bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliable and explainable machine-learning methods for accelerated material discovery
Authors: Kailkhura Bhavya , Gallagher Brian , Kim Sookyung , Hiszpanski Anna , Han T. Yong-Jin 
Published: November 2019

AbstractDespite ML’s impressive performance in commercial applications, several unique challenges exist when applying ML in materials science applications. In such a context, the contributions of this work are twofold. First, we identify common pitfalls of existing ML techniques when learning from underrepresented/imbalanced material data. Specifically, we show that with imbalanced data, standard methods for assessing quality of ML models break down and lead to misleading conclusions. Furthermore, we find that the model’s own confidence score cannot be trusted and model introspection methods (using simpler models) do not help as they result in loss of predictive performance (reliability-explainability trade-off). Second, to overcome these challenges, we propose a general-purpose explainable and reliable machine-learning framework. Specifically, we propose a generic pipeline that employs an ensemble of simpler models to reliably predict material properties. We also propose a transfer learning technique and show that the performance loss due to models’ simplicity can be overcome by exploiting correlations among different material properties. A new evaluation metric and a trust score to better quantify the confidence in the predictions are also proposed. To improve the interpretability, we add a rationale generator component to our framework which provides both model-level and decision-level explanations. Finally, we demonstrate the versatility of our technique on two applications: (1) predicting properties of crystalline compounds and (2) identifying potentially stable solar cell materials. We also point to some outstanding issues yet to be resolved for a successful application of ML in material science.
Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6
Authors: Byrne Alicia B. , Arts Peer , Polyak Steven W. , Feng Jinghua , Schreiber Andreas W. , Kassahn Karin S. , Hahn Christopher N. , Mordaunt Dylan A. , Fletcher Janice M. , Lipsett Jillian , Bratkovic Drago , Booker Grant W. , Smith Nicholas J. , Scott Hamish S. 
Published: November 2019

AbstractWe describe a sibling pair displaying an early infantile-onset, progressive neurodegenerative phenotype, with symptoms of developmental delay and epileptic encephalopathy developing from 12 to 14 months of age. Using whole exome sequencing, compound heterozygous variants were identified in SLC5A6, which encodes the sodium-dependent multivitamin transporter (SMVT) protein. SMVT is an important transporter of the B-group vitamins biotin, pantothenate, and lipoate. The protein is ubiquitously expressed and has major roles in vitamin uptake in the digestive system, as well as transport of these vitamins across the blood–brain barrier. Pathogenicity of the identified variants was demonstrated by impaired biotin uptake of mutant SMVT. Identification of this vitamin transporter as the genetic basis of this disorder guided targeted therapeutic intervention, resulting clinically in improvement of the patient’s neurocognitive and neuromotor function. This is the second report of biallelic mutations in SLC5A6 leading to a neurodegenerative disorder due to impaired biotin, pantothenate and lipoate uptake. The genetic and phenotypic overlap of these cases confirms mutations in SLC5A6 as the genetic cause of this disease phenotype. Recognition of the genetic disorder caused by SLC5A6 mutations is essential for early diagnosis and to facilitate timely intervention by triple vitamin (biotin, pantothenate, and lipoate) replacement therapy.
Tropical forest soils serve as substantial and persistent methane sinks
Authors: Zhao Jun-Fu , Peng Shu-Shi , Chen Meng-Ping , Wang Guan-Ze , Cui Yi-Bin , Liao Li-Guo , Feng Ji-Guang , Zhu Biao , Liu Wen-Jie , Yang Lian-Yan , Tan Zheng-Hong 
Published: November 2019

AbstractAlthough tropical forest soils contributed substantially global soil methane uptake, observations on soil methane fluxes in tropical forests are still sparse, especially in Southeast Asia, leading to large uncertainty in the estimation of global soil methane uptake. Here, we conducted two-year (from Sep, 2016 to Sep, 2018) measurements of soil methane fluxes in a lowland tropical forest site in Hainan island, China. At this tropical forest site, soils were substantial methane sink, and average annual soil methane uptake was estimated at 2.00 kg CH4-C ha−1 yr−1. The seasonality of soil methane uptake showed strong methane uptake in the dry season (−1.00 nmol m−2 s−1) and almost neutral or weak soil methane uptake in the wet season (−0.24 nmol m−2 s−1). The peak soil methane uptake rate was observed as −1.43 nmol m−2 s−1 in February, 2018, the driest and coolest month during the past 24 months. Soil moisture was the dominant controller of methane fluxes, and could explain 94% seasonal variation of soil methane fluxes. Soil temperature could not enhance the explanation of seasonal variation of soil methane fluxes on the top of soil moisture. A positive relationship between soil methane uptake and soil respiration was also detected, which might indicate co-variation in activities of methanotroph and roots and/or microbes for soil heterotrophic respiration. Our study highlights that tropical forests in this region acted as a methane sink.
High Temperature and Power Dependent Photoluminescence Analysis on Commercial Lighting and Display LED Materials for Future Power Electronic Modules
Authors: Sabbar Abbas , Madhusoodhanan Syam , Al-Kabi Sattar , Dong Binzhong , Wang Jiangbo , Atcitty Stanley , Kaplar Robert , Ding Ding , Mantooth Alan , Yu Shui-Qing , Chen Zhong 
Published: November 2019

