bluuebunny/crossref_metadata_2025 huggingface dataset:
Single‐Hemisphere Oxygen Outflow From Earth's Subauroral Zone
Authors: Liu Z.‐Y. , Zong Q.‐G. , Zhou X.‐Z. , Fu S.‐Y. , Hu Z.‐J. , Liu J.‐J. , Yue C.
Published: July 2024

Besides the cusp, polar cap, and auroral oval, the nightside subauroral zone has also recently been reported as a source region of the ionospheric oxygen outflows. However, the detailed mass and energy sources of these ions remain open questions. Here, we address this issue from the perspective of the response of conjugate hemispheres. Investigation of Van Allen Probes data demonstrates a notable preference of oxygen outflows from the nightside subauroral zone from the sunlit hemisphere. This characteristic eliminates the possibility of nightside auroral precipitation playing a significant role, as it is more prominent in darkness. Instead, it highlights sunlight‐induced ionization as the mass source and enhanced plasma waves from the magnetotail as the energy source. The results presented here further support the nightside subauroral zone as an independent source of magnetospheric oxygen ions.
Patient adherence in orthodontics: a scoping review
Authors: van der Bie Ronald Max , Bos Annemieke , Bruers Jan Joseph Mathieu , Jonkman Ronald Edwin Gaston
Published: July 2024

Background

Patient adherence is a key factor in achieving orthodontic treatment success. Despite an evolution in orthodontic healthcare, no recent comprehensive reviews are available on patient adherence in orthodontics. This scoping review provides an evidence-based overview of the literature available on multiple aspects of patient adherence in orthodontics, during both active treatment as well as during the retention phase. Knowledge gaps identified in the literature are listed.

Methods

The protocol for this scoping review was registered in the Open Science Framework (https://doi.org/10.17605/OSF.IO/EC6QD). Electronic databases and reference lists of relevant studies were searched up to 9 February 2023. The inclusion criteria were studies investigating any form of patient adherence in orthodontics published in English from 2006 onwards. The exclusion criteria were studies investigating adherence in the following patients: those with an intellectual or physical disability that could affect their ability to coincide with their therapist’s recommendations and advice, those with oral cleft and craniofacial conditions, and those treated solely for obstructive sleep apnoea. Non-peer-reviewed studies and case reports were also excluded.

Results

A total of 3284 articles were identified, 60 of which met the criteria for final inclusion.

Conclusions

There is no conclusive evidence on which factors have a significant impact on patient adherence and how patient adherence can be promoted. The degree of patient adherence is generally not compared to achieved treatment results or stability of treatment results, making it difficult to provide clear statements about the impact of the degree of adherence on desired treatment results or orthodontic stability.
Mitophagy-related regulated cell death: molecular mechanisms and disease implications
Authors: Yang Molin , Wei Xiang , Yi Xin , Jiang Ding-Sheng
Published: July 2024

During oxidative phosphorylation, mitochondria continuously produce reactive oxygen species (ROS), and untimely ROS clearance can subject mitochondria to oxidative stress, ultimately resulting in mitochondrial damage. Mitophagy is essential for maintaining cellular mitochondrial quality control and homeostasis, with activation involving both ubiquitin-dependent and ubiquitin-independent pathways. Over the past decade, numerous studies have indicated that different forms of regulated cell death (RCD) are connected with mitophagy. These diverse forms of RCD have been shown to be regulated by mitophagy and are implicated in the pathogenesis of a variety of diseases, such as tumors, degenerative diseases, and ischemia‒reperfusion injury (IRI). Importantly, targeting mitophagy to regulate RCD has shown excellent therapeutic potential in preclinical trials, and is expected to be an effective strategy for the treatment of related diseases. Here, we present a summary of the role of mitophagy in different forms of RCD, with a focus on potential molecular mechanisms by which mitophagy regulates RCD. We also discuss the implications of mitophagy-related RCD in the context of various diseases.
Introducing carbon assimilation in yeasts using photosynthetic directed endosymbiosis
Authors: Gao Yang-le , Cournoyer Jay , De Bidhan C. , Wallace Catherine L. , Ulanov Alexander V. , La Frano Michael R. , Mehta Angad P.
Published: July 2024

