bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deubiquitinase Mysm1 regulates neural stem cell proliferation and differentiation by controlling Id4 expression
Authors: Xu Zhenhua , Qin Qiaozhen , Wang Yan , Zhang Heyang , Liu Shuirong , Li Xiaotong , Chen Yue , Wang Yuqing , Ruan Huaqiang , He Wenyan , Zhang Tao , Yan Xinlong , Wang Changyong , Xu Donggang , Jiang Xiaoxia 
Published: February 2024

AbstractNeural stem cells (NSCs) are critical for brain development and maintenance of neurogenesis. However, the molecular mechanisms that regulate NSC proliferation and differentiation remain unclear. Mysm1 is a deubiquitinase and is essential for the self-renewal and differentiation of several stem cells. It is unknown whether Mysm1 plays an important role in NSCs. Here, we found that Mysm1 was expressed in NSCs and its expression was increased with age in mice. Mice with Mysm1 knockdown by crossing Mysm1 floxed mice with Nestin-Cre mice exhibited abnormal brain development with microcephaly. Mysm1 deletion promoted NSC proliferation and apoptosis, resulting in depletion of the stem cell pool. In addition, Mysm1-deficient NSCs skewed toward neurogenesis instead of astrogliogenesis. Mechanistic investigations with RNA sequencing and genome-wide CUT&Tag analysis revealed that Mysm1 epigenetically regulated Id4 transcription by regulating histone modification at the promoter region. After rescuing the expression of Id4, the hyperproliferation and imbalance differentiation of Mysm1-deficient NSCs was reversed. Additionally, knockdown Mysm1 in aged mice could promote NSC proliferation. Collectively, the present study identified a new factor Mysm1 which is essential for NSC homeostasis and Mysm1-Id4 axis may be an ideal target for proper NSC proliferation and differentiation.
Increased thrombospondin-1 levels contribute to epileptic susceptibility in neonatal hyperthermia without seizures via altered synaptogenesis
Authors: Zhai Yujie , Cheng Yao , Yuan Yi , Meng Xianfeng , Li Yang , Wang Yan , Ren Tianpu , Li Shucui , Sun Hongliu 
Published: February 2024

AbstractChildhood febrile seizures (FS) represent one of the most common types of seizures and may lead to severe neurological damage and an increased risk of epilepsy. However, most children with fevers do not show clinical manifestations of convulsions, and the consequences of hyperthermia without seizures remain elusive. This study focused on hyperthermia not reaching the individual’s seizure threshold (sub-FS stimulus). Changes in thrombospondin-1 (TSP-1) levels, synapses, seizure susceptibility, and seizure severity in subsequent FS were investigated in rats exposed to sub-FS stimuli. Pharmacological and genetic interventions were used to explore the role of TSP-1 in sub-FS-induced effects. We found that after sub-FS stimuli, the levels of TSP-1 and synapses, especially excitatory synapses, were concomitantly increased, with increased epilepsy and FS susceptibility. Moreover, more severe neuronal damage was found in subsequent FS. These changes were temperature dependent. Reducing TSP-1 levels by genetic intervention or inhibiting the activation of transforming growth factor-β1 (TGF-β1) by Leu-Ser-Lys-Leu (LSKL) led to lower synapse/excitatory synapse levels, decreased epileptic susceptibility, and attenuated neuronal injury after FS stimuli. Our study confirmed that even without seizures, hyperthermia may promote synaptogenesis, increase epileptic and FS susceptibility, and lead to more severe neuronal damage by subsequent FS. Inhibition of the TSP-1/TGF-β1 pathway may be a new therapeutic target to prevent detrimental sub-FS sequelae.
Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src
Authors: Li Zhenxi , Yang Xinghai , Fu Ruifeng , Wu Zhipeng , Xu Shengzhao , Jiao Jian , Qian Ming , Zhang Long , Wu Chunbiao , Xie Tianying , Yao Jiqiang , Wu Zhixiang , Li Wenjun , Ma Guoli , You Yu , Chen Yihua , Zhang Han-kun , Cheng Yiyun , Tang Xiaolong , Wu Pengfei , Lian Gewei , Wei Haifeng , Zhao Jian , Xu Jianrong , Ai Lianzhong , Siwko Stefan , Wang Yue , Ding Jin , Song Gaojie , Luo Jian , Liu Mingyao , Xiao Jianru 
Published: February 2024

