bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stabilized time‐series expansions for high‐order finite element solutions of partial differential equations
Authors: Deeb Ahmad , Dutykh Denys 
Published: May 2024

AbstractOver the past decade, Finite Element Method (FEM) has served as a foundational numerical framework for approximating the terms of Time‐Series Expansion (TSE) as solutions to transient Partial Differential Equation (PDE). However, the application of high‐order Finite Element (FE) to certain classes of PDEs, such as diffusion equations and the Navier–Stokes (NS) equations, often leads to numerical instabilities. These instabilities limit the number of valid terms in the series, though the efficiency of time‐series integration even when resummation techniques like the Borel–Padé–Laplace (BPL) integrators are employed. In this study, we introduce a novel variational formulation for computing the terms of a TSE associated with a given PDE using higher‐order FEs. Our approach involves the incorporation of artificial diffusion terms on the left‐hand side of the equations corresponding to each power in the series, serving as a stabilization technique. We demonstrate that this method can be interpreted as a minimization of an energy functional, wherein the total variations of the unknowns are considered. Furthermore, we establish that the coefficients of the artificial diffusion for each term in the series obey a recurrence relation, which can be determined by minimizing the condition number of the associated linear system. We highlight the link between the proposed technique and the Discrete Maximum Principle (DMP) of the heat equation. We show, via numerical experiments, how the proposed technique allows having additional valid terms of the series that will be substantial in enlarging the stability domain of the BPL integrators.
In‐situ U‐Pb dating of calcite slickenfibre constraints on Cenozoic multiple‐phase faulting along the eastern segment of Chengkou Fault, Dabashan Fold‐and‐Thrust Belt
Authors: Tong Kui , Li Jinxi , Li Zhiwu , Uysal I. Tonguç , Zhao Jianxin , Feng Yuexing , Hua Tian , Liu Shugen 
Published: May 2024

AbstractThe Dabashan Fold‐and‐Thrust Belt is an important natural laboratory for exploring the Meso‐Cenozoic intracontinental orogenic evolution in China. Due to the severe lack of post‐Early Cretaceous strata, little attention has been paid to Cenozoic tectonic in the Dabashan. This study presents structural analysis, in‐situ U‐Pb dating of calcite in conjunction with petrographic and stable isotopic analyses along the eastern segment of the Chengkou Fault in the Dabashan. Structural analysis coupled with U‐Pb dating of syn‐kinematic calcite slickenfibres suggests two discrete S‐N compressional strike‐slip deformation events associated with localized E‐W extension along the eastern segment of the Chengkou Fault have occurred at the Early Eocene (~57–50 Ma) and Late Oligocene‐Early Miocene (~23–17 Ma), respectively. We tentatively related the Cenozoic deformation events in the study area to the clockwise rotation of the Sichuan Basin, resulting from the combined far‐field stress effects between the India, Eurasia and western Pacific plates.
GEUKE: A geographic entities uniformly explicit knowledge embedding model
Authors: Yang Yongquan , Kong Dehui , Cao Min , Chen Min 
Published: May 2024

AbstractKnowledge embedding for geographic knowledge graphs can effectively improve computational efficiency and provide support for knowledge reasoning, knowledge answering and other applications of knowledge graphs. To maintain a more comprehensive understanding of spatial features through knowledge embedding, it is crucial to integrate the representation and computation of various entity types, encompassing points, lines, and polygons. This article proposes a geographic entities uniformly explicit knowledge embedding model (GEUKE). In GEUKE, spatial data of point, line, and polygon‐type geographic entities are expressed in the form of subgraphs, and space embedding is generated using a SubGNN‐based uniform spatial feature encoder. GEUKE improves the energy function in TransE to train spatial feature‐based embedding and structural‐based embedding of geographic entities into a unified vector space. Experimental results show that GEUKE has higher performance than TransE, TransH, TransD, and TransE‐GDR on link prediction and triple classification task. Within the spatial feature embedding process, GEUKE effectively preserves the inherent features of entities, encompassing location, neighborhood, and structural attributes, while simultaneously ensuring a coherent spatial data representation across all three entity types: points, lines, and polygons. By maintaining the spatial features of geographic entities and their interrelations, this capability unleashes the full potential of applications such as knowledge reasoning and geospatial question answering in a manner that is conducive to diverse geospatial scenarios.
Retrospective evaluation of the effects of a single intraoperative dose of dexamethasone in horses undergoing exploratory laparotomy for small intestinal lesions (2008–2019): 240 cases
Authors: Tallon Rose E. , Allen Sarah E. , Bladon Bruce M. , McGovern Kate F. 
Published: May 2024

