bluuebunny/crossref_metadata_2025 huggingface dataset:
THE STRATEGIC PLANNING OF TRANSPORT INFRASTRUCTURE AND MANAGEMENT OF LOGISTICS SOLUTIONS IN CONDITIONS OF WAR
Authors: KRIACHKO KATERYNA , CHUPRYNA OLENA , MAKSYMOV SERGIY , SHAPOVAL GANNA , VDOVYCHENKO VOLODYMYR , POPOVA YULIIA
Published: June 2024

This article examines the challenges faced by Ukraine, which is embroiled in a military conflict within its borders, particularly the imperative to ensure the efficiency of its transport infrastructure and logistics processes. It has been identified that military actions result in damage to transport networks, restricted access to critical resources, and alterations in logistics operations. It has been established that in wartime conditions, strategic planning of transport infrastructure and effective management of logistics solutions become particularly pertinent as they dictate the country's capacity to meet its own needs and accomplish strategic objectives. Furthermore, it has been determined that Ukraine's future integration into Europe necessitates reforming its transport and logistics system to align with EU standards. Strategic approaches to restoring the transport network and addressing logistics challenges during conflict are discussed, primarily focusing on alternative routes, the development of effective supply chain management systems, and enhancing system redundancy. Strategies for adaptation and response to changes aimed at ensuring the reliability and efficiency of transport and logistics processes in Ukraine have been explored.
Rancang Bangun Mesin Penetas Telur Otomatis Dengan Perata Suhu Kipas Casing CPU
Authors: Wahyu Yani Fatkhur Rohman, Mochammad Arif Irfa'i, Basuki
Published: June 2024

Egg Incubator is a tool that helps the process of hatching eggs. With the egg incubator then the eggs can be hatched without going through the incubation process by the help of the parent. Hatching eggs in principle is to provide a suitable environment so that poultry eggs can hatch. This Egg Incubator aims to increase hatching power with an automatic egg screening system and digital temperature control. With the incubator is able to increase the percentage of success ranges from 80-85% in the process of hatching eggs. In the research of automatic Egg Incubator design with temperature grader CPU casing fan with a capacity of 25 this method used is the method of R&D(research and development). This study authors use a type of digital thermostat that aims to set the temperature stability in accordance with the provisions. Testing tools using descriptive method by asking some questions or questionnaires to the validator. The results of this study obtained the test results of several components and the time required to hatch eggs. The average required component testing shows good performance. While the average testing percentage of hatching eggs showed 82.5%. In the feasibility test and functional tools will be validated by Mr / Ms lecturer (validator). The average amount of percentage tested by validator 1 and validator 2 is 93.5% for feasibility testing. While functional testing the average amount of presntase tested by validator 1 and validator 2 is 93%. So the results of the feasibility and functional testing of the tool validated by 2 validators on the tool are categorized as very good.
PENGARUH VARIASI KADAR PEREKAT TERHADAP LAJU PEMBAKARAN PADA BRIKET BERBAHAN DASAR SERBUK KAYU
Authors: Edi Sunaryo  , Dian Anisa Rokhmah Wati  , Retno Eka Pramitasari  , Mohammad Munib Rosadi
Published: June 2024

Tujuan penelitian ini adalah untuk menganalisa pengaruh variasi kadar perekat pada briket berbahan dasar serbuk kayu terhadap laju pembakaran  variasi komposisi bahan serbuk kayu 95% : 5% perekat, serbuk kayu 90% : 10% perekat, serbuk kayu 85% : 15% perekat, serbuk kayu 80% : 20% perekat, serbuk kayu 75% : 25% perekat. Data yang diperoleh dari penelitian akan dianalisis menggunakan uji kruskal wallis pada aplikasi SPSS 25. Hasil Dari Penelitian ini diketahui nilai signifikan untuk pengaruh kadar perekat pada briket berbahan dasar serbuk kayu terhadap laju pembakaran adalah 0,012 < 0,05 sehingga dapat disimpulkan bahwa hipotesis pertama diterima yang berarti ada perbedaan signifikan.
PENGEMBANGAN MESIN FRAIS WMD-25VL SISTEM KONVENSIONAL MENJADI SISTEM COMPUTER NUMERICAL CONTROL BERBASIS MACH3 CONTROLLER
Authors: Zohan Ardiansyah  , Basuki  , Fajar Satriya Hadi  , Mohammad Munib Rosadi
Published: June 2024

