bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interannual variability on methane emissions in monsoon Asia derived from GOSAT and surface observations
Authors: Wang Fenjuan , Maksyutov Shamil , Janardanan Rajesh , Tsuruta Aki , Ito Akihiko , Morino Isamu , Yoshida Yukio , Tohjima Yasunori , Kaiser Johannes W , Janssens-Maenhout Greet , Lan Xin , Mammarella Ivan , Lavric Jost V , Matsunaga Tsuneo 
Published: December 2020

Abstract
In Asia, much effort is put into reducing methane (CH4) emissions due to the region’s contribution to the recent rapid global atmospheric CH4 concentration growth. Accurate quantification of Asia’s CH4 budgets is critical for conducting global stocktake and achieving the long-term temperature goal of the Paris Agreement. In this study, we present top-down estimates of CH4 emissions from 2009 to 2018 deduced from atmospheric observations from surface network and GOSAT satellite with the high-resolution global inverse model NIES-TM-FLEXPART-VAR. The optimized average CH4 budgets are 63.40 ± 10.52 Tg y−1 from East Asia (EA), 45.20 ± 6.22 Tg y−1 from Southeast Asia (SEA), and 64.35 ± 9.28 Tg y−1 from South Asia (SA) within the 10 years. We analyzed two 5 years CH4 emission budgets for three subregions and 13 top-emitting countries with an emission budget larger than 1 Tg y−1, and interannual variabilities for these subregions. Statistically significant increasing trends in emissions are found in EA with a lower emission growth rate during 2014–2018 compared to that during 2009–2013, while trends in SEA are not significant. In contrast to the prior emission, the posterior emission shows a significant decreasing trend in SA. The flux decrease is associated with the transition from strong La Ninña (2010–2011) to strong El Ninño (2015–2016) events, which modulate the surface air temperature and rainfall patterns. The interannual variability in CH4 flux anomalies was larger in SA compared to EA and SEA. The Southern Oscillation Index correlates strongly with interannual CH4 flux anomalies for SA. Our findings suggest that the interannual variability in the total CH4 flux is dominated by climate variability in SA. The contribution of climate variability driving interannual variability in natural and anthropogenic CH4 emissions should be further quantified, especially for tropical countries. Accounting for climate variability may be necessary to improve anthropogenic emission inventories.
Contact network models matching the dynamics of the COVID-19 spreading
Authors: Medo Matúš 
Published: December 2020

Abstract
We study the epidemic spreading on spatial networks where the probability that two nodes are connected decays with their distance as a power law. As the exponent of the distance dependence grows, model networks smoothly transition from the random network limit to the regular lattice limit. We show that despite keeping the average number of contacts constant, the increasing exponent hampers the epidemic spreading by making long-distance connections less frequent. The spreading dynamics is influenced by the distance-dependence exponent as well and changes from exponential growth to power-law growth. The observed power-law growth is compatible with recent analyses of empirical data on the spreading of COVID-19 in numerous countries.
Remarks on dispersion-improved shallow water equations with uneven bottom
Authors: Clamond Didier 
Published: December 2020

Abstract
It is shown that asymptotically consistent modifications of (Boussinesq-like) shallow water approximations, in order to improve their dispersive properties, can fail for uneven bottoms (i.e., the dispersion is actually not improved). It is also shown that these modifications can lead to ill-posed equations when the water depth is not constant. These drawbacks are illustrated with the (fully nonlinear, weakly dispersive) Serre equations. We also derive asymptotically consistent, well-posed, modified Serre equations with improved dispersive properties for constant slopes of the bottom.
Generalised expression of the noise figure of phase sensitive amplifiers for an arbitrary number of modes
Authors: Bouasria Yousra , Chatterjee Debanuj , Goldfarb Fabienne , Hassouni Yassine , Bretenaker Fabien 
Published: December 2020