AbstractObjectiveTo determine the effect of a single intraoperative dose of dexamethasone on the risk of postoperative reflux (POR) in horses undergoing small intestinal surgery and to investigate its association with incisional complications and short‐term survival.DesignRetrospective cohort study over an 11‐year period (2008–2019).SettingUK‐based private referral center.AnimalsTwo hundred and forty client‐owned horses >6 months of age undergoing exploratory laparotomy for treatment of a small intestinal lesion.InterventionsNinety‐seven horses received a single intraoperative dose of dexamethasone (0.1 mg/kg, IV).Measurements and Main ResultsOf 97 horses that received dexamethasone, 52 (53.6%) required small intestinal resection. Of 143 horses that did not receive dexamethasone, small intestinal resection was performed in 78 (54.5%). A total of 70 horses (29%) developed POR. There was no difference in the risk of POR between horses that received dexamethasone (25/97; 26%) and those that did not (45/143; 31%, P = 0.34). Risk factors associated with the development of POR included small intestinal resection (odds ratio [OR]: 4.55, 95% confidence interval [CI]: 2.27–9.11, P < 0.001), a PCV >40% 24 hours postoperatively (OR: 4.11, 95% CI: 2–8.45, P < 0.001), and a WBC count >10 × 109/L on admission (OR: 3.29, 95% CI: 1.47–7.41, P = 0.004). Dexamethasone was not associated with the odds of POR. Horses undergoing repeat laparotomy had a higher risk of incisional infection (OR: 8.07, 95% CI: 1.98–32.81, P = 0.004). Dexamethasone administration was not associated with incisional infection. The development of POR was negatively associated with short‐term survival (OR: 0.07, 95% CI: 0.03–0.17, P ≤ 0.001). Dexamethasone administration was not retained in the final multivariable model for survival.ConclusionsIntraoperative dexamethasone was not associated with the development of POR in this study population, nor did it have an effect on postoperative survival or incisional infection in horses undergoing surgical management of small intestinal disease.
Retrospective evaluation of the utility of shock index to determine the presence of congestive heart failure in dogs with myxomatous mitral valve disease (2019–2021): 98 cases
Authors: Matson Hannah , Llewellyn Efa A. 
Published: May 2024

AbstractObjectivesTo calculate the shock index (SI) in dogs with myxomatous mitral valve disease (MMVD) and to evaluate its use to predict the presence of congestive heart failure (CHF).DesignRetrospective study.SettingSmall animal university veterinary teaching hospital.AnimalsNinety‐eight dogs with MMVD and 20 healthy dogs as part of a control group.InterventionsHeart rate (HR) and systolic blood pressure (SBP) were recorded, and SI was calculated by dividing HR by SBP for each dog.Measurements and Main ResultsThe mean (SD) HR, SBP, and SI were 123/min (32.6), 147 mm Hg (21.5), and 0.86 (0.3), respectively, for dogs with MMVD and 98/min (20.9), 145 mm Hg (18.7), and 0.68 (0.13), respectively, for control dogs. Dogs with MMVD had a significantly higher HR compared with control dogs (P < 0.01), and an elevation in HR was seen as the severity of MMVD increased. Dogs in stage B2 and C/D MMVD had a significantly higher SI value compared with control dogs (P = 0.04 and P < 0.01, respectively). SI was significantly higher in dogs in stage C/D MMVD compared with dogs in stage B2 MMVD (P < 0.01). Ten of 98 (10%) dogs had an arrhythmia. HR, SBP, and SI were not significantly different between dogs with and without arrhythmias (P = 0.13, P = 0.57, and P = 0.07, respectively), but significantly more dogs with CHF had an arrhythmia (P = 0.01). SI (area under the curve [AUC]: 0.98) and HR (AUC: 0.95) were excellent indicators for the presence of CHF. An optimal SI cutoff value ≥1.1 had 92% sensitivity and 95% specificity for predicting the presence of CHF, and an optimal HR cutoff value of ≥157/min had 92% sensitivity and 93% specificity for the prediction of CHF.ConclusionsWhen there are compatible clinical signs, SI values ≥1.1 may suggest the presence of CHF in dogs with MMVD.
A survey of medication and raw food use among canine blood donors
Authors: Holowaychuk Marie K. 
Published: May 2024

