCP and to identify which HCP interactions are more likely to lead to glove or gown contamination.

Methods

This was a prospective, multicenter cohort study of cultured HCP gloves and gowns for MRSA. Samples were obtained from patients’ anterior nares, perianal area, and skin of the chest and arm to assess bacterial burden.

Results

Among 402 MRSA-colonized patients with 3982 interactions, we found that HCP gloves and gowns were contaminated with MRSA 14.3% and 5.9% of the time, respectively. Contamination of either gloves or gowns occurred in 16.2% of interactions. Contamination was highest among occupational/physical therapists (odds ratio [OR], 6.96; 95% confidence interval [CI], 3.51, 13.79), respiratory therapists (OR, 5.34; 95% CI, 3.04, 9.39), and when any HCP touched the patient (OR, 2.59; 95% CI, 1.04, 6.51). Touching the endotracheal tube (OR, 1.75; 95% CI, 1.38, 2.19), bedding (OR, 1.43; 95% CI, 1.20, 1.70), and bathing (OR, 1.32; 95% CI, 1.01, 1.75) increased the odds of contamination. We found an association between increasing bacterial burden on the patient and HCP glove or gown contamination.

Conclusions

Gloves and gowns are frequently contaminated with MRSA in the ICU. Hospitals may consider using fewer precautions for low-risk interactions and more for high-risk interactions and personnel.
Eosinophil granule major basic protein 1 deposition in eosinophilic esophagitis correlates with symptoms independent of eosinophil counts
Authors: Peterson K A , Gleich G J , Limaye N S , Crispin H , Robson J , Fang J , Saffari H , Clayton F , Leiferman K M
Published: July 2019

In patients with eosinophilic esophagitis (EoE), symptoms often do not correlate with peak eosinophil counts (PEC) determined on histopathological examination of biopsy specimens. This may be because eosinophils degranulate during active disease and lose their morphological identity as intact cells and, therefore, are not enumerated on microscopic examination. Eosinophil granule proteins that are released into tissues with degranulation, including major basic protein 1 (eMBP1), likely contribute to disease pathogenesis and, therefore, may correlate with symptoms better than PEC. We sought to determine whether symptoms in patients with EoE more closely relate to eosinophil granule protein deposition than to eosinophil enumeration, especially in patients with fewer than 15 eosinophils per high power field (HPF). Esophageal biopsy specimens from 34 patients diagnosed with EoE were obtained for histopathological examination and for evaluation of eMBP1 staining by indirect immunofluorescence. PEC by histopathology were compared to extracellular eMBP1 grades by immunostaining. PEC and eMBP1 grades also were analyzed for their relationship to symptoms and clinical course. Biopsy specimens from 19 of the 34 patients had fewer than 15 PEC on histopathological examination, and the other 15 patients had 15 or greater PEC. Positive eMBP1 immunostaining was found in all symptomatic patients. EoE symptoms were related to eMBP1 immunostaining grades (p = 0.0001), but not PEC (P = 0.14). Eosinophil granule protein deposition, specifically eMBP1, is increased in esophageal biopsy specimens from symptomatic patients with EoE and may be a marker of disease activity, including patients with EoE who have ‘resolved’ disease.
Biomechanical Leg Muscle Function During Stair Ambulation in Men Receiving Androgen Deprivation Therapy
Authors: Cheung Ada S , Gray Hans A , Schache Anthony G , Hoermann Rudolf , Bicknell Jarrod , Joon Daryl Lim , Zajac Jeffrey D , Pandy Marcus G , Grossmann Mathis
Published: July 2019

Background

The role of testosterone in maintaining functional performance in older men remains uncertain.

Methods

We conducted a 12-month prospective, observational case–control study including 34 men newly commencing androgen deprivation therapy for prostate cancer and 29 age-matched prostate cancer controls. Video-based motion capture and ground reaction force data combined with computational musculoskeletal modeling, and data were analyzed with a linear mixed model.

