bluuebunny/crossref_metadata_2025 huggingface dataset:
Light-dependent modulation of protein localization and function in living bacteria cells
Authors: Xiao Jie , McQuillen Ryan , Yang Xinxing , Bohrer Christopher , McCausland Joshua , Perez Amilcar , Smith Erika , Chareyre Sylvia , Tsui Ho-Ching , Bruce Kevin , Hla Yin , Winkler Malcolm , Goley Erin , Ramamurthi Kumaran (S)
Published: September 2024

Most bacteria lack membrane-enclosed organelles to compartmentalize cellular processes. In lieu of physical compartments, bacterial proteins are often recruited to macromolecular scaffolds at specific subcellular locations to carry out their functions. Consequently, the ability to modulate a protein’s subcellular location with high precision and speed bears the potential to manipulate its corresponding cellular functions. Here we demonstrate that the CRY2/CIB1 system from Arabidopsis thaliana can be used to rapidly direct proteins to different subcellular locations inside live E. coli cells including the nucleoid, the cell pole, membrane, and the midcell division plane. We further show that such light-induced re-localization can be used to rapidly inhibit cytokinesis in actively dividing E. coli cells and that the CRY2/CIBN binding kinetics can be modulated by green light, adding a new dimension of control to the system. Finally, we tested this optogenetic system in three additional bacterial organisms, B. subtilis, C. crescentus and S. pneumoniae, providing important considerations for the applicability of this system in microbiology and bacterial cell biology.
Microwave-powered liquid metal depolymerization for plastic upcycling
Authors: Gao Jianye , Zhao Jun , Xing Zerong , Guo Minghui , Xie Haijiao , Ma Wangjing , Liu Jing
Published: September 2024

Upcycling waste plastics is highly promising to tackle the global white pollution while achieving sustainable development. However, prevailing approaches often encounter challenges in scalable engineering practices due to either insufficient capability or arduousness in separation, recovery, and purification of catalysts, which inevitably augments the cost of plastic upcycling. Here, we present the microwave-powered liquid metal synergetic depolymerization to facilitate low-cost plastic upcycling. By leveraging the fluidity of liquid metals and their exceptional chemical-bond activation ability under microwave field, this method efficiently converts various polyolefins into narrowband hydrocarbon oil (Oil yield: 81 wt% for PP, 85.9 wt% for PE) and high-value olefin monomers (C2-4= selectivity: 50% for PE, 65.3% for PP) over 30 successive cycles, resulting in a high turnover frequency of 2.83 kgPlastic/mLCatalyst. These captivating advantages offered by electromagnetically-powered liquid metals are also supported by their self-separation features, thereby paving the way for large-scale engineering solutions in waste plastic upcycling.
Assessing population genetic structure and diversity and their driving factors in Phoebe zhennan populations
Authors: Peng Jian , Xie Jiaxin , Gu Yunjie , Guo Hongying , Zhang Shuaiying , Huang Xin , Luo Xiandan , Qian Jianghong , Liu Minhao , Wan Xueqin , Chen Lianghua , Huang Xiong , Zhang Fan , He Fang , Zhu Peng , Zhong Yu , Yang Hanbo
Published: September 2024

Background
Phoebe zhennan, commonly known as “golden-thread nanmu,” is one of the most valuable and protection tree species in China. An accurate understanding of the population genetic structure and its environmental factors is of significance for the protection and selection of new P. zhennan varieties.
Results
Sixteen nSSR and six cpSSR markers were used to determine the genetic diversity and population structure of P. zhennan and the effect of environmental factors on the genetic structure. Low inbreeding (F = 0.237) and high genetic diversity (I = 2.294, h = 0.412) were observed in P. zhennan populations. The genetic differentiation was mainly detected within populations (only 28% and 13% of the variance being between populations according to the nSSR and cpSSR datasets). Among them, the HNSZX (h = 0.469) and SCSZZ (I = 1.943) populations exhibited the highest level of genetic diversity, while the HNXXT (h = 0.041) and SCLJS (I = 0.943) populations exhibited the lowest level of genetic diversity. The average genetic differentiation coefficient (Fst) and gene flow (Nm) were 0.022–0.128 and 1.698–11.373, respectively, which indicated a moderate level of genetic differentiation and a high level of gene flow. STRUCTURE, neighbor-joining clustering, and principal coordinate analysis divided 543 individuals into two or three categories based on the nSSR or cpSSR datasets. Four temperature, three precipitation, five chemical, five physical, and one soil texture variable showed significant effects on the genetic structure and distribution of P. zhennan populations. Compared to nSSR, the genetic differentiation among populations based on cpSSR datasets conformed to the geographic isolation model, suggesting that geographic and genetic distances should be considered for further genetic conservation and breeding utilization. The importance of in situ conservation units, such as populations with a high level of genetic diversity, more private alleles, and haplotypes (e.g., population SCGTS, SCYFS, and YNYJX), should be emphasized. Additionally, breeding, along with artificially assisted population regeneration and restoration, should also be carefully planned, taking into account climate and soil properties at the same time.
Conclusions
In conclusion, this study provided genetic background information for the genetic conservation, management, and utilization of P. zhennan.
Mechanisms of Mechanical Property Degradation and Dynamic Response Characteristics of Hybrid Fiber Reinforced Concrete under High-Temperature Conditions
Authors: Tong Gejun , Pang Jianyong , Tang Bin , Huang Jinkun , Sun Jian
Published: September 2024

