bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Deep Learning Model for Automated Segmentation of Fluorescence Cell images
Authors: Aydın Musa , Kiraz Berna , Eren Furkan , Uysallı Yiğit , Morova Berna , Can Ozcan Selahattin , Acilan Ceyda , Kiraz Alper 
Published: February 2022

Abstract
Deep learning techniques bring together key advantages in biomedical image segmentation. They speed up the process, increase the reproducibility, and reduce the workload in segmentation and classifcation. Deep learning techniques can be used for analysing cell concentration, cell viability, as well as the size and form of each cell. In this study, we develop a deep learning model for automated segmentation of fuorescence cell images, and apply it to fuorescence images recorded with a home-built epi-fuorescence microscope. A deep neural network model based on U-Net architecture was built using a publicly available dataset of cell nuclei images [1]. A model accuracy of 97.3% was reached at the end of model training. Fluorescence cell images acquired with our home-built microscope were then segmented using the developed model. 141 of 151 cells in 5 images were successfully segmented, revealing a segmentation success rate of 93.4%. This deep learning model can be extended to the analysis of diferent cell types and cell viability.
A remarkable dynamical symmetry of the Landau problem
Authors: Dereli Tekin , Nounahon Philippe , Popov Todor 
Published: February 2022

AbstractWe show that the dynamical group of an electron in a constant magnetic feld is the group of symplectomorphisms Sp(4, R). It is generated by the spinorial realization of the conformal algebra so(2,3) considered in Dirac’s seminal paper ”A Remarkable Representation of the 3 + 2 de Sitter Group”. The symplectic groupSp(4,R) is the double covering of the conformal groupSO(2,3) of 2+1 dimensional Minkowski spacetime which is in turn the dynamical group of a hydrogen atom in 2 space dimensions. The Newton-Hooke duality between the 2D hydrogen atom and the Landau problem is explained via the Tits-Kantor-Koecher construction of the conformal symmetries of the Jordan algebra of real symmetric 2 × 2 matrices. The connection between the Landau problem and the 3D hydrogen atom is elucidated by the reduction of a Dirac spinor to a Majorana one in the Kustaanheimo-Stiefel spinorial regularization.
Dark Range of ω In Brans-Dicke Gravity
Authors: Dereli Tekin , Şenikoğlu Yorgo 
Published: February 2022

Abstract
The variational field equations of Brans-Dicke scalar-tensor theory of gravitation that is coupled to a mass-varying sterile neutrino field are presented in Riemannian and non-Riemannian setting in the language of exterior differential forms over four-dimensional spacetime. In a gravitational plane wave geometry in Rosen coordinates, with the scalar field set equal to a constant, the field equations admit ghost neutrino solutions. These correspond to Majorana spinor configurations for which the total neutrino stress-energy-momentum tensor vanishes. We show here that in the absence of a sterile neutrino in the gravitational wave geometry, there are scalar field configurations for which the total scalar field stress-energy-momentum tensor vanishes for negative values of the Brans-Dicke parameter —3/2 < ω < 0.
Statistical geometry and Hessian structures on pre-Leibniz algebroids
Authors: Dogan Keremcan 
Published: February 2022

Abstract
We introduce statistical, conjugate connection and Hessian structures on anti-commutable pre-Leibniz algebroids. Anti-commutable pre-Leibniz algebroids are special cases of local pre-Leibniz algebroids, which are still general enough to include many physically motivated algebroids such as Lie, Courant, metric and higher-Courant algebroids. They create a natural framework for generalizations of differential geometric structures on a smooth manifold. The symmetrization of the bracket on an anti-commutable pre-Leibniz algebroid satisfies a certain property depending on a choice of an equivalence class of connections which are called admissible. These admissible connections are shown to be necessary to generalize aforementioned structures on pre-Leibniz algebroids. Consequently, we prove that, provided certain conditions are met, statistical and conjugate connection structures are equivalent when defined for admissible connections. Moreover, we also show that for ‘projected-torsion-free’ connections, one can generalize Hessian metrics and Hessian structures. We prove that any Hessian structure yields a statistical structure, where these results are completely parallel to the ones in the manifold setting. We also prove a mild generalization of the fundamental theorem of statistical geometry. Moreover, we generalize a-connections, strongly conjugate connections and relative torsion operator, and prove some analogous results.
Echoes from the event horizon of a superfluid vortex
Authors: Güven K , Demirkaya B 
Published: February 2022

