bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics analysis of a case of congenital microtia reveals aldob and oxidative stress associated with microtia etiology
Authors: Liu Wenbo , Wu Yi , Ma Rulan , Zhu Xinxi , Wang Rui , He Lin , Shu Maoguo 
Published: May 2024

Abstract
Background
Microtia is reported to be one of the most common congenital craniofacial malformations. Due to the complex etiology and the ethical barrier of embryonic study, the precise mechanisms of microtia remain unclear. Here we report a rare case of microtia with costal chondrodysplasia based on bioinformatics analysis and further verifications on other sporadic microtia patients.

Results
One hundred fourteen deleterious insert and deletion (InDel) and 646 deleterious SNPs were screened out by WES, candidate genes were ranked in descending order according to their relative impact with microtia. Label-free proteomic analysis showed that proteins significantly different between the groups were related with oxidative stress and energy metabolism. By real-time PCR and immunohistochemistry, we further verified the candidate genes between other sporadic microtia and normal ear chondrocytes, which showed threonine aspartase, cadherin-13, aldolase B and adiponectin were significantly upregulated in mRNA levels but were significantly lower in protein levels. ROS detection and mitochondrial membrane potential (∆ Ψ m) detection proved that oxidative stress exists in microtia chondrocytes.

Conclusions
Our results not only spot new candidate genes by WES and label-free proteomics, but also speculate for the first time that metabolism and oxidative stress may disturb cartilage development and this might become therapeutic targets and potential biomarkers with clinical usefulness in the future.
Hypothalamic protein profiling from mice subjected to social defeat stress
Authors: Mitra Shiladitya , Sameer Kumar Ghantasala S. , Samanta Anumita , Schmidt Mathias V. , Thakur Suman S. 
Published: May 2024

AbstractThe Hypothalmic-Pituitary-Adrenal axis also known as the HPA axis is central to stress response. It also acts as the relay center between the body and the brain. We analysed hypothalamic proteome from mice subjected to chronic social defeat paradigm using iTRAQ based quantitative proteomics to identify changes associated with stress response. We identified greater than 2000 proteins after processing our samples analysed through Q-Exactive (Thermo) and Orbitrap Velos (Thermo) at 5% FDR. Analysis of data procured from the runs showed that the proteins whose levels were affected belonged primarily to mitochondrial and metabolic processes, translation, complement pathway among others. We also found increased levels of fibrinogen, myelin basic protein (MBP) and neurofilaments (NEFL, NEFM, NEFH) in the hypothalamus from socially defeated mice. Interestingly, research indicates that these proteins are upregulated in blood and CSF of subjects exposed to trauma and stress. Since hypothalamus secreted proteins can be found in blood and CSF, their utility as biomarkers in depression holds an impressive probability and should be validated in clinical samples.
Exploring the lung-gut direction of the gut-lung axis in patients with ARDS
Authors: Ziaka Mairi , Exadaktylos Aristomenis 
Published: May 2024

AbstractAcute respiratory distress syndrome (ARDS) represents a life-threatening inflammatory reaction marked by refractory hypoxaemia and pulmonary oedema. Despite advancements in treatment perspectives, ARDS still carries a high mortality rate, often due to systemic inflammatory responses leading to multiple organ dysfunction syndrome (MODS). Indeed, the deterioration and associated mortality in patients with acute lung injury (LI)/ARDS is believed to originate alongside respiratory failure mainly from the involvement of extrapulmonary organs, a consequence of the complex interaction between initial inflammatory cascades related to the primary event and ongoing mechanical ventilation-induced injury resulting in multiple organ failure (MOF) and potentially death. Even though recent research has increasingly highlighted the role of the gastrointestinal tract in this process, the pathophysiology of gut dysfunction in patients with ARDS remains mainly underexplored. This review aims to elucidate the complex interplay between lung and gut in patients with LI/ARDS. We will examine various factors, including systemic inflammation, epithelial barrier dysfunction, the effects of mechanical ventilation (MV), hypercapnia, and gut dysbiosis. Understanding these factors and their interaction may provide valuable insights into the pathophysiology of ARDS and potential therapeutic strategies to improve patient outcomes.
Breast cancer patients enrolled in the Swiss mammography screening program “donna” demonstrate prolonged survival
Authors: Kuklinski David , Blum Marcel , Subelack Jonas , Geissler Alexander , Eichenberger Alena , Morant Rudolf 
Published: May 2024

