bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extrapolation to complete basis-set limit in density-functional theory by quantile random-forest models
Authors: Carbogno Christian , Ghiringhelli Luca , Lubeck Sven , Scheffler Matthias , Draxl Claudia , Speckhard Daniel 
Published: June 2023

Abstract
The numerical precision of density-functional-theory (DFT) calculations depends on a variety of computational parameters, one of the most critical being the basis-set size. The ultimate precision is reached with an infinitely large basis set, \ie in the limit of a complete basis set (CBS). Our aim in this work is to find a machine-learning model that extrapolates finite basis-size calculations to the CBS limit. We start with a data set of 63 binary solids investigated with two all-electron DFT codes, \exciting\ and FHI-aims, which employ very different types of basis sets. A quantile-random-forest model is used to estimate the total-energy correction with respect to a fully converged calculation as a function of the basis-set size. The random-forest model achieves a symmetric mean absolute percentage error of lower than 25\% for both codes and outperforms previous approaches in the literature. Our approach also provides prediction intervals, which quantify the uncertainty of the models' predictions.
Competitive exclusion of a burying beetle by a mongoose
Authors: UEDA AKIRA 
Published: June 2023

Abstract
Competitive exclusion, a mechanism for local extinction of organisms, has been well established among taxonomically related species, including those within the same genus, family, or class in animal communities. This study, however, focuses on competitive exclusion that occurs across phyla, exemplified by the exclusion of a native insect by an invading exotic mammal, where their food resources overlap. The hypothesis proposed in this study is that the small Indian mongoose (Herpestes auropunctatus) has caused the local extinction of a burying beetle (Nicrophorus nepalensis) on Okinawa Is., Japan due to competition for dead bodies of small vertebrates. To test this hypothesis, the beetles were collected from two areas - one where the mongoose has been controlled for over 10 years, including UNESCO’s natural World Heritage, and another where the mongoose has never been controlled or has/had been controlled for only a few years. The use of dead mice bodies laid on the forest floor was also observed in each area. The results showed that the beetle abundance was clearly higher in the former area than in the latter area, and no beetles were collected at sites far from the mongoose controlled area. The beetles often buried the dead mice for their reproduction in the former area, whereas in the latter area, the mongoose frequently fed on the dead mice. The beetle abundance in the former area significantly positively correlated with the canopy cover rate, while no such correlation was observed in the latter area due to the strong impact of the mongoose on the beetle abundance. These results provide the evidence of competitive exclusion of the burying beetle by the mongoose. This conclusion represents the world's first demonstration of competitive exclusion across phyla in the animal community.
Boosting Lipid Production in the Diatom Phaeodactylum tricornutum by Knockdown of the Enoyl CoA Hydratase Using CRISPR Interference
Authors: Guo Wenfeng , Gao Yuqing , Weng Yuwei , Chang Chaofeng , Huang Xuguang , Zhang Feng 
Published: June 2023

Abstract
The oleaginous Phaeodactylum tricornutum is a priming source for biofuel production. However, the contribution of the fatty acid β-oxidation to lipid productivity in this microalga is still poorly understood. In this study, we established a CRISPR interference method to characterize the enoyl CoA hydratase (PtECH), which catalyzed the second step of the β-oxidation pathway. With this method, we generated two transgenic lines: PtECH21 and PtECH1487. RT-qPCR analysis confirmed that the mRNA levels of PtECH in both mutants were significantly impaired as compared to the wild type. Conversely, the lipid content of two PtECH knockdown lines was remarkably elevated, although the growth rates of them were obviously limited. Interestingly, the Fv/Fm values and the expression levels of carbonic anhydrases suggested that both knockdown mutants had a higher photosynthetic efficiency than the wild type. Totally, this study provided a new strategy for enhancing lipid productivity in P. tricornutum, and enlarged our knowledge about the roles of enoyl CoA hydratase in microalgae.
Inactivation of hypocretin receptor-2 signaling in dopaminergic neurons induces hyperarousal and enhanced cognition but impaired inhibitory control
Authors: Bandarabadi Mojtaba , Li Sha , Aeschlimann Lea , Colombo Giulia , Tzanoulinou Stamatina , Tafti Mehdi , Becchetti Andrea , Boutrel Benjamin , Vassalli Anne 
Published: June 2023

