bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of reservoir-forming conditions of Beidong sub-sag in Beier Sag
Authors: Jiang Yongxu 
Published: August 2021

Abstract
Beier Sag is the main oil-rich sag in Hailar District basin. This paper analyzes the structure, source rock, relationship of source and reservoir, and deeply studies the reservoir-forming characteristics of Beidong sub-sag in Beier Sag. The study shows that the structure pattern of the bei-dong sub-sag in Beier Sag is characterized by “concave and uplifted interchangeably”, the present basin pattern is quite different from the prototype basin, develops northeast-east and north-east fault depressions in the Nantun formation during the sedimentary period. After three-stage tectonic transformation, it changes into the north-northeast direction, develops the palaeo-structure and has the geological conditions of reservoir formation. The dark mudstone of Nantun formation in Beidong sub-sag is thick, the abundance of organic matter is higher, and Type II is the main type; it is the medium-good source rocks with favorable conditions for reservoir formation. There are three sets of reservoir-forming assemblages in Beidong sub-sag, forming multi-type reservoirs. The succession of palaeo-structure is the main controlling factor of oil and gas accumulation, the favorable oil-bearing structures, such as reverse fault block and mid-concave uplift, are developed.
Chemical bonding of termination species in 2D carbides investigated through valence band UPS/XPS of Ti3C2T
x
MXene
Authors: Näslund Lars-Åke , Mikkelä Mikko-Heikki , Kokkonen Esko , Magnuson Martin 
Published: August 2021

Abstract
MXenes are technologically interesting 2D materials that show potential in numerous applications. The properties of the MXenes depend at large extent on the selection of elements that build the 2D MX-layer. Another key parameter for tuning the attractive material properties is the species that terminate the surfaces of the MX-layers. Although being an important parameter, experimental studies on the bonding between the MX-layers and the termination species are few and thus an interesting subject of investigation. Here we show that the termination species fluorine (F) bonds to the Ti3C2-surface mainly through Ti 3p—F 2p hybridization and that oxygen (O) bonds through Ti 3p—O 2p hybridization with a significant contribution of Ti 3d and Ti 4p. The study further shows that the Ti3C2-surface is not only terminated by F and O on the threefold hollow face-centered-cubic site. A significant amount of O sits on a bridge site bonded to two Ti surface atoms on the Ti3C2-surface. In addition, the results provide no support for hydroxide (OH) termination on the Ti3C2-surface. On the contrary, the comparison of the valence band intensity distribution obtained through ultraviolet- and x-ray photoelectron spectroscopy with computed spectra by density of states, weighed by matrix elements and sensitivity factors, reveals that OH cannot be considered as an inherent termination species in Ti3C2T
x
. The results from this study have implications for correct modeling of the structure of MXenes and the corresponding materials properties. Especially in applications where surface composition and charge are important, such as supercapacitors, Li-ion batteries, electrocatalysis, and fuel- and solar cells, where intercalation processes are essential.
First passage times over stochastic boundaries for subdiffusive processes
Authors: Constantinescu C. , Loeffen R. , Patie P. 
Published: August 2021

Let

X

=
(

X

t

)

t
≥
0

\mathbb {X}=(\mathbb {X}_t)_{t\geq 0}

be the subdiffusive process defined, for any

t
≥
0

t\geq 0

, by

X

t

=

X

ℓ
t

\mathbb {X}_t = X_{\ell _t}

where

X
=
(

X
t

)

t
≥
0

X=(X_t)_{t\geq 0}

is a Lévy process and

ℓ
t

=
inf
{
s
>
0
;

K

s

>
t
}

\ell _t=\inf \{s>0; \mathcal {K}_s>t \}

with

K

=
(

K

t

)

t
≥
0

\mathcal {K}=(\mathcal {K}_t)_{t\geq 0}

a subordinator independent of

X
X

. We start by developing a composite Wiener-Hopf factorization to characterize the law of the pair

(

T

a

(

b

)

,
(

X

−

b

)

T

a

(

b

)

)

