bluuebunny/crossref_metadata_2025_split huggingface dataset:
The development of pepper (Piper nigrum L.) foot rot disease on agroforestry
Authors: Suhaendah E , Fauziyah E , Manurung G E S 
Published: August 2020

Abstract
Pepper foot rot is one of the most destructive diseases. There were three cropping patterns in the research area, i.e., agroforestry, pepper-cocoa and pepper monoculture patterns. As one of the most common cropping patterns, the observation of foot rots in the agroforestry pattern compared to other cropping patterns. The study was conducted in Simbune Village, East Kolaka Regency, Southeast Sulawesi, from October 2013 to September 2014. The research was conducted by direct observation methods. In each cropping pattern, a permanent measurement plot was made by sampling 30% of the total pepper individuals. The intensity of the disease was observed monthly for 12 months. The observation revealed that the intensity of foot rot disease was getting more severe toward the end of observation. The intensity on agroforestry (26% - 33%) and pepper-cocoa (17% - 35%) patterns were lower than that on pepper monoculture pattern (85% - 90%). The infection rate was lowest on the agroforestry pattern with a value of 0.051. This finding suggested that the agroforestry pattern for pepper showed the best resilience against foot rot disease.
Growth performance of Falcataria moluccana in the mixed cropping pattern and its severity from Gall-rust disease: A case study in Ciamis, West Java
Authors: Dendang B , Sudomo A 
Published: August 2020

Abstract
Monoculture Falcataria moluccana plantation managed by local communities in Ciamis – West Java, is facing a gall-rust disease caused by fungal pathogen Uromycladium tepperianum. A mixed planting crops system is considered less vulnerable to pests and disease problems. In addition, it is possible to increase the productivity of community forest plantations. This study was aimed to evaluate the effects of mixed-crops plantation on the productivity of F. moluccana and the incidence and severity of gall-rust in the plantation. Then it will be compared to the existed monoculture F. moluccana plantation in the area, that was established two years before. The mixed-crop consisted of F. moluccana, Acacia mangium, and Gmelina arborea. These were alternately planted in three different rows with three replications. The observations of growth increments as well as incidence and severity of gall-rust were carried out in 1.5 years after planting. The results showed that the annual height- and diameter- increments of F. moluccana in the mixed-crop plot were 331.2 cm and 2.77 cm, respectively. Meanwhile, the results in the monoculture plot were 325.62 cm and 2.64 cm. The survival rates of F. moluccana in both planting patterns were slightly different (85.3% and 88%). Gall-rust incidence and severity were only observed in the F. moluccana monoculture plot, i.e., 0.15% and 0.48%, respectively. The mixed-planting crops system seems possible to be applied for controlling the gall-rust disease that attacked the F. moluccana stands. Further research on comparing the similar ages of mono- and mixed- cultures of F. moluccana in different locations were suggested.
Effect of POE on mechanical properties and cellular structure of PP/Nano-CaCO3 composites in IMD/MIM process
Authors: Mao Huajie , Cheng Yi , Guo Wei , Meng Zhenghua , Wei Wenting , Hua Lin , Yang Qing 
Published: August 2020

Abstract
Nano-CaCO3 can effectively improve the strength of foamed Polypropylene (PP), ethylene-octene copolymer (POE) can greatly enhance the toughness of PP, and PP-g-MAH can improve the compatibility of Nano-CaCO3 with PP. The supercritical fluid-nitrogen (N2) was used as physical foaming agent, and the PET film was selected to study the effect of POE content on the mechanical properties and cellular structure of PP/nano-CaCO3 blends during combined in-mold decoration and microcellular injection molding (IMD/MIM) process. The results showed that the addition of POE did improve the impact strength of PP/nano-CaCO3 composites, while the tensile strength and flexural strength decreased. On account of the characteristics of POE, the melt strength change of PP/nano-CaCO3 blend system after POE’s addition was studied. The melt strength of the blend system decreased at first and then increased. It can be found that POE distributed uniformly in PP, and POE particle size decreased with the increase of POE content. Besides, it was revealed that POE could improve the cellular structure of the vertical section and the parallel section. The mechanical properties and cellular structure were optimized when 10% POE was added.
Introducing S-RILS and D-RILS as refractive index limited optical biosensors in multiple nanolayers
Authors: Bouzari Nasrin , Amjad Jafar Mostafavi , Mohammadkhani Ramin , Jahanshahi Peyman 
Published: August 2020

