bluuebunny/crossref_metadata_2025_split huggingface dataset:
African food system and biodiversity mainly affected by urbanization via dietary shifts
Authors: De Vos Koen , Janssens Charlotte , Jacobs Liesbet , Campforts Benjamin , Boere Esther , Kozicka Marta , Leclère David , Havlík Petr , Hemerijckx Lisa-Marie , Van Rompaey Anton , Maertens Miet , Govers Gerard 
Published: May 2024

AbstractThe rapid urbanization in Africa profoundly affects local food and ecological systems. According to earlier research, urbanization may cause food production and biodiversity losses as agricultural or natural lands are absorbed by expanding cities. Land-use displacement effects may buffer agricultural production losses or may lead to additional biodiversity losses but are often overlooked. Moreover, impacts of dietary changes associated with urbanization are rarely considered. To address this, we combined spatially explicit projections of African urban area expansion with observed rice consumption shifts to inform a partial equilibrium model (the Global Biosphere Management Model). We demonstrate the importance of displacement effects to identify potential food production or biodiversity issues until 2050 and argue for their integration in land-use planning and policymaking across spatial scales. We identify that because of agricultural displacement, the impact of urban area expansion on food production losses is probably limited (<1%)—at the cost of additional losses of natural lands by 2050 (up to 2 Mt). We also show that considering dietary shifts associated with urbanization increases rice consumption, production (+8.0%), trade (up to +2 Mt of required import) and agricultural methane emissions (up to +12 MtCO2-equivalent yr–1), thereby underscoring the need for a systems approach in future sustainability studies.
Decidual natural killer cells dysfunction is caused by IDO downregulation in dMDSCs with Toxoplasma gondii infection
Authors: Wang Yu , Zhao Xiaoyue , Li Zhidan , Wang Wenxiao , Jiang Yuzhu , Zhang Haixia , Liu Xianbing , Ren Yushan , Xu Xiaoyan , Hu Xuemei 
Published: May 2024

AbstractMyeloid-derived suppressor cells (MDSCs) play a crucial role in maintaining maternal-fetal tolerance by expressing some immune-suppressive molecules, such as indoleamine 2,3-dioxygenase (IDO). Toxoplasma gondii (T. gondii) infection can break the immune microenvironment of maternal-fetal interface, resulting in adverse pregnancy outcomes. However, whether T. gondii affects IDO expression in dMDSCs and the molecular mechanism of its effect are still unclear. Here we show, the mRNA level of IDO is increased but the protein level decreased in infected dMDSCs. Mechanistically, the upregulation of transcriptional levels of IDO in dMDSCs is regulated through STAT3/p52-RelB pathway and the decrease of IDO expression is due to its degradation caused by increased SOCS3 after T. gondii infection. In vivo, the adverse pregnancy outcomes of IDO−/− infected mice are more severe than those of wide-type infected mice and obviously improved after exogenous kynurenine treatment. Also, the reduction of IDO in dMDSCs induced by T. gondii infection results in the downregulation of TGF-β and IL-10 expression in dNK cells regulated through Kyn/AhR/SP1 signal pathway, eventually leading to the dysfunction of dNK cells and contributing the occurrence of adverse pregnancy outcomes. This study reveals a novel molecular mechanism in adverse pregnancy outcome induced by T. gondii infection.
Local dominance unveils clusters in networks
Authors: Shi Dingyi , Shang Fan , Chen Bingsheng , Expert Paul , Lü Linyuan , Stanley H. Eugene , Lambiotte Renaud , Evans Tim S. , Li Ruiqi 
Published: May 2024

AbstractClusters or communities can provide a coarse-grained description of complex systems at multiple scales, but their detection remains challenging in practice. Community detection methods often define communities as dense subgraphs, or subgraphs with few connections in-between, via concepts such as the cut, conductance, or modularity. Here we consider another perspective built on the notion of local dominance, where low-degree nodes are assigned to the basin of influence of high-degree nodes, and design an efficient algorithm based on local information. Local dominance gives rises to community centers, and uncovers local hierarchies in the network. Community centers have a larger degree than their neighbors and are sufficiently distant from other centers. The strength of our framework is demonstrated on synthesized and empirical networks with ground-truth community labels. The notion of local dominance and the associated asymmetric relations between nodes are not restricted to community detection, and can be utilised in clustering problems, as we illustrate on networks derived from vector data.
Unconventional anomalous Hall effect and large anomalous Nernst effect in antiferromagnet SmMnBi2
Authors: Tang Kaixin , Yang Ye , Shen Jianchang , Shi Mengzhu , Zhang Nan , Li Houpu , Li Hongyu , Liu Zhengtai , Shen Dawei , Wang Rui , Gao Yang , He Junfeng , Xiang Ziji , Chen Xianhui 
Published: May 2024

