bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global competing water uses for food and energy
Authors: Qin Yue 
Published: June 2021

Abstract
Water competition between the food and energy sector is a critical component of the food-energy-water nexus. However, few studies have systematically characterized the geospatial and, especially, the sub-annual variations in such competition and the associated environmental impacts and targeted mitigation opportunities. This study characterizes competing water uses for crop-specific irrigated agriculture and fuel-specific power generation across global major river basins to reveal their resulting impacts on local water scarcity for global population under both current and a warming climate. Under annual (and most seasonal) accounting, almost all basins currently suffering from extremely high water scarcity are dominated by agricultural water consumption (e.g. accommodating 26%–49% of basin-total population across seasons), which are often simultaneously exposed to potentially decreasing seasonal water availability under a 4 °C warming scenario. Only 13%–20% of population are located in basins dominated by seasonal power sector water uses, which are predominantly with low water scarcity. Agriculture sector provides the most basin-specific water mitigation opportunities across mid-latitude basins in all four seasons. Nevertheless, power sector becomes more important in affecting seasonal water scarcity and provides unique seasonal water mitigation opportunities, particularly in basins among higher northern latitudes in winter. This analysis highlights irrigated agriculture is currently and will likely remain the key in global water management for basins facing the severest water scarcity, yet increasing attention on the seasonal and spatial variations in cross-sector water use competition is needed to better identify region- and season- specific mitigation opportunities.
Assessing the sequestration time scales of some ocean-based carbon dioxide reduction strategies
Authors: Siegel D A , DeVries T , Doney S C , Bell T 
Published: June 2021

Abstract
Ocean-based carbon dioxide (CO2) removal (CDR) strategies are an important part of the portfolio of approaches needed to achieve negative greenhouse gas emissions. Many ocean-based CDR strategies rely on injecting CO2 or organic carbon (that will eventually become CO2) into the ocean interior, or enhancing the ocean’s biological pump. These approaches will not result in permanent sequestration, because ocean currents will eventually return the injected CO2 back to the surface, where it will be brought into equilibrium with the atmosphere. Here, a model of steady state global ocean circulation and mixing is used to assess the time scales over which CO2 injected in the ocean interior remains sequestered from the atmosphere. There will be a distribution of sequestration times for any single discharge location due to the infinite number of pathways connecting a location at depth with the sea surface. The resulting probability distribution is highly skewed with a long tail of very long transit times, making mean sequestration times much longer than typical time scales. Deeper discharge locations will sequester purposefully injected CO2 much longer than shallower ones and median sequestration times are typically decades to centuries, and approach 1000 years in the deep North Pacific. Large differences in sequestration times occur both within and between the major ocean basins, with the Pacific and Indian basins generally having longer sequestration times than the Atlantic and Southern Oceans. Assessments made over a 50 year time horizon illustrates that most of the injected carbon will be retained for injection depths greater than 1000 m, with several geographic exceptions such as the Western North Atlantic. Ocean CDR strategies that increase upper ocean ecosystem productivity with the goal of exporting more carbon to depth will have mainly a short-term influence on atmospheric CO2 levels because ∼70% will be transported back to the surface ocean within 50 years. The results presented here will help plan appropriate ocean CDR strategies that can help limit climate damage caused by fossil fuel CO2 emissions.
Universal break law for a class of models of polymer rupture
Authors: Aurzada Frank , Betz Volker , Lifshits Mikhail 
Published: June 2021

AbstractWe model a polymer by a finite chain of Brownian particles, interacting through a pairwise potentialU. We investigate what happens when one end of the chain is fixed and the other end slowly pulled away, and when we assume that the chain breaks as soon as the distance between two neighbouring particles exceeds a certain thresholdb. We find that under natural conditions onUand suitable scaling of noise and pulling speed, the laws of the break time and of the place along the chain where the break occurs converge to explicit limits. These limits are universal in the sense that they only depend onU″(b).
Two-dimensional binary metal-oxide quasicrystal approximants
Authors: Huran Ahmad W , Wang Hai-Chen , Marques Miguel A L 
Published: June 2021

Abstract
We investigate, using a systematic computational approach, the possibility of the existence of two-dimensional quasicrystalline phases of binary metal-oxides. Our approach relies on the construction of the complete two-dimensional binary phase diagram through the use of unbiased global structural prediction methods. We then identify, in the low-energy periodic phases, structural elements that can be used to generate quasicrystalline phases through an inflation process. In this way we obtain chemically consistent two-dimensional quasicrystal approximants of both barium and titanium oxides. In the proposed structures, the metallic sites occupy the vertices of the aperiodic square-triangle tiling, while the oxygen atoms decorate the interior of the polygons. We then study the properties of the approximants, both free-standing and deposited on a metallic substrate. Finally, we discuss in which circumstances the formation of these phases seems to be favored.
Computing 𝐿-polynomials of Picard curves from Cartier–Manin matrices
Authors: Asif Sualeh , Fité Francesc , Pentland Dylan 
Published: June 2021