Results

Compared with controls over 12 months, men receiving androgen deprivation therapy had a mean reduction in circulating testosterone from 14.1 nmol/L to 0.4 nmol/L, associated with reductions in peak knee extension torque, mean adjusted difference (MAD) –0.07 Nm/kg (95% confidence interval [CI]: –0.18, 0.04), p = .009, with a corresponding more marked decrease in quadriceps force MAD –0.11 × body weight (BW) [–0.27, 0.06], p = .045 (equating to a 9 kg force reduction for the mean body weight of 85 kg), and decreased maximal contribution of quadriceps to upward propulsion, MAD –0.47 m/s2 [–0.95, 0.02], p = .009. We observed between-group differences in several other parameters, including increased gluteus maximus force in men receiving androgen deprivation therapy, MAD 0.11 × BW [0.02, 0.20], p = .043, which may be compensatory.

Conclusions

Severe testosterone deprivation over 12 months is associated with selective deficits in lower-limb function evident with an important task of daily living.
Anisotropy of magnetic susceptibility in salt rocks from the German Zechstein Basin, Sondershausen mine
Authors: Heinrich Frances C , Schmidt Volkmar , Schramm Michael , Mertineit Michael
Published: July 2019

The anisotropy of magnetic susceptibility (AMS) of rocks reflects the alignment of certain minerals, and therefore it can be used to investigate the deformation history of rocks. However, for salt rocks, very few studies on the AMS of salt rocks and the influence of accessory minerals exist. In this study, we analysed the potential to use the AMS of salt rocks with low impurity content for fabric characterization. Samples of rock salt, sylvinite and carnallitite from a salt mine in Sondershausen (Germany) from the Late Permian (Zechstein 2, Stassfurt series) are investigated. The results of low-field AMS (LF-AMS) measurements show a very weak but significant magnetic anisotropy for sylvinite, carnallitite, and rock salt with an elevated content of accessory minerals. The AMS results are consistent in individual layers of the same rock type. In order to identify the magnetic minerals, which cause the magnetic anisotropy, the high-field AMS (HF-AMS) was measured using a torque magnetometer in order to separate ferrimagnetic and paramagnetic contributions to the AMS. A significant paramagnetic subfabrics exists, which reflects the alignment of phyllosilicates. The magnitude of the LF-AMS is considerably greater than that of the paramagnetic subfabric. This indicates the existence of a ferrimagnetic subfabric due to magnetite, which can have a different orientation than the paramagnetic subfabric. Differences in the orientation of the AMS in samples from two sites suggest a relationship of deformation history and AMS. At a site with dipping layers, the AMS orientation is independent of the bedding and shows large differences between individual lithological layers. In a tight fold, the AMS of all rock types has similar shape and orientation. We conclude that AMS in salt rocks can give meaningful information on the mineral fabric, which could be used in the analysis of the deformation history.
Lasso-based simulation for high-dimensional multi-period portfolio optimization
Authors: Li Zhongyu , Tsang Ka Ho , Wong Hoi Ying
Published: July 2019

This paper proposes a regression-based simulation algorithm for multi-period mean-variance portfolio optimization problems with constraints under a high-dimensional setting. For a high-dimensional portfolio, the least squares Monte Carlo algorithm for portfolio optimization can perform less satisfactorily with finite sample paths due to the estimation error from the ordinary least squares (OLS) in the regression steps. Our algorithm, which resolves this problem e, that demonstrates significant improvements in numerical performance for the case of finite sample path and high dimensionality. Specifically, we replace the OLS by the least absolute shrinkage and selection operator (lasso). Our major contribution is the proof of the asymptotic convergence of the novel lasso-based simulation in a recursive regression setting. Numerical experiments suggest that our algorithm achieves good stability in both low- and higher-dimensional cases.
BOARD INVITED REVIEW: Oxidative stress and efficiency: the tightrope act of mitochondria in health and disease1,2
Authors: Bottje Walter G
Published: July 2019