Abstract
A vortex formed in the superfluid state of a Bose-Einstein condensate may exhibit superradiance a la blackhole for radially propagating acoustic fluctuations. The analogy is usually based on the so-called draining bathtub model of the vortex, in which an event horizon and ergosphere emerges when the radial velocity of the superfluid exceeds the propagation speed of sound in the condensate. The acoustic fluctuations mimic a massless scalar field in the curved Lorentzian space-time of the vortex and are governed by the Klein-Gordon wave equation. One common main approximation is the constant background density of the superfluid even in the presence of the vortex. This sets a constant relativistic sound speed. However, the vortex state solution of the Gross-Pitaevskii equation clearly shows that both the density and the speed of sound vary radially near the vortex core, where the event horizon and thus the superradiance will take place. What changes would this complex interdependence bring to the formulation and to the outcomes of the superradiance based on constant density approximation? Here, we recount this question posed under the guidance of Prof. Tekin Dereli and present recent results. We show that the self-consistent density modifies the amplification dynamics near the event horizon significantly, thereby altering the temporal and spectral fingerprint of the superradiance of the vortex.
A novel approach to autoparallels for the theories of symmetric teleparallel gravity
Authors: Pala Caglar , Adak Muzaffer 
Published: February 2022

Abstract
Although the autoparallel curves and the geodesics coincide in the Riemannian geometry in which only the curvature is nonzero among the nonmetricity, the torsion and the curvature, they define different curves in the non-Riemannian ones. We give a novel approach to autoparallel curves and geodesics for theories of the symmetric teleparallel gravity written in the coincident gauge. Then we apply our autoparallel equation to a Schwarzschild-type metric and give remarks about dark matter and orbit equation.
Quantum Correlations in Jahn-Teller Molecular Systems Simulated with Superconducting Circuits
Authors: Pedram AH , Pusuluk Onur , Müstecaphog`lu Özgür E. 
Published: February 2022

Abstract
We explore quantum correlations, in particular, quantum entanglement, among vibrational phonon modes as well as between electronic and vibrational degrees of freedom in molecular systems, described by Jahn-Teller mechanism. Specifically, to isolate and simplify the phonon- electron interactions in a complex molecular system, the basis of our discussions is taken to be the proposal of simulating two-frequency Jahn- Teller systems using superconducting circuit quantum electrodynamics systems (circuit QED) by Tekin Dereli and co-workers in 2012. We evaluate the quantum correlations, in particular entanglement between the vibrational phonon modes, and present analytical explanations using a single privileged Jahn-Teller mode picture. Furthermore, spin-orbit entanglement or quantum correlations between electronic and vibrational degrees of freedom are examined. We conclude by discussing experimental feasibility to detect such quantum correlations, considering the dephasing and decoherence in state-of-the-art superconducting two-level systems (qubits).
Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction
Authors: Wee JunJie , Xia Kelin 
Published: February 2022

AbstractProtein–protein interactions (PPIs) play a significant role in nearly all cellular and biological activities. Data-driven machine learning models have demonstrated great power in PPIs. However, the design of efficient molecular featurization poses a great challenge for all learning models for PPIs. Here, we propose persistent spectral (PerSpect) based PPI representation and featurization, and PerSpect-based ensemble learning (PerSpect-EL) models for PPI binding affinity prediction, for the first time. In our model, a sequence of Hodge (or combinatorial) Laplacian (HL) matrices at various different scales are generated from a specially designed filtration process. PerSpect attributes, which are statistical and combinatorial properties of spectrum information from these HL matrices, are used as features for PPI characterization. Each PerSpect attribute is input into a 1D convolutional neural network (CNN), and these CNN networks are stacked together in our PerSpect-based ensemble learning models. We systematically test our model on the two most commonly used datasets, i.e. SKEMPI and AB-Bind. It has been found that our model can achieve state-of-the-art results and outperform all existing models to the best of our knowledge.
Co-offending in context: The role of economic hardship
Authors: Rowan Zachary R 
Published: February 2022

Abstract
Scholars have argued that emergence of co-offending depends on the availability, proximity, and convergence of suitable co-offenders. The current study argues that changes in economic conditions may uniquely alter degree to which offenders are motivated to take on criminal accomplices and make engaging in group behaviour a more viable criminal opportunity. This study examines the between and within-MSA effects of economic hardship between 1990-2004 on the rate of co-offences committed using MSA-level data from the National Crime Victimization Survey. Findings indicate that there are similarities in the relationship between economic hardship and crime generally but portray a much more nuanced relationship when viewed through the lens of group behaviour. The discussion evaluates the results from a series of hybrid decomposition model and considers the utility of situating co-offending within broader socio-structural contexts.
The fornix supports episodic memory during childhood
Authors: Hoffman Linda J , Ngo Chi T , Canada Kelsey L , Pasternak Ofer , Zhang Fan , Riggins Tracy , Olson Ingrid R 
Published: February 2022