AbstractOsteoclasts are over-activated as we age, which results in bone loss. Src deficiency in mice leads to severe osteopetrosis due to a functional defect in osteoclasts, indicating that Src function is essential in osteoclasts. G-protein-coupled receptors (GPCRs) are the targets for ∼35% of approved drugs but it is still unclear how GPCRs regulate Src kinase activity. Here, we reveal that GPR54 activation by its natural ligand Kisspeptin-10 (Kp-10) causes Dusp18 to dephosphorylate Src at Tyr 416. Mechanistically, Gpr54 recruits both active Src and the Dusp18 phosphatase at its proline/arginine-rich motif in its C terminus. We show that Kp-10 binding to Gpr54 leads to the up-regulation of Dusp18. Kiss1, Gpr54 and Dusp18 knockout mice all exhibit osteoclast hyperactivation and bone loss, and Kp-10 abrogated bone loss by suppressing osteoclast activity in vivo. Therefore, Kp-10/Gpr54 is a promising therapeutic target to abrogate bone resorption by Dusp18-mediated Src dephosphorylation.
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables
Authors: Burcham Zachary M. , Belk Aeriel D. , McGivern Bridget B. , Bouslimani Amina , Ghadermazi Parsa , Martino Cameron , Shenhav Liat , Zhang Anru R. , Shi Pixu , Emmons Alexandra , Deel Heather L. , Xu Zhenjiang Zech , Nieciecki Victoria , Zhu Qiyun , Shaffer Michael , Panitchpakdi Morgan , Weldon Kelly C. , Cantrell Kalen , Ben-Hur Asa , Reed Sasha C. , Humphry Greg C. , Ackermann Gail , McDonald Daniel , Chan Siu Hung Joshua , Connor Melissa , Boyd Derek , Smith Jake , Watson Jenna M. S. , Vidoli Giovanna , Steadman Dawnie , Lynne Aaron M. , Bucheli Sibyl , Dorrestein Pieter C. , Wrighton Kelly C. , Carter David O. , Knight Rob , Metcalf Jessica L. 
Published: February 2024

AbstractMicrobial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.
Relative synonymous codon usage and codon pair analysis of depression associated genes
Authors: Khandia Rekha , Gurjar Pankaj , Kamal Mohammad Amjad , Greig Nigel H. 
Published: February 2024

AbstractDepression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.
The development of the soderberg electrolyzer electromagnetic field’s state monitoring system
Authors: Yury Ilyushin , Martirosyan Alexander 
Published: February 2024

AbstractThis study is devoted to improving the economic efficiency of the cell, due to the field of the generated electromagnetic field’s accurate diagnostics. To solve this problem, the authors had developed a hardware-software complex for electromagnetic field diagnostics. This complex includes a measurement device and a software package for data collection and analysis. On the laboratory prototype of the aluminum electrolysis complex, a study was carried out on the formation and structure of the electromagnetic field. A number of experiments have been carried out showing the degree of formation of the electromagnetic field by the anode, the relationship of electromagnetic fields in the inter-anode space has been shown. Based on the results of the studies, conclusions were drawn about the possibility of diagnosing the current state of the anode, determining the direction of rotation of aluminum in the electrolytic cell and estimating the life of the anode and its burnout time.
Effect of nutmeg essential oil (Myristica fragrans Houtt.) on methane production, rumen fermentation, and nutrient digestibility in vitro
Authors: Abdillah Achmad Ezar , Sarah Dewi , Ardian Aziz Aji , Anas Muhsin Al , Aprianto Muhammad Anang , Hanim Chusnul , Kurniawati Asih , Muhlisin  , Yusiati Lies Mira 
Published: February 2024