In the context of building fire scenarios, this paper thoroughly investigates the degradation patterns of mechanical properties, dynamic response characteristics, and microstructural evolution of hybrid fiber reinforced concrete (HFRC) under high-temperature conditions. A series of orthogonal design experiments were conducted to quantitatively explore the regulatory effects of rice husk ash content, polypropylene fiber, and steel fiber volume fractions on the mechanical properties of HFRC. Using the Split Hopkinson Pressure Bar (SHPB) technique, the dynamic mechanical behavior of HFRC and ordinary concrete (OC) under various temperature gradients was examined, revealing the interactive influence mechanisms of temperature and strain rate on the dynamic mechanical properties of HFRC. Scanning Electron Microscopy (SEM) was utilized to analyze the microstructure of OC and HFRC samples subjected to high-temperature treatment, elucidating the micro-damage mechanisms behind the mechanical property degradation of HFRC in high-temperature environments. The results indicate that the steel fiber content predominantly determines the compressive and tensile strengths of HFRC, while polypropylene fiber plays a crucial role in enhancing the tensile performance of HFRC. Optimal mechanical performance was achieved with 12% rice husk ash content, 0.1% polypropylene fiber volume fraction, and 0.5% steel fiber volume fraction, resulting in a 10.41% and 50.22% increase in compressive and tensile strengths, respectively. Under high-temperature conditions, HFRC exhibited significantly superior mechanical properties compared to OC, particularly in terms of dynamic response characteristics. As the temperature increased, the dynamic compressive strength, dynamic increase factor, and peak toughness of HFRC initially decreased and then increased, consistently maintaining levels higher than those of OC. The study highlights the critical importance of the interaction between temperature and strain rate on the high-temperature dynamic response characteristics of HFRC, and the significant deteriorative impact of elevated temperatures on its microstructure. This research provides a solid scientific basis for enhancing the disaster resistance of concrete structures in fire environments and offers theoretical support for the effective application of hybrid fiber reinforced concrete in practical engineering.
Seismic response of few realistic typical asymmetric buildings
Authors: CHOWDHURY KRISHNENDU , Chowdhury Utsha
Published: September 2024

Asymmetrical designs have been demonstrated to be extremely hazardous in previous earthquakes. One possible cause of the susceptibility might be a disparity of mass or stiffness. The majority of the investigation was devoted to examining the eccentricity that results from an inconsistent distribution of stiffness. Conversely, the systems exhibiting mass eccentricity as a consequence of the unequal mass distribution at the floor level receive comparatively less awareness. Therefore, stiffness along with mass eccentric systems are jointly thoroughly examined in the current research owing to bidirectional components of ground motion that expose more accurately simulating the actual scenario. In order to provide a relatively precise forecast regarding column elements, the explanation of hysteresis behavior takes into account the impact of biaxial interaction caused by synchronous bidirectional movement. The vulnerability of asymmetric structures to stiffness or mass eccentricity has mostly been studied in idealized single-story systems with different levels of eccentricity. In addition, the subject matter of the research has expanded to cover three-story asymmetric systems in order to examine the impact of higher modes. This study investigates a three-story system with larger eccentricity in the first story for functional reasons and lower eccentricities in the upper stories for a more realistic scenario. The current study demonstrates that stiffness eccentric systems and mass eccentric systems are both susceptible to earthquakes. In addition, three-story systems have a significantly higher reaction than their single-story equivalents. This research could enhance design recommendations by providing a greater comprehension of the behavior of plan asymmetric systems.
Adsorptive and Photocatalytic Degradation of Imidacloprid Pesticide from Wastewater via the ZrP/NiSe 2 nanocomposite
Authors: Izadi Mina , Bahrami Kiumars , Targhan Homa
Published: September 2024

In this study, ZrP/NiSe2 nanocomposite was constructed for the first time. Characterizations were carried out by FT-IR, XRD, EDX mapping and FESEM, confirming the nanocomposite formation. The resulting sustainable ZrP/NiSe2 nanocomposite exhibit improved photocatalytic activity in the visible area to remove imidacloprid from water compared to pure ZrP and NiSe2 nanoparticles. Improving the performance of this nanocomposite can be the result of the integration of ZrP and NiSe2 at the nanoscale and the synergistic enhancement of their activity. Furthermore, ZrP/NiSe2 and ZrP can remove significant percentages of imidacloprid from aqueous solutions through adsorption. This result can be explained by the high adsorption affinity of ZrP toward organic pollutants with protonable groups.
Case report: Recurrent enteritis and intestinal obstruction in a patient with chronic mucocutaneous candidiasis due to STAT1 Gain-of-function mutation
Authors: LUO Mingfen , Huang Huan , Nie Hanhui , Liu Yinghui , Chen Yangxia , Zheng Fuying , Xi Liyan , Liu Hongfang
Published: September 2024