We study the sequence of zeta functions

Z
(

C
p

,
T
)

Z(C_p,T)

of a generic Picard curve

C
:

y
3

=
f
(
x
)

C:y^3=f(x)

defined over

Q

\mathbb {Q}

at primes

p
p

of good reduction for

C
C

. We define a degree 9 polynomial

ψ
f

∈

Q

[
x
]

\psi _f\in \mathbb {Q}[x]

such that the splitting field of

ψ
f

(

x
3

/

2
)

\psi _f(x^3/2)

is the

2
2

-torsion field of the Jacobian of

C
C

. We prove that, for all but a density zero subset of primes, the zeta function

Z
(

C
p

,
T
)

Z(C_p,T)

is uniquely determined by the Cartier–Manin matrix

A
p

A_p

of

C
C

modulo

p
p

and the splitting behavior modulo

p
p

of

f
f

and

ψ
f

\psi _f

; we also show that for primes

≡
1

(
mod

3
)

\equiv 1 \pmod {3}

the matrix

A
p

A_p

suffices and that for primes

≡
2

(
mod

3
)

\equiv 2 \pmod {3}

the genericity assumption on

C
C

is unnecessary. An element of the proof, which may be of independent interest, is the determination of the density of the set of primes of ordinary reduction for a generic Picard curve. By combining this with recent work of Sutherland, we obtain a practical deterministic algorithm that computes

Z
(

C
p

,
T
)

Z(C_p,T)

for almost all primes

p
≤
N

p \le N

using

N
log
⁡
(
N

)

3
+
o
(
1
)

N\log (N)^{3+o(1)}

bit operations. This is the first practical result of this type for curves of genus greater than 2.
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
Authors: Lee Joon-Yong , Bilbao Aivett , Conant Christopher R , Bloodsworth Kent J , Orton Daniel J , Zhou Mowei , Wilson Jesse W , Zheng Xueyun , Webb Ian K , Li Ailin , Hixson Kim K , Fjeldsted John C , Ibrahim Yehia M , Payne Samuel H , Jansson Christer , Smith Richard D , Metz Thomas O 
Published: June 2021

Abstract

Motivation
Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required.

Results
We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing.

Availability and implementation
https://github.com/PNNL-Comp-Mass-Spec/AutoCCS.

Supplementary information
Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).
Metabolo-epigenetics: the interplay of metabolism and epigenetics during early germ cells development†
Authors: Verdikt Roxane , Allard Patrick 
Published: June 2021

Abstract
Metabolites control epigenetic mechanisms, and conversly, cell metabolism is regulated at the epigenetic level in response to changes in the cellular environment. In recent years, this metabolo-epigenetic control of gene expression has been implicated in the regulation of multiple stages of embryonic development. The developmental potency of stem cells and their embryonic counterparts is directly determined by metabolic rewiring. Here, we review the current knowledge on the interplay between epigenetics and metabolism in the specific context of early germ cell development. We explore the implications of metabolic rewiring in primordial germ cells in light of their epigenetic remodeling during cell fate determination. Finally, we discuss the relevance of concerted metabolic and epigenetic regulation of primordial germ cells in the context of mammalian transgenerational epigenetic inheritance.
The tailor-made treatment in a particular case of pulmonary hypertension in thalassaemia intermedia: a case report
Authors: Blasi Federico B M , Rota Irene , Graziadei Giovanna , Vicenzi Marco 
Published: June 2021

Abstract

Background
Pulmonary hypertension (PH) is a haemodynamic condition, secondary to different causes. Thalassaemia may lead to PH of different origin and needs a comprehensive analysis to be correctly characterized and possibly treated.

Case summary
We present a case study of a patient with a non-transfusion-dependent thalassaemia and a previous diagnosis of group 5 PH. A complete diagnostic assessment led to a specific diagnosis of chronic thromboembolic PH. Thus, we were able to start a specific therapy with riociguat that provided an improvement in terms of haemodynamic, imaging, and functional status.