AbstractThe study evaluated the effect of adding of nutmeg (Myristica fragrans Houtt.) essential oil (NEO) as a feed additive on methane production, rumen fermentation parameters, rumen enzyme activity, and nutrient digestibility in vitro. This study was divided into three treatments based on the level of NEO addition, which included 0 µL/L (T0), 100 µL/L (T1), and 200 µL/L (T2). The feed substrate composition consisted of king grass as forage and concentrate in a 60:40 ratio. Feed fermentation was conducted using the Menke and Steingass gas production and two-step Tilley and Terry in-vitro digestibility technique. The data obtained from the study were analyzed using one-way ANOVA and if there were differences between means, they were further assessed using DMRT. The results showed that T2 treatment significantly decreased (P < 0.05) ammonia (NH3) levels, total VFA, acetate, propionate, butyrate, and microbial protein (P < 0.05). Methane production and the activity of rumen protease enzyme significantly decreased (P < 0.05) at T1 and T2 treatment. The T2 treatment significantly reduced (P < 0.05) protein digestibility (IVCPD) at 48 h, while IVCPD at 96 h significantly increased (P < 0.05). On the other hand, the addition of nutmeg essential oil did not effect the activity of the amylase, carboxymethyl cellulase, and β-glucosidase enzymes, as well as the in-vitro digestibility of dry matter (IVDMD), crude fiber (IVCFD), and organic matter (IVOMD). The conclusion drawn from this study is that the optimum level for NEO is 200 µL/L, which can reduce methane production and increase crude protein digestibility at 96 h without any negative effect on rumen fermentation and nutrient digestibility.
Tissue-specific proteome profile analysis reveals regulatory and stress responsive networks in passion fruit during storage
Authors: Garcia Ellen , Koh Jin , Wu Xingbo , Sarkhosh Ali , Liu Tie 
Published: February 2024

AbstractPassiflora edulis, commonly known as passion fruit, is a crop with a fragrant aroma and refreshingly tropical flavor that is a valuable source of antioxidants. It offers a unique opportunity for growers because of its adaptability to tropical and subtropical climates. Passion fruit can be sold in the fresh market or used in value-added products, but its postharvest shelf life has not been well-researched, nor have superior cultivars been well-developed. Understanding the proteins expressed at the tissue level during the postharvest stage can help improve fruit quality and extend shelf life. In this study, we carried out comparative proteomics analysis on four passion fruit tissues, the epicarp, mesocarp, endocarp, and pulp, using multiplexed isobaric tandem mass tag (TMT) labeling quantitation. A total of 3352 proteins were identified, including 295 differentially expressed proteins (DEPs). Of these DEPs, 213 showed a fold increase greater than 1.45 (50 proteins) or a fold decrease less than 0.45 (163 proteins) with different patterns among tissue types. Among the DEPs, there were proteins expressed with functions in oxygen scavenging, lipid peroxidation, response to heat stress, and pathogen resistance. Thirty-six proteins were designated as hypothetical proteins were characterized for potential functions in immunity, cell structure, homeostasis, stress response, protein metabolism and miraculin biosynthesis. This research provides insight into tissue-specific pathways that can be further studied within fruit physiology and postharvest shelf life to aid in implementing effective plant breeding programs. Knowing the tissue-specific function of fruit is essential for improving fruit quality, developing new varieties, identifying health benefits, and optimizing processing techniques.
Vertical and horizontal reading training in patients with hemianopia and its effect on reading eye movements
Authors: Kuester-Gruber S. , Kabisch P. , Cordey-Henke A. , Martus P. , Karnath H.-O. , Trauzettel-Klosinski S. 
Published: February 2024