We presented a case of chronic mucocutaneous candidiasis (CMC) due to STAT1 GOF mutation with recurrent enteritis and intestinal obstruction. A 33-year-old woman complained of recurrent oral erosion and finger (toe) nails damage for over 30 years. Candida albicans were cultured from the oral mucosa and nails. Sanger sequencing revealed a gain-of-function mutation in STAT1 (c.A1159 G, p.T387A). Since the age of 37, she developed recurrent enteritis and intestinal obstruction. Laboratory examinations revealed an increased pSTAT1 protein expression and a decreased proportion of Th17 cells in peripheral blood lymphocyte (PBMC), with a high expression of pSTAT1 and a scarce expression of IL17A observed in intestinal immunohistochemistry. Intestinal obstruction had not previously been reported as the main clinical manifestation in STAT1 GOF patients. We speculated that the low levels of IL17A impaired the intestinal barrier, which might lead to gastrointestinal disorders in this patient. This case expanded the clinical phenotype of heterozygous STAT1 GOF patients.
The Therapeutic Efficacy of MS473, a Fully Human Single-Chain Variable Fragment Specific to Staphylococcus aureus Toxic Shock Syndrome Toxin-1, in a Mouse Model of Toxic Shock
Authors: Jamnani Fatemeh Rahimi , Moradi Hamid Reza , Soezi Mahdieh , Azizi Masoumeh , Nazari Farzaneh , Fateh Abolfazl , Siadat Seyed Davar
Published: September 2024

Toxic shock syndrome toxin-1 (TSST-1), produced by Staphylococcus aureus, is one of the most potent superantigens involved in causing life-threatening toxic shock syndrome (TSS) and contributes to the onset of some autoimmune diseases. To this end, we have previously identified a fully human single-chain variable fragment antibody (scFv), MS473, exhibiting high binding affinity and specificity for TSST-1 and demonstrating in vitro neutralization activity. In the present study, the therapeutic activity of MS473 was assessed in a D-galactosamine-sensitized mouse model of lethal shock. D-galactosamine-sensitized mice were injected with TSST-1 and then received a single dose of MS473 intraperitoneally (15 mg/kg) after five minutes or intravenously (3 mg/kg) after 10 minutes. The survival rate was examined for seven days. Furthermore, mice were killed after 24 hours, and their kidneys and liver were histopathologically examined. The findings demonstrated a 100% survival rate and no significant pathology damage on tissue samples in both treated groups, administered with MS473 in two different routes compared to the control groups, including toxin-injected mice receiving normal saline or an unrelated scFv. Targeting disseminated TSST-1 with scFvs, which have appropriate permeability and distribution throughout the body, may be an effective way to alleviate the malfunctioning of the immune system caused by TSST-1.
Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize
Authors: Martinez-Feria Rafael , Simmonds Maegen B , Ozaydin Bilge , Lewis Stacey , Schwartz Allison , Pluchino Alex , McKellar Megan , Gottlieb Shayin S. , Kayatsky Tasha , Vital Richelle , Mehlman Sharon E. , Caron Zoe , Colaianni Nicholas R. , Ané Jean-Michel , Maeda Junko , Infante Valentina , Karlsson Bjorn H , McLimans Caitlin , Vyn Tony , Hanson Brendan , Verhagen Garrett , Nevins Clayton , Reese Lori , Otyama Paul , Robinson Alice , Learmonth Timothy , Miller Christine , Havens Keira , Tamsir Alvin , Temme Karsten
Published: September 2024

Increasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha− 1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.
Development of an Industrial-Size Aeroponic Rooting System and Plant Cutting Rooting Studies
Authors: KARADAĞ Hakan , Polatcı Hakan , Saraçoğlu Onur , Cömert Mehmet , Vural Güzella Yılmaz , Yıldız Kenan
Published: September 2024

Aeroponic agriculture is an innovative system that allows plants to grow and develop by fogging and applying water directly to the bare root area. Thus, oxygen and water, which are the limiting factors of traditional agriculture, can be supplied at sufficient levels in this system. Within the scope of the study, an industrial-sized aeroponic rooting unit was designed and manufactured. After drawings were made in the digital environment, the manufacturing process started. The unit consists of 3 lines, each with 3 floors. Nine cabins were produced, each cabin measuring 2x0.4x1 m. The control unit is designed to independently control each cabin's humidity, temperature, lighting, and ventilation features. In the study, research and findings on the potential of aeroponic agriculture were examined, focusing primarily on the effects of the aeroponic system on the growth of plant roots and its performance on various plant species. Within the scope of the study, the rooting performances of black mulberry (Morus nigra) and Judas tree (Cercis siliquastrum) cuttings, which are very difficult to root with traditional methods, were examined in perlite and aeroponic environments. The effect of cutting time, growth regulator doses, and various parameters on root formation and development during the rooting process were examined. Applying 6000 ppm IBA on black mulberry wood cuttings in the aeroponic system reached the highest rooting rate (85.19%) and callus formation rate (96.30%). The rooting rate of black mulberry wood cuttings in perlite medium with 6000 ppm IBA application was 59.26%. Application of 4000 ppm IBA on black mulberry green cuttings in the aeroponic system reached the highest callus formation rate (92.59%) and rooting rate (81.48%). These values ​​show a significant increase compared to the control group. At the same time, the highest rooting rate (74.08%) in perlite medium was again obtained with 4000 ppm IBA application. Application of 6000 ppm IBA to Judas tree green cuttings in the aeroponic system reached the highest rooting rate (29.63%) and callus formation rate (25.92%). It has been observed that the aeroponic system is more successful in terms of rooting rates and number of roots compared to perlite media.
Maternal and Fetal Factors Affecting the Effectiveness of Vaginal Dinoprostone in Labor Induction
Authors: Atlihan Ufuk , Yavuz Onur , Ata Can , Avsar Huseyin Aytug
Published: September 2024