(\mathbb {T}_a^{({b})}, (\mathbb {X} - {b})_{\mathbb {T}_a^{({b})}})

where

T

a

(

b

)

=
inf
{
t
>
0
;

X

t

>
a
+

b

t

}

\begin{equation*}\mathbb {T}_a^{({b})} = \inf \{t>0; \mathbb {X}_t > a+ {b}_t \} \end{equation*}

with

a
∈

R

a \in \mathbb {R}

and

b

=
(

b

t

)

t
≥
0

{b}=({b}_t)_{t\geq 0}

a (possibly degenerate) subordinator independent of

X
X

and

K

\mathcal {K}

. We proceed by providing a detailed analysis of the cases where either

X

\mathbb {X}

is a self-similar or is spectrally negative. For the later, we show the fact that the process

(

T

a

(

b

)

)

a
≥
0

(\mathbb {T}_a^{({b})})_{a\geq 0}

is a subordinator. Our proofs hinge on a variety of techniques including excursion theory, change of measure, asymptotic analysis and on establishing a link between subdiffusive processes and a subclass of semi-regenerative processes. In particular, we show that the variable

T

a

(

b

)

\mathbb {T}_a^{({b})}

has the same law as the first passage time of a semi-regenerative process of Lévy type, a terminology that we introduce to mean that this process satisfies the Markov property of Lévy processes for stopping times whose graph is included in the associated regeneration set.
High-dimensional generalized propensity score with application to omics data
Authors: Gao Qian , Zhang Yu , Liang Jie , Sun Hongwei , Wang Tong 
Published: August 2021

AbstractPropensity score (PS) methods are popular when estimating causal effects in non-randomized studies. Drawing causal conclusion relies on the unconfoundedness assumption. This assumption is untestable and is considered more plausible if a large number of pre-treatment covariates are included in the analysis. However, previous studies have shown that including unnecessary covariates into PS models can lead to bias and efficiency loss. With the ever-increasing amounts of available data, such as the omics data, there is often little prior knowledge of the exact set of important covariates. Therefore, variable selection for causal inference in high-dimensional settings has received considerable attention in recent years. However, recent studies have focused mainly on binary treatments. In this study, we considered continuous treatments and proposed the generalized outcome-adaptive LASSO (GOAL) to select covariates that can provide an unbiased and statistically efficient estimation. Simulation studies showed that when the outcome model was linear, the GOAL selected almost all true confounders and predictors of outcome and excluded other covariates. The accuracy and precision of the estimates were close to ideal. Furthermore, the GOAL is robust to model misspecification. We applied the GOAL to seven DNA methylation datasets from the Gene Expression Omnibus database, which covered four brain regions, to estimate the causal effects of epigenetic aging acceleration on the incidence of Alzheimer’s disease.
Using molecular embeddings in QSAR modeling: does it make a difference?
Authors: Sabando María Virginia , Ponzoni Ignacio , Milios Evangelos E , Soto Axel J 
Published: August 2021

Abstract
With the consolidation of deep learning in drug discovery, several novel algorithms for learning molecular representations have been proposed. Despite the interest of the community in developing new methods for learning molecular embeddings and their theoretical benefits, comparing molecular embeddings with each other and with traditional representations is not straightforward, which in turn hinders the process of choosing a suitable representation for Quantitative Structure–Activity Relationship (QSAR) modeling. A reason behind this issue is the difficulty of conducting a fair and thorough comparison of the different existing embedding approaches, which requires numerous experiments on various datasets and training scenarios. To close this gap, we reviewed the literature on methods for molecular embeddings and reproduced three unsupervised and two supervised molecular embedding techniques recently proposed in the literature. We compared these five methods concerning their performance in QSAR scenarios using different classification and regression datasets. We also compared these representations to traditional molecular representations, namely molecular descriptors and fingerprints. As opposed to the expected outcome, our experimental setup consisting of over $25 000$ trained models and statistical tests revealed that the predictive performance using molecular embeddings did not significantly surpass that of traditional representations. Although supervised embeddings yielded competitive results compared with those using traditional molecular representations, unsupervised embeddings tended to perform worse than traditional representations. Our results highlight the need for conducting a careful comparison and analysis of the different embedding techniques prior to using them in drug design tasks and motivate a discussion about the potential of molecular embeddings in computer-aided drug design.
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins
Authors: Zaitzeff Alexander , Leiby Nicholas , Motta Francis C , Haase Steven B , Singer Jedediah M 
Published: August 2021