Abstract
The amplitude and phase sensitivities of a sensor with a multiple nanolayers consisting of gold-silicon dioxide-gold (Au-SiO2-Au) are investigated. The proposed sensor has the ability to limit to the certain regions of the sensing medium refractive index n

s
. The number of these regions can be increased by increasing the thickness of the silicon dioxide layer (

d

SiO

2

). The results show that for the

d

SiO

2

=
200

nm

the sensitivity has a nearly Gaussian in shape which its position depends on the refractive index of the prism n

p
. This type of sensor is introduced as a singlet refractive index limited sensor (S-RILS) that is useful tool in the detection of the target sample optical properties with certain refractive indices. It is found that two nearly Gaussian curves are generated in the amplitude and phase sensitivities for the

d

SiO

2

=
450

nm

, which is introduced as a doublet refractive index limited sensor (D-RILS). The optical properties of the mixture samples can be detected by D-RILS, in while the S-RILS is used to detect the optical properties of single samples. The efficiency of the sensors can be improved by adding the titanium or titanium-graphene layers. The results exhibit that the optimal amplitude and phase sensitivities occur for multiple nanolayers (Ti-Au-SiO2-Ti-Au).
Deep-patterning of complex oxides by focused ion beam with PMMA-assisted hybrid protective layer
Authors: Shiue Jessie , Kuo Pai-Chia 
Published: August 2020

Abstract
Studying novel properties of complex oxides in nanoscale has become a popular research interest. Nanofabrication of complex oxides without damaging its intrinsic structure, however, is still challenging. In this work, we investigated the commonly used focused ion beam (FIB) technique for deep-patterning SrTiO3 (STO) using Cr as a surface protective layer and found that it was insufficient in protecting STO against the damage caused by the FIB beam tail effect. We further developed a new method for effectively deep-patterning STO using FIB. Our approach adopted a hybrid surface layer of Cr and polymethyl methacrylate (PMMA) to protect the STO surface during the FIB milling process against the damage caused by the beam tail. This PMMA-assisted hybrid protective layer can effectively prevent the damage resulting from the energetic ion beam, as verified by high-resolution transmission electron microscopy characterization. It was found that PMMA is not spun off during the FIB process but forms bubbles and likely absorbs the energy from the ion beam during this process. At the same time, a thin Cr layer of this hybrid served as a charge-releasing path and kept the patterning precise. This mechanism is very different from simply using Cr as a scarifying surface layer for ion bombardment.
A thin transferable blue light-emitting diode by electrochemical lift-off
Authors: Hou Yaonan , Wang Yong , Ai Qingkang 
Published: August 2020

Abstract
We demonstrate a transferable blue light-emitting diode (LED) fabricated using a cost-effective approach. By means of solution-based electrochemical etching, an ultrathin free-standing membrane can be obtained from a commercial III-nitride LED wafer. The membrane, containing a full LED structure (including p-/n-type layers and multiple quantum wells) epitaxially grown on a sapphire substrate, is transferable to foreign substrates with a simple lift-off process facilitated by electrochemical etching. After fabrication, optical properties of the thin film are massively improved, accompanied by a 17-fold enhanced photoluminescence normal to the film surface. Prototype transferable blue LEDs are realized on both a copper-coated glass substrate and a polypropylene substrate. The devices exhibit a high performance with bright emission at 447 nm under electrical injection at room temperature.
Maternal Prenatal Smoking and Autism Spectrum Disorder in Offspring: A California Statewide Cohort and Sibling Study
Authors: von Ehrenstein Ondine S , Cui Xin , Yan Qi , Aralis Hilary , Ritz Beate 
Published: August 2020