Abstract

Hypocretin/Orexin (HCRT/OX) and dopamine (DA) are two key effectors of salience processing, reward and stress-associated behavior and motivational states, yet their respective roles and interactions are poorly delineated. We inactivated HCRT-to-DA connectivity by genetic disruption of Hypocretin receptor type-1 (Hcrtr1), Hypocretin receptor type-2 (Hcrtr2), or both receptors (Hcrtr1&2) in dopamine neurons and analyzed the consequences on vigilance states, brain oscillations, and cognitive performance in freely behaving mice. Unexpectedly, loss of Hcrtr2, but not Hcrtr1 or Hcrtr1&2, led to dramatic increases in theta (7-11 Hz) electroencephalographic (EEG) activity during both wakefulness and rapid-eye-movement (REM) sleep. Compared to controls, DAHcrtr2-deficient mice spent more time in an active (or theta activity-enriched) substate of wakefulness, as well as exhibited prolonged REM sleep. Additionally, both wake and REM sleep displayed enhanced theta-gamma phase-amplitude coupling. The baseline waking EEG of DAHcrtr2-deficient mice exhibited diminished infra-theta, but increased theta power, two hallmarks of EEG hyperarousal, which however were found to be uncoupled from the mice’ locomotor activity. Upon exposure to novel, either rewarding or stress-inducing environments, DAHcrtr2-deficient mice’ waking state featured more pronounced surges in theta and fast-gamma (52-80 Hz) EEG activities compared to their littermate controls, further suggesting increased alertness. Cognition was next evaluated using an operant conditioning paradigm, demonstrating that DAHcrtr2-ablated mice exhibit faster learning, and once performance was stable and attentional demands were increased, they manifested higher attentional capabilities. Concomitantly, the mice however displayed maladaptive patterns of reward-seeking, with behavioral indices of increased impulsivity as well as compulsivity. None of the EEG changes observed in DAHcrtr2-deficient mice were seen in dopaminergic Hcrtr1-ablated mice, which tended to show opposite EEG phenotypes. Our findings establish a clear, genetically-defined link between monosynaptic HCRT-to-dopaminergic neurotransmission and theta oscillations, with a differential and novel role of HCRTR2 in cross-frequency coupling, attentional processes, and executive functions, relevant to disorders including narcolepsy, attention-deficit/hyperactivity disorder, and Parkinson’s disease.
Submonolayer Biolasers for Ultrasensitive Biomarker Detection
Authors: Gong Chaoyang , Yang Xi , Tang Shui-Jing , Zhang Qian-Qian , Wang Yanqiong , Liu Yi-Ling , Chen Yu-Cheng , Peng Gang-Ding , Fan Xudong , Xiao Yun-Feng , Rao Yun-Jiang , Gong Yuan 
Published: June 2023

Abstract
Biomarker detection is key to identifying health risks. However, designing sensitive and single-use biosensors for early diagnosis remains a major challenge. Here, we report submonolayer lasers on optical fibers as ultrasensitive and disposable biosensors. Telecom optical fibers serve as distributed optical microcavities with high Q-factor, great repeatability, and ultralow cost, which enables whispering-gallery laser emission to detect biomarkers. It is found that the sensing performance strongly depends on the number of gain molecules. The submonolayer lasers obtained a six-order-of-magnitude improvement in the lower limit of detection (LOD) when compared to saturated monolayer lasers. We further achieve an ultrasensitive immunoassay for a Parkinson's disease biomarker, alpha-synuclein, with a lower LOD of 0.32 pM in serum. Our demonstration of submonolayer biolaser offers great potentials in high-throughput clinical diagnosis with ultimate sensitivity.
Reduction of p11 in Dorsal Raphe Nucleus Serotonergic Neurons Mediates Depression-like Behaviors
Authors: Li Wei , Shen Zuqi , Yin Xuan , Chang Weiqi , Chen Xiaorong , Yu Jin , Xu Shifen 
Published: June 2023