Abstract

Motivation
Accurate automatic annotation of protein function relies on both innovative models and robust datasets. Due to their importance in biological processes, the identification of DNA-binding proteins directly from protein sequence has been the focus of many studies. However, the datasets used to train and evaluate these methods have suffered from substantial flaws. We describe some of the weaknesses of the datasets used in previous DNA-binding protein literature and provide several new datasets addressing these problems. We suggest new evaluative benchmark tasks that more realistically assess real-world performance for protein annotation models. We propose a simple new model for the prediction of DNA-binding proteins and compare its performance on the improved datasets to two previously published models. In addition, we provide extensive tests showing how the best models predict across taxa.

Results
Our new gradient boosting model, which uses features derived from a published protein language model, outperforms the earlier models. Perhaps surprisingly, so does a baseline nearest neighbor model using BLAST percent identity. We evaluate the sensitivity of these models to perturbations of DNA-binding regions and control regions of protein sequences. The successful data-driven models learn to focus on DNA-binding regions. When predicting across taxa, the best models are highly accurate across species in the same kingdom and can provide some information when predicting across kingdoms.

Availability and Implementation
The data and results for this article can be found at https://doi.org/10.5281/zenodo.5153906. The code for this article can be found at https://doi.org/10.5281/zenodo.5153683. The code, data and results can also be found at https://github.com/AZaitzeff/tools_for_dna_binding_proteins.
Assassin bugs can reduce the aggression of their spider prey before an attack
Authors: Wignall Anne E , Soley Fernando G 
Published: August 2021

AbstractPredators that hunt dangerous prey require specialized predatory tactics to avoid counter-attack. Usually, these predatory tactics reduce the probability of detection. The assassin bugs Stenolemus bituberus and S. giraffa rely on stealth or mimicry to prey on dangerous web-building spiders. Paradoxically, however, these assassin bugs tap the spiders with their antennae prior to attacking, leaving the bugs vulnerable to detection and counter-attack. Here, we tested the function of prey tapping. We used a controlled, repeated-measures experiment to assess the responses of spiders (Pholcus phalangioides) to simulated prey and compared their responses after being tapped on the leg (mimicking tapping by Stenolemus) or sham-tapped. We show that tapping can reduce the likelihood that spiders will behave aggressively, in turn lowering the risks of injury for assassin bug predators. Tapping may be an adaptation to reduce intraspecific aggression in prey that is being exploited by their predators.
Orienting to the sun improves camouflage for bilaterally symmetrical prey
Authors: Mavrovouna Veronica , Penacchio Olivier , Allen William L 
Published: August 2021

AbstractHere, we investigate the camouflage consequences of animal orientation behaviour. Shadows can be a conspicuous cue to the presence of prey. For bilaterally symmetrical animals, light field modelling indicates that camouflage will be improved when an animal orients its longitudinal axis directly towards or away from the sun, because the appearance of shadows is minimized. We test this prediction with a field predation experiment, in which wild birds hunt for artificial camouflaged prey oriented with the longitudinal axis either parallel or perpendicular to the sun. We find that prey oriented parallel to the sun are 3.93 times more likely to survive than prey oriented perpendicular to the sun. This result demonstrates the strong orientation dependence of camouflage. Given the dramatic difference in survival of prey with different orientations, we suggest that camouflage should be investigated as an important determinant of the positional behaviour of animals.
Enhancing endocannabinoid signalling in astrocytes promotes recovery from traumatic brain injury
Authors: Hu Mei , Zhu Dexiao , Zhang Jian , Gao Fei , Hashem Jack , Kingsley Philip , Marnett Lawrence J , Mackie Ken , Chen Chu 
Published: August 2021