AbstractWe examined associations between maternal smoking and autism spectrum disorder (ASD) in children in a statewide population-based cohort and sibling-comparison design using California birth records (n = 2,015,104) with information on maternal smoking, demographic factors, and pregnancy (2007–2010). ASD cases (n = 11,722) were identified through California Department of Developmental Services records with diagnoses based on the Diagnostic and Statistical Manual of Mental Disorders–IV-TR. We estimated odds ratios for ASD with and without intellectual disability in the full cohort using logistic regression and in a sibling comparison using conditional logistic regression. In the full cohort, the adjusted odds ratio for ASD and maternal smoking 3 months before/during pregnancy compared with nonsmoking was 1.15 (95% confidence interval (CI): 1.04, 1.26), and it was similar in cases with (odds ratio = 1.12, 95% CI: 0.84, 1.49) and without intellectual disability (odds ratio = 1.15, 95% CI: 1.04, 1.27). Heavy prenatal smoking (≥20 cigarettes/day in any trimester) was related to an odds ratio of 1.55 (95% CI: 1.21, 1.98). In the sibling comparison, the odds ratio for heavy smoking was similarly elevated but the confidence interval was wide. Our findings are consistent with an increased risk for ASD in offspring of mothers who smoked ≥20 cigarettes/day during pregnancy; associations with lighter smoking were weaker.
CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Authors: Träger Sylvain , Tamò Giorgio , Aydin Deniz , Fonti Giulia , Audagnotto Martina , Dal Peraro Matteo 
Published: August 2020

Abstract

Motivation
Proteins are intrinsically dynamic entities. Flexibility sampling methods, such as molecular dynamics or those arising from integrative modeling strategies, are now commonplace and enable the study of molecular conformational landscapes in many contexts. Resulting structural ensembles increase in size as technological and algorithmic advancements take place, making their analysis increasingly demanding. In this regard, cluster analysis remains a go-to approach for their classification. However, many state-of-the-art algorithms are restricted to specific cluster properties. Combined with tedious parameter fine-tuning, cluster analysis of protein structural ensembles suffers from the lack of a generally applicable and easy to use clustering scheme.

Results
We present CLoNe, an original Python-based clustering scheme that builds on the Density Peaks algorithm of Rodriguez and Laio. CLoNe relies on a probabilistic analysis of local density distributions derived from nearest neighbors to find relevant clusters regardless of cluster shape, size, distribution and amount. We show its capabilities on many toy datasets with properties otherwise dividing state-of-the-art approaches and improves on the original algorithm in key aspects. Applied to structural ensembles, CLoNe was able to extract meaningful conformations from membrane binding events and ligand-binding pocket opening as well as identify dominant dimerization motifs or inter-domain organization. CLoNe additionally saves clusters as individual trajectories for further analysis and provides scripts for automated use with molecular visualization software.

Availability and implementation
www.epfl.ch/labs/lbm/resources, github.com/LBM-EPFL/CLoNe.

Supplementary information
Supplementary data are available at Bioinformatics online.
Immune correlates analysis using vaccinees from test negative designs
Authors: Follmann Dean A , Dodd Lori 
Published: August 2020

Summary
Determining the effect of vaccine-induced immune response on disease risk is an important goal of vaccinology. Typically, immune correlates analyses are conducted prospectively with immune response measured shortly after vaccination and subsequent disease status regressed on immune response. In outbreaks and rare disease settings, collecting samples from all vaccinees is not feasible. The test negative design is a retrospective design used to measure vaccine efficacy where symptomatic individuals who present at a clinic are assessed for relevant disease (cases) or some other disease (controls) and vaccination status ascertained. This article proposes that test negative vaccinees have immune response to vaccine assessed both for relevant (e.g., Ebola) and irrelevant (e.g., vector) proteins. If the latter immune response is unaffected by active (Ebola) infection, and is correlated with the relevant immune response, it can serve as a proxy for the immune response of interest proximal to infection. We show that logistic regression using imputed immune response as the covariate and case disease as outcome can estimate the prospective immune response slope and detail the assumptions needed for unbiased inference. The method is evaluated by simulation under various scenarios including constant and decaying immune response. A simulated dataset motivated by ring vaccination for an ongoing Ebola outbreak is analyzed.
Individual Differences in Intrinsic Brain Networks Predict Symptom Severity in Autism Spectrum Disorders
Authors: Pua Emmanuel Peng Kiat , Thomson Phoebe , Yang Joseph Yuan-Mou , Craig Jeffrey M , Ball Gareth , Seal Marc 
Published: August 2020