AbstractCommercial light emitting diode (LED) materials - blue (i.e., InGaN/GaN multiple quantum wells (MQWs) for display and lighting), green (i.e., InGaN/GaN MQWs for display), and red (i.e., Al0.05Ga0.45In0.5P/Al0.4Ga0.1In0.5P for display) are evaluated in range of temperature (77–800) K for future applications in high density power electronic modules. The spontaneous emission quantum efficiency (QE) of blue, green, and red LED materials with different wavelengths was calculated using photoluminescence (PL) spectroscopy. The spontaneous emission QE was obtained based on a known model so-called the ABC model. This model has been recently used extensively to calculate the internal quantum efficiency and its droop in the III-nitride LED. At 800 K, the spontaneous emission quantum efficiencies are around 40% for blue for lighting and blue for display LED materials, and it is about 44.5% for green for display LED materials. The spontaneous emission QE is approximately 30% for red for display LED material at 800 K. The advance reported in this paper evidences the possibility of improving high temperature optocouplers with an operating temperature of 500 K and above.
Relative sorption coefficient: Key to tracing petroleum migration and other subsurface fluids
Authors: Zhang L. , Wang Y. , Li M.-W. , Yin Q.-Z. , Zhang W. 
Published: November 2019

AbstractThe accumulation and spatial distribution of economically important petroleum in sedimentary basins are primarily controlled by its migration from source rocks through permeable carrier beds to reservoirs. Tracing petroleum migration entails the use of molecular indices established according to sorption capacities of polar molecules in migrating petroleum. However, little is known about molecular sorption capacities in natural migration systems, rendering these indices unreliable. Here, we present a new approach based on a novel concept of relative sorption coefficient for quantitatively assessing sorption capacities of polar molecules during natural petroleum migration. Using this approach, we discovered previously unrecognized “stripping” and “impeding” effects that significantly reduce the sorption capacities of polar compounds. These discoveries provide new insights into the behaviors of polar compounds and can easily explain why traditional molecular indices yield incorrect information about petroleum migration. In light of these new findings, we established new molecular indices for tracing petroleum migration. We demonstrate via case studies that the newly established indices, unlike traditional molecular indices, are reliable and effective in tracing petroleum migration. Our approach can be applied to diverse basins around the world to reveal distribution patterns of petroleum, which would decrease environmental risks of exploration by reducing unsuccessful wells.
Complex life histories discovered in a critically endangered fish
Authors: Hobbs James A. , Lewis Levi S. , Willmes Malte , Denney Christian , Bush Eva 
Published: November 2019

AbstractEffective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California’s endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized “hot-spots” of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.
Effect of Water Compressibility, Sea-floor Elasticity, and Field Gravitational Potential on Tsunami Phase Speed
Authors: Abdolali Ali , Kadri Usama , Kirby James T. 
Published: November 2019

AbstractTsunamis can propagate thousands of kilometres across the ocean. Precise calculations of arrival times are essential for reliable early warning systems, determination of source and earth properties using the inverse problem, and time series modulation due to frequency dependency of phase speed. Far field observatories show a systematic discrepancy between observed and calculated arrival times. Models in present use and based on incompressible hydrodynamics and interaction with a rigid ocean floor overestimate the phase speed of tsunamis, leading to arrival time differences exceeding tens of minutes. These models neglect the simultaneous effects of the slight compressibility of water, sea-bed elasticity, and static compression of the ocean under gravity, hereinafter gravity. Here, we show that taking these effects into account results in more accurate phase speeds and travel times that agree with observations. Moreover, the semi-analytical model that we propose can be employed near real-time, which is essential for early warning inverse models and mitigation systems that rely on accurate phase speed calculations.
Dopamine D2 receptor modulates Wnt expression and control of cell proliferation
Authors: Han Fei , Konkalmatt Prasad , Mokashi Chaitanya , Kumar Megha , Zhang Yanrong , Ko Allen , Farino Zachary J. , Asico Laureano D. , Xu Gaosi , Gildea John , Zheng Xiaoxu , Felder Robin A. , Lee Robin E. C. , Jose Pedro A. , Freyberg Zachary , Armando Ines 
Published: November 2019