Mesin frais kovensional adalah suatu mesin perkakas yang mempunyai 3 sumbu utama pada pergerakanya. Mesin frais konvensional dapat ditingkatkan kinerja dan efektifitasnya dengan menambahkan motor stepper dengan sistem kendali menggunakan Mach3 Controller sehingga menjadi sistem otomatis. Pengembangan mesin frais WMD-25VL kovensional menjadi CNC ini untuk mengetahui desain mesin frais CNC WMD-25VL dan mengetahui kinerja dari mesin frais CNC WMD-25VL dengan menggunakan metode Research And Development. Proses awal pengembangan dengan studi literatur dari berbagai sumber, membuat desain awal meliputi desain rangka, desain bracket motor stepper, perakitan wiring hardware, serta penginstalan sistem kendali Mach3 Controller. Hasil dari pengembangan mesin frais WMD-25VL konvensional menjadi CNC ini adalah mesin sesuai dengan desain, dapat bekerja dengan baik setiap axisnya dan dapat mengikuti kode perintah program. Hasil uji fungsional dari tim validator mendapatkan persentase 96.65 %. Pada uji kelayakan mesin frais CNC WMD-25VL mendapatkan persentase 100%. Pada uji pemakaian mendapatkan persentase 93.3%. Kesimpulan pada pengembangan mesin frais ini menunjukkan mesin frais CNC WMD-25VL dikategorikan dengan kriteria sangat baik.
KEPUTUSAN ALTERNATIF DALAM MEMFUNGSIKAN PERAN AUDIT INTERNAL MELALUI FOCUS GROUP DISCUSSION
Authors: Yunita
Published: June 2024

Penelitian ini bertujuan untuk menganalisis manajemen pengelolaan lembaga pendidikan Preschool X di Jakarta Selatan. Penelitian ini merupakan penelitian kualitatif dengan observasi partisipatif dimana peneliti terlibat dalam kegiatan sehari – hari di Preschool X dan digunakan sebagai sumber data penelitian. Pendekatan Focus Group Discussion digunakan sebagai metode analisis atas data yang terkumpul dari hasil wawancara dan observasi. Hasil penelitian ini adalah Lembaga Pendidikan Preschool X memerlukan audit internal sebagai fungsi pengawasan pengendalian internal namun karena faktor biaya dan memilih memperbaiki sistem pengendalian sehingga manajemen memutuskan untuk tidak menggunakan audit internal.
Determination of muscle shape deformations of the tibialis anterior during dynamic contractions using 3D ultrasound
Authors: Sahrmann Annika S. , Vosse Lukas , Siebert Tobias , Handsfield Geoffrey G. , Röhrle Oliver
Published: June 2024

Purpose

In this paper, we introduce a novel method for determining 3D deformations of the human tibialis anterior (TA) muscle during dynamic movements using 3D ultrasound.

Materials and Methods

An existing automated 3D ultrasound system is used for data acquisition, which consists of three moveable axes, along which the probe can move. While the subjects perform continuous plantar- and dorsiflexion movements in two different controlled velocities, the ultrasound probe sweeps cyclically from the ankle to the knee along the anterior shin. The ankle joint angle can be determined using reflective motion capture markers. Since we considered the movement direction of the foot, i.e., active or passive TA, four conditions occur: slow active, slow passive, fast active, fast passive. By employing an algorithm which defines ankle joint angle intervals, i.e., intervals of range of motion (ROM), 3D images of the volumes during movement can be reconstructed.

Results

We found constant muscle volumes between different muscle lengths, i.e., ROM intervals. The results show an increase in mean cross-sectional area (CSA) for TA muscle shortening. Furthermore, a shift in maximum CSA towards the proximal side of the muscle could be observed for muscle shortening. We found significantly different maximum CSA values between the fast active and all other conditions, which might be caused by higher muscle activation due to the faster velocity.

Conclusion

In summary, we present a method for determining muscle volume deformation during dynamic contraction using ultrasound, which will enable future empirical studies and 3D computational models of skeletal muscles.
STIM1, ORAI1, and KDM2B in circulating tumor cells (CTCs) isolated from prostate cancer patients
Authors: Roumeliotou Argyro , Alkahtani Saad , Alarifi Saud , Alkahtane Abdullah A. , Stournaras Christos , Kallergi Galatea
Published: June 2024

Introduction: Previous publications have shown that STIM1, ORAI1, and KDM2B, are implicated in Ca2+ signaling and are highly expressed in various cancer subtypes including prostate cancer. They play multiple roles in cancer cell migration, invasion, and metastasis. In the current study we investigated the expression of the above biomarkers in circulating tumor cells from patients with metastatic prostate cancer.

Methods: Thirty-two patients were enrolled in this study and CTCs’ isolation was performed with Ficoll density gradient. Two different triple immunofluorescence stainings were conducted with the following combination of antibodies: CK/KDM2B/CD45 and CK/STIM1/ORAI1. Slides were analyzed using VyCAP microscopy technology.

Results: CTC-positive patients were detected in 41% for (CK/KDM2B/CD45) staining and in 56% for (CK/STIM1/ORAI1) staining. The (CK+/KDM2B+/CD45–) and the (CK+/STIM1+/ORAI1+) were the most frequent phenotypes as they were detected in 85% and 94% of the CTC-positive patients, respectively. Furthermore, the expression of ORAI1 and STIM1 in patients’ PBMCs was very low exhibiting them as interesting specific biomarkers for CTC detection. The (CK+/STIM1+/ORAI1+) phenotype was correlated to bone metastasis (p = 0.034), while the (CK+/STIM1+/ORAI1–) to disease relapse (p = 0.049).