AbstractBackgroundBlood donors are screened for medication use to determine their health status and to ensure that the collection will be safe and efficacious for transfusion. Although stringent medication deferral guidelines exist for human blood donors, no consensus exists as to which medications should be permitted among canine donors.MethodsA brief survey regarding canine donor screening methods was distributed to an online hematology and transfusion medicine group and included questions pertaining to commonly prescribed medications and consumption of a raw food diet.Key FindingsThe survey results demonstrate that more than half of the respondents accept canine donors given thyroid supplements, whereas respondents were split as to whether they accept canine donors given antihistamines chronically. Most survey respondents exclude canine donors taking anti‐inflammatory or anti‐itch medications unless in acute circumstances and only after a washout period. More than half of the survey respondents exclude dogs fed a raw food diet.SignificanceThe survey results demonstrate that there is no obvious agreement regarding which medications to permit in canine donors. Evidence‐based guidelines are needed to inform best practices and the subsequent decisions made by donor programs.
Discrete spectrum of the magnetic Laplacian on perturbed half‐planes
Authors: Bonnaillie‐Noël Virginie , Fournais Søren , Kachmar Ayman , Raymond Nicolas 
Published: May 2024

AbstractThe existence of bound states for the magnetic Laplacian in unbounded domains can be quite challenging in the case of a homogeneous magnetic field. We provide an affirmative answer for almost flat corners and slightly curved half‐planes when the total curvature of the boundary is positive.
Discussion of “A Multi-Objective Comprehensive Evaluation of Heat Transfer Performance of a Direct-Contact Heat Exchanger” (Li, B., Yang, P., Li, Z., Xu, J., and Wang, H., 2023, ASME J. Therm. Sci. Eng. Appl., 15(1), p. 011014)
Authors: Awad M. M. 
Published: May 2024

Abstract
The units of entransy dissipation (G) in Nomenclature are wrong. Also, an opinion on the concept of entransy is presented.
Zafirlukast, as a viral inactivator, potently inhibits infection of several flaviviruses, including Zika virus, dengue virus, and yellow fever virus
Authors: Chen Yongkang , Li Yuan , Lu Lu , Zou Peng 
Published: May 2024

ABSTRACT

Zika virus (ZIKV) is one of the mosquito-borne flaviviruses that exhibits a unique tropism to nervous systems and is associated with Guillain-Barre syndrome and congenital Zika syndrome (CZS). Dengue virus (DENV) and yellow fever virus (YFV), the other two mosquito-borne flaviviruses, have also been circulating for a long time and cause severe diseases, such as dengue hemorrhagic fever and yellow fever, respectively. However, there are no safe and effective antiviral drugs approved for the treatment of infections or coinfections of these flaviviruses. Here, we found that zafirlukast, a pregnancy-safe leukotriene receptor antagonist, exhibited potent antiviral activity against infections of ZIKV strains from different lineages in diﬀerent cell lines, as well as against infections of DENV-2 and YFV 17D. Mechanistic studies demonstrated that zafirlukast directly and irreversibly inactivated these flaviviruses by disrupting the integrity of the virions, leading to the loss of viral infectivity, hence inhibiting the entry step of virus infection. Considering its efficacy against flaviviruses, its safety for pregnant women, and its neuroprotective effect, zafirlukast is a promising candidate for prophylaxis and treatment of infections or coinfections of ZIKV, DENV, and YFV, even in pregnant women.
Enhancing glucaric acid production from
myo
-inositol in
Escherichia coli
by eliminating cell-to-cell variation
Authors: Ding Nana , Sun Lei , Zhou Xuan , Zhang Linpei , Deng Yu , Yin Lianghong 
Published: May 2024