AbstractStudy goalWe compared the survival rates of women with breast cancer (BC) detected within versus outside the mammography screening program (MSP) “donna”.MethodsWe merged data from the MSP with the data from corresponding cancer registries to categorize BC cases as within MSP (screen-detected and interval carcinomas) and outside the MSP. We analyzed the tumor stage distribution, tumor characteristics and the survival of the women. We further estimated hazard ratios using Cox-regressions to account for different characteristics between groups and corrected the survival rates for lead-time bias.ResultsWe identified 1057 invasive (ICD-10: C50) and in-situ (D05) BC cases within the MSP and 1501 outside the MSP between 2010 and 2019 in the Swiss cantons of St. Gallen and Grisons. BC within the MSP had a higher share of stage I carcinoma (46.5% vs. 33.0%;p < 0.01), a smaller (mean) tumor size (19.1 mm vs. 24.9 mm,p < 0.01), and fewer recurrences and metastases in the follow-up period (6.7% vs. 15.6%,p < 0.01). The 10-year survival rates were 91.4% for women within and 72.1% for women outside the MSP (p < 0.05). Survival difference persisted but decreased when women within the same tumor stage were compared. Lead-time corrected hazard ratios for the MSP accounted for age, tumor size and Ki-67 proliferation index were 0.550 (95% CI 0.389, 0.778;p < 0.01) for overall survival and 0.469 (95% CI 0.294, 0.749;p < 0.01) for BC related survival.ConclusionWomen participating in the “donna” MSP had a significantly higher overall and BC related survival rate than women outside the program. Detection of BC at an earlier tumor stage only partially explains the observed differences.
Current status of community resources and priorities for weed genomics research
Authors: Montgomery Jacob , Morran Sarah , MacGregor Dana R. , McElroy J. Scott , Neve Paul , Neto Célia , Vila-Aiub Martin M. , Sandoval Maria Victoria , Menéndez Analia I. , Kreiner Julia M. , Fan Longjiang , Caicedo Ana L. , Maughan Peter J. , Martins Bianca Assis Barbosa , Mika Jagoda , Collavo Alberto , Merotto Aldo , Subramanian Nithya K. , Bagavathiannan Muthukumar V. , Cutti Luan , Islam Md. Mazharul , Gill Bikram S. , Cicchillo Robert , Gast Roger , Soni Neeta , Wright Terry R. , Zastrow-Hayes Gina , May Gregory , Malone Jenna M. , Sehgal Deepmala , Kaundun Shiv Shankhar , Dale Richard P. , Vorster Barend Juan , Peters Bodo , Lerchl Jens , Tranel Patrick J. , Beffa Roland , Fournier-Level Alexandre , Jugulam Mithila , Fengler Kevin , Llaca Victor , Patterson Eric L. , Gaines Todd A. 
Published: May 2024

AbstractWeeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
Nasal profile changes after LeFort I osteotomy (maxillary advancement) with and without ANS reduction in class III skeletal patients: a study protocol for a randomized clinical trial
Authors: Sezavar Mehdi , Moghaddamshaldoozi Hossein Rastegar , Haraji Afshin , Ghanipour Nima , Salmasi Salar Chaychi 
Published: May 2024

Abstract
Background
Dentofacial malformation is a common condition that affects a significant portion of the population, resulting in functional and aesthetic defects. Orthognathic surgeries, such as LeFort I osteotomy, are performed to correct these abnormalities. However, the impact of these surgeries on nasal profile changes remains unclear. Additionally, the role of anterior nasal spine (ANS) reduction in maxillary advancement surgeries of 3–5 mm range is yet to be determined. This study aims to investigate the effect of ANS reduction on soft tissue profile changes following LeFort I osteotomy with a maxillary advancement range of 3–5 mm in class III skeletal patients. The hypothesis is that the changes in nasolabial angle and upper lip length will not significantly differ between patients who undergo LeFort I osteotomy with and without ANS reduction.

