bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photophysical properties and sensing mechanism of fluorescent coumarin–chalcone hybrid for biothiols: A theoretical study
Authors: Zhang Ling , Chen Mohan , Li Zheng , Teng Yangxin , Wang Guirong , Xue Yunsheng 
Published: February 2022

AbstractThe photophysical properties and sensing mechanism of a novel coumarin–chalcone hybrid fluorescent probe (CCH) for biothiols were investigated by density functional theory (DFT) and time‐dependent density functional theory (TDDFT) methods. The theoretical calculations well reproduced the experimental spectra and clarified the experimental observed fluorescence “on–off” switching. Potential energy surface (PES) results revealed that the excited‐state intramolecular proton transfer (ESIPT) process is thermodynamically and kinetically viable for CCH, with the keto form more stable than the enol form. ESIPT process and the significant changes of the orbital energies should be responsible for the red fluorescence of CCH. The results revealed that the lowest lying transition of probe CCH corresponds to electronic transition between HOMO and LUMO with charge transfer (CT) character. The addition of cysteine to CCH breaks the conjugation and the intramolecular CT. A nonclassical photoinduced electron transfer (PET) process should contribute to the fluorescence quenching of CCH‐Cys. Thermodynamic and kinetic calculations on the recognition reaction predicted a moderate Gibbs free energy barrier, which proves the possibility of the Michael addition reaction and induces the rapid response of the probe CCH for cysteine.
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery
Authors: Firouzi Rohoullah , Ashouri Mitra , Karimi‐Jafari Mohammad Hossein 
Published: February 2022

AbstractAn attractive drug target to combat COVID‐19 is the main protease (Mpro) because of its key role in the viral life cycle by processing the polyproteins translated from the viral RNA. Studying the crystal structures of the protease is important to enhance our understanding of its mechanism of action at the atomic‐level resolution, and consequently may provide crucial structural insights for structure‐based drug discovery. In the current study, we report a comparative structural analysis of the Mpro substrate binding site for both apo and holo forms to identify key interacting residues and conserved water molecules during the ligand‐binding process. It is shown that in addition to the catalytic dyad residues (His41 and Cys145), the oxyanion hole residues (Asn142–Ser144) and residues His164–Glu166 form essential parts of the substrate‐binding pocket of the protease in the binding process. Furthermore, we address the issue of the substrate‐binding pocket flexibility and show that two adjacent loops in the Mpro structures (residues Thr45–Met49 and Arg188–Ala191) with high flexibility can regulate the binding cavity’ accessibility for different ligand sizes. Moreover, we discuss in detail the various structural and functional roles of several important conserved and mobile water molecules within and around the binding site in the proper enzymatic function of Mpro. We also present a new docking protocol in the framework of the ensemble docking strategy. The performance of the docking protocol has been evaluated in predicting ligand binding pose and affinity ranking for two popular docking programs; AutoDock4 and AutoDock Vina. Our docking results suggest that the top‐ranked poses of the most populated clusters obtained by AutoDock Vina are the most important representative docking runs that show a very good performance in estimating experimental binding poses and affinity ranking.
Composite optimization with coupling constraints via dual proximal gradient method with applications to asynchronous networks
Authors: Wang Jianzheng , Hu Guoqiang 
Published: February 2022

AbstractIn this article, we consider solving a composite optimization problem with affine coupling constraints in a multi‐agent network based on proximal gradient method. In this problem, all the agents jointly minimize the sum of individual cost functions composed of smooth and possibly non‐smooth parts. To this end, we derive the dual problem by the concept of Fenchel conjugate, which gives rise to the dual proximal gradient (DPG) algorithm by allowing for the asymmetric individual interpretations of the coupling constraints. Then, an asynchronous DPG (Asyn‐DPG) algorithm is proposed for the asynchronous networks with heterogeneous step‐sizes and communication delays. For both the two algorithms, if the non‐smooth parts of the objective functions are simple‐structured, we only need to update dual variables by some simple operations, accounting for the reduction of the overall computational complexity. Analytical convergence rate of the proposed algorithms is derived and their efficacy is verified by solving a social welfare optimization problem of electricity market in the numerical simulation.
Monitoring invasive alien macroinvertebrate species with environmental DNA
Authors: Blackman Rosetta C. , Brantschen Jeanine , Walser Jean‐Claude , Wüthrich Remo , Altermatt Florian 
Published: February 2022