Objective
Induction of labor (IOL) is a common obstetric intervention used to encourage the onset of labor. The aim of study was to evaluate the maternal and fetal factors that play a role in the efficacy of vaginal dinoprostone in labor induction.
Materials and Methods
Our study included 780 patients who underwent pregnancy follow-up and delivery in our hospital between March 2018 and 2024. All data including body mass index (BMI), age, parity, induction criteria, obstetric history, bishop score, time of delivery, newborn weight and Apgar score were entered by the delivery room physician. Data from 620 patients who had a successful delivery with vaginal dinoprostone application and 120 patients who could not have a vaginal delivery were evaluated retrospectively.
Results
The BMI value of women in Group 2 at admission to the hospital was found to be significantly higher than that of women in Group 1 (p < 0.001). The Bishop score of women in Group 1 at admission to the hospital was found to be significantly higher than that of women in Group 2 (p < 0.001). The nulliparity rate of women in Group 2 was found to be significantly higher than those in Group 1 (p < 0.001). The uterocervical angle measurement of women in Group 2 was found to be significantly lower than those in Group 1 (p < 0.001). The rate of newborns with 1st and 5th minute Apgar scores ≥ 8 in Group 1 was found to be significantly higher than those in Group 2 (p = 0.006, p = 0.04, respectively).
Conclusion
It was determined that parity was one of the important determinants in achieving vaginal delivery in pregnancies where dinoprostone vaginal insert was applied. It was determined that multiparous women benefited more from induction with dinoprostone. However, according to the results of our study, more research is needed to evaluate nulliparous pregnancies requiring induction.
The performance of LaAlO x gate dielectric films prepared by sol-gel method at different temperatures of annealing
Authors: Huang Zhenhua , Tuokedaerhan Kamale , Yang Linyu , Guo Chaozhong , Cai Zhengang , Ibraimov Margulan , Sailanbek Serikbek
Published: September 2024

In recent years, there has been growing interest in the exploration of rare earth oxides for their potential as high-k gate dielectrics. Lanthanum oxide (La2O3) has emerged as a particularly noteworthy candidate due to its impressive dielectric properties, wide bandgap, strong thermodynamic stability, and remarkable compatibility with silicon substrates. However, La2O3 has a significant problem for MOS device applications due to its hygroscopicity and low crystallization temperature, making it unsuitable for high-temperature treatment during fabrication. To improve its oxide quality, it can be doped. Al-doped La2O3 (LaAlOx) thin films annealed at different temperatures were prepared on n-type Si substrates by sol-gel method and the effect of temperature variation on LaAlOx thin films as gate dielectrics were investigated in terms of root-mean-square, interfacial properties, and electrical properties. The findings indicate that the introduction of Al doping raises the crystallization temperature of La2O3. Additionally, it was observed that the root-mean-square roughness of the LaAlOx films decreases from 0.919 nm to 0.320 nm with an increase in annealing temperature from 500 to 700°C. XPS has the capability to assess the interfacial characteristics of LaAlOx. It is evident that elevated temperatures promote the formation of M-O bonds, diminish film defects, and enhance the overall interfacial quality of the film. In addition, analyzed the electrical properties of the Al/ LaAlOx/Si/Al metal-oxide-semiconductor capacitors The findings indicate that the samples annealed at 700°C exhibit favorable electrical characteristics, demonstrating a dielectric constant of 20.91 under a gate voltage of 1 V and a leakage current density of 3.54×10− 3A/cm2.
Models-based study of radiative Hybrid nanofluid flow over a vertical porous stretching cylinder
Authors: Abbas Nadeem , Shatanawi Wasfi , Hasan Fady , Shatnawi Taqi A. M.
Published: September 2024

This research aims to develop and analyze different models, such as the Yamada-Ota, Xue, and Tiwari-Das models. The study examines how thermal radiation affects the flow of a mixture of single-walled and multi-walled carbon nanotubes (SWCNT-MWCNT) in water over a vertical porous stretching cylinder with heat generation. The goal is to understand the impact of these models on thermal performance, boundary layer behavior, and heat transfer enhancement. The study offers valuable insights for optimizing industrial applications that involve advanced nanofluid cooling and heating systems. The governing momentum and energy conservation equations are formulated to include thermal radiation and heat generation terms. These equations are transformed using similarity transformations and solved numerically using the bvp4c method. A comparative analysis evaluates model performance, focusing on temperature distribution, velocity profiles, and heat transfer rates. The results are validated against existing literature to ensure the accuracy and reliability of the proposed models. Thermal radiation improves heat transfer; the Tiwari-Das model exhibits the highest thermal conductivity enhancement. Velocity profiles show a thicker boundary layer for the Yamada-Ota model, while the Xue model predicts higher heat generation effects.
DomHMM – Analysis of Membrane Domains
Authors: Tunç Eren , Trollmann Marius , Böckmann Rainer
Published: September 2024