ABSTRACT

Glucaric acid (GA) is a value-added chemical and can be used to manufacture food additives, anticancer drugs, and polymers. The non-genetic cell-to-cell variations in GA biosynthesis are naturally inherent, indicating the presence of both high- and low-performance cells in culture. Low-performance cells can lead to nutrient waste and inefficient production. Furthermore,
myo
-inositol oxygenase (MIOX) is a key rate-limiting enzyme with the problem of low stability and activity in GA production. Therefore, eliminating cell-to-cell variations and increasing MIOX stability can select high-performance cells and improve GA production. In this study, an
in vivo
GA bioselector was constructed based on GA biosensor and tetracycline efflux pump protein TetA to continuously select GA-efficient production strains. Additionally, the upper limit of the GA biosensor was improved to 40 g/L based on ribosome-binding site optimization, achieving efficient enrichment of GA high-performance cells. A small ubiquitin-like modifier (SUMO) enhanced MIOX stability and activity. Overall, we used the GA bioselector and SUMO-MIOX fusion in fed-batch GA production and achieved a 5.52-g/L titer in
Escherichia coli
, which was 17-fold higher than that of the original strain.

IMPORTANCE

Glucaric acid is a non-toxic valuable product that was mainly synthesized by chemical methods. Due to the problems of non-selectivity, inefficiency, and environmental pollution, GA biosynthesis has attracted significant attention. The non-genetic cell-to-cell variations and MIOX stability were both critical factors for GA production. In addition, the high detection limit of the GA biosensor was a key condition for performing high-throughput screening of GA-efficient production strains. To increase GA titer, this work eliminated the cell-to-cell variations by GA bioselector constructed based on GA biosensor and TetA, and improved the stability and activity of MIOX in the GA biosynthetic pathway through fusing the SUMO to MIOX. Finally, these approaches improved the GA production by 17-fold to 5.52 g/L at 65 h. This study represents a significant step toward the industrial application of GA biosynthetic pathways in
E. coli
.
The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon
hdrBCA
in
Methanosarcina barkeri
Authors: Zhang Sicheng , Chen Yi , Wang Shuxin , Yang Qing , Leng Huan , Zhao Pengyan , Guo Leizhou , Dai Lirong , Bai Liping , Cha Guihong 
Published: May 2024

ABSTRACT

Methanogenic archaea play a key role in the global carbon cycle because these microorganisms remineralize organic compounds in various anaerobic environments. The microorganism
Methanosarcina barkeri
is a metabolically versatile methanogen, which can utilize acetate, methanol, and H
2
/CO
2
to synthesize methane. However, the regulatory mechanisms underlying methanogenesis for different substrates remain unknown. In this study, RNA-seq analysis was used to investigate
M. barkeri
growth and gene transcription under different substrate regimes. According to the results,
M. barkeri
showed the best growth under methanol, followed by H
2
/CO
2
and acetate, and these findings corresponded well with the observed variations in genes transcription abundance for different substrates. In addition, we identified a novel regulator, MSBRM_RS03855 (designated as HdrR), which specifically activates the transcription of the heterodisulfide reductase
hdrBCA
operon in
M. barkeri
. HdrR was able to bind to the
hdrBCA
operon promoter to regulate transcription. Furthermore, the structural model analyses revealed a helix-turn-helix domain, which is likely involved in DNA binding. Taken together, HdrR serves as a model to reveal how certain regulatory factors control the expression of key enzymes in the methanogenic pathway.