Abstract
Traumatic brain injury is an important risk factor for development of Alzheimer’s disease and dementia. Unfortunately, no effective therapies are currently available for prevention and treatment of the traumatic brain injury-induced Alzheimer’s disease-like neurodegenerative disease. This is largely due to our limited understanding of the mechanisms underlying traumatic brain injury-induced neuropathology. Previous studies showed that pharmacological inhibition of monoacylglycerol lipase, a key enzyme degrading the endocannabinoid 2-arachidonoylglycerol, attenuates traumatic brain injury-induced neuropathology. However, the mechanism responsible for the neuroprotective effects produced by inhibition of monoacylglycerol lipase in traumatic brain injury remains unclear.
Here we first show that genetic deletion of monoacylglycerol lipase reduces neuropathology and averts synaptic and cognitive declines in mice exposed to repeated mild closed head injury. Surprisingly, these neuroprotective effects result primarily from inhibition of 2-arachidonoylglycerol metabolism in astrocytes, rather than in neurons. Single-cell RNA-sequencing data reveal that astrocytic monoacylglycerol lipase knockout mice display greater resilience to traumatic brain injury-induced changes in expression of genes associated with inflammation or maintenance of brain homeostasis in astrocytes and microglia. The monoacylglycerol lipase inactivation-produced neuroprotection is abrogated by deletion of the cannabinoid receptor-1 or by adeno-associated virus vector-mediated silencing of astrocytic peroxisome proliferator-activated receptor-γ. This is further supported by the fact that overexpression of peroxisome proliferator-activated receptor-γ in astrocytes prevents traumatic brain injury-induced neuropathology and impairments in spatial learning and memory.
Our results reveal a previously undefined cell type-specific role of 2-arachidonoylglycerol metabolism and signalling pathways in traumatic brain injury-induced neuropathology, suggesting that enhanced 2-arachidonoylglycerol signalling in astrocytes is responsible for the monoacylglycerol lipase inactivation-produced alleviation of neuropathology and deficits in synaptic and cognitive functions in traumatic brain injury.
Lymphatic contractile function: a comprehensive review of drug effects and potential clinical application
Authors: Russell Peter S , Hong Jiwon , Trevaskis Natalie L , Windsor John A , Martin Niels D , Phillips Anthony R J 
Published: August 2021

Abstract
The lymphatic system and the cardiovascular (CV) system work together to maintain body fluid homeostasis. Despite that, the lymphatic system has been relatively neglected as a potential drug target and a source of adverse effects from CV drugs. Like the heart, the lymphatic vessels undergo phasic contractions to promote lymph flow against a pressure gradient. Dysfunction or failure of the lymphatic pump results in fluid imbalance and tissue oedema. While this can be due to drug effects, it is also a feature of breast cancer-associated lymphoedema, chronic venous insufficiency, congestive heart failure, and acute systemic inflammation. There are currently no specific drug treatments for lymphatic pump dysfunction in clinical use despite the wealth of data from pre-clinical studies. The aim of this study was to identify (i) drugs with direct effects on lymphatic tonic and phasic contractions with potential for clinical application, and (ii) drugs in current clinical use that have a positive or negative side effect on lymphatic function. We comprehensively reviewed all studies that tested the direct effect of a drug on the contractile function of lymphatic vessels. Of the 208 drugs identified from 193 studies, about a quarter had only stimulatory effects on lymphatic tone, contraction frequency, and/or contraction amplitude. Of Food and Drug Administration-approved drugs, there were 14 that increased lymphatic phasic contractile function. The most frequently used class of drugs with inhibitory effects on lymphatic pump function were the calcium channels blockers. This review highlights the opportunity for specific drug treatments of lymphatic dysfunction in various disease states and for avoiding adverse drug effects on lymphatic contractile function.
“Systemic, Transhistoric, Institutionalized, and Legitimized Antipathy”: Epistemic and Sexual Violence inA Girl Is a Half-formed ThingandMilkman
Authors: Darling Orlaith 
Published: August 2021