Abstract
The neurobiology of heterogeneous neurodevelopmental disorders such as Autism Spectrum Disorders (ASD) is still unknown. We hypothesized that differences in subject-level properties of intrinsic brain networks were important features that could predict individual variation in ASD symptom severity. We matched cases and controls from a large multicohort ASD dataset (ABIDE-II) on age, sex, IQ, and image acquisition site. Subjects were matched at the individual level (rather than at group level) to improve homogeneity within matched case–control pairs (ASD: n = 100, mean age = 11.43 years, IQ = 110.58; controls: n = 100, mean age = 11.43 years, IQ = 110.70). Using task-free functional magnetic resonance imaging, we extracted intrinsic functional brain networks using projective non-negative matrix factorization. Intrapair differences in strength in subnetworks related to the salience network (SN) and the occipital-temporal face perception network were robustly associated with individual differences in social impairment severity (T = 2.206, P = 0.0301). Findings were further replicated and validated in an independent validation cohort of monozygotic twins (n = 12; 3 pairs concordant and 3 pairs discordant for ASD). Individual differences in the SN and face-perception network are centrally implicated in the neural mechanisms of social deficits related to ASD.
Aging Modulates Prefrontal Plasticity Induced by Executive Control Training
Authors: Najberg Hugo , Wachtl Laura , Anziano Marco , Mouthon Michael , Spierer Lucas 
Published: August 2020

AbstractWhile declines in inhibitory control, the capacity to suppress unwanted neurocognitive processes, represent a hallmark of healthy aging, whether this function is susceptible to training-induced plasticity in older populations remains largely unresolved. We addressed this question with a randomized controlled trial investigating the changes in behavior and electrical neuroimaging activity induced by a 3-week adaptive gamified Go/NoGo inhibitory control training (ICT). Performance improvements were accompanied by the development of more impulsive response strategies, but did not generalize to impulsivity traits nor quality of life. As compared with a 2-back working-memory training, the ICT in the older adults resulted in a purely quantitative reduction in the strength of the activity in a medial and ventrolateral prefrontal network over the 400 ms P3 inhibition-related event-related potentials component. However, as compared with young adults, the ICT induced distinct configurational modifications in older adults’ 200 ms N2 conflict monitoring medial–frontal functional network. Hence, while older populations show preserved capacities for training-induced plasticity in executive control, aging interacts with the underlying plastic brain mechanisms. Training improves the efficiency of the inhibition process in older adults, but its effects differ from those in young adults at the level of the coping with inhibition demands.
Predicting the fMRI Signal Fluctuation with Recurrent Neural Networks Trained on Vascular Network Dynamics
Authors: Sobczak Filip , He Yi , Sejnowski Terrence J , Yu Xin 
Published: August 2020