Abstract
Phase sensitive amplifiers (PSA), contrary to usual phase insensitive amplifiers (PIA), are in principle capable to achieve noiseless amplification, i.e. exhibit a quantum-limited noise figure (NF) of 0 db. When implemented using four-wave mixing (FWM) in a non-linear fibre, extra waves can be generated by undesired FWM processes, which may introduce extra input ports for vacuum fluctuations, thus potentially degrading the NF. In this situation, we give here a general analytical quantum derivation of the PSA NF, valid for an arbitrary number of nonlinearly coupled modes. This expression is usable as soon as a linear input-output relation can be found for the annihilation and creation operators of the involved modes. It predicts that the noise level depends on the number of interacting waves. We illustrate the usefulness of this expression in the case of six waves, corresponding to four interacting quantum modes. In this example the signal NF is degraded by 0.4 db, compared to 10 db obtained for PIA operation of the same scheme.
Automated measurements of morphological parameters of muscles and tendons
Authors: Jabbar Shaima Ibraheem , Day Charles , Chadwick Edward 
Published: December 2020

Abstract
Capturing accurate representations of musculoskeletal system morphology is a core aspect of musculoskeletal modelling of the upper limb. Measurements of important geometric parameters such as the thickness of muscles and tendons are key descriptors of the underlying morphology. Though the measurement of those parameters can be estimated manually using cadaveric measurements, this is not an appropriate technique for constructing a personalised musculoskeletal model for an individual. Therefore, this work proposes and applies a novel method for evaluating the geometric parameters of the upper extremity based on automated ultrasound image analysis. The proposed algorithm involves advanced techniques from artificial intelligence and image processing to outline the necessary details of the musculoskeletal morphology from appropriately enhanced ultrasound images. The ultrasound images were collected from 25 healthy volunteers from different parts of upper limb. The results were compared with measurements of a manual evaluation. Our results showed that the average discrepancy between the manual and automatic measures of triceps thickness is 0.115 mm. This represents improved accuracy compared to several current approaches.
Mg
x
Zn1−x
O contact to CuGa3Se5 absorber for photovoltaic and photoelectrochemical devices
Authors: Khan Imran S , Muzzillo Christopher P , Perkins Craig L , Norman Andrew G , Young James L , Gaillard Nicolas , Zakutayev Andriy 
Published: December 2020

Abstract
CuGa3Se5 is a promising candidate material with wide band gap for top cells in tandem photovoltaic and photoelectrochemical (PEC) devices. However, traditional CdS contact layers used with other chalcopyrite absorbers are not suitable for CuGa3Se5 due to the higher position of its conduction band (CB) minimum. Mg
x
Zn1−

x
O (MZO) is a transparent oxide with adjustable band gap and CB position as a function of magnesium composition, but its direct application is hindered by CuGa3Se5 surface oxidation. Here, MZO is investigated as a contact (n-type ‘buffer’ or ‘window’) material to CuGa3Se5 absorbers pretreated in Cd2+ solution, and an onset potential close to 1 V vs reversible hydrogen electrode in 10 mM hexaammineruthenium (III) chloride electrolyte is demonstrated. The Cd2+ surface treatment changes the chemical composition and electronic structure of the CuGa3Se5 surface, as demonstrated by photoelectron spectroscopy measurements. The performance of CuGa3Se5 absorber with Cd2+ treated surface in the solid-state test structure depends on the Zn/Mg ratio in the MZO layer. The measured open circuit voltage of 925 mV is promising for tandem PEC water splitting with CuGa3Se5/MZO top cells.
Pathways to help-seeking for sexual difficulties in older adults: qualitative findings from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3)
Authors: Hinchliff Sharron , Lewis Ruth , Wellings Kaye , Datta Jessica , Mitchell Kirstin 
Published: December 2020

Abstract

Background
Older adults are at an increased risk of sexual difficulties due to ageing and chronic health conditions. While they experience barriers to seeking and receiving help for sexual difficulties there is a dearth of research about the help-seeking journey.

Objective
To explore decision-making in context; particularly, the reasons why older adults do, or do not, seek help for sexual difficulties.

Methods
Semi-structured interviews were conducted with 11 men and 12 women aged 58–75 who reported having a health condition, disability or medication that had affected their sex life in the last year. Participants were part of the third British National Survey of Sexual Attitudes and Lifestyles (Natsal-3). Data were analysed thematically.