Conversion of heterotrophic organisms into partially or completely autotrophic organisms is primarily accomplished by extensive metabolic engineering and laboratory evolution efforts that channel CO2 into central carbon metabolism. Here, we develop a directed endosymbiosis approach to introduce carbon assimilation in budding yeasts. Particularly, we engineer carbon assimilating and sugar-secreting photosynthetic cyanobacterial endosymbionts within the yeast cells, which results in the generation of yeast/cyanobacteria chimeras that propagate under photosynthetic conditions in the presence of CO2 and in the absence of feedstock carbon sources like glucose or glycerol. We demonstrate that the yeast/cyanobacteria chimera can be engineered to biosynthesize natural products under the photosynthetic conditions. Additionally, we expand our directed endosymbiosis approach to standard laboratory strains of yeasts, which transforms them into photosynthetic yeast/cyanobacteria chimeras. We anticipate that our studies will have significant implications for sustainable biotechnology, synthetic biology, and experimentally studying the evolutionary adaptation of an additional organelle in yeast.
A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment
Authors: Pérez Raúl F. , Tezanos Patricia , Peñarroya Alfonso , González-Ramón Alejandro , Urdinguio Rocío G. , Gancedo-Verdejo Javier , Tejedor Juan Ramón , Santamarina-Ojeda Pablo , Alba-Linares Juan José , Sainz-Ledo Lidia , Roberti Annalisa , López Virginia , Mangas Cristina , Moro María , Cintado Reyes Elisa , Muela Martínez Pablo , Rodríguez-Santamaría Mar , Ortea Ignacio , Iglesias-Rey Ramón , Castilla-Silgado Juan , Tomás-Zapico Cristina , Iglesias-Gutiérrez Eduardo , Fernández-García Benjamín , Sanchez-Mut Jose Vicente , Trejo José Luis , Fernández Agustín F. , Fraga Mario F.
Published: July 2024

Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
Hippocampal connectivity patterns echo macroscale cortical evolution in the primate brain
Authors: Eichert Nicole , DeKraker Jordan , Howard Amy F. D. , Huszar Istvan N. , Zhu Silei , Sallet Jérôme , Miller Karla L. , Mars Rogier B. , Jbabdi Saad , Bernhardt Boris C.
Published: July 2024

While the hippocampus is key for human cognitive abilities, it is also a phylogenetically old cortex and paradoxically considered evolutionarily preserved. Here, we introduce a comparative framework to quantify preservation and reconfiguration of hippocampal organisation in primate evolution, by analysing the hippocampus as an unfolded cortical surface that is geometrically matched across species. Our findings revealed an overall conservation of hippocampal macro- and micro-structure, which shows anterior-posterior and, perpendicularly, subfield-related organisational axes in both humans and macaques. However, while functional organisation in both species followed an anterior-posterior axis, we observed a marked reconfiguration in the latter across species, which mirrors a rudimentary integration of the default-mode-network in non-human primates. Here we show that microstructurally preserved regions like the hippocampus may still undergo functional reconfiguration in primate evolution, due to their embedding within heteromodal association networks.
Surface properties of the seas of Titan as revealed by Cassini mission bistatic radar experiments
Authors: Poggiali Valerio , Brighi Giancorrado , Hayes Alexander G. , Nicholson Phil D. , MacKenzie Shannon , Lalich Daniel E. , Bonnefoy Léa E. , Oudrhiri Kamal , Lorenz Ralph D. , Soderblom Jason M. , Tortora Paolo , Zannoni Marco
Published: July 2024

Saturn’s moon Titan was explored by the Cassini spacecraft from 2004 to 2017. While Cassini revealed a lot about this Earth-like world, its radar observations could only provide limited information about Titan’s liquid hydrocarbons seas Kraken, Ligeia and Punga Mare. Here, we show the results of the analysis of the Cassini mission bistatic radar experiments data of Titan’s polar seas. The dual-polarized nature of bistatic radar observations allow independent estimates of effective relative dielectric constant and small-scale roughness of sea surface, which were not possible via monostatic radar data. We find statistically significant variations in effective dielectric constant (i.e., liquid composition), consistent with a latitudinal dependence in the methane-ethane mixing-ratio. The results on estuaries suggest lower values than the open seas, compatible with methane-rich rivers entering seas with higher ethane content. We estimate small-scale roughness of a few millimeters from the almost purely coherent scattering from the sea surface, hinting at the presence of capillary waves. This roughness is concentrated near estuaries and inter-basin straits, perhaps indicating active tidal currents.
Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments
Authors: Vilarrasa-Blasi Josep , Vellosillo Tamara , Jinkerson Robert E. , Fauser Friedrich , Xiang Tingting , Minkoff Benjamin B. , Wang Lianyong , Kniazev Kiril , Guzman Michael , Osaki Jacqueline , Barrett-Wilt Gregory A. , Sussman Michael R. , Jonikas Martin C. , Dinneny José R.
Published: July 2024

Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allows us to infer their evolutionary conservation and divergence across these lineages. 76 genes, acting across diverse cellular compartments, were found to be important for osmotic-stress tolerance in Chlamydomonas through their functions in cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs for five of these genes have conserved functions in stress tolerance in Arabidopsis and reveal a novel PROFILIN-dependent stage of acclimation affecting the actin cytoskeleton that ensures tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants, and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.
OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing
Authors: Zeng Zehua , Ma Yuqing , Hu Lei , Tan Bowen , Liu Peng , Wang Yixuan , Xing Cencan , Xiong Yuanyan , Du Hongwu
Published: July 2024