Method and design
This study is designed as a randomized controlled trial. A total of 26 class III skeletal patients with maxillofacial abnormalities will be recruited from the maxillofacial clinic of Bu-Ali and Farahikhtegan Hospitals in Tehran, Iran. Patients meeting the inclusion criteria will be randomly assigned to two groups: one group will undergo LeFort I osteotomy with ANS reduction, and the other group will undergo LeFort I osteotomy without ANS reduction. The soft tissue profile changes, specifically the nasolabial angle and upper lip length, will be evaluated and compared between the two groups.

Discussion
Achieving facial harmony through orthognathic surgery requires careful planning and consideration of the impact on surrounding soft tissue. The primary objective is to predict and plan for the effects on the nasolabial region. LeFort I osteotomy is a common procedure used to correct dentofacial deformities, particularly in class III patients. Maxillary advancement during this surgery can lead to changes in nasal tip position, width, and rotation, potentially due to repositioning of the anterior nasal spine and soft tissue dissection. In this study, soft tissue changes will be assessed in non-growing class III patients using cephalometric radiographs. The impact of reducing the anterior nasal spine (ANS) on nasal profile changes will be investigated for maxillary advancements of 3–5 mm. Objective measurements and patient-reported outcomes will be evaluated to gain insights into the aesthetic outcomes of orthognathic surgery. The findings will provide valuable guidance for treatment decisions and alternative options based on expected nasal profile changes.

Trial registration
This project was registered at The Iranian Registry of Clinical Trials (Identifier No. IRCT20210928052625N1, Website: https://www.irct.ir/trial/59171) and Open Science Framework (OSF) (Registration https://doi.org/10.17605/OSF.IO/X3HD4). 2021-06-09.
Size-dependent enhancement of gene expression by Plasmodium 5’UTR introns
Authors: Lin Lirong , Liu Yanjing , Liang Rui , Guo Yue , Xu Ruixue , Fan Ruoxi , Jiao Zhiwei , Zhao Wenting , Yue Lixia , Lu Mingke , Liu Shengfa , Su Xin-zhuan , Li Jian 
Published: May 2024

Abstract
Background
Eukaryotic genes contain introns that are removed by the spliceosomal machinery during mRNA maturation. Introns impose a huge energetic burden on a cell; therefore, they must play an essential role in maintaining genome stability and/or regulating gene expression. Many genes (> 50%) in Plasmodium parasites contain predicted introns, including introns in 5′ and 3′ untranslated regions (UTR). However, the roles of UTR introns in the gene expression of malaria parasites remain unknown.

Methods
In this study, an episomal dual-luciferase assay was developed to evaluate gene expression driven by promoters with or without a 5′UTR intron from four Plasmodium yoelii genes. To investigate the effect of the 5′UTR intron on endogenous gene expression, the pytctp gene was tagged with 3xHA at the N-terminal of the coding region, and parasites with or without the 5′UTR intron were generated using the CRISPR/Cas9 system.

Results
We showed that promoters with 5′UTR introns had higher activities in driving gene expression than those without 5′UTR introns. The results were confirmed in recombinant parasites expressing an HA-tagged gene (pytctp) driven by promoter with or without 5′UTR intron. The enhancement of gene expression was intron size dependent, but not the DNA sequence, e.g. the longer the intron, the higher levels of expression. Similar results were observed when a promoter from one strain of P. yoelii was introduced into different parasite strains. Finally, the 5′UTR introns were alternatively spliced in different parasite development stages, suggesting an active mechanism employed by the parasites to regulate gene expression in various developmental stages.

Conclusions
Plasmodium 5′UTR introns enhance gene expression in a size-dependent manner; the presence of alternatively spliced mRNAs in different parasite developmental stages suggests that alternative slicing of 5′UTR introns is one of the key mechanisms in regulating parasite gene expression and differentiation.