Lateral nano- or microdomains are a major hallmark of biological membranes. A key challenge in analyzing membrane domains from molecular dynamics (MD) simulations lies in accurately assigning lipids to more ordered (Lo) or disordered (Ld) membrane domains, particularly when these domains exhibit similar chemical compositions but differ in structural characteristics. To address this issue, we present the implementation of DomHMM, a novel application previously developed for the unsupervised classification of Lo and Ld domains based on coarse-grained or all-atom MD simulations. DomHMM employs a Gaussian-based Hidden MarkovModel (HMM) for initial lipid state assignment based on specific lipid characteristics, followed by state reweighing through local spatial correlations andsubsequent clustering. This approach significantly improves the efficiency and accuracy of membrane domain analysis, establishing DomHMM as a robust tool for investigating membrane domain behavior.
Antimicrobial strategies of Lower Respiratory Tract Infection in Immunocompromised Patients based on Metagenomic Next-Generation Sequencing：a retrospective study
Authors: Meng Beibei , Liu Haichao , Wu Qinliang , Qu Lei , Mao Congzheng , Yang Fang , Lan Tianzhou , Fang Juan , Hu Zhenhong , Fang Yao
Published: September 2024

Background
Immunocompromised patients with Lower Respiratory Tract Infection(LRTI) frequently encounter a diverse range of pathogenic infections, characterized by rapid disease progression and significant mortality rates due to reckless or excessive utilization of antibiotics. Therefore, it is crucial to promptly and accurately identify the causative microorganisms for pathogen diagnosis and clinical decision-making. The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses.
Methods
We conducted a comparative analysis of positivity rate, detection accuracy, pathogen spectrum, duration of treatment (DOT), and antibiotic management in a cohort of 283 patients diagnosed with lower respiratory tract infections.
Results
The positive detection rate was higher in mNGS compared to conventional culture in both immunocompetent group (89.92% vs. 28.57%, P < 0.001) and immunocompromised group (84.44% vs. 33.33%, P < 0.001). The antibiotic escalation in the immunocompromised group was more frequent than that in the immunocompetent group (49.00% vs. 31.00%, P = 0.018), but no difference was observed for antibiotic de-escalation (20.00% vs. 15.00%, P = 0.458).
Conclusions
The application of mNGS can significantly enhance the pathogen detection rate and optimize antimicrobial drug management in immunocompromised patients with LRTI.
Pioneering Precision in Lumbar Spine MRI Segmentation with Advanced Deep Learning and Data Enhancement
Authors: Ahmed Istiak , Hossain Md. Tanzim , Nahid Md. Zahirul Islam , Sanjid Kazi Shahriar , Junayed Md. Shakib Shahariar , Uddin M. Monir , Khan Mohammad Monirujjaman
Published: September 2024

This study presents an advanced approach to lumbar spine segmentation using deep learning techniques, focusing on addressing key challenges such as class imbalance and data preprocessing. Magnetic resonance imaging (MRI) scans of patients with low back pain are meticulously preprocessed to accurately represent three critical classes: vertebrae, spinal canal, and intervertebral discs (IVDs). By rectifying class inconsistencies in the data preprocessing stage, the fidelity of the training data is ensured. The modified U-Net model incorporates innovative architectural enhancements, including an upsample block with leaky Rectified Linear Units (ReLU) and Glorot uniform initializer, to mitigate common issues such as the dying ReLU problem and improve stability during training. Introducing a custom combined loss function effectively tackles class imbalance, significantly improving segmentation accuracy. Evaluation using a comprehensive suite of metrics showcases the superior performance of this approach, outperforming existing methods and advancing the current techniques in lumbar spine segmentation. These findings hold significant advancements for enhanced lumbar spine MRI and segmentation diagnostic accuracy.
A rapid and accurate method for determining titers of baculovirus for protein expression
Authors: Ding Feng , Wang Jinyang , Shi Hui , Peng Jinrong
Published: September 2024

The Baculovirus Expression Vector System (BEVS) is extensively used for expressing target proteins, necessitating accurate baculovirus titration to ensure the output. Traditional plaque assay assisted titration, while reliable, is labor-intensive and time consuming. Here, we introduce an improved quantitative real-time polymerase chain reaction (qPCR)-based method for determining baculovirus titers. Briefly, target-gene specific primers are designed to produce a 180-bp PCR product using viral DNA as the template. The PCR products are purified and the mass weight of the PCR products are quantified based on 260-nm absorbance. Based on the molecular weight of the 180bp PCR product, the mass weight is then converted to the molar concentration which is finally converted to molecule number by applying the Avogadro constant. Such PCR product is serially diluted and used as the template for qPCR. The qPCR Ct values between serial dilutions are used to generate the standard curve. Finally, the Avogadro’s number (i.e. titer) of the test viral DNA is inferred from its qPCR Ct value by comparing with the standard curve. Our method eliminates the need for a pre-titrated viral stock, reducing variability caused by storage conditions. This advancement is particularly beneficial for large-scale production of the target protein using the BEVS.
Discriminating activating, deactivating and resistance variants in protein kinases
Authors: Singh Gurdeep , Schmenger Torsten , Gonzalez-Sanchez Juan Carlos , Kutkina Anastasiia , Bremec Nina , Diwan Gaurav , Mozas Pablo , López Cristina , Siebert Reiner , Sotillo Rocio , Russell Robert B
Published: September 2024