Single-cell sequencing is frequently affected by “omission” due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly “omitted” cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of “omitted” cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
Closing Kok’s cycle of nature’s water oxidation catalysis
Authors: Guo Yu , He Lanlan , Ding Yunxuan , Kloo Lars , Pantazis Dimitrios A. , Messinger Johannes , Sun Licheng
Published: July 2024

The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.
Unidirectional guided-wave-driven metasurfaces for arbitrary wavefront control
Authors: Li Shiqing , Tsakmakidis Kosmas L. , Jiang Tao , Shen Qian , Zhang Hang , Yan Jinhua , Sun Shulin , Shen Linfang
Published: July 2024

Metasurfaces are capable of fully reshaping the wavefronts of incident beams in desired manners. However, the requirement for external light excitation and the resonant nature of their meta-atoms, make challenging their on-chip integration. Here, we introduce the concept and design of a fresh class of metasurfaces, driven by unidirectional guided waves, capable of arbitrary wavefront control based on the unique dispersion properties of unidirectional guided waves rather than resonant meta-atoms. Upon experimentally demonstrating the feasibility of our designs in the microwave regime, we numerically validate the introduced principle through the design of several microwave meta-devices using metal-air-gyromagnetic unidirectional surface magneto-plasmons, agilely converting unidirectional guided modes into the wavefronts of 3D Bessel beams, focused waves, and controllable vortex beams. We, further, numerically demonstrate sub-diffraction focusing, which is beyond the capability of conventional metasurfaces. Our unfamiliar yet practical designs may enable full, broadband manipulation of electromagnetic waves on deep subwavelength scales.
Membrane protein MHZ3 regulates the on-off switch of ethylene signaling in rice
Authors: Li Xin-Kai , Huang Yi-Hua , Zhao Rui , Cao Wu-Qiang , Lu Long , Han Jia-Qi , Zhou Yang , Zhang Xun , Wu Wen-Ai , Tao Jian-Jun , Wei Wei , Zhang Wan-Ke , Chen Shou-Yi , Ma Biao , Zhao He , Yin Cui-Cui , Zhang Jin-Song
Published: July 2024

Ethylene regulates plant growth, development, and stress adaptation. However, the early signaling events following ethylene perception, particularly in the regulation of ethylene receptor/CTRs (CONSTITUTIVE TRIPLE RESPONSE) complex, remains less understood. Here, utilizing the rapid phospho-shift of rice OsCTR2 in response to ethylene as a sensitive readout for signal activation, we revealed that MHZ3, previously identified as a stabilizer of ETHYLENE INSENSITIVE 2 (OsEIN2), is crucial for maintaining OsCTR2 phosphorylation. Genetically, both functional MHZ3 and ethylene receptors prove essential for OsCTR2 phosphorylation. MHZ3 physically interacts with both subfamily I and II ethylene receptors, e.g., OsERS2 and OsETR2 respectively, stabilizing their association with OsCTR2 and thereby maintaining OsCTR2 activity. Ethylene treatment disrupts the interactions within the protein complex MHZ3/receptors/OsCTR2, reducing OsCTR2 phosphorylation and initiating downstream signaling. Our study unveils the dual role of MHZ3 in fine-tuning ethylene signaling activation, providing insights into the initial stages of the ethylene signaling cascade.
Phase interface engineering enables state-of-the-art half-Heusler thermoelectrics
Authors: Zhang Yihua , Peng Guyang , Li Shuankui , Wu Haijun , Chen Kaidong , Wang Jiandong , Zhao Zhihao , Lyu Tu , Yu Yuan , Zhang Chaohua , Zhang Yang , Ma Chuansheng , Guo Shengwu , Ding Xiangdong , Sun Jun , Liu Fusheng , Hu Lipeng
Published: July 2024

In thermoelectric, phase interface engineering proves effective in reducing the lattice thermal conductivity via interface scattering and amplifying the density-of-states effective mass by energy filtering. However, the indiscriminate introduction of phase interfaces inevitably leads to diminished carrier mobility. Moreover, relying on a singular energy barrier is insufficient for comprehensive filtration of low-energy carriers throughout the entire temperature range. Addressing these challenges, we advocate the establishment of a composite phase interface using atomic layer deposition (ALD) technology. This design aims to effectively decouple the interrelated thermoelectric parameters in ZrNiSn. The engineered coherent dual-interface energy barriers substantially enhance the density-of-states effective mass across the entire temperature spectrum while preser carrier mobility. Simultaneously, the strong interface scattering on phonons is crucial for curtailing lattice thermal conductivity. Consequently, a 40-cycles TiO2 coating on ZrNi1.03Sn0.99Sb0.01 achieves an unprecedented zT value of 1.3 at 873 K. These findings deepen the understanding of coherent composite-phase interface engineering.
Molecularly specific detection towards trace nitrogen dioxide by utilizing Schottky-junction-based Gas Sensor
Authors: Xu Shipu , Zhou Xuehan , Xu Shidang , Zhang Yan , Shi Yiwen , Cong Xuzhong , Xu Qijia , Tian Ye , Jiang Ying , Guo Hanjie , Zhao Jinkui , Sun Fengqiang , Peng Hailin
Published: July 2024