AbstractVertical reading training (VRTr) increases reading speed (RS) significantly in patients with hemianopic field defects (HFD). We ask, how eye movements (EM) contribute to this improvement and whether EM-behavior is affected by the side of HFD. Twenty-one patients, randomly assigned to VRTr or horizontal RTr, trained reading single lines from a screen at home, for 4 weeks. In the clinic, we recorded EM while reading short sentences aloud from a screen before training (T1), directly (T2) and 4 weeks afterwards (T3). RS-screen was correlated with RS during reading printed paragraphs (RS-print) to assess the transfer to everyday life. RS-screen and RS-print correlated positively (horizontal: r > 0.8, vertical: r > 0.9) at all times. Vertical RS did not exceed horizontal RS. We found significant negative correlations of EM-variables and RS-print: in right-HFD with the number of forward saccades (T1: r =  − 0.79, T2: r =  − 0.94), in left-HFD with the steps during return sweeps (T1: r =  − 0.83, T2: r =  − 0.56). Training effects remained stable at T3. EM-improvement was specific for the RTr and the side of the HFD: in right-HFD fewer forward saccades after VRTr, in left-HFD fewer steps during return sweeps after HRTr. RTr on a screen transfers to reading printed text in real-life situations.Trial registration: The study was retrospectively registered in the German Clinical Trials register: DRKS-ID: DRKS00018843, March 13th, 2020.
Impact of simulated acid rain on chemical properties of Nyalau series soil and its leachate
Authors: Ibrahim Mohamad Hilmi , Kasim Susilawati , Ahmed Osumanu Haruna , Mohd. Rakib Mohd. Rashid , Hasbullah Nur Aainaa , Islam Shajib Md. Tariqul 
Published: February 2024

AbstractGreenhouse gases can cause acid rain, which in turn degrades soil chemical properties. This research was conducted to determine the effects of simulated acid rain (SAR) on the chemical properties of Nyalau series (Typic paleudults). A 45-day laboratory leaching and incubation study (control conditions) was conducted following standard procedures include preparing simulated acid rain with specific pH levels, followed by experimental design/plan and systematically analyzing both soil and leachate for chemical changes over the 45-day period. Six treatments five of which were SAR (pH 3.5, 4.0, 4.5, 5.0, and 5.5) and one control referred to as natural rainwater (pH 6.0) were evaluated. From the study, the SAR had significant effects on the chemical properties of the soil and its leachate. The pH of 3.5 of SAR treatments decreased soil pH, K+, and fertility index. In contrast, the contents of Mg2+, Na+, SO42−, NO3−, and acidity were higher at the lower SAR pH. Furthermore, K+ and Mg2+ in the leachate significantly increased with increasing acidity of the SAR. The changes in Ca2+ and NH4+ between the soil and its leachate were positively correlated (r = 0.84 and 0.86), whereas the changes in NO3− negatively correlated (r = − 0.82). The novelty of these results lies in the discovery of significant alterations in soil chemistry due to simulated acid rain (SAR), particularly impacting soil fertility and nutrient availability, with notable positive and negative correlations among specific ions where prolonged exposure to acid rain could negatively affect the moderately tolerant to acidic and nutrient-poor soils. Acid rain can negatively affect soil fertility and the general soils ecosystem functions. Long-term field studies are required to consolidate the findings of this present study in order to reveal the sustained impact of SAR on tropical forest ecosystems, particularly concerning soil health, plant tolerance, and potential shifts in biodiversity and ecological balance.
White blood cells classification using multi-fold pre-processing and optimized CNN model
Authors: Saidani Oumaima , Umer Muhammad , Alturki Nazik , Alshardan Amal , Kiran Muniba , Alsubai Shtwai , Kim Tai-Hoon , Ashraf Imran 
Published: February 2024

AbstractWhite blood cells (WBCs) play a vital role in immune responses against infections and foreign agents. Different WBC types exist, and anomalies within them can indicate diseases like leukemia. Previous research suffers from limited accuracy and inflated performance due to the usage of less important features. Moreover, these studies often focus on fewer WBC types, exaggerating accuracy. This study addresses the crucial task of classifying WBC types using microscopic images. This study introduces a novel approach using extensive pre-processing with data augmentation techniques to produce a more significant feature set to achieve more promising results. The study conducts experiments employing both conventional deep learning and transfer learning models, comparing performance with state-of-the-art machine and deep learning models. Results reveal that a pre-processed feature set and convolutional neural network classifier achieves a significantly better accuracy of 0.99. The proposed method demonstrates superior accuracy and computational efficiency compared to existing state-of-the-art works.
Vault changes in eyes with a vertically implanted implantable collamer lens
Authors: Ouchi Masayuki 
Published: February 2024