AbstractRegular monitoring of ecosystems can be used for the early detection of invasive alien species (IAS), and provide information for management and preventing them from becoming established or advancing into new areas. Current methods of monitoring freshwater systems for IAS can be both financially costly and time‐consuming, with routine monitoring often carried out at low intensity and at only a small number of sites. In this study, we evaluate how environmental DNA (eDNA) metabarcoding for monitoring freshwater macroinvertebrate IAS compares to traditional kick‐net sampling as part of a national (Switzerland) and a catchment monitoring programme. Kick‐net sampling was more fruitful for the detection of several well‐known target macroinvertebrate IAS. However, eDNA samples proved complementary for the detection of IAS that belong to species often being unnoticed by traditional sampling due to methodological or taxonomic reasons. Specifically, the invasive jellyfish Craspedacusta sowerbii, hardly detectable using classic kick‐net sampling, was found to be widespread in both the national and the catchment‐scale monitoring with the eDNA method only. Our study shows that IAS detection using eDNA is easily implemented in both national‐ and catchment‐scale monitoring campaigns. However, successful detection of target IAS is still highly dependent on primer choice, species' biology, and availability of adequate markers. Specifically, multiple markers should be considered for detecting IAS from several different taxonomic groups, such as those under the ‘freshwater macroinvertebrate’ umbrella term. While eDNA is still developing in terms of these fundamental methodological requirements, surveillance for both target and non‐target IAS using eDNA is likely to increase efficiency in early detection of IAS in freshwater systems.
Teachers' ability to diagnose and deal with alternative student conceptions of evolution
Authors: Hartelt Tim , Martens Helge , Minkley Nina 
Published: February 2022

AbstractStudents possess alternative conceptions of many science topics, and these conceptions can act as obstacles for learning scientific concepts. In the field of biology education, students' alternative conceptions of evolution have been widely investigated. However, there is little research on how teachers diagnose and deal with these alternative conceptions, although these abilities are a crucial part of teachers' pedagogical content knowledge. Additionally, little is known about how these abilities are connected to professional experience and content knowledge. Thus, our study investigated how (prospective) biology teachers at various points in their teaching careers diagnosed and reported dealing with alternative conceptions. Therefore, 182 preservice biology teachers, biology teachers in practical training, and in‐service biology teachers were surveyed using a questionnaire. The participants were confronted with students' explanations of evolutionary phenomena, most of them based on common student conceptions, such as anthropomorphism, teleology, and essentialism. These student conceptions are rooted in cognitive biases and are common in evolutionary and other contexts. We found that the participants diagnosed only approximately half of the alternative conceptions, with the in‐service teachers diagnosing significantly more of the alternative conceptions than the preservice teachers. Furthermore, the analyses revealed a variety of ways to deal with student conceptions. The in‐service teachers more often suggested scientifically correct approaches that address student conceptions, whereas the preservice teachers more often did not respond or responded incorrectly. Moreover, the ability to diagnose and deal with alternative conceptions correlated with teachers' content knowledge regarding the topic of evolution and their acceptance of evolution.
SO2F2‐Promoted Dehydroxylative Fluorination of Alcohols
Authors: Zhang Guofu , Wang Huimin , Wu Wenliang , Fan Qiankun , Ding Chengrong 
Published: February 2022

AbstractReported here is the development of a novel, mild and practical protocol for the SO2F2‐promoted dehydroxylative fluorination of readily available alcohols. The advantages of this protocol include an inexpensive and available reagent, and operational simplicity. This method enables the transformation of many kinds of primary, secondary and tertiary (hetero) arene alcohols into the corresponding fluorides and tolerates a range of functional groups. And the reactions occur smoothly to give the desired products in moderate to high yields. And a tentative mechanism was proposed involving formation and elimination of key intermediate, sulfonyl ester.
Leaf mold compost reduces waste, improves soil and microbial properties, and increases tomato productivity
Authors: Richardville Kyle , Egel Dan , Flachs Andrew , Jaiswal Amit , Perkins Dan , Thompson Aaron , Hoagland Lori 
Published: February 2022