AbstractThe Wnt/β-catenin pathway is one of the most conserved signaling pathways across species with essential roles in development, cell proliferation, and disease. Wnt signaling occurs at the protein level and via β-catenin-mediated transcription of target genes. However, little is known about the underlying mechanisms regulating the expression of the key Wnt ligand Wnt3a or the modulation of its activity. Here, we provide evidence that there is significant cross-talk between the dopamine D2 receptor (D2R) and Wnt/β-catenin signaling pathways. Our data suggest that D2R-dependent cross-talk modulates Wnt3a expression via an evolutionarily-conserved TCF/LEF site within the WNT3A promoter. Moreover, D2R signaling also modulates cell proliferation and modifies the pathology in a renal ischemia/reperfusion-injury disease model, via its effects on Wnt/β-catenin signaling. Together, our results suggest that D2R is a transcriptional modulator of Wnt/β-catenin signal transduction with broad implications for health and development of new therapeutics.
A Frailty Index based on clinical data to quantify mortality risk in dogs
Authors: Banzato Tommaso , Franzo Giovanni , Di Maggio Roberta , Nicoletto Elisa , Burti Silvia , Cesari Matteo , Canevelli Marco 
Published: November 2019

AbstractFrailty is defined as a decline in an organism’s physiological reserves resulting in increased vulnerability to stressors. In humans, a single continuous variable, the so-called Frailty Index (FI), can be obtained by multidimensionally assessing the biological complexity of an ageing organism. Here, we evaluate this variability in dogs and compare it to the data available for humans. In dogs, there was a moderate correlation between age and the FI, and the distribution of the FI increased with age. Deficit accumulation was strongly related to mortality. The effect of age, when combined with the FI, was negligible. No sex-related differences were evident. The FI could be considered in epidemiological studies and/or experimental trials to account for the potential confounding effects of the health status of individual dogs. The age-related deficit accumulation reported in dogs is similar to that demonstrated in humans. Therefore, dogs might represent an excellent model for human aging studies.
Emotional learning promotes perceptual predictions by remodeling stimulus representation in visual cortex
Authors: Meaux E. , Sterpenich V. , Vuilleumier P. 
Published: November 2019

AbstractEmotions exert powerful effects on perception and memory, notably by modulating activity in sensory cortices so as to capture attention. Here, we examine whether emotional significance acquired by a visual stimulus can also change its cortical representation by linking neuronal populations coding for different memorized versions of the same stimulus, a mechanism that would facilitate recognition across different appearances. Using fMRI, we show that after pairing a given face with threat through conditioning, viewing this face activates the representation of another viewpoint of the same person, which itself was never conditioned, leading to robust repetition-priming across viewpoints in the ventral visual stream (including medial fusiform, lateral occipital, and anterior temporal cortex). We also observed a functional-anatomical segregation for coding view-invariant and view-specific identity information. These results indicate emotional signals may induce plasticity of stimulus representations in visual cortex, serving to generate new sensory predictions about different appearances of threat-associated stimuli.
Characterization of GUCA1A-associated dominant cone/cone-rod dystrophy: low prevalence among Japanese patients with inherited retinal dystrophies
Authors: Mizobuchi Kei , Hayashi Takaaki , Katagiri Satoshi , Yoshitake Kazutoshi , Fujinami Kaoru , Yang Lizhu , Kuniyoshi Kazuki , Shinoda Kei , Machida Shigeki , Kondo Mineo , Ueno Shinji , Terasaki Hiroko , Matsuura Tomokazu , Tsunoda Kazushige , Iwata Takeshi , Nakano Tadashi 
Published: November 2019