AbstractThe anomalous Hall effect (AHE) and its thermoelectric counterpart, the anomalous Nernst effect (ANE), are two transverse transport coefficients that are intensely studied in condensed matter physics. While conventional wisdom links AHE and ANE to ferromagnetism, recent achievements reveal that they can emerge in nonmagnetic and antiferromagnetic topological materials with a diversity of mechanisms—many of which await further elucidation. Here, both an unconventional AHE (UAHE) that does not scale with the magnetization and a sizable ANE ( ≈ 1.8 μV K−1) are shown to be possessed by the metallic tetragonal antiferromagnet SmMnBi2. Electronic band structure of SmMnBi2 is investigated by angle-resolved photoemission spectroscopy and first-principles calculations. It is demonstrated that the UAHE reflects the intrinsic Berry curvature contribution stemming from the spin-canted antiferromagnetism, whereas the ANE is possibly further amplified by extrinsic mechanisms. These results identify SmMnBi2 as a promising candidate for exploring unusual transverse transport effects and the extremely rich underlying physics.
Global forest gaps reduce litterfall but increase litter carbon and phosphorus release
Authors: Zhang Xiaoyue , Heděnec Petr , Yue Kai , Ni Xiangyin , Wei Xinyu , Chen Zihao , Yang Jing , Wu Fuzhong 
Published: May 2024

AbstractOngoing global climate change and conventional forestry have led to a dramatic increase in new forest gaps, predicted to strongly impact litter turnover and nutrient cycling. Here we synthesized 8739 paired observations to quantify the impacts of naturally occurring and artificially created gaps on litterfall, litter decomposition, and the release of carbon and nutrients. Globally, forest gaps decreased annual litterfall by 29.5% and litter remaining carbon and phosphorus by 5.6%, while litter decomposition increased in the 0–20% mass loss interval. Climate and litter quality showed a major contribution to forest gap effects on litter decomposition, with gap characteristics further influencing the release of carbon and nutrients during decomposition. Our results uncovered the potential impact of escalating forest gaps on reducing litter turnover and carbon sequestration, providing support for the inclusion of gaps into global litter dynamic models to improve predictions of ecosystem material cycling responses to ongoing climate change.
IL-27 maintains cytotoxic Ly6C+ γδ T cells that arise from immature precursors
Authors: Wiesheu Robert , Edwards Sarah C , Hedley Ann , Hall Holly , Tosolini Marie , Fares da Silva Marcelo Gregorio Filho , Sumaria Nital , Castenmiller Suzanne M , Wardak Leyma , Optaczy Yasmin , Lynn Amy , Hill David G , Hayes Alan J , Hay Jodie , Kilbey Anna , Shaw Robin , Whyte Declan , Walsh Peter J , Michie Alison M , Graham Gerard J , Manoharan Anand , Halsey Christina , Blyth Karen , Wolkers Monika C , Miller Crispin , Pennington Daniel J , Jones Gareth W , Fournie Jean-Jacques , Bekiaris Vasileios , Coffelt Seth B 
Published: May 2024