Trace NO2 detection is essential for the production and life, where the sensing strategy is appropriate for rapid detection but lacks molecular specificity. This investigation proposes a sensing mechanism dominated by surface-scattering to achieve the molecularly-specific detection. Two-dimensional Bi2O2Se is firstly fabricated into a Schottky-junction-based gas-sensor. Applied with an alternating excitation, the sensor simultaneously outputs multiple response signals (i.e., resistance, reactance, and the impedance angle). Their response times are shorter than 200 s at room temperature. In NO2 sensing, these responses present the detection limit in ppt range and the sensitivity is up to 16.8 %·ppb−1. This NO2 sensitivity presents orders of magnitude higher than those of the common gases within the exhaled breath. The impedance angle is involved in the principle component analysis together with the other two sensing signals. Twelve kinds of typical gases containing NO2 are acquired with molecular characteristics. The change in dipole moment of the target molecule adsorbed is demonstrated to correlate with the impedance angle via surface scattering. The proposed mechanism is confirmed to output ultra-sensitive sensing responses with the molecular characteristic.
First-principles predictions of HfO2-based ferroelectric superlattices
Authors: Mukherjee Binayak , Fedorova Natalya S. , Íñiguez-González Jorge
Published: July 2024

The metastable nature of the ferroelectric phase of HfO2 is a significant impediment to its industrial application as a functional ferroelectric material. In fact, no polar phases exist in the bulk phase diagram of HfO2, which shows a dominant non-polar monoclinic ground state. As a consequence, ferroelectric orthorhombic HfO2 is stabilized either kinetically or via epitaxial strain. Here, we propose an alternative approach, demonstrating the feasibility of thermodynamically stabilizing polar HfO2 in superlattices with other simple oxides. Using the composition and stacking direction of the superlattice as design parameters, we obtain heterostructures that can be fully polar, fully antipolar or mixed, with improved thermodynamic stability compared to the orthorhombic polar HfO2 in bulk form. Our results suggest that combining HfO2 with an oxide that does not have a monoclinic ground state generally drives the superlattice away from this non-polar phase, favoring the stability of the ferroelectric structures that minimize the elastic and electrostatic penalties. As such, these diverse and tunable superlattices hold promise for various applications in thin-film ferroelectric devices
A neural modeling approach to study mechanisms underlying the heterogeneity of visual spatial frequency sensitivity in schizophrenia
Authors: Dugan Caroline , Zikopoulos Basilis , Yazdanbakhsh Arash
Published: July 2024

Patients with schizophrenia exhibit abnormalities in spatial frequency sensitivity, and it is believed that these abnormalities indicate more widespread dysfunction and dysregulation of bottom-up processing. The early visual system, including the first-order Lateral Geniculate Nucleus of the thalamus (LGN) and the primary visual cortex (V1), are key contributors to spatial frequency sensitivity. Medicated and unmedicated patients with schizophrenia exhibit contrasting changes in spatial frequency sensitivity, thus making it a useful probe for examining potential effects of the disorder and antipsychotic medications in neural processing. We constructed a parameterized, rate-based neural model of on-center/off-surround neurons in the early visual system to investigate the impacts of changes to the excitatory and inhibitory receptive field subfields. By incorporating changes in both the excitatory and inhibitory subfields that are associated with pathophysiological findings in schizophrenia, the model successfully replicated perceptual data from behavioral/functional studies involving medicated and unmedicated patients. Among several plausible mechanisms, our results highlight the dampening of excitation and/or increase in the spread and strength of the inhibitory subfield in medicated patients and the contrasting decreased spread and strength of inhibition in unmedicated patients. Given that the model was successful at replicating results from perceptual data under a variety of conditions, these elements of the receptive field may be useful markers for the imbalances seen in patients with schizophrenia.
Co-inheritance of recombined chromatids maintains heterozygosity in a parthenogenetic ant
Authors: Lacy Kip D. , Hart Taylor , Kronauer Daniel J. C.
Published: July 2024