We present a data-driven approach to predict the functional consequence of genetic changes in protein kinases. We first created a large curated dataset of 375 activating/gain-of-function, 1028 deactivating/loss, 98 resistance and 1004 neutral protein variants in 441 human kinases by scouring the literature and various databases. For any variant, we defined a vector of 7 types of sequence, evolutionary and structural features. We used these vectors to train machine learning predictors of kinase variant classes that obtain excellent performance (Mean AUC = 0.941), which we then applied to uncharacterized variants found in somatic cancer samples, hereditary diseases and genomes from healthy individuals. Encouragingly we predicted a greater tendency of activating variants in cancers, deactivating in hereditary diseases and few of both in healthy individuals. Using this method on clinical data can identify potential functional variants. In cancer samples we experimentally assessed the impact of several such mutations, including potential activating variants p.Ser97Asn in PIM1, where phosphorylation analysis suggests an increase in activity, and p.Ala84Thr in MAP2K3, where gene expression and mitochondrial staining shows a reduction in mitochondrial function when contrasting mutant to wild type, the opposite having been observed previously during deletion experiments. We provide an online application to study any variant in the kinase domain that provides prediction scores in addition to a detailed list of what is known across all kinases near the position of interest. Besides supporting the interpretation of genomic variants of unknown significance, knowledge of kinase activation can lead to immediate therapeutic suggestions, we thus believe our approach will be a key component in the repertoire of tools for personalised medicine.
Zinc-mediated regulation of TMEM106B function in the endolysosomal pathway revealed through the systematic identification of TRIM2/3 ubiquitination substrates
Authors: Perez-Borrajero Cecilia , Stein Frank , Schweimer Kristian , Kotova Iuliia , Fernandez-Novel Nadine , Rettel Mandy , Schwarz Jennifer , Haberkant Per , Lapouge Karine , Loedige Inga , Gayk Jesse , Stachera Weronika , Trovato Matteo , Hoffmann Thomas , Murciano Brice , Bhogaraju Sagar , Savitski Mikhail , Mahamid Julia , Noh Kyung-Min , Hennig Janosch
Published: September 2024

The understanding of ubiquitin E3 ligase function hinges on thoroughly identifying their cellular targets, but the transient nature of signaling complexes leading to ubiquitination poses a significant challenge for detailed mechanistic studies. TRIM2 and TRIM3 are paralogous mammalian E3 ligases with particularly high expression in the brain, where they contribute to neuronal development and homeostasis. Here, we tailored recently developed ubiquitin-specific proximity labelling tools to identify substrates of TRIM2 and TRIM3 activity. We show that despite their high amino acid sequence identity, the ligases have distinct intracellular dynamics, binding partners, and ubiquitination substrates. Using biochemical and structural studies, we show that TRIM2 ubiquitinates the lysosomal protein TMEM106B at lysine residues located in the cytosolic N-terminal region. Substrate recognition involves a direct interaction between TRIM2 and a newly identified zinc-coordination motif in TMEM106B that mediates homodimerization and is required for lysosomal size regulation. We found that in addition to catalysis, the tripartite motif is involved in substrate recruitment, and we provide insights into the assembly of the ubiquitination complex. Deletion of TRIM2/TRIM3 in mouse embryonic stem-cell derived neurons impacted the extracellular matrix composition, likely through acting on the endolysosomal pathway. Our study thus contributes a catalogue of TRIM2 and TRIM3-associated effectors and supports a key role at the interface of vesicle trafficking and the cytoskeleton.
Experimental confirmation of secondary flows in granular media
Authors: Einav Itai , Escobar Andres , Baker James , Guillard Francois , Faug Thierry
Published: September 2024

As collections of grains flow, their free surface rarely remains flat. We can observe this first-hand during laboratory flow experiments or infer from undulating deposits left after landslides on Earth or Mars. The free-surface disturbances that develop suggest the presence of secondary flows, smaller in magnitude than the primary motion but driving complex three-dimensional structures inside the flow. While one can infer such behaviour from the boundaries or simulations, until now we have not been able to directly observe secondary flows experimentally. In this paper we present the first experimental confirmation of secondary kinematics in granular media using dynamic x-ray radiography, without needing to stop the motion for tomography. Specifically, we create a bulldozing mechanism by driving granular material with a conveyor belt. This sets up a unidirectional primary flow, but also generates a non-uniform, indented free-surface, hinting that secondary mechanisms are at play. Modelling of the system using discrete element method simulations is consistent with this secondary-flow explanation. We then probe further experimentally using two perpendicular pairs of x-ray sources and detectors to measure the velocity field inside the bulk. This indeed unveils a complex three-dimensional flow pattern that must include vortices and convection rolls. This advancement is pertinent for many industrial and natural scenarios where grains impact obstacles, and has even broader relevance for secondary rheology of other amorphous soft materials such as dense emulsions, pastes and colloidal suspensions.
AI vs. Humans: A Comparative Analysis of Time, Cost, and Performance on a Clinical Code Conversion Task
Authors: Hudson Carly , Randall Marcus , Bowman Candice , Joy Anu , Goldsworthy Adrian
Published: September 2024