Discussion
A correct characterization and treatment of PH are essential in order to change the patient’s prognosis. Chronic thromboembolic PH is a treatable cause of PH in thalassemic patients and should be investigated.
The multiple mediating effects of social connectedness and self-care confidence on the relationship between subjective social status and emotional well-being in patients with heart failure: a cross-sectional study
Authors: Chen Cancan , Zhang Yanting , Zhao Qiuge , Wang Lyu , An Yan , Fan Xiuzhen 
Published: June 2021

Abstract

Background
Previous studies have shown that subjective social status (SSS) was positively associated with well-being in various populations. However, little is known about the relationship considering the underlying mechanism in patients with heart failure (HF).

Aims
The aim was to study the effects of social connectedness and self-care confidence on the relationship between SSS and well-being in patients with HF according to the Reserve Capacity Model.

Methods and results
We recruited 296 patients from a general hospital using convenience sampling. SSS, social connectedness, self-care confidence, and well-being were assessed using self-reported questionnaires. A multiple mediation model was examined using the PROCESS macro in SPSS.
Higher levels of SSS (r = 0.18, P &lt; 0.01), social connectedness (r = 0.21, P &lt; 0.01), and self-care confidence (r = 0.20, P &lt; 0.01) were positively correlated with better emotional well-being, but not with physical well-being. The multiple mediation analysis revealed that the relationship between SSS and emotional well-being was mediated by social connectedness (effect: 0.061, 95% CI [0.014, 0.148]) and self-care confidence (effect: 0.110, 95% CI [0.006, 0.249]) separately, and together in serial (effect: 0.008, 95% CI [0.001, 0.028]).

Conclusions
Social connectedness and self-care confidence are multiple mediators of the relationship between SSS and emotional well-being. Interventions targeting to strengthening social connectedness and self-care confidence may improve emotional well-being directly. In addition, emotional well-being may be improved by enhancing SSS indirectly in patients with HF.
Bacterial colonization of bladder urothelial cells in women with refractory Detrusor Overactivity: the effects of antibiotic therapy
Authors: Ognenovska S , Chen Z , Mukerjee C , Moore K H , Mansfield K J 
Published: June 2021

AbstractBacterial infection may have a pathophysiological role in refractory Detrusor Overactivity (DO). The aim of this study was to observe any impact of antibiotic therapy upon bacterial colonization of urothelial cells, and to determine whether a relationship existed between colonization and symptom severity. Mid-stream urine samples were collected as part of a clinical trial of antibiotics in women with refractory DO. Wright stained urothelial cells were categorized according to the degree of bacterial colonization as; ‘clear’ (free of bacteria), or as associated with bacteria that were ‘adjacent’ to the cell or ‘intracellular’ at low or high density. The average percentages were compared with routine microbiology cultures, over the 26 week trial, and with patient clinical outcome measures of DO severity. In patients receiving placebo, ‘high-density intracellular bacteria’ significantly increased during urinary tract infection (P = 0.0008). In antibiotic patients, ‘clear’ cells were more prevalent. Amoxicillin & Clavulanic Acid significantly decreased bacterial colonization within urothelial cells, suggesting that these antibiotics possess the greatest intracellular efficacy. ‘High-density intracellular bacteria’ positively correlated with symptom severity, measured by leakage on pad test (P = 0.014), leaks per day (P = 0.004), and voids per day (P = 0.005). Thus, by decreasing high density intracellular bacteria, antibiotic treatment may improve the refractory DO condition.
A screen for sleep and starvation resistance identifies a wake-promoting role for the auxiliary channel unc79
Authors: Murakami Kazuma , Palermo Justin , Stanhope Bethany A , Gibbs Allen G , Keene Alex C 
Published: June 2021

Abstract
The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in both the regulation of sleep and starvation resistance. Genetic knockdown or mutation of unc79 results in flies with increased sleep duration, as well as increased starvation resistance. Previous findings have shown that unc79 is required in pacemaker for 24-hours circadian rhythms. Here, we find that unc79 functions in the mushroom body, but not pacemaker neurons, to regulate sleep duration and starvation resistance. Together, these findings reveal spatially localized separable functions of unc79 in the regulation of circadian behavior, sleep, and metabolic function.
Smoothened and ARL13B are critical in mouse for superior cerebellar peduncle targeting
Authors: Suciu Sarah K , Long Alyssa B , Caspary Tamara 
Published: June 2021