According to Mendel’s second law, chromosomes segregate randomly in meiosis. Non-random segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte. Here we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi, in which both alleles are co-inherited at all loci across the entire genome. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole-genome sequencing, we show that crossover recombination is, in fact, common but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel’s law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular ‘memory’ of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
The Tropical Andes Biodiversity Hotspot: A Comprehensive Dataset for the Mira-Mataje Binational Basins
Authors: Yánez-Muñoz Mario H. , Jarrín-V. Pablo , Brito M. Jorge , Román-RR Roberto , Astorquiza Juranny M. , Baca Aida E. , Baker Paul A. , Bejarano-Muñoz Patricia , Cuesta R. Eric Y. , Freire Efraín , Garzón César , Gómez-Paredes Jorge , Klinger William , Lagos Luz E. , Medina Wilderson , Mena-Valenzuela Patricio , Mosquera R. Luis J. , Mosquera M. Robinson S. , Murillo Yirsela , Murillo A. Yiscar D. , Nagle R. Edsson , Narváez Germán , Pimm Stuart , Proaño Cecilia , Prieto A. Francisco J. , Quezada Zoraida , Ramírez Giovanny , Rengifo I. Reimer , Rentería M. Luis E. , Urgilés-Merchán Miguel A. , Vargas Lady , Valdospinos Carla , Valolyes Zulmary , Inclán Diego J.
Published: July 2024

We present a flora and fauna dataset for the Mira-Mataje binational basins. This is an area shared between southwestern Colombia and northwestern Ecuador, where both the Chocó and Tropical Andes biodiversity hotspots converge. We systematized data from 120 sources in the Darwin Core Archive (DwC-A) standard and geospatial vector data format for geographic information systems (GIS) (shapefiles). Sources included natural history museums, published literature, and citizen science repositories across 13 countries. The resulting database has 33,460 records from 6,821 species, of which 540 have been recorded as endemic, and 612 as threatened. The diversity represented in the dataset is equivalent to 10% of the total plant species and 26% of the total terrestrial vertebrate species in both hotspots. The dataset can be used to estimate and compare biodiversity patterns with environmental parameters and provide value to ecosystems, ecoregions, and protected areas. The dataset is a baseline for future assessments of biodiversity in the face of environmental degradation, climate change, and accelerated extinction processes.
Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis
Authors: Devanna Basavantraya Navadagi , Sucharita Sumali , Sunitha N. C. , Anilkumar C. , Singh Pankaj K. , Pramesh D. , Samantaray Sanghamitra , Behera Lambodar , Katara Jawahar Lal , Parameswaran C. , Rout Prachitara , Sabarinathan Selvaraj , Rajashekara Hosahatti , Sharma Tilak Raj
Published: July 2024

Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS–LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.
Magnetic field and initial stress on a rotating photothermal semiconductor medium with ramp type heating and internal heat source
Authors: Salah Doaa M. , Abd-Alla A. M. , Abo-Dahab S. M. , Alharbi F. M. , Abdelhafez M. A.
Published: July 2024

This manuscript addresses a significant research gap in the study by employing a mathematical model of photo thermoelastic wave propagation in a rotator semiconductor medium under the effect of a magnetic field and initial stress, as well as ramp-type heating. The considered model is formulated during the photothermal theory and in two-dimensional (2D) electronic-elastic deformation. The governing equations represent the interaction between the primary physical parameters throughout the process of photothermal transfer. Computational simulations are performed to determine the temperature, carrier density, displacement components, normal stress, and shear stress using the application of Lame’s potential and normal mode analysis. Numerical calculations are carried out and graphically displayed for an isotropic semiconductor like silicon (Si) material. Furthermore, comparisons are made with the previous results obtained by the others, as well as in the presence and absence of magnetic field, rotation, and initial stress. The obtained results illustrate that the rotation, initial stress, magnetic field, and ramp-type heating parameter all have significant effects. This investigation provides valuable insights into the synergistic dynamics among a magnetization constituent, semiconducture structures, and wave propagation, enabling advancements in nuclear reactors' construction, operation, electrical circuits, and solar cells.
Predicting pathological complete response after neoadjuvant chemotherapy in breast cancer by clinicopathological indicators and ultrasound parameters using a nomogram
Authors: Zhang Tingjian , Liu Yuyao , Tian Tian
Published: July 2024