Results
Help-seeking was rarely a predictable or linear process. Participants tended to wait and see if the sexual difficulty got better on its own or improved as a result of lifestyle changes. An often-lengthy period of thinking, researching and planning could end with a decision to seek professional help, to not seek help, or do nothing for now. A significant barrier was concern about the interaction of medicines prescribed for the sexual difficulty with those already taken for chronic health conditions. Patient fear of not being taken seriously and doctor reticence to ask thwarted potential conversations. Help-seeking journeys often ended without resolution, even when professional help was sought.

Conclusions
To give patients and practitioners permission to raise the topic, suggestions include providing patients with a pre-consultation card which lists topics they would like to talk about, including sexual issues.
Are you my baby? Testing whether paternity affects behavior of cobreeder male acorn woodpeckers
Authors: Koenig Walter D , Prinz Anna C B , Haydock Joseph , Dugdale Hannah L , Walters Eric L 
Published: December 2020

AbstractNatural selection is expected to favor males that invest more in offspring they sire. We investigated the relationship between paternity and male behavior in the acorn woodpecker (Melanerpes formicivorus), a cooperative breeder that lives in family groups including offspring that remain on their natal territory, sometimes for years, and cobreeders of both sexes. Regardless of group composition, only one communal nest is attended at a time. Whereas cobreeding females share maternity equally, one male usually sires the majority of young in the group’s communal nest. Copulations are rarely observed, and thus it has not been possible to link paternity to sexual behavior. There were no differences among cobreeder males that did or did not sire young in their propensity to roost in the nest cavity at night. However, cobreeder males that attended females continuously prior to egg-laying were more likely to successfully sire young than males that did not, and the relative share of feeding visits and time spent at the subsequent nest were positively related to a male’s realized paternity. These differences in male behavior were partly due to differences among males and partly to plasticity in male behavior covarying with paternity share. Feedings by males successfully siring young also involved a larger proportion of nutritionally valuable insect prey. Males are aware of their paternity success, apparently because of their relative access to females prior to egg laying, and provide more paternal care at nests in which they are more likely to have sired young.
ChemGenerator: a web server for generating potential ligands for specific targets
Authors: Yang Jing , Hou Ling , Liu Kun-Meng , He Wen-Bin , Cai Yong , Yang Feng-Qing , Hu Yuan-Jia 
Published: December 2020

Abstract
In drug discovery, one of the most important tasks is to find novel and biologically active molecules. Given that only a tip of iceberg of drugs was founded in nearly one-century’s experimental exploration, it shows great significance to use in silico methods to expand chemical database and profile drug-target linkages. In this study, a web server named ChemGenerator was proposed to generate novel activates for specific targets based on users’ input. The ChemGenerator relies on an autoencoder-based algorithm of Recurrent Neural Networks with Long Short-Term Memory by training of 7 million of molecular Simplified Molecular-Input Line-Entry System as the basic model, and further develops target guided generation by transfer learning. As results, ChemGenerator gains lower loss (&lt;0.01) than existing reference model (0.2~0.4) and shows good performance in the case of Epidermal Growth Factor Receptor. Meanwhile, ChemGenerator is now freely accessible to the public by http://smiles.tcmobile.org. In proportion to endless molecular enumeration and time-consuming expensive experiments, this work demonstrates an efficient alternative way for the first virtual screening in drug discovery.
BiCoN: network-constrained biclustering of patients and omics data
Authors: Lazareva Olga , Canzar Stefan , Yuan Kevin , Baumbach Jan , Blumenthal David B , Tieri Paolo , Kacprowski Tim , List Markus 
Published: December 2020

Abstract

Motivation
Unsupervised learning approaches are frequently used to stratify patients into clinically relevant subgroups and to identify biomarkers such as disease-associated genes. However, clustering and biclustering techniques are oblivious to the functional relationship of genes and are thus not ideally suited to pinpoint molecular mechanisms along with patient subgroups.