Abstract
Episodic memory relies on the coordination of widespread brain regions that reconstruct spatiotemporal details of an episode. These topologically dispersed brain regions can rapidly communicate through structural pathways. Research in animal and human lesion studies implicate the fornix—the major output pathway of the hippocampus—in supporting various aspects of episodic memory. Because episodic memory undergoes marked changes in early childhood, we tested the link between the fornix and episodic memory in an age window of robust memory development (ages 4–8 years). Children were tested on the stories subtest from the Children’s Memory Scale, a temporal order memory task, and a source memory task. Fornix streamlines were reconstructed using probabilistic tractography to estimate fornix microstructure. In addition, we measured fornix macrostructure and computed free water. To assess selectivity of our findings, we also reconstructed the uncinate fasciculus. Findings show that children’s memory increases from ages 4 to 8 and that fornix micro- and macrostructure increases between ages 4 and 8. Children’s memory performance across nearly every memory task correlated with individual differences in fornix, but not uncinate fasciculus, white matter. These findings suggest that the fornix plays an important role in supporting the development of episodic memory, and potentially semantic memory, in early childhood.
Selective impairment of circuits between prefrontal cortex glutamatergic neurons and basal forebrain cholinergic neurons in a tauopathy mouse model
Authors: Zhong Ping , Cao Qing , Yan Zhen 
Published: February 2022

Abstract
Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder linked to cognitive decline. To understand how specific neuronal circuits are impaired in AD, we have used optogenetic and electrophysiological approaches to reveal the functional changes between prefrontal cortex (PFC) and basal forebrain (BF), 2 key regions controlling cognitive processes, in a tauopathy mouse model. We found that the glutamatergic synaptic responses in BF cholinergic neurons from P301S Tau mice (6–8 months old) were markedly diminished. The attenuated long-range PFC to BF pathway in the AD model significantly increased the failure rate of action potential firing of BF cholinergic neurons triggered by optogenetic stimulations of glutamatergic terminals from PFC. In contrast, the projection from PFC to other regions, such as amygdala and striatum, was largely unaltered. On the other hand, optogenetic stimulation of cholinergic terminals from BF induced a persistent reduction of the excitability of PFC pyramidal neurons from Tau mice, instead of the transient reduction exhibited in wild-type mice. Taken together, these data have revealed a selective aberration of the pathway between PFC pyramidal neurons and BF cholinergic neurons in a tauopathy mouse model. This circuit deficit may underlie the loss of attention and executive function in AD.
Micellar Thin Layer Chromatography and Computer-Aided Analysis of Empagliflozin, Linagliptin and Metformin HCl Ternary Mixture
Authors: Abbas Noha S , Mohamed Yahya Abduh Salim , Derayea Sayed M , Omar Mahmoud A , Saleh Gamal A 
Published: February 2022

Abstract
The present work was performed in order to study the mechanism of micellar thin layer chromatography (MTLC) and to develop a new simple and sensitive simultaneous MTLC method for separation of empagliflozin, Linagliptin and metformin hydrochloride ternary mixture. The study was done using three different surfactants; sodium dodecyl sulphate (SDS), benzalkonium chloride (BAC) and polysorbate 80 (tween 80). Chromatographic procedure was performed using micellar mobile phase that composed of aqueous solution of each surfactant and methanol (6: 4 v/v) and micellar TLC determination at λmax 237 nm. Separation using SDS (anionic surfactant) and BAC (cationic surfactant) depends on ionization potential (AMI-IP), partition coefficient (logP (o/w)) and hydrogen bond donor atoms (a-don), whereas separation using tween 80 depends mainly on the lipophilicity (RM0), solvation energy (E-sol) and Van der Waals energy (E-vdw). Quantitative structure–retention relationships study was carried out, modeled, evaluated and validated using molecular operating environment software.
Screening and Identification of Croton Fruit Poisoning in Food Using GC–MS and HPLC–MS/MS
Authors: Chen Dongyang , Li Tanyao , Fan Xiang , Li Bangrui , Zhang Hao , Zeng Dong , Feng Jiali , Jiang Dingguo 
Published: February 2022

Abstract
Croton fruit poisoning was successfully identified through a series of chromatographic technologies. A suspected compound named 2-methyl-butenoic acid was screened out using gas chromatography–mass spectrometry, and the hydrolysate of isoguanosine in soup sample was further detected by high performance liquid chromatography–tandem mass spectrometry. The identification of croton fruit poisoning was confirmed basing on these laboratory tests together with the clinical symptoms of the patients. Especially, the false-negative result and the interferences were successfully excluded through simulation test, spectral analysis and chromatographic separation technique. Such study is significant for croton poisoning identification and provides beneficial references for disposing untargeted food poisoning incident.
What Can IBD Specialists Learn from IL-23 Trials in Dermatology?
Authors: Valenti Mario , Narcisi Alessandra , Pavia Giulia , Gargiulo Luigi , Costanzo Antonio 
Published: February 2022

Abstract

Background and Aims
The advent of biologic drugs revolutionised the treatment of many chronic inflammatory diseases in rheumatology, dermatology, and gastroenterology. The introduction of different targeted agents closely followed the increase in knowledge of pathogenic mechanisms. The identification of IL-23 as a master regulator of ‘pathogenic’ inflammation and the consequent efficacy of IL-23 blocking agents were first proofed in psoriasis and then in other inflammatory diseases such as psoriatic arthritis and Crohn’s disease.