AbstractResting-state functional MRI (rs-fMRI) studies have revealed specific low-frequency hemodynamic signal fluctuations (&lt;0.1 Hz) in the brain, which could be related to neuronal oscillations through the neurovascular coupling mechanism. Given the vascular origin of the fMRI signal, it remains challenging to separate the neural correlates of global rs-fMRI signal fluctuations from other confounding sources. However, the slow-oscillation detected from individual vessels by single-vessel fMRI presents strong correlation to neural oscillations. Here, we use recurrent neural networks (RNNs) to predict the future temporal evolution of the rs-fMRI slow oscillation from both rodent and human brains. The RNNs trained with vessel-specific rs-fMRI signals encode the unique brain oscillatory dynamic feature, presenting more effective prediction than the conventional autoregressive model. This RNN-based predictive modeling of rs-fMRI datasets from the Human Connectome Project (HCP) reveals brain state-specific characteristics, demonstrating an inverse relationship between the global rs-fMRI signal fluctuation with the internal default-mode network (DMN) correlation. The RNN prediction method presents a unique data-driven encoding scheme to specify potential brain state differences based on the global fMRI signal fluctuation, but not solely dependent on the global variance.
Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Asymptomatic Infections in 2 Large Academic Health Systems in Wisconsin
Authors: Rivera Frida , Safdar Nasia , Ledeboer Nathan , Schaack Grace , Chen Derrick J , Munoz-Price L Silvia 
Published: August 2020

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at 2 hospital systems in 2 counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of coronavirus disease 2019 (COVID-19) in Milwaukee County.
Labour market polarisation as a localised process: evidence from Sweden
Authors: Henning Martin , Eriksson Rikard H 
Published: August 2020

Abstract
The present article creates a link between contemporary labour market polarisation and regional divergence and analyses the spatial patterns of labour market polarisation in Swedish municipalities during the period 2002–2012. The results show that the national pattern of labour market polarisation is driven by polarisation in clusters of previously manufacturing-dominated municipalities with low- and medium-skill production, as well as increasing labour market polarisation and spatial selection within the fast-growing top-tier metropolitan regions. Outside these polarising spaces, most municipalities still experience job upgrading. The much-discussed abandonment of the traditional Western European job-upgrading model towards a polarising trajectory is thus not unequivocal. Regional labour market change and metropolitan selection cause great variation in labour market trajectories across space.
Breast Cancer Detection and Treatment Monitoring Using a Noninvasive Prenatal Testing Platform: Utility in Pregnant and Nonpregnant Populations
Authors: Lenaerts Liesbeth , Che Huiwen , Brison Nathalie , Neofytou Maria , Jatsenko Tatjana , Lefrère Hanne , Maggen Charlotte , Villela Darine , Verheecke Magali , Dehaspe Luc , Croitor Anca , Hatse Sigrid , Wildiers Hans , Neven Patrick , Vandecaveye Vincent , Floris Giuseppe , Vermeesch Joris Robert , Amant Frédéric 
Published: August 2020

Abstract

Background
Numerous publications have reported the incidental detection of occult malignancies upon routine noninvasive prenatal testing (NIPT). However, these studies were not designed to evaluate the NIPT performance for cancer detection.

Methods
We investigated the sensitivity of a genome-wide NIPT pipeline, called GIPSeq, for detecting cancer-specific copy number alterations (CNAs) in plasma tumor DNA (ctDNA) of patients with breast cancer. To assess whether a pregnancy itself, with fetal cell-free DNA (cfDNA) in the maternal circulation, might influence the detection of ctDNA, results were compared in pregnant (n = 25) and nonpregnant (n = 25) cancer patients. Furthermore, the ability of GIPSeq to monitor treatment response was assessed.

Results
Overall GIPSeq sensitivity for detecting cancer-specific CNAs in plasma cfDNA was 26%. Fifteen percent of detected cases were asymptomatic at the time of blood sampling. GIPSeq sensitivity mainly depended on the tumor stage. Also, triple negative breast cancers (TNBC) were more frequently identified compared to hormone-positive or HER2-enriched tumors. This might be due to the presence of high-level gains and losses of cfDNA or high ctDNA loads in plasma of TNBC. Although higher GIPSeq sensitivity was noted in pregnant (36%) than in nonpregnant women (16%), the limited sample size prohibits a definite conclusion. Finally, GIPSeq profiling of cfDNA during therapy allowed monitoring of early treatment response.

Conclusions
The results underscore the potential of NIPT-based tests, analyzing CNAs in plasma cfDNA in a genome-wide and unbiased fashion for breast cancer detection, cancer subtyping and treatment monitoring in a pregnant and nonpregnant target population.