Results
We developed the network-constrained biclustering approach Biclustering Constrained by Networks (BiCoN) which (i) restricts biclusters to functionally related genes connected in molecular interaction networks and (ii) maximizes the difference in gene expression between two subgroups of patients. This allows BiCoN to simultaneously pinpoint molecular mechanisms responsible for the patient grouping. Network-constrained clustering of genes makes BiCoN more robust to noise and batch effects than typical clustering and biclustering methods. BiCoN can faithfully reproduce known disease subtypes as well as novel, clinically relevant patient subgroups, as we could demonstrate using breast and lung cancer datasets. In summary, BiCoN is a novel systems medicine tool that combines several heuristic optimization strategies for robust disease mechanism extraction. BiCoN is well-documented and freely available as a python package or a web interface.

Availability and implementation
PyPI package: https://pypi.org/project/bicon.

Web interface
https://exbio.wzw.tum.de/bicon.

Supplementary information
Supplementary data are available at Bioinformatics online.
Teaching an Old Shell New Tricks: Extracting DNA from Current, Historical, and Ancient Mollusk Shells
Authors: Martin Kelly R , Waits Lisette P , Parent Christine E 
Published: December 2020

ABSTRACTThe use of unconventional DNA sources has increased because the acquisition of traditional samples can be invasive, destructive, or impossible. Mollusks are one group for which novel genetic sources are crucial, but methodology remains relatively undeveloped. Many species are important ecologically and in aquaculture production. However, mollusks have the highest number of extinctions of any taxonomic group. Traditionally, mollusk shell material was used for morphological research and only recently has been used in DNA studies. In the present article, we review the studies in which shell DNA was extracted and found that effective procedures consider taxon-specific biological characteristics, environmental conditions, laboratory methods, and the study objectives. Importantly, these factors cannot be considered in isolation because of their fundamental, sometimes reciprocal, relationships and influence in the long-term preservation and recovery of shell DNA. Successful recovery of shell DNA can facilitate research on pressing ecological and evolutionary questions and inform conservation strategies to protect molluscan diversity.
Rapid and Sensitive LC-MS/MS Method for Simultaneous Determination of Three First-Line Oral Antituberculosis Drug in Plasma
Authors: Han Fei , Li Weiwei , Jin Yi , Wang Fang , Yuan Bo , Xu Haiyan 
Published: December 2020

Abstract
A bioanalytical method for simultaneous quantification of isoniazid (INH), pyrazinamide (PZA) and ethambutol (EMB) in plasma was developed and validated using high-performance liquid chromatography with tandem mass spectrometry. After extracted by protein precipitation with acetonitrile, the analytes were separated on a Waters XBridge Amide column by isocratic elution with acetonitrile and 5 mM ammonium acetate solution containing 0.3% formic acid (77:23, v/v) at a flow rate of 0.5 mL/min. The detection was carried out on a triple quadrupole tandem mass spectrometer equipped with an electrospray ionization source in positive mode by monitoring the selected ion transitions at m/z 205.2 → 116.1, m/z 137.9 → 121.2, m/z 124.3 → 78.9 and m/z 213.1 → 122.4 for EMB, INH, PZA and EMB-d8 Internal standard (IS), respectively. The calibration curves were linear over the range of 0.0125–2.00 μg/mL for EMB, 0.0625–10.0 μg/mL for INH and 0.250–40.0 μg/mL for PZA. Neither cross-analytes inter-conversion nor matrix effects were observed. The intra- and inter-assay precision (%RSD) values were within 8.80%, and accuracy (%RE) ranged from −11.13 to 13.49%, indicating that the precision and accuracy were well within the acceptable limits of variation. The method would be helpful for analysis of EMB, INH and PZA in plasma samples from clinical pharmacokinetics and therapeutic drug monitoring.
Channel Estimation for Millimeter Wave Massive MIMO System: Proposed Hybrid Optimization with Heuristic-Enabled Precoding and Combining
Authors: Srinivasa Rao Y , Madhu R 
Published: December 2020