Abstract
The pathology of depression is related to the imbalance of various neurotransmitters. The dorsal raphe nucleus (DRN), the main brain region producing 5-hydroxytryptamine (5-HT), is crucially involved in the pathophysiology of depression. It contains several neuron types, in which GABAergic neurons are activated by stimuli associated with negative experiences and 5-HT neurons are activated by reward signals. However, little is known about its underlying molecular mechanisms. Here, we found that p11, a multifunctional protein associated with depression, was down-regulated by chronic social defeat stress in 5-HTDRN neurons. Knockdown of p11 in DRN induced depression-like behaviors, while its overexpression in 5-HTDRN neurons alleviated depression-like behavior caused by chronic social defeat stress. Further, p11 affected neuronal activity by regulating glutamate receptor signaling pathways in DRN neurons, suggesting a possible molecular mechanism underlying the participation of p11 in the pathological process of depression. This may facilitate the understanding of the molecular and cellular basis of depression.
Alamandine attenuates ovariectomy-induced osteoporosis by promoting osteogenic differentiation via AMPK/eNOS axis
Authors: Luo Wanxin , Yao Chen , Sun Jie , Zhang Bo , Chen Hao , Miao Jin , Zhang Yafeng 
Published: June 2023

Abstract
Background
Alamandine is a newly characterized peptide of renin angiotensin system. Our study aims to investigate the osteo-preservative effects of alamandine, explore underlying mechanism and bring a potential preventive strategy for postmenopausal osteoporosis in the future.
Methods
An ovariectomy (OVX)-induced rat osteoporosis model was established for in vivo experiments. Micro-computed tomography and three-point bending test were used to evaluate bone strength. Histological femur slices were processed for immunohistochemistry (IHC). Bone turnover markers and nitric oxide (NO) concentrations in serum were determined with enzyme-linked immunosorbent assay (ELISA). The mouse embryo osteoblast precursor (MC3T3-E1) cells were used for in vitro experiments. The cell viability was analysed with a Cell Counting Kit‑8. We performed Alizarin Red S staining and alkaline phosphatase (ALP) activity assay to observe the differentiation status of osteoblasts. Western blotting was adopted to detect the expression of osteogenesis related proteins and AMP-activated protein kinase/endothelial nitric oxide synthase (AMPK/eNOS) in osteoblasts. DAF-FM diacetate was used for semi-quantitation of intracellular NO.
Results
In OVX rats, alamandine alleviated osteoporosis and maintained bone strength. The IHC showed alamandine increased osteocalcin and collagen type I α1 (COL1A1) expression. The ELISA revealed alamandine decreased bone turnover markers and restored NO level in serum. In MC3T3-E1 cells, alamandine promoted osteogenic differentiation. Western blotting demonstrated that alamandine upregulated the expression of osteopontin, Runt-related transcription factor 2 and COL1A1. The intracellular NO was also raised by alamandine. Additionally, the activation of AMPK/eNOS axis mediated the effects of alamandine on MC3T3-E1 cells and bone tissue. PD123319 and dorsomorphin could repress the regulating effect of alamandine on bone metabolism.
Conclusion
Alamandine attenuates ovariectomy-induced osteoporosis by promoting osteogenic differentiation via AMPK/eNOS axis.
Increasing Energy Efficiency and Flow Coefficient by Determining Fluid Behaviours with Computer Aided Design and CFD Analysis in Isolation Valves
Authors: OZKAN ERHAN 
Published: June 2023