The study explored the impact of pretreatment serum albumin-to-alkaline phosphatase ratio (AAPR) and changes in tumor blood supply on pathological complete response (pCR) in breast cancer (BC) patients following neoadjuvant chemotherapy (NACT). Additionally, a nomogram for predicting pCR was established and validated. The study included BC patients undergoing NACT at Yongchuan Hospital of Chongqing Medical University from January 2019 to October 2023. We analyzed the correlation between pCR and clinicopathological factors, as well as tumor ultrasound features, using chi-square or Fisher's exact test. We developed and validated a nomogram predicting pCR based on regression analysis results. The study included 176 BC patients. Logistic regression analysis identified AAPR [odds ratio (OR) 2.616, 95% confidence interval (CI) 1.140–5.998, P = 0.023], changes in tumor blood supply after two NACT cycles (OR 2.247, 95%CI 1.071–4.716, P = 0.032), tumor histological grade (OR 3.843, 95%CI 1.286–10.659, P = 0.010), and HER2 status (OR 2.776, 95%CI 1.057–7.240, P = 0.038) as independent predictors of pCR after NACT. The nomogram, based on AAPR, changes in tumor blood supply after two NACT cycles, tumor histological grade, and HER2 status, demonstrated a good predictive capability.
Improvement of Bacillus subtilis PI agarase production, hydrolysate scavenging capability assessment, and saccharification of algal biomass for green ethanol generation
Authors: Goda Doaa A. , Shalaby Nagham H. , Soliman Nadia A.
Published: July 2024

The goal of the current work was to optimize the growth parameters needed to manufacture agarase enzyme from a non-marine PI strain of Bacillus subtilis on an agar-based medium. Using Plackett–Burman design (PBD), nine process parameters were evaluated, and agar, peptone, and yeast-extract were identified as the most significant independent factors influencing agarase production with confidence levels more than 90%. To evaluate the optimal concentrations of the indicated process parameters on agarase production, the Box–Behnken design (BBD) was applied. After optimization, B. subtilis strain PI produced 119.8 U/ml of agarase, representing a 1.36-fold increase. In addition the agar hydrolysate fermented products contain the liberated oligosaccharide acts as strong antioxidant which has 62.4% scavenging activity. Also, the agarase yields increased (1141.12, 1350.253, 1684.854 and 1921.863 U/ml) after substitution the agar with algal biomass of Carolina officinalis at different concentrations (2, 5, 10 and 15%), respectively. After completing the saccharification process, the resulted hydrolysate was used to produce ethanol through fermentation with Pichia pastoris yeast strain as an economical method giving yields (6.68317, 7.09748, 7.75648 and 8.22332 mg/ml), that are higher than using yeast extract peptone dextrose (YPD) medium (4.461 mg/ml).
Systematic analysis of microorganisms’ metabolism for selective targeting
Authors: Dehghan Manshadi Mehdi , Setoodeh Payam , Zare Habil
Published: July 2024

Selective drugs with a relatively narrow spectrum can reduce the side effects of treatments compared to broad-spectrum antibiotics by specifically targeting the pathogens responsible for infection. Furthermore, combating an infectious pathogen, especially a drug-resistant microorganism, is more efficient by attacking multiple targets. Here, we combined synthetic lethality with selective drug targeting to identify multi-target and organism-specific potential drug candidates by systematically analyzing the genome-scale metabolic models of six different microorganisms. By considering microorganisms as targeted or conserved in groups ranging from one to six members, we designed 665 individual case studies. For each case, we identified single essential reactions as well as double, triple, and quadruple synthetic lethal reaction sets that are lethal for targeted microorganisms and neutral for conserved ones. As expected, the number of obtained solutions for each case depends on the genomic similarity between the studied microorganisms. Mapping the identified potential drug targets to their corresponding pathways highlighted the importance of key subsystems such as cell envelope biosynthesis, glycerophospholipid metabolism, membrane lipid metabolism, and the nucleotide salvage pathway. To assist in the validation and further investigation of our proposed potential drug targets, we introduced two sets of targets that can theoretically address a substantial portion of the 665 cases. We expect that the obtained solutions provide valuable insights into designing narrow-spectrum drugs that selectively cause system-wide damage only to the target microorganisms.
CXCL9, IL2RB, and SPP1, potential diagnostic biomarkers in the co-morbidity pattern of atherosclerosis and non-alcoholic steatohepatitis
Authors: Wu Xize , Yuan Changbin , Pan Jiaxiang , Zhou Yi , Pan Xue , Kang Jian , Ren Lihong , Gong Lihong , Li Yue
Published: July 2024