Discussion: STIM1, ORAI1, and KDM2B were overexpressed in CTCs from patients with metastatic prostate cancer. STIM1 and ORAI1 expression was related to disease recurrence and bone metastasis. Further investigation of these biomarkers in a larger cohort of patients will clarify their clinical significance for prostate cancer patients.
Beyond the double helix: the multifaceted landscape of extracellular DNA in Staphylococcus aureus biofilms
Authors: Bowden Lucy C. , Finlinson Jenny , Jones Brooklyn , Berges Bradford K.
Published: June 2024

Staphylococcus aureus forms biofilms consisting of cells embedded in a matrix made of proteins, polysaccharides, lipids, and extracellular DNA (eDNA). Biofilm-associated infections are difficult to treat and can promote antibiotic resistance, resulting in negative healthcare outcomes. eDNA within the matrix contributes to the stability, growth, and immune-evasive properties of S. aureus biofilms. eDNA is released by autolysis, which is mediated by murein hydrolases that access the cell wall via membrane pores formed by holin-like proteins. The eDNA content of S. aureus biofilms varies among individual strains and is influenced by environmental conditions, including the presence of antibiotics. eDNA plays an important role in biofilm development and structure by acting as an electrostatic net that facilitates protein-cell and cell-cell interactions. Because of eDNA’s structural importance in biofilms and its ubiquitous presence among S. aureus isolates, it is a potential target for therapeutics. Treatment of biofilms with DNase can eradicate or drastically reduce them in size. Additionally, antibodies that target DNABII proteins, which bind to and stabilize eDNA, can also disperse biofilms. This review discusses the recent literature on the release, structure, and function of eDNA in S. aureus biofilms, in addition to a discussion of potential avenues for targeting eDNA for biofilm eradication.
Environmental variation predicts patterns of genomic variation in an African tropical forest frog
Authors: Miller Courtney A. , Tasse Taboue Geraud C. , Fokam Eric B. , Morgan Katy , Zhen Ying , Harrigan Ryan J. , Le Underwood Vinh , Ruegg Kristen , Clee Paul R. Sesink , Ntie Stephan , Mickala Patrick , Mboumba Jean Francois , Fuller Trevon , Zimkus Breda M. , Smith Thomas B. , Anthony Nicola M.
Published: June 2024

Central African rainforests are predicted to be disproportionately affected by future climate change. How species will cope with these changes is unclear, but rapid environmental changes will likely impose strong selection pressures. Here we examined environmental drivers of genomic variation in the central African puddle frog (Phrynobatrachus auritus) to identify areas of elevated environmentally-associated turnover. We also compared current and future climate models to pinpoint areas of high genomic vulnerability where allele frequencies will have to shift the most in order to keep pace with future climate change. Neither physical landscape barriers nor the effects of past Pleistocene refugia influenced genomic differentiation. Alternatively, geographic distance and seasonal aspects of precipitation are the most important drivers of SNP allele frequency variation. Patterns of genomic differentiation coincided with key ecological gradients across the forest-savanna ecotone, montane areas, and a coastal to interior rainfall gradient. Areas of greatest vulnerability were found in the lower Sanaga basin, the southeastern region of Cameroon, and southwest Gabon. In contrast with past conservation efforts that have focused on hotspots of species richness or endemism, our findings highlight the importance of maintaining environmentally heterogeneous landscapes to preserve genomic variation and ongoing evolutionary processes in the face of climate change.
Exploring the effects of real-time online cardiac telerehabilitation using wearable devices compared to gym-based cardiac exercise in people with a recent myocardial infarction: a randomised controlled trial
Authors: Mitropoulos A. , Anifanti M. , Koukouvou G. , Ntovoli A. , Alexandris K. , Kouidi E.
Published: June 2024

Background

Exercise-based cardiac rehabilitation (CR) is a non-pharmacological multidisciplinary programme for individuals after myocardial infarction (MI) that offers multiple health benefits. One of the greatest barriers to CR participation is the travel distance to the rehabilitation centre. Remotely monitored CR appears to be at least as effective in improving cardiovascular risk factors and exercise capacity as traditional centre-based CR. Nevertheless, the efficacy of remotely monitored CR in individuals with a recent MI has yet to be examined.

Methods

A total of 30 individuals (8 women, 22 men) after a recent (i.e., <4 weeks) MI were randomly allocated into two groups (online home-based and gym-based groups). Both groups underwent a 26-week CR programme three times per week. All patients performed baseline and 24-week follow-up measurements where peak oxygen uptake (VO2peak), mean daily steps, distance, and calories were assessed.

Results

The online group showed an improvement in mean daily steps (p < 0.05) and mean daily distance (p < 0.05) at 24 weeks compared to the gym-based group. The paired-sample t-test showed that all the assessed variables were statistically (p < 0.001) improved for both groups at 24 weeks. Pearson's r demonstrated positive correlations between VO2peak and mean daily distance (r = 0.375), and negative correlations between VO2peak and muscle (r = −0.523) and fat masses (r = −0.460). There were no exercise-induced adverse events during the study.