Graphical Abstract
Impact of squat set configuration on mechanical performance in paired sets of upper-body exercises
Authors: Janicijevic Danica , Miras-Moreno Sergio , Morenas-Aguilar Maria Dolores , Chacon-Ventura Sara , Weakley Jonathon , García-Ramos Amador 
Published: May 2024

Abstract
Background
Paired sets and alternative set configurations (e.g., cluster sets) are frequently employed by strength and conditioning practitioners; however, their synergistic impact remains underexplored in research. This study aimed to elucidate whether the set configuration used in a lower-body exercise affects mechanical performance during paired sets of upper-body exercises.

Methods
Twenty-one resistance-trained individuals (14 men and 7 women) randomly completed three experimental sessions that involved four sets of five repetitions at 75%1RM during both the bench press and bench pull exercises. The three experimental sessions varied solely in the activity conducted during the inter-set rest periods of each upper-body exercise: (i) Traditional squat – six squat repetitions without intra-set rest at 65%1RM; (ii) Rest redistribution squat – two clusters of three repetitions of the squat exercise at 65%1RM with 30 s of intra-set rest; and (iii) Passive rest – no exercise.

Results
The rest redistribution set configuration allowed the sets of the squat exercise to be performed at a faster velocity than the traditional set configuration (p = 0.037). However, none of the mechanical variables differed between the exercise protocols neither in the bench press (p ranged from 0.279 to 0.875) nor in the bench pull (p ranged from 0.166 to 0.478).

Conclusions
Although rest redistribution is an effective strategy to alleviate fatigue during the sets in which it is implemented, it does not allow subjects to perform better in subsequent sets of the training session.
In-silico analysis of ribosome inactivating protein (RIP) of the Cucurbitaceae family
Authors: Maqsood Quratulain , Sumrin Aleena , Ali Qurban , Hussain Nazim , Malook Saif Ul , Ali Daoud 
Published: May 2024

AbstractRibosome-inactivating proteins (RIPs) are highly active N-glycosidases that depurinate both bacterial and eukaryotic rRNAs, halting protein synthesis during translation. Found in a diverse spectrum of plant species and tissues, RIPs possess antifungal, antibacterial, antiviral, and insecticidal properties linked to plant defense. In this study, we investigated the physiochemical properties of RIP peptides from the Cucurbitaceae family through bioinformatics approaches. Molecular weight, isoelectric point, aliphatic index, extinction coefficient, and secondary structures were analyzed, revealing their hydrophobic nature. The novelty of this work lies in the comprehensive examination of RIPs from the Cucurbitaceae family and their potential therapeutic applications. The study also elucidated the binding interactions of Cucurbitaceae RIPs with key biological targets, including Interleukin-6 (IL-6). Strong hydrogen bond interactions between RIPs and these targets suggest potential for innovative insilico drug design and therapeutic applications, particularly in cancer treatment. Comprehensive analysis of bond lengths using Ligpolt + software provides insights for optimizing molecular interactions, offering a valuable tool for drug design and structural biology studies.
Stochastic dynamics of an SIR model for respiratory diseases coupled air pollutant concentration changes
Authors: He Sha , Tan Yiping , Wang Weiming 
Published: May 2024

AbstractIndustrial development has made air pollution increasingly severe, and many respiratory diseases are closely related to air quality in terms of infection and transmission. In this work, we used the classic stochastic susceptible–infectious–recovered (SIR) model to reflect the spread of respiratory disease, coupled with the diffusion process of air pollutants to the infectious disease model, and we investigated the impact of various environmental noises on the process of disease transmission and air pollutant diffusion. The value of this study lies in two aspects. Mathematically, we define threshold $\mathcal{R}_{1}^{s}$

R
1
s

for extinction and threshold $\mathcal{R}_{2}^{s}$

R
2
s

for persistence of the disease in the stochastic model ($\mathcal{R}_{2}^{s}<\mathcal{R}_{1}^{s}$

R
2
s

<

R
1
s

) when the parameters are constant, and we show that (i) when $\mathcal{R}_{1}^{s}$

R
1
s

is less than 1, the disease will go to stochastic extinction; (ii) when $\mathcal{R}_{2}^{s}$

R
2
s

is larger than 1, the disease will persist almost surely and the model has a unique ergodic stationary distribution; (iii) when $\mathcal{R}_{1}^{s}$