AbstractIn mice, γδ-T lymphocytes that express the co-stimulatory molecule, CD27, are committed to the IFNγ-producing lineage during thymic development. In the periphery, these cells play a critical role in host defense and anti-tumor immunity. Unlike αβ-T cells that rely on MHC-presented peptides to drive their terminal differentiation, it is unclear whether MHC-unrestricted γδ-T cells undergo further functional maturation after exiting the thymus. Here, we provide evidence of phenotypic and functional diversity within peripheral IFNγ-producing γδ T cells. We found that CD27+ Ly6C− cells convert into CD27+Ly6C+ cells, and these CD27+Ly6C+ cells control cancer progression in mice, while the CD27+Ly6C− cells cannot. The gene signatures of these two subsets were highly analogous to human immature and mature γδ-T cells, indicative of conservation across species. We show that IL-27 supports the cytotoxic phenotype and function of mouse CD27+Ly6C+ cells and human Vδ2+ cells, while IL-27 is dispensable for mouse CD27+Ly6C− cell and human Vδ1+ cell functions. These data reveal increased complexity within IFNγ-producing γδ-T cells, comprising immature and terminally differentiated subsets, that offer new insights into unconventional T-cell biology.
Targeting ATP2B1 impairs PI3K/Akt/FOXO signaling and reduces SARS-COV-2 infection and replication
Authors: de Antonellis Pasqualino , Ferrucci Veronica , Miceli Marco , Bibbo Francesca , Asadzadeh Fatemeh , Gorini Francesca , Mattivi Alessia , Boccia Angelo , Russo Roberta , Andolfo Immacolata , Lasorsa Vito Alessandro , Cantalupo Sueva , Fusco Giovanna , Viscardi Maurizio , Brandi Sergio , Cerino Pellegrino , Monaco Vittoria , Choi Dong-Rac , Cheong Jae-Ho , Iolascon Achille , Amente Stefano , Monti Maria , Fava Luca L , Capasso Mario , Kim Hong-Yeoul , Zollo Massimo 
Published: May 2024

AbstractATP2B1 is a known regulator of calcium (Ca2+) cellular export and homeostasis. Diminished levels of intracellular Ca2+ content have been suggested to impair SARS-CoV-2 replication. Here, we demonstrate that a nontoxic caloxin-derivative compound (PI-7) reduces intracellular Ca2+ levels and impairs SARS-CoV-2 infection. Furthermore, a rare homozygous intronic variant of ATP2B1 is shown to be associated with the severity of COVID-19. The mechanism of action during SARS-CoV-2 infection involves the PI3K/Akt signaling pathway activation, inactivation of FOXO3 transcription factor function, and subsequent transcriptional inhibition of the membrane and reticulum Ca2+ pumps ATP2B1 and ATP2A1, respectively. The pharmacological action of compound PI-7 on sustaining both ATP2B1 and ATP2A1 expression reduces the intracellular cytoplasmic Ca2+ pool and thus negatively influences SARS-CoV-2 replication and propagation. As compound PI-7 lacks toxicity in vitro, its prophylactic use as a therapeutic agent against COVID-19 is envisioned here.
Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx)
Authors: Madill-Thomsen Katelynn S. , Halloran Philip F. 
Published: May 2024

Abstract
There is a major unmet need for improved accuracy and precision in the assessment of transplant rejection and tissue injury. Diagnoses relying on histologic and visual assessments demonstrate significant variation between expert observers (as represented by low kappa values) and have limited ability to assess many biological processes that produce little histologic changes, for example, acute injury. Consensus rules and guidelines for histologic diagnosis are useful but may have errors. Risks of over- or under-treatment can be serious: many therapies for transplant rejection or primary diseases are expensive and carry risk for significant adverse effects. Improved diagnostic methods could alleviate healthcare costs by reducing treatment errors, increase treatment efficacy, and serve as useful endpoints for clinical trials of new agents that can improve outcomes. Molecular diagnostic assessments using microarrays combined with machine learning algorithms for interpretation have shown promise for increasing diagnostic precision via probabilistic assessments, recalibrating standard of care diagnostic methods, clarifying ambiguous cases, and identifying potentially missed cases of rejection. This review describes the development and application of the Molecular Microscope® Diagnostic System (MMDx), and discusses the history and reasoning behind many common methods, statistical practices, and computational decisions employed to ensure that MMDx scores are as accurate and precise as possible. MMDx provides insights on disease processes and highly reproducible results from a comparatively small amount of tissue and constitutes a general approach that is useful in many areas of medicine, including kidney, heart, lung, and liver transplants, with the possibility of extrapolating lessons for understanding native organ disease states.
Targeting the long non-coding RNA MIAT for the treatment of fibroids in an animal model
Authors: Chuang Tsai-Der , Ton Nhu , Manrique Nathaly , Rysling Shawn , Khorram Omid 
Published: May 2024