Non-alcoholic steatohepatitis (NASH) is a hepatocyte inflammation based on hepatocellular steatosis, yet there is no effective drug treatment. Atherosclerosis (AS) is caused by lipid deposition in the endothelium, which can lead to various cardiovascular diseases. NASH and AS share common risk factors, and NASH can also elevate the risk of AS, causing a higher morbidity and mortality rate for atherosclerotic heart disease. Therefore, timely detection and diagnosis of NASH and AS are particularly important. In this study, differential gene expression analysis and weighted gene co-expression network analysis were performed on the AS (GSE100927) and NASH (GSE89632) datasets to obtain common crosstalk genes, respectively. Then, candidate Hub genes were screened using four topological algorithms and externally validated in the GSE43292 and GSE63067 datasets to obtain Hub genes. Furthermore, immune infiltration analysis and gene set variation analysis were performed on the Hub genes to explore the underlying mechanisms. The DGIbd database was used to screen candidate drugs for AS and NASH. Finally, a NASH model was constructed using free fatty acid-induced human L02 cells, an AS model was constructed using lipopolysaccharide-induced HUVECs, and a co-morbidity model was constructed using L02 cells and HUVECs to verify Hub gene expression. The result showed that a total of 113 genes common to both AS and NASH were identified as crosstalk genes, and enrichment analysis indicated that these genes were mainly involved in the regulation of immune and metabolism-related pathways. 28 candidate Hub genes were screened according to four topological algorithms, and CXCL9, IL2RB, and SPP1 were identified as Hub genes after in vitro experiments and external dataset validation. The ROC curves and SVM modeling demonstrated the good diagnostic efficacy of these three Hub genes. In addition, the Hub genes are strongly associated with immune cell infiltration, especially macrophages and γ–δ T cell infiltration. Finally, five potential therapeutic drugs were identified. has-miR-185 and hsa-miR-335 were closely related to AS and NASH. This study demonstrates that CXCL9, IL2RB, and SPP1 may serve as potential biomarkers for the diagnosis of the co-morbidity patterns of AS and NASH and as potential targets for drug therapy.
A microtomographic and histopathological evaluation of dental cements as late-stage peri-implant complication in a rat model
Authors: Lakkasetter Chandrashekar Bhuvana , Biguetti Claudia C. , Arteaga Alexandra , Miramontes Andres J. , Rios Evelin , Rodrigues Danieli C.
Published: July 2024

Cement mediated peri-implantitis accounts for 1.9–75% of dental implant failures associated with peri-implant diseases. This study evaluated the biological impact of dental cements on osseointegrated implants using Lewis rats. Twenty-two rats were distributed into 6 groups: negative control (NC) soft diet (SD), and hard diet (HD); positive control SD and HD (n = 3); Implant + bio-ceramic Cement (BC) SD and HD which included contralateral Sham sites (n = 5). Titanium implants were placed on either side of the maxillae and allowed to heal for 14 days. Later, both sides of experimental groups underwent a re-entry surgery to simulate clinical cementation. The right side received 0.60 mg of BC. At 14 days post cement application, maxillae were harvested for clinical, microtomographic, and histological evaluations. Clinical and microtomographic evaluations indicated evidence of extensive inflammation and circumferential bone resorption around BC implants in comparison to NC. Histology revealed cement particles surrounded by inflammatory infiltrate in the implant area accompanied by biofilm for SD groups. Both sides of BC indicated intensive bone resorption accompanied by signs of osteolysis when compared to NC. Cemented groups depicted significantly lower bone to implant contact when compared to NC. In conclusion, residual cement extravasation negatively impacted osseointegrated implants after re-entry surgeries.
Effect of gamma irradiation on properties of the synthesized PANI-Cu nanoparticles assimilated into PS polymer for electromagnetic interference shielding application
Authors: Bekhit Mohamad , Fathy E. S. , Sharaf A.
Published: July 2024

Conductive polymer nanocomposites for electromagnetic interference (EMI) shielding are important materials that can be combat the increasingly dangerous radiation pollution arising from electronic equipment and our surrounding environment. In this work, we have synthesized polyaniline-copper nanoparticles (PANI-Cu NPs) by the copper salt based oxidative polymerization method at room temperature and then added with different concentration (0, 1, 3 and 5 wt%) in polystyrene polymer forming PS/ PANI-Cu nanocomposites films by means of the traditional solution casting technique. The formed PANI-Cu NPs were investigated by UV/Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM) and SEM/EDX elemental mapping techniques. On the other hand, the prepared PS/PANI-Cu nanocomposites films were evaluated by UV and SEM, the mechanical properties of the nanocomposites films were evaluated and showed an improvement by added PANI-Cu NPs up to 3 wt% and 50 kGy gamma exposure dose. The PS/PANI-Cu nanocomposites films were examined as electromagnetic interference shielding material. Electromagnetic shielding effectiveness of the produced nanocomposites were tested in the X-band of the radio frequency range namely from 8 to 12 GHz using the vector network analyzer (VNA) and a proper wave guide. All samples were studied before and after 50 kGy gamma-ray irradiation under the same condition of pressure and temperature. The results showed that the nanocomposites have improved shielding properties.
Protozoan communities serve as a strong indicator of water quality in the Nile River
Authors: El-Tohamy Wael S. , Taher Mohamed E. , Ghoneim Ahmed M. , Hopcroft Russell R.
Published: July 2024