Conclusion

Our findings might indicate that a real-time online supervised CR exercise programme using wearable technology to monitor the haemodynamic responses in post-MI patients is equally effective as a gym-based exercise programme.
Staying connected: implementing avatar robots at schools in Germany and Japan
Authors: Spoden Celia , Ema Arisa
Published: June 2024

Introduction

With advancements in communication technologies and internet connectivity, avatar robots for children who cannot attend school in person due to illness or disabilities have become more widespread. Introducing these technologies to the classroom aims to offer possibilities of social and educational inclusion. While implementation is still at an experimental level, several of these avatars have already been introduced as a marketable service. However, various obstacles impede widespread acceptance.

Methods

In our explorative qualitative case study we conducted semi-structured interviews with eight individuals involved in the implementation of the avatar robots AV1 in Germany and eleven participants involved with implementing OriHime in Japan. We analyzed and compared implementation processes, application areas, access and eligibility, and the potential and limitations of avatars at schools.

Results

We identified structural similarities and differences in both countries. In the German cases the target is defined as temporary use for children who cannot attend school in person because of childhood illness, with the clear goal of returning to school. Whereas in Japan OriHime is also implemented for children with physical or developmental disabilities, or who cannot attend school in person for other reasons.

Discussion

Our study suggests that avatar technologies bear high potential for children to stay socially and educationally connected. Yet, structures need establishing that grant equal access to avatar technologies. These include educational board regulations, budgets for funding avatar technologies and making them accessible to the public, and privacy protection standards that are adequate, yet do not create implementation hurdles that are too high. Furthermore, guidelines or training sessions on technical, educational and psychosocial aspects of including avatar technologies in the classroom for teachers are important for successful implementation. Since our Japanese cases suggest that expanding the area of application beyond childhood illness is promising, further research on the benefits for different groups is needed.
Transitional experiences of Australian health science researchers: where is academic teaching preparedness?
Authors: Lamon Séverine , Knowles Olivia , Currey Judy
Published: June 2024

Academic career development relies on a combination of teaching and research skills. In Australia, it is common for recent Doctor of Philosophy graduates to have a short-term post-doctoral research experience to build publication track-record and increase grant competitiveness, before securing a combined research and teaching or ‘academic’ role at a university. Other scientists work as full-time researchers for several years before transitioning to academic roles with expectations they can teach. The aim of this study was to explore the experiences of health and biomedical science researchers transitioning into academic roles using a mixed methods design. Sixty-six participants working in health and biomedical sciences at over 20 Australian Universities who had been in an academic role for 5 years or less completed an online survey. Of 66 participants, 18 (27%) had never been in a research-only role before, while 48 (63%) had held a research-only role for up to 11 years before starting their current academic role. Findings showed most academics were not trained nor equipped to successfully undertake scholarly teaching. They reported a lack of awareness of teaching expectations, practical resources, and direct support provision at the start of their appointment. For former researchers specifically, these experiences led to low confidence and poor enjoyment in their academic role, with the potential to decrease overall teaching quality, student learning and student satisfaction. We postulate that these issues may be mitigated by the implementation of teaching-specific training programs catering for the research-only background of staff entering health and biomedical academic roles in the higher education workforce.
A CFD numerical simulation of particle deposition characteristics in automobile tailpipe: power abatement pathways
Authors: Zhang Rui , Gao Ming , Fan Mao
Published: June 2024

The study of the movement of pollutants through ducts facilitates the assessment and control of ambient air quality problems (AQ). Among other things, understanding the deposition and distribution of particulate matter in elbows is important for practical engineering applications. In this study, the turbulent flow field and particle deposition in a 90° bend is investigated using RANS simulation. The RNG k-ε turbulence model was employed to calculate the airflow flow field and the discrete phase model (DPM) was used to simulate the particle phase motion. Where for the discrete phase, the Discrete Random Wander (DRW) model was considered and the deposition of particles with sizes of 1, 3, 5, 10, 20, and 40 μm in the flow field was investigated separately. Grid-independent validation of the models used in the simulations was performed. The effects of inlet velocity, particle size, and direction of gravity on the flow field and particle deposition in the elbow were considered. The results show that the flow field in the bend is strongly influenced by the above parameters. Among them, the turbulent disturbance in the bend section is the most intense, with high turbulent energy value, and it is also the region with the largest energy loss. The inlet velocity is negatively correlated with the deposition rate, and the particle size is positively correlated with the deposition rate.
The barrier risk to the ecological connectivity of plant diversity in karst landscapes in Guizhou Province, China
Authors: Zhou Baichi , Lou Hezhen , Yang Shengtian , Li Chaojun , Pan Zihao , Zhang Yujia , Li Hao , Yi Yin , Gong Jiyi
Published: June 2024