Oxidative stress is an unavoidable consequence of aerobic metabolism. Whereas high amounts of mitochondrial reactive oxygen species (ROS) can cause oxidation, low levels play important roles in signal transduction. In a Pedigree male (PedM) broiler model of feed efficiency (FE), the low FE phenotype was characterized by increased ROS in isolated mitochondria (muscle, liver, and duodenum) with a pervasive protein oxidation in mitochondria and tissues. Subsequent proteogenomic studies in muscle revealed evidence of enhanced mitoproteome abundance, enhanced mitochondrial phosphocreatine shuttling expression, and enhanced ribosome assembly in the high FE phenotype. Surprisingly, an enhanced infrastructure would foster greater repair of damaged proteins or organelles through the autophagy and proteosome pathways in the high FE phenotype. Although protein and organelle degradation, recycling, and reconstruction would be energetically expensive, it is possible that energy invested into maintaining optimal function of proteins and organelles contributes to cellular efficiency in the high FE phenotype. New findings in mitochondrial physiology have been reported in the last several years. Reverse electron transport (RET), once considered an artifact of in vitro conditions, now is recognized to play significant roles in inflammation, ischemia–reperfusion, muscle differentiation, and energy utilization. A topology of ROS production indicates that ROS derived from Complex I of the respiratory chain primarily causes oxidation, whereas ROS generated from Complex III are primarily involved in cell signaling. It is also apparent that there is a constant fission and fusion process that mitochondria undergo that help maintain optimal mitochondrial function and enables mitochondria to adjust to periods of nutrient limitation and nutrient excess. Understanding the balancing act that mitochondria play in health and disease will continue to be a vital biological component in health-production efficiency and disease in commercial animal agriculture.
Baryon acoustic oscillation, Hubble parameter, and angular size measurement constraints on the Hubble constant, dark energy dynamics, and spatial curvature
Authors: Ryan Joseph , Chen Yun , Ratra Bharat
Published: July 2019

In this paper, we use all available baryon acoustic oscillation, Hubble parameter, and quasar angular size data to constrain six dark energy cosmological models, both spatially flat and non-flat. Depending on the model and data combination considered, these data mildly favour closed spatial hypersurfaces (by as much as 1.7σ) and dark energy dynamics (up to a little over 2σ) over a cosmological constant Λ. The data also favour, at 1.8σ to 3.4σ, depending on the model and data combination, a lower Hubble constant than what is measured from the local expansion rate.
Structural and phenotypic analysis of Chikungunya virus RNA replication elements
Authors: Kendall Catherine , Khalid Henna , Müller Marietta , Banda Dominic H , Kohl Alain , Merits Andres , Stonehouse Nicola J , Tuplin Andrew
Published: July 2019

Chikungunya virus (CHIKV) is a re-emerging, pathogenic Alphavirus transmitted to humans by Aedes spp. mosquitoes. We have mapped the RNA structure of the 5′ region of the CHIKV genome using selective 2′-hydroxyl acylation analysed by primer extension (SHAPE) to investigate intramolecular base-pairing at single-nucleotide resolution. Taking a structure-led reverse genetic approach, in both infectious virus and sub-genomic replicon systems, we identified six RNA replication elements essential to efficient CHIKV genome replication - including novel elements, either not previously analysed in other alphaviruses or specific to CHIKV. Importantly, through a reverse genetic approach we demonstrate that the replication elements function within the positive-strand genomic copy of the virus genome, in predominantly structure-dependent mechanisms during efficient replication of the CHIKV genome. Comparative analysis in human and mosquito-derived cell lines reveal that a novel element within the 5′UTR is essential for efficient replication in both host systems, while those in the adjacent nsP1 encoding region are specific to either vertebrate or invertebrate host cells. In addition to furthering our knowledge of fundamental aspects of the molecular virology of this important human pathogen, we foresee that results from this study will be important for rational design of a genetically stable attenuated vaccine.
Myroides injenensis Bacteremia and Severe Cellulitis
Authors: LaVergne Stephanie , Gaufin Thaidra , Richman Douglas
Published: July 2019