Background: Healthcare services generate and store large quantities of data which historically required significant resources to manually analyse and gain meaningful insights to assist in informing healthcare policy and system design. Recent advancements in automation tools, such as generative artificial intelligence (GAI), provides new opportunities to disencumber human labour and thinking for difficult tasks. This study explores the potential utilisation of GAI for a healthcare data analysis task, specifically, the conversion of clinical data from one diagnostic classification system to another (i.e., SNOMED-CT-AU to the ICD-10-CM). Additionally, it examines the time and cost benefit of performing this using GAI when compared to a human rater.
Methods: Conversions were completed on SNOMED-CT-AU codes to the ICD-10-CM using three methods: 1) manual conversion using the National Library of Medicine’s I-MAGIC tool, 2) conversion using ChatGPT 4o, and 3) conversion using Claude Sonnet 3.5. The accuracy of the GAI tools was mapped against the manually extracted codes, and examined in terms of a perfect, partial, or incorrect match. Researchers’ time was recorded and extrapolated to calculate and compare the cost associated with each method.
Results: When compared to the manually extracted codes, Claude Sonnet 3.5 yielded the highest level of agreement over ChatGPT 4o, whilst also being the most time and cost effective.
Conclusion: GAI tools have greater utility than they have currently been given credit for. The automation of big data healthcare analytics, whilst still the domain of humans is increasingly capable of being undertaken using automation tools with low barriers to entry. The further development of the capability of GAI alongside the capability of the healthcare system to use it appropriately has the potential to result in significant resource savings.
Advanced Blockchain-Enabled Deep Quantum Computing Model for Secured Machine-to-Machine Communication
Authors: Arora Rajeev Kumar , Tiwari Aniruddh , Mohd.Muqeem
Published: September 2024

Machine-to-machine (M2M) communication has become an integral part of various industries, facilitating efficient data exchange and enabling autonomous decision-making processes. However, the proliferation of interconnected devices has brought about unprecedented security challenges. Conventional cryptographic methods may not be sufficient to protect sensitive data in the face of rapidly evolving cyber threats. To address this issue, a novel approach combining blockchain technology and deep quantum computing has been proposed to enhance the security and privacy of M2M communication. This paper presents an advanced blockchain-enabled deep quantum computing model designed to safeguard machine-to-machine communication from potential cyber threats. At the core of the model is a quantum key distribution (QKD) protocol, which enables the secure establishment of cryptographic keys between communicating devices. To ensure the scalability and immutability of the M2M communication network, a blockchain framework is integrated into the system. Additionally, the model incorporates deep learning techniques to bolster the security infrastructure further. In this paper we introduce an innovative solution to address the security challenges in machine-to-machine communication. By integrating advanced quantum computing, blockchain technology, and deep learning, the proposed model establishes a robust and secure framework that ensures the confidentiality, integrity, and authenticity of M2M data exchanges.
Direct vocabulary teaching practices by preschool teachers
Authors: Chlapana Elissavet , Vasileiou Varvara
Published: September 2024

The purpose of the present study was to investigate preschool teachers’ practices. The sample consisted of 274 preschool teachers working in different regions of Crete in Greece. The data were collected via an online questionnaire comprised of 22 items inquiring about the sample teachers’ demographic characteristics and occupational status, as well as about the activity settings and the techniques they use to teach vocabulary directly in their classrooms. In relation to the indicated activity settings and the direct vocabulary teaching techniques, the sample teachers recorded the frequency of their use on 5-point Likert scales. The results showed that story reading was the most frequent activity setting for implementing direct vocabulary teaching. Furthermore, data analysis showed that contextualized and de-contextualized vocabulary teaching with an emphasis on the receptive aspect of vocabulary and multimodal vocabulary teaching with an emphasis on the productive aspect of vocabulary were the two basic dimensions that described the preschool teachers’ practices. In addition, the results showed that contextualized and de-contextualized vocabulary teaching was reported to be used more frequently than multimodal teaching, while both teaching practices were related more strongly to the other activity settings besides story reading.
The importance of retail behavior quality to maintain consumers’ loyalty: findings from Indonesian micro retail businesses
Authors: Fatimah Feti , Suroso Imam , Irawan Bambang , Barokah Suryaningsih Ika
Published: September 2024

The rapid retail development has led to increasingly fierce competition, and micro retail businesses need innovation to survive and thrive. Retail innovation is reflected in the quality of consumers’ behavior in making purchase decisions. Therefore, this study aimed to analyze the role of retail behavior quality as an intervening variable on merchandise offer and store image on consumers’ loyalty in micro retail businesses. In this study, the confirmatory and explanatory methods were used, and it was conducted in Jember Regency, East Java, Indonesia with a sample size of 306 consumers of micro retail businesses. Moreover, the data were obtained through a questionnaire, and Partial Least Squares-Structural Equation Modeling analysis was used to determine the direct and indirect effects. The results showed that merchandise offer had a positive and significant effect on consumers loyalty both directly and indirectly through retail behavior quality with total effect of 50.4%. Store image had no significant direct effect on consumers loyalty. However, it had a positive and significant direct effect on consumers through retail behavior quality with total effect of 22%. In this context, retail behavior quality played an important role in increasing consumers’ loyalty to micro retail businesses. These results contributed to improved retail quality behavior oriented towards transparency in quality of goods, employee attitudes, in-store environment, product arrangement, and established good relationships with consumers to maintain loyalty.
AcknowledgmentThe authors are grateful to the Muhammadiyah University of Jember for funding thisresearch.
Y VE Z KUŞAKLARININ BAĞLANMA STİLLERİ İLE EVLİLİK BEKLENTİLERİNİN İNCELENMESİ
Authors: Türk Ahmet , Aydemir İshak
Published: September 2024