AbstractSoils in urban settings are often degraded, which can prevent growers from optimizing the health and productivity of their crops. In this study, we investigated whether amending soil with a locally made leaf‐mold compost could (a) improve soil chemical and biological properties, (b) increase survival of a microbial inoculant with plant growth promoting and disease suppressive capabilities, and (c) enhance the yield and quality of a tomato crop. Results were promising, with dramatically greater concentrations of active soil organic matter (SOM) and marketable fruit in plots receiving the amendment in both years of the study. Foliar disease severity was also lower in compost‐amended plots in the second year of the trial. Inoculating tomato (Solanum lycopersicum L.) transplants with Trichoderma harzianum T‐22 reduced deaths that are due to transplant stress in one of the cultivars evaluated, and the compost supported greater populations of this microbe in soil demonstrating that it is possible to enhance the efficacy of beneficial microbial inoculants in field settings using targeted practices. These results indicate that urban farmers can improve the productivity of their farms by amending soils with leaf mold compost, which will help ensure the long‐term sustainability of urban farming initiatives. However, all composts should be tested to ensure they do not contain toxic levels of heavy metals or pathogens, and farmers should avoid overapplication since this can reduce crop health and lead to environmental challenges.
Climate change and phenology
Authors: Inouye David W. 
Published: February 2022

AbstractClimate change is a defining element of the current ecological landscape, with consequences ranging from global to local environments. One of the first indices of the ecological impact of the ongoing environmental changes was measurement of their effects on phenology, the seasonal timing of recurring annual events such as the beginning of the growing season, timing of flowering, and breeding seasons of animals. Research has moved beyond simple descriptions of these temporal changes to investigations of their root causes, impacts, and consequences at both ecological and evolutionary time scales. This changing landscape, environmental, ecological, and evolutionary, makes this an exciting, albeit sometimes depressing, time to be a scientist.This article is categorized under:
Assessing Impacts of Climate Change > Observed Impacts of Climate Change
Climate, Ecology, and Conservation > Observed Ecological Changes
Environmental Stress in Military Settings
Authors: Sullivan-Kwantes Wendy , Cramer Matthew , Bouak Fethi , Goodman Leonard 
Published: February 2022

AbstractDuring military training and operations, exposure to extremes of noise, temperature, humidity, pressure, or acceleration can induce levels of physiological strain that degrade cognitive and physical capabilities, threaten health and safety, and affect behavior and performance. The overarching purpose of this chapter is to discuss the impact of environmental stress on military personnel. Because each of the aforementioned stressors induces disparate effects, each section addresses a unique stressor in terms of (i) the nature of the threat, (ii) physiological and biomedical effects, (iii) the impact on performance, and (iv) management strategies. The evolution of next-generation wearable biosensors, smart performance algorithms, and scientifically based operational training methods including stress inoculation exposure that will contribute to improved training, adaptation, and tolerance to these operational stresses is discussed.
Toroidal and elliptic quiver BPS algebras and beyond
Authors: Galakhov Dmitry , Li Wei , Yamazaki Masahito 
Published: February 2022

Abstract
The quiver Yangian, an infinite-dimensional algebra introduced recently in [1], is the algebra underlying BPS state counting problems for toric Calabi-Yau three-folds. We introduce trigonometric and elliptic analogues of quiver Yangians, which we call toroidal quiver algebras and elliptic quiver algebras, respectively. We construct the representations of the shifted toroidal and elliptic algebras in terms of the statistical model of crystal melting. We also derive the algebras and their representations from equivariant localization of three-dimensional $$ \mathcal{N} $$
N
= 2 supersymmetric quiver gauge theories, and their dimensionally-reduced counterparts. The analysis of supersymmetric gauge theories suggests that there exist even richer classes of algebras associated with higher-genus Riemann surfaces and generalized cohomology theories.
Bootstrap bounds on closed hyperbolic manifolds
Authors: Bonifacio James 
Published: February 2022