Myroides spp. are environmental bacterial organisms that rarely cause disease in humans. Myroides spp. infections are infrequently reported in the literature, and Myroides injenensis infections are quite uncommon. Myroides spp. usually infect immunocompromised hosts and can have highly resistant antibiotic susceptibility patterns. Here we report a case of Myroides injenensis bacteremia and severe cellulitis in a patient with cirrhosis and review the literature of other Myroides spp. infections.
Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development
Authors: Neogy Ananya , Garg Tushar , Kumar Anil , Dwivedi Anuj K , Singh Harshita , Singh Urminder , Singh Zeenu , Prasad Kalika , Jain Mukesh , Yadav Shri Ram
Published: July 2019

Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control the architecture of adventitious root remain largely unknown. Here, we studied the modulations in global genes activity in developing rice adventitious root by genome-wide RNA sequencing in response to external auxin and cytokinin signaling cues. We further analyzed spatiotemporal regulations of key developmental regulators emerged from our global transcriptome analysis. Interestingly, some of the key cell fate determinants such as homeodomain transcription factor (TF), OsHOX12, no apical meristem protein, OsNAC39, APETALA2/ethylene response factor, OsAP2/ERF-40 and WUSCHEL-related homeobox, OsWOX6.1 and OsWOX6.2, specifically expressed in adventitious root primordia. Functional analysis of one of these regulators, an auxin-induced TF containing AP2/ERF domain, OsAP2/ERF-40, demonstrates its sufficiency to confer the adventitious root fate. The ability to trigger the root developmental program is largely attributed to OsAP2/ERF-40-mediated dose-dependent transcriptional activation of genes that can facilitate generating effective auxin response, and OsERF3–OsWOX11–OsRR2 pathway. Our studies reveal gene regulatory network operating in response to hormone signaling pathways and identify a novel TF regulating adventitious root developmental program, a key agronomically important quantitative trait, upstream of OsERF3–OsWOX11–OsRR2 pathway.
Reboot Online: A Randomized Controlled Trial Comparing an Online Multidisciplinary Pain Management Program with Usual Care for Chronic Pain
Authors: Smith Jessica , Faux Steven G , Gardner Tania , Hobbs Megan J , James Mathew A , Joubert Amy E , Kladnitski Natalie , Newby Jill M , Schultz Regina , Shiner Christine T , Andrews Gavin
Published: July 2019

Objective

Chronic pain is a prevalent and burdensome condition. Reboot Online was developed to address treatment barriers traditionally associated with accessing face-to-face chronic pain management programs. It is a comprehensive multidisciplinary online treatment program, based on an existing and effective face-to-face multidisciplinary pain program (the Reboot program).

Design & Participants

A CONSORT-compliant randomized controlled trial was conducted, enrolling adults who had experienced pain for three months or longer.

Methods

Participants were randomly allocated to either an eight-lesson multidisciplinary pain management program, Reboot Online (N = 41), or to a usual care (UC) control group (N = 39). Clinical oversight was provided by a multidisciplinary team remotely, including physiotherapists and clinical psychologists. Participants were measured at baseline, post-treatment (week 16), and three-month follow-up (week 28).

Results

Intention-to-treat analyses revealed that Reboot Online was significantly more effective than UC at increasing pain self-efficacy (g = 0.69) at post-treatment, and these gains were maintained at follow-up. Similarly, Reboot Online was significantly more effective than UC on several secondary measures at post-treatment and follow-up, including movement-based fear avoidance and pain-related disability, but it did not significantly reduce pain interference or depression compared with UC. Clinician input was minimal, and adherence to Reboot Online was moderate, with 61% of participants (N = 25) completing all eight lessons.

Conclusions

Reboot Online presents a novel approach to multidisciplinary pain management and offers an accessible, efficacious alternative and viable treatment option for chronic pain management.
Mechanical Performance of a Thermoelectric Composite in the Vicinity of an Elliptic Inhomogeneity
Authors: Song K , Song H P , Schiavone P , Gao C F
Published: July 2019