Abstract
In this study, it was aimed to convey theoretical and practical development of the double eccentric butterfly valve, which would be the first in the sector, with highly efficient, saves energy, has a long life, and requires less maintenance. For this purpose, a prototype with lower weight and higher flow coefficient has been developed by the Computational Fluid Dynamics (CFD) method. Thanks to the use of computer aided design and simulation techniques, environmentally friendly and highly efficient valves have been produced, improving competitive conditions and an innovative product has been obtained in the sector. The design, CFD analysis, and casting simulation were carried out by Solidworks, ANSYS, and Anycasting computer programs respectively. At the same time, as a result of this study, a design suitable for an innovative production technique that leads to less energy and less waste has been obtained. Innovative material selection and casting techniques were used by optimizing the total material weight and valve cost.
Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments
Authors: Wang Victor , Liu Zichao , Martinek Jan , Zhou Jie , Boruchov Hannah , Ray Kelly , Palucka Karolina , Chuang Jeffrey 
Published: June 2023

Abstract

The tumor microenvironment (TME) and the cellular interactions within it can be critical to tumor progression and treatment response. Although technologies to generate multiplex images of the TME are advancing, the many ways in which TME imaging data can be mined to elucidate cellular interactions are only beginning to be realized. Here, we present a novel approach for multipronged computational immune synapse analysis (CISA) that reveals T-cell synaptic interactions from multiplex images. CISA enables automated discovery and quantification of immune synapse interactions based on the localization of proteins on cell membranes. We first demonstrate the ability of CISA to detect T-cell:APC (antigen presenting cell) synaptic interactions in two independent human melanoma imaging mass cytometry (IMC) tissue microarray datasets. We then generate melanoma histocytometry whole slide images and verify that CISA can detect similar interactions across data modalities. Interestingly, CISA histoctyometry analysis also reveals that T-cell:macrophage synapse formation is associated with T-cell proliferation. We next show the generality of CISA by extending it to breast cancer IMC images, finding that CISA quantifications of T-cell:B-cell synapses are predictive of improved patient survival. Our work demonstrates the biological and clinical significance of spatially resolving cell-cell synaptic interactions in the TME and provides a robust method to do so across imaging modalities and cancer types.
A new adaptive differential evolution-hybrid fuzzy PIDN controller for performance amelioration of power systems
Authors: Chintu Jagan Mohana Rao , Sahu Rabindra Kumar , ARYA YOGENDRA , Panda Sidhartha , Gorripotu Tulasichandra Sekhar 
Published: June 2023

Abstract
Rapidly returning back the synchronism of an inter-connected multi-area power system under continuous varying load demand conditions is documented as a distinguished issue to be tackled by automatic generation control (AGC). AGC supports to alleviate both the frequency and tie-line power deviations on occurrence of load perturbations. Therefore, a robust and intelligent controller is indispensable for an effective AGC in power system. In the current work, a hybrid fuzzy proportional-integral-derivative with filter (FPIDN) controller is employed for AGC of 2-area non-reheat/reheat thermal power systems. A new adaptive differential evolution (ADE) is exploited to adjust parameters of the controller. The dominance of the endorsed technique is revealed by evaluating it with lately published approaches. Then, the recommended scheme is extended to a realistic 4-area interconnected reheat thermal system, which includes all possible uncertainties such as generation rate constraint, boiler dynamics and governor dead band. It is perceived that the performance of the suggested ADE aided hybrid FPIDN controller provides a better response than other control techniques. Lastly, the robustness of the advocated method is tested for an extensive variety of system parameters. The stability analysis is validated by analyzing frequency domain specifications such as gain margin and phase margin. Finally, real-time hardware-in-the-loop simulations are performed to confirm the applicability of the advocated controller for AGC.
Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1
Authors: Glunčić Matko , Vlahović Ines , Rosandić Marija , Paar Vladimir 
Published: June 2023