Abstract
Our previous studies indicated that there is overexpression of MIAT in fibroids and MIAT is a sponge for the miR-29 family in these tumors. The objective of the present study was to determine if the knockdown of MIAT in fibroid xenografts will increase miR-29 levels and reduce the expression of genes targeted by this miRNA such as collagen and cell cycle regulatory proteins in a mouse model for fibroids. Ovariectomized CB-17 SCID/Beige mice bearing estrogen/progesterone pellets were implanted subcutaneously in the flank with equal weight of fibroid explants which had been transduced by lentivirus for either control (empty vector) or MIAT knockdown for four weeks (n=7). Knockdown of MIAT in fibroid xenografts resulted in a 30% reduction of tumor weight and a marked increase in miR-29a, -b, and -c levels in the xenografts. There was reduced cell proliferation and expression of cell cycle regulatory genes CCND1, CDK2, and E2F1 and no significant changes in apoptosis. The xenografts with MIAT knockdown expressed lower mRNA and protein levels of FN1, COL3A1, and TGF-β3, and total collagen protein. Targeting MIAT, which sponges the pro-fibrotic miR-29 family, is an effective therapy for fibroids by reducing cell proliferation and thereby, tumor growth and accumulation of ECM, which is a hallmark of these benign gynecologic tumors.
Malate dehydrogenase: a story of diverse evolutionary radiation
Authors: Wolyniak Michael J. , Frazier Robert H. , Gemborys Peter K. , Loehr Henry E. 
Published: May 2024

Abstract
Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH’s ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and ‘big data’ analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.
Development of a Dysphagia Pathway Program for Head and Neck Cancer in a Rural Patient Population
Authors: Chan Kimberly , Keane Allison , Fisher Nicole , King Tonya S. , Yang Yanxu , Allibone Melissa , Ayala Aaron , Choi Karen Y. 
Published: May 2024

Purpose:
The purpose of this study is to discuss the feasibility of developing, and the challenges of implementing, a structured dysphagia program in a rural patient population with preliminary data.

Method:
The Dysphagia Pathway Program (DPP) is a standardized, prophylactic swallow therapy program for head and neck cancer patients initiated in 2019 as a multidisciplinary approach at Penn State Hershey Medical Center. An interrupted time series study was conducted comparing the swallow and nutritional status of patients pre- and postimplementation of the DPP. Data were analyzed using the chi-square test and linear mixed-effects models to determine statistical significance for categorical and continuous variables, respectively.

Results:

The DPP group included 52 patients, and the pre-implementation group included 109 patients. A higher percentage of patients in the DPP group tolerated a by mouth (PO)-only diet at the last day of treatment time point (
p
< .001). The DPP group showed similar changes in body mass index and albumin over time but had lower rates of gastrostomy tube placements (
p
= .002) compared to the pre-implementation group. The average adherence to speech and swallow therapy in the DPP group decreased over time.

Conclusions:
Although we encountered many obstacles in the development of the DPP, we found prophylactic swallow therapy to be feasible to implement and beneficial in our rural patient population. In this pilot study, our results demonstrated that prophylactic swallow therapy shows a favorable trend in swallowing and nutritional status. Future improvements include improving documentation of swallowing outcomes, patient adherence, and utilizing telehealth.
Turn‐to‐turn and phase‐to‐phase short circuit fault detection of wind turbine permanent magnet generator based on equivalent magnetic network modelling by wavelet transform approach
Authors: Ghods Mehrage , Tabarniarami Zabihollah , Faiz Jawad , Bazrafshan Mohammad Amin 
Published: May 2024