Thermal stress induced by an uneven temperature field and mismatched thermal expansion is known to be a dominating factor in the debonding mechanism that threatens reliability and ultimately leads to failure in thermoelectric (TE) composites. Accordingly, we analyse the stress distributions in a TE composite induced by the presence of an elliptic inhomogeneity embedded in the surrounding matrix material. Using complex variable methods, we obtain closed-form representations of the thermal–electric and thermal–elastic fields and find that the temperature field around the inhomogeneity is reduced dramatically by the application of a remote electric current density without affecting the temperature difference across the inhomogeneity–matrix interface. This ensures the conversion efficiency of the TE composite while improving its reliability. Numerical results illustrate that a suitable choice of electric current density can prevent interfacial debonding via the suppression of the maximum positive normal stress on the interface.
Biodegradable harmonophores for targeted high-resolution in vivo tumor imaging
Authors: Sonay Ali Yasin , Yaganoglu Sine , Konantz Martina , Teulon Claire , Sieber Sandro , Jiang Shuai , Behzadi Shahed , Crespy Daniel , Landfester Katharina , Roke Sylvie , Langerke Claudia , Pantazis Periklis
Published: July 2019

Optical imaging probes have played a major role in detecting and monitoring of a variety of diseases1. In particular, nonlinear optical imaging probes, such as second harmonic generating (SHG) nanoprobes, hold great promise as clinical contrast agents, as they can be imaged with little background signal and unmatched long-term photostability2. As their chemical composition often includes transition metals, the use of inorganic SHG nanoprobes can raise long-term health concerns. Ideally, contrast agents for biomedical applications should be degraded in vivo without any long-term toxicological consequences to the organism. Here, we developed biodegradable harmonophores (bioharmonophores) that consist of polymer-encapsulated, self-assembling peptides that generate a strong SHG signal. When functionalized with tumor cell surface markers, these reporters can target single cancer cells with high detection sensitivity in zebrafish embryos in vivo. Thus, bioharmonophores will enable an innovative approach to cancer treatment using targeted high-resolution optical imaging for diagnostics and therapy.
Insight into mosquito GnRH-related neuropeptide receptor specificity revealed through analysis of naturally occurring and synthetic analogs of this neuropeptide family
Authors: Wahedi Azizia , Gäde Gerd , Paluzzi Jean-Paul
Published: July 2019

Adipokinetic hormone (AKH), corzazonin (CRZ) and the AKH/CRZ-related peptide (ACP) are peptides considered homologous to the vertebrate gonadotropin-releasing hormone (GnRH). All threeAedes aegyptiGnRH-related neuropeptide receptors have been characterized and functionally deorphanized, which individually exhibit high specificity for their native ligands, which prompted us to investigate the contribution of ligand structures in conferring receptor specificity. In the current study, we designed a series of analogs based on the native ACP sequence inA. aegyptiand screened them against the ACP receptor using a heterologous system to identify critical residues required for receptor activation. Specifically, analogs lacking the carboxy-terminal amidation, replacing aromatic residues, as well as truncated analogs were either completely inactive or had very low activities even at high concentration. The next most critical residues were the polar threonine in position 3 and the blocked amino-terminal pyroglutamate, with activity of the latter partially recovered using an alternatively blocked analog. ACP analogs with alanine substitutions at position 2 (valine), 5 (serine), 6 (arginine) and 7 (aspartic acid) positions were less detrimental as were replacements of charged residues. Interestingly, replacing asparagine with an alanine at position 9, creating a C-terminal WAA-amide, resulted in a 5-fold more active analog which may be useful as a lead superagonist compound. Similarly, we utilized this high-throughput approach against anA. aegyptiAKH receptor (AKHR-IA) testing a number of mostly naturally-occurring AKH analogs from other insects to determine how substitutions of specific amino acids in the AKH ligand influences receptor activation. AKH analogs having single substitutions compared to the endogenousA. aegyptiAKH revealed position 7 (serine) was well tolerated whereas changes to position 6 (proline) had pronounced effects, with receptor activity compromised nearly ten-fold. Substitution of position 3 (threonine) or analogs with combinations of substitutions were quite detrimental with a significant decrease in AKHR-IA activation. Interestingly, analogs with an asparagine residue at position seven displayed improved receptor activation compared to the native mosquito AKH. Collectively, these results advance our understanding of how two GnRH-related systems inA. aegyptisharing the most recent evolutionary origin sustain independence of function and signalling despite their relatively high degree of ligand and receptor homology.
Assembly of a functional ribozyme from short oligomers by enhanced non-enzymatic ligation
Authors: Zhou Lijun , O’Flaherty Derek K. , Szostak Jack W.
Published: July 2019