R
1
s

is larger than 1 and $\mathcal{R}_{2}^{s}$

R
2
s

is less than 1, the extinction of the disease has randomness, which is demonstrated through numerical experiments. In addition, we derive the exact expression of the probability density function of the stationary distribution by solving the corresponding Fokker–Planck equation under the condition of disease persistence and analyze the effects of random noises on stationary distribution characteristics and the disease extinction. Epidemiologically, the change of the concentration of air pollutants affects the conditions for disease extinction and persistence. The increase in the inflow of pollutants and the increase in the clearance rate have negative and positive impacts on the spread of diseases, respectively. We found that an increase in random noise intensity will increase the variance, reduce the kurtosis of distribution, which is not conducive to predicting and controlling the development status of the disease; however, large random noise intensity can also increase the probability of disease extinction and accelerates disease extinction. We further investigate the dynamic of the stochastic model, assuming that the inflow rate switches between two levels by numerical experiments. The results show that the random noise has a significant impact on disease extinction. The data fitting of the switching model shows that the model can effectively depict the relationship and changes in trends between air pollution and diseases.
Natural variation in tocopherols, B vitamins, and isoflavones in seeds of 13 Korean conventional soybean varieties
Authors: Kim Eun-Ha , Jung Jung-Won , Yu Oh Suk , Lee So-Young , Kim Myeong-Ji , Lee Sang-Gu , Park Hyoun-Min , Jo Yongmin , Joo Yongsung , Oh Seon-Woo 
Published: May 2024

AbstractSoybean seeds are excellent sources of tocopherols, B vitamins, and isoflavones, which are well known for their health benefits. This study investigated the influence of environment and genotype on these constituents across 13 Korean soybean varieties cultivated in three locations during the 2017–2019 growing seasons. Statistical analyses, employing both univariate and multivariate methods, revealed significant impacts of genetic and environmental factors on the composition of tocopherols, B vitamins, and isoflavones. Through permutational univariate analysis of variance, the primary contributors to each measured component were identified. Genotype strongly influenced the levels of β- and δ-tocopherols, whereas the interaction between location and year predominantly affected α- and γ-tocopherols. Vitamin B1 content was predominantly determined by genotype, whereas B3 and B6 were influenced by annual variations. Vitamin B2 level was primarily affected by the interplay between environmental and genotypic effects. Genotype had a significant effect on isoflavone components, with the exception of daidzein. Furthermore, early maturing varieties and those with black seed coats exhibited low levels of isoflavone components and total isoflavones, suggesting a relationship between maturity group and seed coat color in isoflavone variation. These findings can be used as reference values for compositional equivalence assessment of genetically modified soybeans.
Analysis of urban sprawl dynamics using machine learning, CA-Markov chain, and the Shannon entropy model: a case study in Mbombela City, South Africa
Authors: Mhangara Paidamwoyo , Gidey Eskinder , Manjoo Rabia 
Published: May 2024

AbstractOver half of the world’s population resides in urban areas. We anticipate that this pattern will become more evident, notably in South Africa. Therefore, research on urban spirals, both past and projected, is necessary for efficient urban land use planning and management. This study aims to assess the spatio-temporal urban sprawl dynamics from 2003 to 2033 in Mbombela, South Africa. We employed robust approaches such as machine learning, the cellular automata-Markov chain, and the Shannon entropy model to look at how urban sprawl changes over time using both the Landsat 4–5 Thematic Mapper and the 8 Operational Land Imagers. We conducted this study to bridge the gaps in existing research, which primarily focuses on past and current urban growth trends rather than future trends. The findings indicated that the coverage of built-up areas and vegetation has expanded by 1.98 km2 and 13.23 km2 between the years 2003 and 2023. On the other hand, the amount of land continues to decrease by -12.56 km2 and − 2.65 km2 annually, respectively. We anticipate an increase in the built-up area and vegetation to a total of 7.60 km2 and 0.57 km2, respectively, by the year 2033. We anticipate a total annual decline of -7.78 km2 and − 0.39 km2 in water bodies and open land coverage, respectively. This work has the potential to assist planners and policymakers in improving sustainable urban land-use planning.