Toplumsal yapıda oluşan değişim ve dönüşümler yalnızca toplumların değerleri, gelenekleri ve kültürlerini değil aynı zamanda bireylerin kendine özgü yapılarını, davranışlarını ve tutumlarını da etkilemektedir. Buna bağlı olarak sosyo-kültürel açıdan kuşaklar arası farklılıklar daha da belirgin hale gelmiştir. Bu kapsamda bu araştırma Y ve Z kuşaklarının evlilik beklentileri ile bağlanma stillerinin incelenmesi amacıyla gerçekleştirilmiştir. Tarama modelinin kullanıldığı araştırmaya 542’si (%51.4) Y kuşağı ve 512’si (%48.6) Z kuşağı olmak üzere 1054 kişi katılmıştır. Katılımcıların 558’i (%52.9) kadın ve 496’sı (%47.1) erkektir. 18 ile 42 yaş aralığındaki katılımcıların yaş ortalaması x̄=23.62±3.58’dir. Araştırmanın verileri Kişisel Bilgi Formu, Evlilik Beklentisi Ölçeği ve Üç Boyutlu Bağlanma Stilleri Ölçeği kullanılarak toplanmıştır. Verilerin analizinde betimsel istatistikler ile Ki kare, bağımsız örneklem t testi ve tek yönlü varyans analizi (ANOVA) kullanılmıştır. Bulgular hem Y kuşağının hem de Z kuşağının evlilikten en önemli beklentilerinin samimiyet olduğunu, her iki kuşağın da gerçekçi olmayan-idealist evlilik beklentisine ve güvenli bağlanma stiline sahip olduğunu; bağlanma stillerinin evlilik beklentisi türlerine göre farklılaştığını göstermektedir.
Entrevista com Jurandyr Luciano Sanches Ross
Authors: Revista Brasileira de Geografia Conselho Editorial da
Published: September 2024

Entrevista com o professor Jurandyr Luciano Sanches Ross sobre Aziz Nacib Ab’Saber por ocasião do centenário de seu nascimento .
Tão verde quanto possível
Authors: Xavier-Sampaio Laymara , Rodrigues Queiroz Liana , Maciel Gomes Manuella , Farias Costa Maria Ligia , Elisa Zanella Maria , Freire Moro Marcelo
Published: September 2024

Este estudo tem como objetivo computar o total de áreas de vegetação remanescentes no município de Fortaleza, de modo a: calcular a extensão total de áreas que estão dentro de unidades de conser-vação e o grau de degradação da cobertura vege-tal em Unidades de Conservação (UC); mensurar o total de áreas remanescentes que estão sem pro-teção jurídica pelo Sistema Nacional de Unidades de Conservação; identificar fragmentos de cobertu-ra vegetal nativa vulneráveis à destruição. A análi-se é baseada em técnicas de geoprocessamento, identificando as áreas remanescentes do municí-pio e o total de áreas desmatadas dentro e fora das UC. Fortaleza perdeu mais de 80% de sua cobertu-ra vegetal natural ou seminatural ao longo dos últimos séculos. O nível de proteção efetiva da cobertura vegetal nessas UC é baixo. O estudo identificou 60 áreas com vegetação remanescente vulneráveis ao desmatamento.
Analysing Indoor Air Pollution: A Study on Pollutant Levels and Air Quality Assessment in Social Housing Properties
Authors: Narayanan Vishnupriya , Shaikh Roshina , Hashemi Arman , Elsharkawy Heba , Newport Darryl , Basaly Lucienne
Published: September 2024

Amid growing concerns over Indoor Air Quality (IAQ), this paper presents a comprehensive analysis of pollutants to assess the environmental health in a few Case Study Buildings (CSBs). The main objectives were to evaluate the levels of key Indoor Air Pollutants (IAPs) (PM10, PM2.5, CO, CO2, TVOCs) and relative humidity across multiple social housing properties and to analyze how occupant behaviormay affect IAQ. Utilizing quantitative measurements, the study investigates the range and exposure of the building occupants to IAPs. The methodology involves the systematic measurement of IAPs through the installation of data loggers, focusing on pollutant levels to evaluate air quality across multiple CSBs. Findings show fluctuation in pollutant levels, with some IAPs demonstrating consistently within the acceptable range while others exhibit sporadic spikes in pollutant concentrations. The results indicate that significant attention should be given to PM10, CO, and VOCs. This study underscores the importance of continuous monitoring and targeted interventions to mitigate poor IAQ and ensure healthier indoor environments for building occupants. Further research and implementation of effective measures are imperative to safeguard public health and well-being.