AbstractThis article concerns the interrelations of epistemic and physical gendered violence in two award-winning contemporary Irish novels, A Girl Is a Half-formed Thing (2013) and Milkman (2018) by Eimear McBride and Anna Burns, respectively. It argues that patriarchal naming power which defines women as sexual objects is inextricable from the physical violence featured in both texts. Using theories of violence and naming, it examines how, faced with a climate of constant and submerged sexual threat, “middle sister” (as the narrator is called) and “Girl” (the protagonist of A Girl Is a Half-formed Thing) attempt to appropriate dominant patriarchal narratives to retain subjectivity in the face of violence. While “middle sister” comes to recognize and articulate the violence done to her, Girl’s internalization of violence leads to the annihilation of both self and body.
Seasonal Appearance, Abundance, and Host Preference of Philaenus spumarius and Neophilaenus campestris (Hemiptera: Aphrophoridae) in Olive Groves in Greece
Authors: Antonatos Spyridon , Papachristos Dimitrios P , Varikou Kyriaki , Vahamidis Petros , Kapranas Apostolos , Milonas Panagiotis 
Published: August 2021

Abstract
Xylella fastidiosa Wells et al. (Xanthomonadales: Xanthomonadaceae) is a xylem inhabiting bacterium which is exclusively transmitted by xylem sap feeding insects. Among them, Philaenus spumarius Linnaeus and Neophilaenus campestris Fallén are the most abundant species in Europe. During 2018 and 2019 a survey was conducted in olive groves in Greece aimed to improve the knowledge about the biology and ecology of those spittlebugs in areas with Mediterranean climate. Moreover, the host preference of the nymphs was studied. The nymphs of P. spumarius and N. campestris were observed between early March and middle May depending on geographic location and year. The spittlebug adults were present during two periods every year, one in spring and another one in autumn and early winter. During summer months the spittlebugs were totally absent from olive groves. Our observation on host plant selection revealed that there was a strong preference of N. campestris nymphs for plants belonging to the family Poaceae. On the contrary, P. spumarius nymphs were polyphagous. The most preferable plants for the nymphs of this species belonged to the families Asteraceae and Fabaceae. The importance of these findings for control measures for these spittlebugs is discussed.
Discontinuation of direct oral anticoagulants among patients with atrial fibrillation according to gender and cohabitation status: a nationwide cohort study
Authors: Binding Casper , Olesen Jonas Bjerring , Lee Christina Ji-Young , Lip Gregory Y H , Sindet-Pedersen Caroline , Gislason Gunnar , Bonde Anders Nissen 
Published: August 2021

Abstract

Aims
The aim of this study was to evaluate the risk of discontinuing treatment with direct oral anticoagulants (DOACs) among patients with atrial fibrillation (AF) according to cohabitation status and gender.

Methods and results
Using the Danish national registers, we identified 32 364 patients with AF aged 40–90 years undergoing treatment with DOACs. The study period was from 2013 to 2017, and patients were followed for 2 years, or until death, outcome, or emigration. The main outcome was discontinuation of DOAC treatment for at least 30 days. The absolute 2-year risk of DOAC discontinuation was highest among men living alone [35.7%, 95% confidence interval (CI): 37.3–34.1%]. Men living alone had a 4.6% (95% CI: 6.4–2.8%) higher absolute risk of discontinuation and a 12% [hazard ratio (HR): 1.12, 95% CI: 1.04–1.20] higher relative risk of discontinuation compared with men living with a partner. Female patients living alone likewise had a higher absolute risk of DOAC discontinuation (2.6%, 95% CI: 4.4–0.09%) compared with female patients living with a partner, yet no statistically significant difference in relative risk. In an analysis evaluating gender, we found male gender to be associated with a significantly higher relative risk of DOAC discontinuation (HR: 1.33, 95% CI: 1.26–1.40) compared with female gender (P-value for interaction with cohabitant status = 0.5996).

Conclusion
In this nationwide population study, male gender and living alone were associated with a higher risk of DOAC discontinuation among patients with AF.