Methods
We reviewed all available results from anti-Il-23 clinical trials for psoriasis, focusing on data of IBDologists’ interest. Regarding guselkumab, we analysed data from phase III clinical trials VOYAGE1, VOYAGE2, and NAVIGATE. For risankizumab, we reported efficacy and safety results from UltIMMa-1, UltIMMa-2, and IMMvent clinical trials, and tildrakizumab was evaluated by analysing data from reSURFACE1 and reSURFACE2 studies.

Results
Data from all the clinical trials that we reported showed both the efficacy of all three anti-IL-23 drugs in psoriasis and the safety of this class; in particular, no gastrointestinal side effects were observed in those studies. IL-23 blockers have shown promising short- and long-term results in psoriasis, with a major safety profile and no negative interactions with gastrointestinal system.

Conclusions
Anti-IL-23 indication for psoriatic arthritis is very recent and for IBD is still to come. Therefore, dermatologists are accumulating long-term experience with these drugs, both in clinical trials and in real-world evidence, which can help gastroenterologists in the management of IBD patients.
Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All
Authors: Sudhakar Padhmanand , Alsoud Dahham , Wellens Judith , Verstockt Sare , Arnauts Kaline , Verstockt Bram , Vermeire Severine 
Published: February 2022

Abstract
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
Proteasome activity modulates amyloid toxicity
Authors: Galvin John , Curran Elizabeth , Arteaga Francisco , Goossens Alicia , Aubuchon-Endsley Nicki , McMurray Michael A , Moore Jeffrey , Hansen Kirk C , Chial Heidi J , Potter Huntington , Brodsky Jeffrey L , Coughlan Christina M 
Published: February 2022

Abstract
Alzheimer's disease (AD) is responsible for 60%–80% of identified cases of dementia. While the generation and accumulation of amyloid precursor protein (APP) fragments is accepted as a key step in AD pathogenesis, the precise role of these fragments remains poorly understood. To overcome this deficit, we induced the expression of the soluble C-terminal fragment of APP (C99), the rate-limiting peptide for the generation of amyloid fragments, in yeast that contain thermosensitive mutations in genes encoding proteasome subunits. Our previous work with this system demonstrated that these proteasome-deficient yeast cells, expressing C99 when proteasome activity was blunted, generated amyloid fragments similar to those observed in AD patients. We now report the phenotypic repercussions of inducing C99 expression in proteasome-deficient cells. We show increased levels of protein aggregates, cellular stress and chaperone expression, electron-dense accumulations in the nuclear envelope/ER, abnormal DNA condensation, and an induction of apoptosis. Taken together, these findings suggest that the generation of C99 and its associated fragments in yeast cells with compromised proteasomal activity results in phenotypes that may be relevant to the neuropathological processes observed in AD patients. These data also suggest that this yeast model should be useful for testing therapeutics that target AD-associated amyloid, since it allows for the assessment of the reversal of the perturbed cellular physiology observed when degradation pathways are dysfunctional.
A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects
Authors: Isaacson Joshua R , Berg Matthew D , Charles Brendan , Jagiello Jessica , Villén Judit , Brandl Christopher J , Moehring Amanda J 
Published: February 2022

Abstract
Transfer RNAs (tRNAs) are the adaptor molecules required for reading the genetic code and producing proteins. Transfer RNA variants can lead to genome-wide mistranslation, the misincorporation of amino acids not specified by the standard genetic code into nascent proteins. While genome sequencing has identified putative mistranslating transfer RNA variants in human populations, little is known regarding how mistranslation affects multicellular organisms. Here, we create a multicellular model of mistranslation by integrating a serine transfer RNA variant that mistranslates serine for proline (tRNAUGG,G26ASer) into the Drosophila melanogaster genome. We confirm mistranslation via mass spectrometry and find that tRNAUGG,G26ASer misincorporates serine for proline at a frequency of ∼0.6% per codon. tRNAUGG,G26ASer extends development time and decreases the number of flies that reach adulthood. While both sexes of adult flies containing tRNAUGG,G26ASer present with morphological deformities and poor climbing performance, these effects are more pronounced in female flies and the impact on climbing performance is exacerbated by age. This model will enable studies into the synergistic effects of mistranslating transfer RNA variants and disease-causing alleles.