Ecological connectivity in landscapes is crucial for plant diversity conservation. The barrier risk to ecological connectivity represents the risk to ecological connectivity loss or weakening, resulting from the barrier to biological information exchange among habitats. Therefore, clarifying the barrier risk to the ecological connectivity of plant diversity in space can reveal the spatial impacts of reduced ecological connectivity on plant diversity. This study analyzed effects of karst peak, river network, arable land, and impervious surface on plant diversity in karst natural, countryside, urban, and island landscapes in Guizhou Province with fragile environment. Then, we calculated the barrier distance of ecological connectivity to reveal the barrier risk to the ecological connectivity of plant diversity in space. The results showed that karst peak was the source of high plant diversity, and plant diversity could diffuse about 400 m around karst peaks. River network and arable land enhanced the connectivity among karst peaks to maintain plant diversity, and the effect on enhancing the connectivity was about 300 m and 450 m, respectively, while the weakening effect of impervious surface on connectivity was about 350 m. Based on the distance for plant diversity diffusing around karst peaks, the barrier distance of ecological connectivity was determined by the combination type of river network, arable land and impervious surface in landscapes. From low to high, the barrier risk to the ecological connectivity of plant diversity was about 1,110 m in the combination of river network and arable land, about 790 m in the combination of river network, arable land and impervious surface, about 520 min the combination of arable land and impervious surface, about 400 m in the combination of river network and impervious surface. Our findings clarify the barrier risk to the ecological connectivity of plant diversity in space, and provide a scientific basis for plant diversity conservation from the perspective of ecological connectivity.
Study on the effect of carbon trading on the carbon emission intensity of enterprises—a mechanism test based on ESG performance
Authors: Han Anzi , Yu Tinglei , Ke Yihu , Liu Chang , Liu Yunqiang
Published: June 2024

Facing the double constraints of the “double carbon” target and high-quality economic development, carbon trading policy is an important tool for realizing the emission reduction commitment; based on the perspective of microenterprises, the specific mechanism and spatial effect of carbon trading policy still need to be evaluated. Taking China’s carbon emissions trading pilot as a quasi-natural experiment, this paper empirically investigates the impact of carbon trading policy on the carbon emission intensity of pilot enterprises and its mechanism of action, and its impact on the carbon emission intensity of neighboring enterprises, based on the multi-temporal double-difference model, moderating effect model, and spatial Durbin model with the A-share-listed enterprises in the period of 2009–2019 as the samples. It is found that: 1) Carbon trading policy will reduce the carbon emission intensity of enterprises to different degrees, and there are significant differences under different ownership types, degrees of marketization and the level of digitization. 2) Under the influence of environmental uncertainty, ESG disclosure will weaken the effectiveness of carbon emission reduction in the pre-pilot stage of the policy; with the gradual improvement of the carbon trading policy and ESG disclosure mechanism, ESG ratings will positively regulate the inhibitory effect of the carbon trading policy on the carbon emission intensity of enterprises through multiple paths. 3) Carbon trading policy effectively reduces multiple negative spillovers through the demonstration effect and competition effect of neighboring enterprises, driving the carbon emission reduction behavior of non-pilot enterprise. The research in this paper enriches the research paradigm of carbon emission intensity influencing factors, provides reference suggestions for the government to improve its policies, and better contributes to the realization of the “dual-carbon” vision in China as soon as possible.
Constructing ecological security pattern based on spatio-temporal evaluation of ecosystem services and ecological health in Chengdu, Southwest China
Authors: Zhong Bo , Wu Shuang , Wu Ning , Sun Geng , He Chunmei , Liu Liangfeng , Chen Huai
Published: June 2024

Introduction

With the acceleration of urbanization, human population and built surface in urban areas have increased rapidly, triggering numerous environmental problems. Identification of ecological security pattern (ESP) can be helpful to optimize the interaction and relationship between ecological conservation and socioeconomic development in a given region. In this study, taking Chengdu City as an example, a methodology was used to analyze the city’s ESP.

Methodology

Ecological sources were identified based on their ecological security values, which were derived from the spatio-temporal evaluation of ecosystem services and ecological health. The ecological resistance surface was revised with nighttime light index. Linkage Mapper combined with circuit theory was used to extracted ecological corridors and key ecological nodes.

Results:

The results showed that the mean values of ecological security in Chengdu City presented a downward and then upward trend from 2000 to 2018. In 2018, the ESP in Chengdu City was formed by 140 ecological sources with the total area of 8,819.78 km2, 302 ecological corridors with the area of 456.91 km2, as well as 61 pinch-points and 17 barrier points. The ecological sources in Chengdu City were mainly distributed in or nearby Longmen Mountain and Longquan Mountain, two flanks of the Chengdu Plain, and connected each other with hundreds of ecological corridors. Most of ecological sources and corridors were composited of forests in mountainous areas and linpan units (wooded lots) in rural plain areas. On the contrary, pinch-points and barrier points were mainly distributed in the districts nearby the metropolitan urban center.