AbstractIn multiple-input multiple-output (MIMO), millimeter wave (mmWave) is considered as a promising technology for advanced communication over wireless networks due to its rich frequency spectral resources. However, recognizing the mmWave in MIMO remains a complex task that faces the issues like increased propagation loss. Therefore, this paper proposes a new optimization-assisted estimation algorithm to estimate the mmWave channel parameters. The channel estimation and hybrid precoding performance on mmWave massive MIMO system are proposed by adopting optimization process in the codebook design principles. In fact, the existing works have performed uniform distribution of azimuth angles in the codebook design, whereas the proposed work evaluates it as a single objective optimization problem without excluding the angle characteristics. In order to solve the mentioned optimization problem, dragonfly-evaluated gray wolf optimization (DA-GWO) model is introduced that hybridizes the concepts of dragonfly algorithm and GWO, respectively. Finally, the performance of proposed work is compared and validated over other state-of-the-art models with respect to channel state information and error measures. Accordingly, from the analysis, the proposed DA-GWO model concerning (64, 64) combination for 400th channel bandwidth is 80% and 95.53% superior to adaptive channel estimation and projected gradient factorization algorithms.
Cannabinoid Receptor Activation on Haematopoietic Cells and Enterocytes Protects against Colitis
Authors: Becker William , Alrafas Haider Rasheed , Busbee Philip B , Walla Michael D , Wilson Kiesha , Miranda Kathryn , Cai Guoshuai , Putluri Vasanta , Putluri Nagireddy , Nagarkatti Mitzi , Nagarkatti Prakash S 
Published: December 2020

Abstract

Background and Aims
Cannabinoid receptor [CB] activation can attenuate inflammatory bowel disease [IBD] in experimental models and human cohorts. However, the roles of the microbiome, metabolome, and the respective contributions of haematopoietic and non-haematopoietic cells in the anti-colitic effects of cannabinoids have yet to be determined.

Methods
Female C57BL/6 mice were treated with either cannabidiol [CBD], Δ 9-tetrahydrocannabinol [THC], a combination of CBD and THC, or vehicle, in several models of chemically induced colitis. Clinical parameters of colitis were assessed by colonoscopy, histology, flow cytometry, and detection of serum biomarkers; single-cell RNA sequencing and qRT-PCR were used to evaluate the effects of cannabinoids on enterocytes. Immune cell transfer from CB2 knockout mice was used to evaluate the contribution of haematopoietic and non-haematopoietic cells to colitis protection.

Results
We found that THC prevented colitis and that CBD, at the dose tested, provided little benefit to the amelioration of colitis, nor when added synergistically with THC. THC increased colonic barrier integrity by stimulating mucus and tight junction and antimicrobial peptide production, and these effects were specific to the large intestine. THC increased colonic Gram-negative bacteria, but the anti-colitic effects of THC were independent of the microbiome. THC acted both on immune cells via CB2 and on enterocytes, to attenuate colitis.

Conclusions
Our findings demonstrate how cannabinoid receptor activation on both immune cells and colonocytes is critical to prevent colonic inflammation. These studies also suggest how cannabinoid receptor activation can be used as a preventive and therapeutic modality against colitis.
Weather Conditions Affect the Visitation Frequency, Richness and Detectability of Insect Flower Visitors in the Australian Alpine Zone
Authors: Goodwin Emma K , Rader Romina , Encinas-Viso Francisco , Saunders Manu E 
Published: December 2020

Abstract
Weather conditions, such as humidity, temperature, and wind speed, affect insect activity. Understanding how different taxa respond to varying environmental conditions is necessary to determine the extent to which environmental change may impact plant-pollinator networks. This is particularly important in alpine regions where taxa may be more susceptible to extreme climatic events and overall increases in temperature. We observed plant–flower visitor interactions in Australian alpine plant communities to determine 1) the structure of the plant-flower visitor community, and 2) how floral visitation and diversity of insect taxa varied according to environmental conditions and habitat type. Coleoptera and Diptera were the most dominant flower visitors in the visitation networks. Most insect orders were moderately generalized in their interactions, but Hymenoptera showed greater specialization (d′) at exposed sites compared to other insect orders. Importantly, insect orders behaved differently in response to changes in environmental conditions. Hymenoptera visitation increased with higher temperatures. Diptera was the only taxon observed actively moving between flowers under inclement conditions. Our results demonstrate the value in sampling across the spectrum of environmental conditions to capture the differences among flower visiting insect taxa in their responses to varying environmental conditions. A diversity of responses among insect taxa could facilitate community-level resilience to changing environmental conditions.