The relationship between the protozoan communities and environmental variables was studied in the Nile River to evaluate their potential as water quality indicators. Protozoans were sampled monthly at six sampling sites in the Nile's Damietta Branch across a spatial gradient of environmental conditions during a 1-year cycle (February 2016–January 2017). The Protozoa community was comprised of 54 species belonging to six main heterotrophic Protozoa phyla. The abundance (average, 1089 ± 576.18 individuals L−1) and biomass (average, 86.60 ± 106.13 μg L−1) were comparable between sites. Ciliates comprised the majority of protozoan species richness (30 species), abundance (79.72%), and biomass (82.90%). Cluster analysis resulted in the distribution of protozoan species into three groups, with the most dominant species being the omnivorous ciliate Paradileptus elephantinus. Aluminium, fluoride, and turbidity negatively affected abundance and biomass, while dissolved oxygen and potassium positively impacted biomass. Of the dominant species recorded over the study area, the amoebozoa Centropyxis aculeata was associated with runoff variables, while the bacterivorous ciliates Colpidium colpoda, Glaucoma scintillans, and Vorticella convallaria were related to the abundance of heterotrophic bacteria, phytoplankton biomass, and total organic carbon. Total dissolved salts, PO4, NH3, NO2, dissolved oxygen, and total organic carbon were the strongest causative factors for protozoa distribution. The α-Mesosaprobic environment at site VI confirmed a high load of agricultural runoffs compared to other sites. This study demonstrates that protozoans can be a potential bioindicator of water quality status in this subtropical freshwater river system.
Rifabutin loaded inhalable β-glucan microparticle based drug delivery system for pulmonary TB
Authors: Ahmad Firoz , Ahmad Shad , Upadhyay Tarun Kumar , Singh Sanjay , Khubaib Mohd , Singh Jyotsna , Saeed Mohd , Ahmad Irfan , Al-Keridis Lamya Ahmed , Sharma Rolee
Published: July 2024

Inhalable microparticle-based anti TB drug delivery systems are being investigated extensively for Tuberculosis [TB] treatment as they offer efficient and deep lung deposition with several advantages over conventional routes. It can reduce the drug dose, treatment duration and toxic effects and optimize the drug bioavailability. Yeast derived β-glucan is a β-[1–3/1–6] linked biocompatible polymer and used as carrier for various biomolecules. Due to presence of glucan chains, particulate glucans act as PAMP and thereby gets internalized via receptor mediated phagocytosis by the macrophages. In this study, β-glucan microparticles were prepared by adding l-leucine as excipient, and exhibited 70% drug [Rifabutin] loading efficiency. Further, the sizing and SEM data of particles revealed a size of 2–4 µm with spherical dimensions. The FTIR and HPLC data confirmed the β-glucan composition and drug encapsulations efficiency of the particles. The mass median aerodynamic diameter [MMAD] and geometric standard deviation [GSD] data indicated that these particles are inhalable in nature and have better thermal stability as per DSC thermogram. These particles were found to be non-toxic upto a concentration of 80 µg/ml and were found to be readily phagocytosed by human macrophage cells in-vitro as well as in-vivo by lung alveolar macrophage. This study provides a framework for future design of inhalable β-glucan particle based host-directed drug delivery system against pulmonary TB.
Association of dietary and lifestyle inflammation score (DLIS) with chronic migraine in women: a cross-sectional study
Authors: Bakhshimoghaddam Farnush , Shalilahmadi Davood , Mahdavi Reza , Nikniaz Zeinab , Karandish Majid , Hajjarzadeh Samaneh
Published: July 2024

Due to more frequent and intense attacks, chronic migraine (CM) sufferers usually report more disability compared to patients with episodic migraine (EM). There is increasing evidence that points to inflammatory diet and lifestyle as a probable underlying cause of migraine. The present study investigated the association of dietary and lifestyle inflammation scores (DLIS) with the odds of CM in Iranian women. In the current study, 285 women with migraine enrolled. Migraine was diagnosed by a single neurologist based on the third edition of the International Classification of Headache Disorders (ICHD-III). The women were categorized into CM and EM groups based on their attack frequency per month. Adherence to the dietary inflammation score (DIS), Lifestyle Inflammatory Score (LIS), and DLIS (DIS + LIS) was assessed based on last year’s dietary intakes collected using a semi-quantitative food frequency questionnaire (FFQ). The Odds Ratio (OR) for CM across the DIS, LIS, and DLIS tertiles were assessed through logistic regression. Most of the participants were overweight or obese (74.4%). The percentage of women with CM was 40.7%. Women with CM had significantly higher DIS (P = 0.002) and DLIS (P = 0.04) than women with EM. There was a significant positive association between CM and DIS. Those in the third tertile of the DIS had almost two times higher chance of experiencing chronic migraine compared with those in the first tertile [OR = 2.02; 95% CI 1.06–3.82; P = 0.03]. the P-value for the trend also was significant (0.03). In terms of LIS and DLIS tertiles, no significant association was observed. Adherence to the more inflammatory diets was associated with higher chances of experiencing CM in women.