IMPORTANCE

The microorganism
Methanosarcina barkeri
has a pivotal role in the global carbon cycle and contributes to global temperature homeostasis. The consequences of biological methanogenesis are far-reaching, including impacts on atmospheric methane and CO
2
concentrations, agriculture, energy production, waste treatment, and human health. As such, reducing methane emissions is crucial to meeting set climate goals. The methanogenic activity of certain microorganisms can be drastically reduced by inhibiting the transcription of the
hdrBCA
operon, which encodes heterodisulfide reductases. Here, we provide novel insight into the mechanisms regulating
hdrBCA
operon transcription in the model methanogen
M. barkeri
. The results clarified that HdrR serves as a regulator of heterodisulfide reductase
hdrBCA
operon transcription during methanogenesis, which expands our understanding of the unique regulatory mechanisms that govern methanogenesis. The findings presented in this study can further our understanding of how genetic regulation can effectively reduce the methane emissions caused by methanogens.
Biological puzzles solved by using
Streptococcus pneumoniae
: a historical review of the pneumococcal studies that have impacted medicine and shaped molecular bacteriology
Authors: Hiller N. Luisa , Orihuela Carlos J. 
Published: May 2024

ABSTRACT

The major human pathogen
Streptococcus pneumoniae
has been the subject of intensive clinical and basic scientific study for over 140 years. In multiple instances, these efforts have resulted in major breakthroughs in our understanding of basic biological principles as well as fundamental tenets of bacterial pathogenesis, immunology, vaccinology, and genetics. Discoveries made with
S. pneumoniae
have led to multiple major public health victories that have saved the lives of millions. Studies on
S. pneumoniae
continue today, where this bacterium is being used to dissect the impact of the host on disease processes, as a powerful cell biology model, and to better understand the consequence of human actions on commensal bacteria at the population level. Herein we review the major findings, i.e., puzzle pieces, made with
S. pneumoniae
and how, over the years, they have come together to shape our understanding of this bacterium’s biology and the practice of medicine and modern molecular biology.
Identification and characterization of zinc importers in
Corynebacterium diphtheriae
Authors: Peng Eric D. , Lyman Lindsey R. , Schmitt Michael P. 
Published: May 2024

ABSTRACT

Corynebacterium diphtheriae
is the causative agent of diphtheria, a severe respiratory disease in humans.
C. diphtheriae
colonizes the human upper respiratory tract, where it acquires zinc, an essential metal required for survival in the host. While the mechanisms for zinc transport by
C. diphtheriae
are not well characterized, four putative zinc ABC-type transporter loci were recently identified in strain 1737:
iutABCD/E
(
iut
),
znuACB
(
znu
),
nikABCD1
(
nik1
), and
nikABCD2
(
nik2
). A mutant deleted for all four loci (Δ4) exhibited similar growth to that of the wild-type strain in a zinc-limited medium, suggesting there are additional zinc transporters. Two additional gene loci predicted to be associated with metal import,
mntABCD
(
mnt
) and
sidAB
(
sid
)
,
were deleted in the Δ4 mutant to construct a new mutant designated Δ6. The
C. diphtheriae
Δ6 mutant exhibited significantly reduced growth under zinc limitation relative to the wild type, suggesting a deficiency in zinc acquisition. Strains retaining the
iut
,
znu
,
mnt,
or
sid
loci grew to near-wild-type levels in the absence of the other five loci, indicating that each of these transporters may be involved in zinc uptake. Plasmid complementation with cloned
iut
,
znu
,
mnt
, or
nik1
loci also enhanced the growth of the Δ6 mutant. Quantification of intracellular zinc content by inductively coupled plasma mass spectrometry was consistent with reduced zinc uptake by Δ6 relative to the wild type and further supports a zinc uptake function for the transporters encoded by
iut
,
znu
, and
mnt
. This study demonstrates that
C. diphtheriae
zinc transport is complex and involves multiple zinc uptake systems.

IMPORTANCE

Zinc is a critical nutrient for all forms of life, including human bacterial pathogens. Thus, the tools that bacteria use to acquire zinc from host sources are crucial for pathogenesis. While potential candidates for zinc importers have been identified in
Corynebacterium diphtheriae
from gene expression studies, to date, no study has clearly demonstrated this function for any of the putative transporters. We show that
C. diphtheriae
encodes at least six loci associated with zinc import, underscoring the extent of redundancy for zinc acquisition. Furthermore, we provide evidence that a previously studied manganese-regulated importer can also function in zinc import. This study builds upon our knowledge of bacterial zinc transport mechanisms and identifies potential targets for future diphtheria vaccine candidates.