Conclusion

Finally, this study proposed that constructing ESP must adopt a dynamic and holistic approach in considering the change of restoring ecosystems, shift of urban demands for ecosystem services and transformation of urban-rural land use/cover. Restoring and managing corridors sustainably are important for improving the ecological connectivity of all over ecological sources in a city, all of which together, if functioning well, could further support the realization of sustainable urbanization.
LGC-DBP: the method of DNA-binding protein identification based on PSSM and deep learning
Authors: Zhu Yiqi , Sun Ailun
Published: June 2024

The recognition of DNA Binding Proteins (DBPs) plays a crucial role in understanding biological functions such as replication, transcription, and repair. Although current sequence-based methods have shown some effectiveness, they often fail to fully utilize the potential of deep learning in capturing complex patterns. This study introduces a novel model, LGC-DBP, which integrates Long Short-Term Memory (LSTM), Gated Inception Convolution, and Improved Channel Attention mechanisms to enhance the prediction of DBPs. Initially, the model transforms protein sequences into Position Specific Scoring Matrices (PSSM), then processed through our deep learning framework. Within this framework, Gated Inception Convolution merges the concepts of gating units with the advantages of Graph Convolutional Network (GCN) and Dilated Convolution, significantly surpassing traditional convolution methods. The Improved Channel Attention mechanism substantially enhances the model’s responsiveness and accuracy by shifting from a single input to three inputs and integrating three sigmoid functions along with an additional layer output. These innovative combinations have significantly improved model performance, enabling LGC-DBP to recognize and interpret the complex relationships within DBP features more accurately. The evaluation results show that LGC-DBP achieves an accuracy of 88.26% and a Matthews correlation coefficient of 0.701, both surpassing existing methods. These achievements demonstrate the model’s strong capability in integrating and analyzing multi-dimensional data and mark a significant advancement over traditional methods by capturing deeper, nonlinear interactions within the data.
MicroRNA-939 amplifies Staphylococcus aureus-induced matrix metalloproteinase expression in atopic dermatitis
Authors: Wang Jiating , Huang Yejing , Wu Xinfeng , Li Dongqing
Published: June 2024

Background

Atopic dermatitis (AD) is a common chronic inflammatory skin diseases that seriously affects life quality of the patients. Staphylococcus aureus (S. aureus) colonization on the skin plays an important role in the pathogenesis of AD; however, the mechanism of how it modulates skin immunity to exacerbate AD remains unclear. MicroRNAs are short non-coding RNAs that act as post-transcriptional regulators of genes. They are involved in the pathogenesis of various inflammatory skin diseases.

Methods

In this study, we established miRNA expression profiles for keratinocytes stimulated with heat-killed S. aureus (HKSA). The expression of miR-939 in atopic dermatitis patients was analyzed by fluorescence in situ hybridization (FISH). miR-939 mimic was transfected to human primary keratinocyte to investigate its impact on the expression of matrix metalloproteinase genes (MMPs) in vitro. Subsequently, miR-939, along with Polyplus transfection reagent, was administered to MC903-induced atopic dermatitis skin to assess its function in vivo.

Results

MiR-939 was highly upregulated in HKSA-stimulated keratinocytes and AD lesions. In vitro studies revealed that miR-939 increased the expression of matrix metalloproteinase genes, including MMP1, MMP3, and MMP9, as well as the cell adhesion molecule ICAM1 in human primary keratinocytes. In vivo studies indicated that miR-939 increased the expression of matrix metalloproteinases to promote the colonization of S. aureus and exacerbated S. aureus-induced AD-like skin inflammation.

Conclusions

Our work reveals miR-939 is an important regulator of skin inflammation in AD that could be used as a potential therapeutic target for AD.
Dynamic immune status analysis of peripheral blood mononuclear cells in patients with Klebsiella pneumoniae bloodstream infection sepsis using single-cell RNA sequencing
Authors: Zhang Shengwei , Zhang Nan , Han Jing , Sun Zeyu , Jiang Hua , Huang Wenhua , Kong Decong , Li Qian , Ren Yuhao , Zhao Shishun , Jiang Yongqiang , Liu Peng
Published: June 2024

Background

Klebsiella pneumoniae is a common Gram-negative bacterium. Blood infection caused by K. pneumoniae is one of the most common causes of human sepsis, which seriously threatens the life of patients. The immune status of peripheral blood mononuclear cells (PBMCs) based on single-cell RNA sequencing (scRNA-seq) in acute stage and recovery stage of sepsis caused by K. pneumoniae bloodstream infection has not been studied.

Methods

A total of 13 subjects were included in this study, 3 healthy controls, 7 patients with K. pneumoniae bloodstream infection in the acute stage (4 patients died), and 3 patients in the recovery stage. Peripheral blood of all patients was collected and PBMCs were isolated for scRNA-seq analysis. We studied the changes of PBMCs components, signaling pathways, differential genes, and cytokines in acute and recovery stages.