AbstractGUCA1A gene variants are associated with autosomal dominant (AD) cone dystrophy (COD) and cone-rod dystrophy (CORD). GUCA1A-associated AD-COD/CORD has never been reported in the Japanese population. The purpose of this study was to investigate clinical and genetic features of GUCA1A-associated AD-COD/CORD from a large Japanese cohort. We identified 8 variants [c.C50_80del (p.E17VfsX22), c.T124A (p.F42I), c.C204G (p.D68E), c.C238A (p.L80I), c.T295A (p.Y99N), c.A296C (p.Y99S), c.C451T (p.L151F), and c.A551G (p.Q184R)] in 14 families from our whole exome sequencing database composed of 1385 patients with inherited retinal diseases (IRDs) from 1192 families. Three variants (p.Y99N, p.Y99S, and p.L151F), which are located on/around EF-hand domains 3 and 4, were confirmed as “pathogenic”, whereas the other five variants, which did not co-segregate with IRDs, were considered “non-pathogenic”. Ophthalmic findings of 9 patients from 3 families with the pathogenic variants showed central visual impairment from early to middle-age onset and progressive macular atrophy. Electroretinography revealed severely decreased or non-recordable cone responses, whereas rod responses were highly variable, ranging from nearly normal to non-recordable. Our results indicate that the three pathogenic variants, two of which were novel, underlie AD-COD/CORD with progressive retinal atrophy, and the prevalence (0.25%, 3/1192 families) of GUCA1A-associated IRDs may be low among Japanese patients.
Spatial-temporal risk assessment of urbanization impacts on ecosystem services based on pressure-status - response framework
Authors: Kang Peng , Chen Weiping , Hou Ying , Li Yuanzheng 
Published: November 2019

AbstractRapid urbanization is a global phenomenon that has altered many ecosystems, generating ecological risks such as causing a decline in many ecosystem services. In this study, ecosystem service oriented risk assessment combined with PSR were quantifying how urbanization influences the ecosystem services about Beijing-Tianjin-Hebei urban agglomeration of China between 2000 year and 2010 year. The mean value of ecosystem services in three gradient (rural areas, suburban, and urban area) declined from 4.12 Yuan/m2 to 1.75 Yuan/m2 in 2000 year, while the mean value in 2010 year showed significant decrease and also represented urban-rural gradient. The average of pressure in PSR framework increased from 0.145 to 0.162 between two periods, while the average of status decrease from 0.378 to 0.311, and the status value decrease from 0.096 to 0.087. The higher risk degree V increased 6.95% between two periods, while the lower risk degree I decrease 6.89%. Two main types including high value gathering field and low value gathering field existed between two periods, the higher gathering field owned the ratio of 9.85%, mainly distributed around the urban area of Beijing and Tianjin, while the lower gathering field possess the ratio of 10.69%, mainly distributed in the northern and western in region. Overall, the analytical framework proposed in this study can provide comprehensive information to evaluate the impacts of complex practice in land-use planning and region ecosystem management.
Using bear rub data and spatial capture-recapture models to estimate trend in a brown bear population
Authors: Kendall Katherine C. , Graves Tabitha A. , Royle J. Andrew , Macleod Amy C. , McKelvey Kevin S. , Boulanger John , Waller John S. 
Published: November 2019

AbstractTrends in population abundance can be challenging to quantify during range expansion and contraction, when there is spatial variation in trend, or the conservation area is large. We used genetic detection data from natural bear rubbing sites and spatial capture-recapture (SCR) modeling to estimate local density and population growth rates in a grizzly bear population in northwestern Montana, USA. We visited bear rubs to collect hair in 2004, 2009—2012 (3,579—4,802 rubs) and detected 249—355 individual bears each year. We estimated the finite annual population rate of change 2004—2012 was 1.043 (95% CI = 1.017—1.069). Population density shifted from being concentrated in the north in 2004 to a more even distribution across the ecosystem by 2012. Our genetic detection sampling approach coupled with SCR modeling allowed us to estimate spatially variable growth rates of an expanding grizzly bear population and provided insight into how those patterns developed. The ability of SCR to utilize unstructured data and produce spatially explicit maps that indicate where population change is occurring promises to facilitate the monitoring of difficult-to-study species across large spatial areas.
An evaluation of the SureID 23comp Human Identification Kit for kinship testing
Authors: Alsafiah Hussain M. , Aljanabi Ali A. , Hadi Sibte , Alturayeif Saleh S. , Goodwin William 
Published: November 2019

AbstractShort tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38–40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.
DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples
Authors: Alawi Malik , Burkhardt Lia , Indenbirken Daniela , Reumann Kerstin , Christopeit Maximilian , Kröger Nicolaus , Lütgehetmann Marc , Aepfelbacher Martin , Fischer Nicole , Grundhoff Adam 
Published: November 2019

AbstractWe describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.