AbstractPatients with the ciliopathy Joubert syndrome present with physical anomalies, intellectual disability, and a hindbrain malformation described as the “molar tooth sign” due to its appearance on an MRI. This radiological abnormality results from a combination of hypoplasia of the cerebellar vermis and inappropriate targeting of the white matter tracts of the superior cerebellar peduncles. ARL13B is a cilia-enriched regulatory GTPase established to regulate cell fate, cell proliferation, and axon guidance through vertebrate Hedgehog signaling. In patients, mutations in ARL13B cause Joubert syndrome. To understand the etiology of the molar tooth sign, we used mouse models to investigate the role of ARL13B during cerebellar development. We found that ARL13B regulates superior cerebellar peduncle targeting and these fiber tracts require Hedgehog signaling for proper guidance. However, in mouse, the Joubert-causing R79Q mutation in ARL13B does not disrupt Hedgehog signaling nor does it impact tract targeting. We found a small cerebellar vermis in mice lacking ARL13B function but no cerebellar vermis hypoplasia in mice expressing the Joubert-causing R79Q mutation. In addition, mice expressing a cilia-excluded variant of ARL13B that transduces Hedgehog normally showed normal tract targeting and vermis width. Taken together, our data indicate that ARL13B is critical for the control of cerebellar vermis width as well as superior cerebellar peduncle axon guidance, likely via Hedgehog signaling. Thus, our work highlights the complexity of ARL13B in molar tooth sign etiology.
Elder Mistreatment Methods and Measures in Round 3 of the National Social Life, Health, and Aging Project
Authors: Wong Jaclyn S , Howe Melissa J K , Breslau Hannah , Wroblewski Kristen E , McSorley V Eloesa , Waite Linda J 
Published: June 2021

Abstract

Objectives
Elder mistreatment has negative consequences for older adults’ health and well-being. As such, scholars aim to understand its causes, the contexts in which it occurs, how to prevent victimization, and how to design interventions for mistreated older adults. This paper provides a detailed overview of the 2015–2016 National Social Life, Health, and Aging Project (NSHAP) Round 3 Elder Mistreatment Module (EMM) to encourage further research on the topic.

Method
This paper reviews previous elder mistreatment scholarship, describes the EMM, provides descriptive analyses of elder mistreatment among community-dwelling older adults, and discusses promising approaches and limitations to future research with these data.

Results
The EMM includes 10 stem questions to measure elder mistreatment behaviors experienced since age 60 and 2 follow-up questions about perceived severity and the identity of the perpetrator. The stem questions can be analyzed individually or combined into a scale, and researchers can account for severity as a robustness check. Analysts can also group the measures into specific types of elder mistreatment. A major strength of the EMM is its ability to identify perpetrators in victims’ core social networks.

Discussion
The NSHAP Round 3 EMM provides scholars an opportunity to study older Americans’ mistreatment experiences, particularly as they relate to their physical and mental health, their social networks and personal relationships, and their broader social contexts.
Global Analysis of GG Systems
Authors: Matsubara-Heo Saiei-Jaeyeong 
Published: June 2021

Abstract
This paper deals with some analytic aspects of GG system introduced by I.M. Gelfand and M.I. Graev: we compute the dimension of the solution space of GG system over the field of meromorphic functions periodic with respect to a lattice. We describe the monodromy invariant subspace of the solution space. We provide a connection formula between a pair of bases consisting of $\Gamma $-series solutions of GG system associated with a pair of regular triangulations adjacent to each other in the secondary fan.
Increasing trust in real-world evidence through evaluation of observational data quality
Authors: Blacketer Clair , Defalco Frank J , Ryan Patrick B , Rijnbeek Peter R 
Published: June 2021

Abstract

Objective
Advances in standardization of observational healthcare data have enabled methodological breakthroughs, rapid global collaboration, and generation of real-world evidence to improve patient outcomes. Standardizations in data structure, such as use of common data models, need to be coupled with standardized approaches for data quality assessment. To ensure confidence in real-world evidence generated from the analysis of real-world data, one must first have confidence in the data itself.

Materials and Methods
We describe the implementation of check types across a data quality framework of conformance, completeness, plausibility, with both verification and validation. We illustrate how data quality checks, paired with decision thresholds, can be configured to customize data quality reporting across a range of observational health data sources. We discuss how data quality reporting can become part of the overall real-world evidence generation and dissemination process to promote transparency and build confidence in the resulting output.

Results
The Data Quality Dashboard is an open-source R package that reports potential quality issues in an OMOP CDM instance through the systematic execution and summarization of over 3300 configurable data quality checks.

Discussion
Transparently communicating how well common data model-standardized databases adhere to a set of quality measures adds a crucial piece that is currently missing from observational research.

Conclusion
Assessing and improving the quality of our data will inherently improve the quality of the evidence we generate.