Results

During K. pneumoniae acute infection we observed a decrease in the proportion of T cells, most probably due to apoptosis and the function of T cell subtypes was disorder. The proportion of monocytes increased in acute stage. Although genes related to their phagocytosis function were upregulated, their antigen presentation capacity-associated genes were downregulated. The expression of IL-1β, IL-18, IFNGR1 and IFNGR2 genes was also increased in monocytes. The proportion of DCs was depleted during the acute stage and did not recover during sepsis recovery. DCs antigen presentation was weakened during the acute stage but recovered fast during the recovery stage. pDCs response to MCP-1 chemokine was weakened, they recovered it quickly during the recovery stage. B cells showed apoptosis both in the acute stage and recovery stage. Their response to complement was weakened, but their antigen presentation function was enhanced. The proportion of NK cells stable during all disease’s stages, and the expression of IFN-γ gene was upregulated.

Conclusion

The proportion of PBMCs and their immune functions undergo variations throughout the course of the disease, spanning from the acute stage to recovery. These findings provide new insights into the mechanism of PBMCs immune function during K. pneumoniae bloodstream infection sepsis and recovery and sets the basis for further understanding and treatment.
Granzyme K mediates IL-23-dependent inflammation and keratinocyte proliferation in psoriasis
Authors: Richardson Katlyn C. , Aubert Alexandre , Turner Christopher T. , Nabai Layla , Hiroyasu Sho , Pawluk Megan A. , Cederberg Rachel A. , Zhao Hongyan , Jung Karen , Burleigh Angela , Crawford Richard I. , Granville David J.
Published: June 2024

Psoriasis is an inflammatory disease with systemic manifestations that most commonly presents as itchy, erythematous, scaly plaques on extensor surfaces. Activation of the IL-23/IL-17 pro-inflammatory signaling pathway is a hallmark of psoriasis and its inhibition is key to clinical management. Granzyme K (GzmK) is an immune cell-secreted serine protease elevated in inflammatory and proliferative skin conditions. In the present study, human psoriasis lesions exhibited elevated GzmK levels compared to non-lesional psoriasis and healthy control skin. In an established murine model of imiquimod (IMQ)-induced psoriasis, genetic loss of GzmK significantly reduced disease severity, as determined by delayed plaque formation, decreased erythema and desquamation, reduced epidermal thickness, and inflammatory infiltrate. Molecular characterization in vitro revealed that GzmK contributed to macrophage secretion of IL-23 as well as PAR-1-dependent keratinocyte proliferation. These findings demonstrate that GzmK enhances IL-23-driven inflammation as well as keratinocyte proliferation to exacerbate psoriasis severity.
Unraveling the phylogeny of Chaetopteridae (Annelida) through mitochondrial genome analysis
Authors: Wu Xiu , Su Xuechun , Wang Yu , He Caifang , Qiu Jian-Wen , Zhang Yanjie
Published: June 2024

Mitochondrial genomes serve as valuable markers for phylogenetic and evolutionary studies across diverse invertebrate taxa, but their application within Annelida remains limited. In this study, we report the mitochondrial genomes of seven species from four genera of Chaetopteridae (Annelida), obtained by high-throughput sequencing. Phylogenetic analysis was performed using cox1, 18S, 28S and all mitochondrial genes. Our results reveal Chaetopterus and Mesochaetopterus as well-supported monophyletic sister clades, while Phyllochaetopterus and Spiochaetopterus appear paraphyletic, with species from both genera in a mixed clade sister to Chaetopterus + Mesochaetopterus. While mitochondrial gene orders remain conserved within Chaetopteridae, they appear substantially different from those of the ancestral patterns in Annelida. All 13 protein-coding genes found in Chaetopteridae evolved under strong purification selection, although Phyllochaetopterus exhibited the highest base-substitution rate for most of them, suggesting a more relaxed purified selection. Overall, our study provides molecular resources for phylogenetic studies of Chaetopteridae, highlighting the necessity for a comprehensive revision of the family, particularly dealing with the paraphyletic Phyllochaetopterus and Spiochaetopterus.
Construction of a large-scale maritime element semantic schema based on knowledge graph models for unmanned automated decision-making
Authors: Li Yong , Liu Xiaotong , Wang Zhishan , Mei Qiang , Xie Wenxin , Yang Yang , Wang Peng
Published: June 2024