Abstract
It is known that the ~ 1.6 kb NBPF repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo and collaborators, comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga and collaborators, identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
A computational approach to demonstrate the control of gene expression via chromosomal access in colorectal cancer
Authors: Pecka Caleb J. , Thapa Ishwor , Singh Amar , Bastola Dhundy 
Published: June 2023

Abstract
Improved technologies for chromatin accessibility sequencing such as ATAC-seq have increased our understanding of gene regulation mechanisms, particularly in disease conditions such as cancer. This study introduces a computational tool that quantifies and establishes connections between chromatin accessibility, transcription factor binding, transcription factor mutations, and gene expression using publicly available colorectal cancer data. The tool has been packaged using a workflow management system to allow biologists and researchers to reproduce the results of this study. Through the application of this pipeline, we present compelling evidence linking chromatin accessibility to gene expression, with particular emphasis on SNP mutations and the accessibility of transcription factor genes. Furthermore, we have identified significant upregulation of key transcription factor interactions in colon cancer patients, including the apoptotic regulation facilitated by E2F1, MYC, and MYCN, as well as activation of the BCL-2 protein family facilitated by TP73. The code for this project is openly available on GitHub at the following address: https://github.com/CalebPecka/ATAC-Seq-Pipeline/.
Exploring the Learning Curve of Medical Students in Orthopedic Special Tests for ACL Tear Diagnosis
Authors: Dawod Moh'd S. , Alswerki Mohammad N. , Darabah Asem J. , Darabah Yazeed J. 
Published: June 2023

AbstractObjectives Teaching medical students proper physical examination techniques is an integral component of their clinical training. Multiple physical examination tests exist in orthopedics, with tests for anterior cruciate ligament (ACL) tears being conducted frequently due to the prevalence of this injury. The three most common physical examination tests are Lachman's test, anterior drawer test, and Lilli's test. The aim of this study was to evaluate the clinical accuracy, competence, and motor skill acquisition of medical students while performing these tests. Methods Four patients with a complete ACL tear were selected using a cross-sectional study design. Over the course of one month, the four patients were examined for ACL injury using the three specialized tests. The results of these examinations were recorded, and a statistical evaluation of the student's performance and diagnostic metrics was conducted. Results In terms of sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, we find that the Lachman's and anterior drawer tests perform considerably lower than Lilli's test. When compared to the other tests, students demonstrated a faster learning curve for Lilli's test. Conclusion Orthopedic special tests are notoriously difficult for medical students, despite their apparent simplicity. Special tests that are less technically demanding (Lilli's) have a shorter learning curve and can be implemented more rapidly by the students. Level of Evidence: Level 4, Cross sectional Descriptive
Memory reactivation in slow wave sleep enhances relational learning.
Authors: Kashif Ibad , McGinley Niall , Lewis Penelope , Santamaria Lorena 
Published: June 2023

Abstract
Sleep has been shown to boost the integration of memories, and thus to facilitate relational learning. This benefit is thought to rely upon memory reactivation during non-REM sleep. We set out to test this possibility by explicitly cueing such reactivation using a technique called targeted memory reactivation (TMR), in which sounds are paired with learned material in wake and then softly played back to the participant in sleep, triggering reactivation of the associated memories. Specifically, we tested whether TMR during slow wave sleep leads to enhancements in inferential thinking in a transitive inference task. Because the Up-phase of the slow oscillation is more responsive to external cues than the Down-phase, we also asked whether stimulation at this specific phase is more beneficial for such integration. Our data show that Up-phase TMR boosts the ability to make inferences, but only for the most distant inferential leaps. Such stimulation was also associated with detectable memory reinstatement, whereas Down-phase stimulation produced no such trace and led to below-chance performance. These findings demonstrate that cueing memory reactivation at the right time points in sleep can provide a direct benefit to difficult relational learning problems.