AbstractThe eigenvalues of the Laplace-Beltrami operator and the integrals of products of eigenfunctions must satisfy certain consistency conditions on compact Riemannian manifolds. These consistency conditions are derived by using spectral decompositions to write quadruple overlap integrals in terms of products of triple overlap integrals in multiple ways. In this paper, we show how these consistency conditions imply bounds on the Laplacian eigenvalues and triple overlap integrals of closed hyperbolic manifolds, in analogy to the conformal bootstrap bounds on conformal field theories. We find an upper bound on the gap between two consecutive nonzero eigenvalues of the Laplace-Beltrami operator in terms of the smaller eigenvalue, an upper bound on the smallest eigenvalue of the rough Laplacian on symmetric, transverse-traceless, rank-2 tensors, and bounds on integrals of products of eigenfunctions and eigentensors. Our strongest bounds involve numerically solving semidefinite programs and are presented as exclusion plots. We also prove the analytic boundλi+1≤ 1/2 + 3λi+$$ \sqrt{\lambda_i^2+2{\lambda}_i+1/4} $$λi2+2λi+1/4for consecutive nonzero eigenvalues of the Laplace-Beltrami operator on closed orientable hyperbolic surfaces. We give examples of genus-2 surfaces that nearly saturate some of these bounds. To derive the consistency conditions, we make use of a transverse-traceless decomposition for symmetric tensors of arbitrary rank.
Non-decoupling new particles
Authors: Banta Ian , Cohen Timothy , Craig Nathaniel , Lu Xiaochuan , Sutherland Dave 
Published: February 2022

Abstract
We initiate the study of a new class of beyond the Standard Model states that we call “Loryons.” They have the defining characteristic of being non-decoupling, in the sense that their physical mass is dominated by a contribution from the vacuum expectation value of the Higgs boson. The stakes are high: the discovery of a Loryon would tell us that electroweak symmetry must be non-linearly realized in the effective field theory of the Standard Model. Loryons have their masses bounded from above by perturbative unitarity considerations and thus define a finite parameter space for exploration. After providing a complete catalog of Loryon representations under mild assumptions, we turn to examining the constraints on the parameter space from Higgs couplings measurements, precision electroweak tests, and direct collider searches. We show that most fermionic candidates are already ruled out (with some notable exceptions), while much of the scalar Loryon parameter space is still wide open for discovery.
Coupled Domain-Boundary Variational Formulations for Hodge–Helmholtz Operators
Authors: Schulz Erick , Hiptmair Ralf 
Published: February 2022

AbstractWe couple the mixed variational problem for the generalized Hodge–Helmholtz or Hodge–Laplace equation posed on a bounded 3D Lipschitz domain with the first-kind boundary integral equations arising from the latter when constant coefficients are assumed in the unbounded complement. Recently developed Calderón projectors for the relevant boundary integral operators are used to perform a symmetric coupling. We prove stability of the coupled problem away from resonant frequencies by establishing a generalized Gårding inequality (T-coercivity). The resulting system of equations describes the scattering of monochromatic electromagnetic waves at a bounded inhomogeneous isotropic body possibly having a “rough” surface. The low-frequency robustness of the potential formulation of Maxwell’s equations makes this model a promising starting point for Galerkin discretization.
On simultaneous linearization of certain commuting nearly integrable diffeomorphisms of the cylinder
Authors: Chen Qinbo , Damjanović Danijela , Petković Boris 
Published: February 2022

AbstractLet $$\mathcal {F}$$
F
and $$\mathcal {K}$$
K
be commuting $$C^\infty $$

C
∞

diffeomorphisms of the cylinder $$\mathbb {T}\times \mathbb {R}$$

T
×
R

that are, respectively, close to $$\mathcal {F}_0 (x, y)=(x+\omega (y), y)$$

F
0

(
x
,
y
)

=

(
x
+
ω

(
y
)

,
y
)

and $$T_\alpha (x, y)=(x+\alpha , y)$$

T
α

(
x
,
y
)

=

(
x
+
α
,
y
)

, where $$\omega (y)$$

ω
(
y
)

is non-degenerate and $$\alpha $$
α
is Diophantine. Using the KAM iterative scheme for the group action we show that $$\mathcal {F}$$
F
and $$\mathcal {K}$$
K
are simultaneously $$C^\infty $$