The non-enzymatic replication of the primordial genetic material is thought to have enabled the evolution of the first ribozymes, leading to early forms of RNA-based life. However, the reported rate of chemical RNA ligation is extremely slow. Here we show that the rate of ligation can be greatly enhanced by employing a 3′-amino group at the 3′-end of each oligonucleotide, in combination with an N-alkyl imidazole organocatalyst. These modifications allow the rapid copying of long RNA templates by multi-step ligation of tetranucleotides, as well as the assembly of long oligonucleotides from short template splints. Our work shows that a functional RNA ligase ribozyme can be assembled from relatively short oligonucleotides, demonstrating a transition from non-enzymatic ligation to enzymatic ligation. We suggest that the genomes of primitive protocells could have consisted of relatively easily replicated oligonucleotides as short as 10 to 12 nucleotides in length.
Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping
Authors: Ramilowski Jordan A , Yip Chi Wai , Agrawal Saumya , Chang Jen-Chien , Ciani Yari , Kulakovskiy Ivan V , Mendez Mickaël , Ooi Jasmine Li Ching , Ouyang John F , Parkinson Nick , Petri Andreas , Roos Leonie , Severin Jessica , Yasuzawa Kayoko , Abugessaisa Imad , Akalin Altuna , Antonov Ivan V , Arner Erik , Bonetti Alessandro , Bono Hidemasa , Borsari Beatrice , Brombacher Frank , Cameron Chris JF , Cannistraci Carlo Vittorio , Cardenas Ryan , Cardon Melissa , Chang Howard , Dostie Josée , Ducoli Luca , Favorov Alexander , Fort Alexandre , Garrido Diego , Gil Noa , Gimenez Juliette , Guler Reto , Handoko Lusy , Harshbarger Jayson , Hasegawa Akira , Hasegawa Yuki , Hashimoto Kosuke , Hayatsu Norihito , Heutink Peter , Hirose Tetsuro , Imada Eddie L , Itoh Masayoshi , Kaczkowski Bogumil , Kanhere Aditi , Kawabata Emily , Kawaji Hideya , Kawashima Tsugumi , Kelly S. Thomas , Kojima Miki , Kondo Naoto , Koseki Haruhiko , Kouno Tsukasa , Kratz Anton , Kurowska-Stolarska Mariola , Kwon Andrew Tae Jun , Leek Jeffrey , Lennartsson Andreas , Lizio Marina , López-Redondo Fernando , Luginbühl Joachim , Maeda Shiori , Makeev Vsevolod J , Marchionni Luigi , Medvedeva Yulia A , Minoda Aki , Müller Ferenc , Muñoz-Aguirre Manuel , Murata Mitsuyoshi , Nishiyori Hiromi , Nitta Kazuhiro R , Noguchi Shuhei , Noro Yukihiko , Nurtdinov Ramil , Okazaki Yasushi , Orlando Valerio , Paquette Denis , Parr Callum JC , Rackham Owen JL , Rizzu Patrizia , Martinez Diego Fernando Sánchez , Sandelin Albin , Sanjana Pillay , Semple Colin AM , Shibayama Youtaro , Sivaraman Divya M , Suzuki Takahiro , Szumowski Suzannah C , Tagami Michihira , Taylor Martin S , Terao Chikashi , Thodberg Malte , Thongjuea Supat , Tripathi Vidisha , Ulitsky Igor , Verardo Roberto , Vorontsov Ilya , Yamamoto Chinatsu , Young Robert S , Baillie J Kenneth , Forrest Alistair RR , Guigó Roderic , Hoffman Michael M , Hon Chung Chau , Kasukawa Takeya , Kauppinen Sakari , Kere Juha , Lenhard Boris , Schneider Claudio , Suzuki Harukazu , Yagi Ken ,   FANTOM consortium, de Hoon Michiel , Shin Jay W , Carninci Piero
Published: July 2019

Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNA exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest to-date lncRNA knockdown dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.