AbstractSulcus-to-sulcus vertical diameter is longer than the horizontal. However, the effect of vertical positioning of the implantable collamer lens (ICL) on the vault compared to preoperative prediction is unclear. This prospective consecutive case series aimed to examine postoperative and preoperative predicted vaults during vertical ICL fixation. This study assessed 180 right eyes in 180 patients with myopic astigmatism. For the 90 eyes in 90 patients who underwent horizontal fixation (horizontal group) and 90 eyes in 90 patients who underwent vertical fixation (vertical group), biometrics by three-dimensional tomography of the anterior segment optical coherence tomography (A-OCT) was performed before surgery and 2 h, 1 day, 1 week, 1 month and 3 months after surgery. The anterior chamber depth did not change over time in both groups, and there was no significant difference from preoperative values. The postoperative vault values were significantly lower in the vertical group than in horizontal group over time. The difference between vault measurements and preoperative predictions at all postoperative time points was significantly greater in the vertical group than in horizontal group. Vertical fixation of the ICL reduced the vault by > 100 μm compared with horizontal fixation, which was different from the A-OCT preoperative predicted value.
A new function for drug combination dose finding trials
Authors: Xiao Jiacheng , Zhang Weijia 
Published: February 2024

AbstractCombination drugs play an essential role in treating cancers. The challenging part of the combination drugs are to specify the dose-toxicity ordering, which means the sequences of dose escalation and de-escalation in process of dose findings should be pre-determined. In the paper, we extend a novel function of the continual reassessment method based on the combination of the normal distribution for drug-combination dose-finding trials and systematically evaluate its performance using a template of four performance measures EARS (Efficiency, Accuracy, Reliability, Selection). Dose escalation and deescalation rules are based on the nearest neighborhood continual reassessment method for a combination drug, and we specify all possible dose-toxicity orderings in the trial. Simulation demonstrates that the new design is efficient, accurate and reasonably reliable.
GWAS-identified hyperuricemia-associated IGF1R variant rs6598541 has a limited role in urate mediated inflammation in human mononuclear cells
Authors: Gaal Orsolya I. , Liu Ruiqi , Marginean Dragoș , Badii Medeea , Cabău Georgiana , Hotea Ioana , Nica Valentin , Colcear Doina ,   HINT Consortium, Joosten Leo A. B. , Pop Ioan V. , Crişan Tania O. , Farcaş Marius , Marginean Dragoş H. , Badii Medeea O. , Peca Loredana , Mirea Andreea-Manuela , Pop Mariana S. , Rus Ancuta , Pamfil Cristina , Merriman Tony R. , Rednic Simona , Popp Radu A. , Crișan Tania O. , Joosten Leo A. B. 
Published: February 2024

AbstractGout is a common autoinflammatory joint diseases characterized by deposition of monosodium urate (MSU) crystals which trigger an innate immune response mediated by inflammatory cytokines. IGF1R is one of the loci associated with both urate levels and gout susceptibility in GWAS to date, and IGF-1-IGF-1R signaling is implicated in urate control. We investigate the role of IGF-1/IGF1R signaling in the context of gouty inflammation. Also, we test the gout and urate-associated IGF1R rs6598541 polymorphism for association with the inflammatory capacity of mononuclear cells. For this, freshly isolated human peripheral blood mononuclear cells (PBMCs) were exposed to recombinant IGF-1 or anti-IGF1R neutralizing antibody in the presence or absence of solubilized urate, stimulated with LPS/MSU crystals. Also, the association of rs6598541 with IGF1R and protein expression and with ex vivo cytokine production levels after stimulation with gout specific stimuli was tested. Urate exposure was not associated with IGF1R expression in vitro or in vivo. Modulation of IGF1R did not alter urate-induced inflammation. Developing urate-induced trained immunity in vitro was not influenced in cells challenged with IGF-1 recombinant protein. Moreover, the IGF1R rs6598541 SNP was not associated with cytokine production. Our results indicate that urate-induced inflammatory priming is not regulated by IGF-1/IGF1R signaling in vitro. IGF1R rs6598541 status was not asociated with IGF1R expression or cytokine production in primary human PBMCs. This study suggests that the role of IGF1R in gout is tissue-specific and may be more relevant in the control of urate levels rather than in inflammatory signaling in gout.