C
∞

-linearizable if $$\mathcal {F}$$
F
has the intersection property (including the exact symplectic maps) and $$\mathcal {K}$$
K
satisfies a semi-conjugacy condition. We also provide examples showing necessity of these conditions. As a consequence, we get local rigidity of certain class of $$\mathbb {Z}^2$$

Z

2

-actions on the cylinder, generated by commuting twist maps.
Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics
Authors: Salek Mogjiborahman , Förster Jonas D. , Lehmann Wolf-Dieter , Riemer Angelika B. 
Published: February 2022

Abstract
In mass spectrometry-based proteomics, heavy internal standards are used to validate target peptide detections and to calibrate peptide quantitation. Here, we report light contamination present in heavy labelled synthetic peptides of high isotopic enrichment. Application of such peptides as assay-internal standards potentially compromises the detection and quantitation especially of low abundant cellular peptides. Therefore, it is important to adopt guidelines to prevent false-positive identifications of endogenous light peptides as well as errors in their quantitation from biological samples.
Loss of luminal carbonic anhydrase XIV results in decreased biliary bicarbonate output, liver fibrosis, and cholangiocyte proliferation in mice
Authors: Zhou Zhenzhen , Qian Jiajie , Kini Archana , Riederer Brigitte , Römermann Dorothee , Gros Gerolf , Seidler Ursula 
Published: February 2022

AbstractCarbonic anhydrase XIV (Car14) is highly expressed in the hepatocyte, with predominance in the canalicular membrane and its active site in the extracellular milieu. The aim of this study is to determine the physiological relevance of Car14 for biliary fluid and acid/base output, as well as its role in the maintenance of hepatocellular and cholangiocyte integrity. The common bile duct of anesthetized car14−/− and car14+/+ mice was cannulated and hepatic HCO3− output was measured by microtitration and bile flow gravimetrically before and during stimulation with intravenously applied tauroursodeoxycholic acid (TUDCA). Morphological alterations and hepatic damage were assessed histologically and immunohistochemically in liver tissue from 3- to 52-week-old car14−/− and car14+/+ mice, and gene and/or protein expression was measured for pro-inflammatory cytokines, fibrosis, and cholangiocyte markers. Biliary basal and more so TUDCA-stimulated HCO3− output were significantly reduced in car14−/− mice of all age groups, whereas bile flow and hepatic and ductular morphology were normal at young age. Car14−/− mice developed fibrotic and proliferative changes in the small bile ducts at advanced age, which was accompanied by a reduction in bile flow, and an upregulation of hepatic cytokeratin 19 mRNA and protein expression. Membrane-bound Car14 is essential for biliary HCO3− output, and its loss results in gradual development of small bile duct disease and hepatic fibrosis. Bile flow is not compromised in young adulthood, suggesting that Car14-deficient mice may be a model to study the protective role of biliary canalicular HCO3− against luminal noxi to the cholangiocyte.
Pararectus approach to the AO B2.2 pelvic fracture: early functional and radiological outcomes
Authors: Yu Yi-Hsun , Liu Chang-Heng , Hsu Yung-Heng , Chou Ying-Chao , Chen I-Jung 
Published: February 2022

Abstract
Purpose
The pararectus approach is used to treat acetabular fractures; however, it remains unclear whether it can be used to treat pelvic fractures. This study aimed to examine the outcomes of patients with a pelvic ring fracture treated with this approach.

Methods
Seven patients with AO B2.2 pelvic fractures treated with the pararectus approach were included. Patients’ pain was assessed pre- and postoperatively with a numerical rating scale. Radiological evaluations included inlet and outlet ratios and pelvic symmetry. Functional outcomes, including Merle d’Aubigné and Majeed scores, were also recorded for 12 months.

Results
One patient experienced obturator nerve neuropraxia. Pain scores ranged from 2.3–8.0 to 2.0–3.1 points before and after surgery, respectively. Radiological findings revealed satisfactory outcomes. The maximal gap of the affected ilium reduced from 8.6–20.2 to 0–3.4 mm, from 6.8–17.9 to 0–4.4 mm, and from 3.7–20.3 to 0–3.2 mm in the axial, sagittal, and coronal views, respectively. Based on multiple evaluations, functional outcomes were improved for all patients.

Conclusion
The pararectus approach can be used safely and satisfactorily to treat AO B 2.2 pelvic fractures.