AbstractOne of the most common faults in electric machines is a turn‐to‐turn short circuit (TTSC), which may destroy coil insulation and demagnetise the magnet. In addition, the phase‐to‐phase short circuit (PPSC) fault, which can have even more destructive effects than the TTSC fault, is introduced and analysed. The equivalent magnetic network (EMN) method, with high modelling accuracy and a short computation time, is employed for healthy and faulty machines. The current signal under fault conditions is analysed in the dqo frame, showing the presence of the second harmonic component in its waveform. This fault detection index is processed using the signal processing technique of discrete(wavelet transform (DWT). Besides, energy analysis is used to distinguish TTSC and PPSC faults. Finally, finite element and EMN modelling results are compared with the experimental data of the prototyped permanent magnet generator. The results show that the combination of the proposed EMN method and DWT has very good accuracy and speed. Furthermore, the proposed fault detection method remains unaffected by various linear loads with different power factors.The cover image is based on the article Turn‐to‐turn and phase‐to‐phase short circuit fault detection of wind turbine permanent magnet generator based on equivalent magnetic network modelling by wavelet transform approach by Mehrage Ghods et al., https://doi.org/10.1049/elp2.12452
Multi‐objective capacity estimation of wind ‐ solar ‐ energy storage in power grid planning consideration policy effect
Authors: Huan Jiajia , Zhang Xiaohui , He Yuling , Sun Kai , Han Zhicheng , Wang Haipeng 
Published: May 2024

AbstractNumerous policies have been implemented to advance the growth of renewable energy. Nonetheless, certain policies have not yielded the anticipated impact on the progression of renewable energy development. In order to maximize the promotion effect of renewable energy policies, this study proposes a capacity allocation optimization method of wind power generation, solar power and energy storage in power grid planning under different policy objectives. First, based on the policy quantification, grey relation analysis (GRA) is used to calculate the correlation degree of the policy indicators on the planning capacity of renewable energy. Further, a multi‐objective capacity estimation model for wind, solar and energy storage is comprehensively presented. Some highly correlated policy indicators are transformed into the special constraints. And the economy and the stability of the power grid are integrated as the objective function. Meanwhile, the carbon trading and punishment for wind power and solar power abandonment are considered. Finally, the proposed model is solved by NSGA‐II‐PSO (particle swarm optimization) algorithm. The novelty of the algorithm is that the crossover operation of NSGA‐II is replaced by the position updating of particle swarm. The calculation result of the case study can effectively evaluate the optimal planning capacity of renewable energy under different policies, while ensuring the economic and the stability of the power system. The study can provide the reasonable basis and the valid analytical method for the policy formulation and the renewable energy development.
Emergence of high-mass stars in complex fiber networks (EMERGE)
Authors: Bonanomi Francesca , Hacar Alvaro , Socci Andrea , Petry Dirk , Suri Sümeyye 
Published: May 2024

Context. High-resolution images from Atacama Large Millimetre Array (ALMA) allow for the filamentary structure of the interstellar medium (ISM) to be resolved down to a few thousand astronomical units (au) in star-forming regions located at kiloparsec (kpc) distances.
Aims. We aim to systematically quantify the impact of the interferometric response and the effects of the short-spacing information during the characterization of the ISM structure using ALMA observations.
Methods. We created a series of continuum ALMA synthetic observations to test the recovery of the fundamental observational properties of dense cores and filaments (i.e., intensity peak, radial profile, and width) at different spatial scales. We homogeneously compared the results obtained with and without different data combination techniques and using different ALMA arrays and SD telescopes in both simulated data and real observations.
Results. Our analysis illustrates the severity of interferometric filtering effects. ALMA-12 m-alone observations show significant scale-dependent flux losses that systematically corrupt (>30% error) all the physical properties inferred in cores and filaments (i.e., column density, mass, and size) well before the maximum recoverable scale of the interferometer. These effects are only partially mitigated by the addition of the ALMA ACA-7 m array, although at the expenses of degrading the telescope point-spread-function (PSF). Our results demonstrate that only the addition of the ALMA Total Power(TP) information allows for the true sky emission to be recovered down to a few times the ALMA beamsize with sufficient accuracy (<10% error). Additional tests show that the emission recovery of cores and filaments at all scales is further improved if the 7 m+TP data are replaced by additional maps obtained by a larger SD telescope (e.g., IRAM-30 m), even if the latter are noisier than expected. In particular, these observational biases affect partially resolved targets, which becomes especially critical for studies in nearby regions such as Taurus or Orion.
Conclusions. Our results demonstrate the need for the use of the state-of-the-art data combination techniques to accurately characterize the complex physical structure of the ISM in the ALMA era.