In maritime logistics optimization, considerable research efforts are focused on the extraction of deep behavioral characteristics from comprehensive shipping data to discern patterns in maritime vessel behavior. The effective linkage of these characteristics with maritime infrastructure, such as berths, is critical for the enhancement of ship navigation systems. This endeavor is paramount not only as a research focus within maritime information science but also for the progression of intelligent maritime systems. Traditional methodologies have primarily emphasized the analysis of navigational paths of vessels without an extensive consideration of the geographical dynamics between ships and port infrastructure. However, the introduction of knowledge graphs has enabled the integration of disparate data sources, facilitating new insights that propel the development of intelligent maritime systems. This manuscript presents a novel framework using knowledge graph technology for profound analysis of maritime data. Utilizing automatic identification system (AIS) data alongside spatial information from port facilities, the framework forms semantic triplet connections among ships, anchorages, berths, and waterways. This enables the semantic modeling of maritime behaviors, offering precise identification of ships through their diverse semantic information. Moreover, by exploiting the semantic relations between ships and berths, a reverse semantic knowledge graph for berths is constructed, which is specifically tailored to ship type, size, and category. The manuscript critically evaluates a range of graph embedding techniques, dimensionality reduction methods, and classification strategies through experimental frameworks to determine the most efficacious methodologies. The findings reveal that the maritime knowledge graph significantly enhances the semantic understanding of unmanned maritime equipment, thereby improving decision-making capabilities. Additionally, it establishes a semantic foundation for the development of expansive maritime models, illustrating the potential of knowledge graph technology in advancing intelligent maritime systems.
Evaluation of the probiotic, technological, safety attributes, and GABA-producing capacity of microorganisms isolated from Iranian milk kefir beverages
Authors: Moghimani Minoo , Onyeaka Helen , Hashemi Mohammad , Afshari Asma
Published: June 2024

Introduction

Kefir beverage has beneficial microorganisms that have health-giving properties; therefore, they have a good potential to be probiotic. This study evaluated the probiotic potential, technological, and safety characteristics of Enterococcus faecalis, Lactococcus lactis, and Pichia fermentans isolated from traditional kefir beverages.

Method

First, isolates were evaluated in terms of resistance to acid, alkali, bile salts, trypsin, and pepsin of the gastrointestinal tract. The auto-aggregation and co-aggregation ability of isolates were measured using spectrophotometry. Antimicrobial activities were assayed against important food-borne pathogens using the agar well diffusion method. Moreover, gamma-aminobutyric acid (GABA) production was investigated by thin-layer chromatography (TLC).

Result

Among the isolates, P. fermentans had an 85% total survival rate, but its amount reached below 6 log CFU/ml which is considered non-resistant, and it showed the highest auto-aggregation (74.67%). Moreover, only L. lactis showed antimicrobial activity and had the highest co-aggregation with E. coli PTCC 1338 (54.33%) and L. monocytogenes ATCC 7644 (78%). Finally, an evaluation of the technological and safety characteristics of the strains showed that the strains produced GABA and were safe.

Discussion

Although the isolates were not resistant to the gastrointestinal tract, their supernatant contained valuable natural compounds, including antioxidants, GABA, and antimicrobials, which can be used to produce functional foods and medicines. In addition, other approaches, such as increasing the initial number of strains, using foods as carriers of isolates, and encapsulating the isolates, can effectively increase the survivability of isolates in the gastrointestinal tract.
Catabolism and interactions of syntrophic propionate- and acetate oxidizing microorganisms under mesophilic, high-ammonia conditions
Authors: Weng Nils , Singh Abhijeet , Ohlsson Jonas A. , Dolfing Jan , Westerholm Maria
Published: June 2024

Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) “Candidatus Syntrophopropionicum ammoniitolerans”, a syntrophic acetate-oxidizing bacterium (SAOB) Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen, for which we propose the provisional name “Candidatus Methanoculleus ammoniitolerans”. The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation.
Metabarcoding reveals a high diversity and complex eukaryotic microalgal community in coastal waters of the northern Beibu Gulf, China
Authors: Wang Chaofan , Gu Junning , Li Weiguo , Wang Jian , Wang Zhaohui , Lin Qiuqi
Published: June 2024

Beibu Gulf is an important semi-enclosed bay located in the northwestern South China Sea, and is famous for its high bio-productivity and rich bio-diversity. The fast development along the Beibu Gulf Economical Rim has brought pressure to the environment, and algal blooms occurred frequently in the gulf. In this study, surface water samples and micro-plankton samples (20–200 μm) were collected in the northern Beibu Gulf coast. Diversity and distribution of eukaryotic planktonic microalgae were analyzed by both metabarcoding and microscopic analyses. Metabarcoding revealed much higher diversity and species richness of microalgae than morphological observation, especially for dinoflagellates. Metabarcoding detected 144 microalgal genera in 8 phyla, while microscopy only detected 40 genera in 2 phyla. The two methods revealed different microalgal community structures. Dinoflagellates dominated in microalgal community based on metabarcoding due to their high copies of 18 s rRNA gene, and diatoms dominated under microscopy. Altogether 48 algal bloom and/or toxic species were detected in this study, 34 species by metabarcoding and 19 species by microscopy. Our result suggested a high potential risk of HABs in the Beibu Gulf. Microalgal community in the surface water samples demonstrated significantly higher OTU/species richness, alpha diversity, and abundance than those in the micro-plankton samples, although more HAB taxa were detected by microscopic observations in the micro-plankton samples. Furthermore, nano-sized taxa, such as those in chlorophytes, haptophytes, and chrysophyceans, occurred more abundantly in the surface water samples. This study provided a comprehensive morphological and molecular description of microalgal community in the northern Beibu Gulf.