bluuebunny/crossref_metadata_2025 huggingface dataset:
PRODUKTIVITAS KERJA PADA PELAYANAN TIKET DI PT. PELNI SORONG DENGAN METODE STOPWATCH TIME STUDY
Authors: Masniar Masniar , Ashar Ashar , Atanay Orgenes Paulus
Published: January 2023

Pengukuran produktivitas kerja atau work measurement merupakan usaha untuk menentukan lama kerja yang dibutuhkan oleh seorang operator atau pekerja dalam menyelesaikan suatu pekerjaan yang spesifik pada tingkat kecepatan kerja yang normal dalam lingkungan kerja yang terbaik pada saat itu. Sebagai perusahaan nasional PT. Pelni selalu dituntut untuk memberikan pelayanan yang baik. Untuk itu perlu diketahui standar waktu pelayanan untuk pelayanan PT. Pelni cabang Sorong dan mengukur produktivitas karyawan. Pada penelitian ini duganakan Stopwatch Time Study untuk mengumpulkan data-data yang diperlukan untuk memenuhi kebutuhan proses perhitungan work sampling. Setelah dilakukan penelitian diperoleh total waktu baku yaitu sebagai berikut: (1) untuk karyawan 1 pada hari 1 yaitu sebesar 390,225 detik atau 6,504 menit (2) untuk karyawan 2 pada hari 1 yaitu sebesar 390,590 detik atau 6,526 menit (3) untuk karyawan 1 pada hari 2 yaitu sebesar 388,366 detik atau 6,473 menit (4) untuk karyawan 2 pada hari 2 yaitu sebesar 402,87 detik atau 6,715 menit, masing-masing untuk melayani 1 pembelian tiket. Hasil perhitungan menunjukkan tingkat produktivitas kerja sebagai berikut : (1) pada karyawan 1 pada hari 1 mencapai 77% (2) pada karyawan 2 pada hari 1 sebesar 68% (3) pada karyawan 1 pada hari 2 sebesar 68% (4) pada karyawan 2 pada hari 2 sebesar 67%.
USULAN RANCANGAN SISTEM USAHA WARALABA PADA RUMAH MAKAN SAWAYAKA SUSHI
Authors: Tamrin Tajuddin  , Aprisa Rian Histiarini  , Asih Ahistasari  , Hamunta Muhammad Rizky
Published: January 2023

Franchise is a business activity using the method of granting licenses, trademarks, copyrights, or patents from the franchisor to the franchisee. Sawayaka Sushi is a franchise business that offers Japanese food products. Sawayaka Sushi is currently incomplete and does not cover all activities at Sawayaka Sushi. The restaurant owner has plans to expand his business by applying the improved franchise system to the new Sawayaka Sushi restaurant. The system that will be used is a franchise system that matches the Sawayaka Sushi restaurant. Therefore, the old Sawayaka Sushi business system will be evaluated and with this evaluation a new system will be created and can be proposed as a franchise business system at the Sawayaka Sushi restaurant. To find out whether Sawayaka Sushi's business is eligible to become a franchise or not, a franchisability study is used, namely from a qualitative and quantitative perspective. In the marketing strategy used SWOT analysis. The results obtained based on the business feasibility aspect show that the Sawayaka Sushi business can be said to be feasible. The payback period of the Sawayaka Sushi franchise is 2 years 7 months, the NPV generates a positive value of IDR 57,639,635. Internal Rate of Return (IRR) of 28.316% is declared acceptable.
Current Developments and Perspectives in Multiple Myeloma
Authors: Delforge Michel , Knop Stefan , Mohty Mohamad
Published: January 2023

In the last decades, advances in the therapeutic management of multiple myeloma (MM) with new drug armamentarium and strategies have significantly improved the outcome and survival of newly diagnosed and relapsed patients. However, the continuing challenges physicians are facing within specific clinical settings and patient subpopulations, whose prognosis with current strategies is extremely poor, call for a paradigm change. New immunomodulators, proteasome inhibitors, histone deacetylase inhibitors, and monoclonal antibodies are being explored to improve first-line outcomes so that a smaller proportion of patients relapse early or fail to respond to induction treatment. Moreover, recent advances and clinical evidence with novel therapies seem to provide patients with relapsed or refractory MM additional survival benefits. Improving clinical outcomes and refining standard of care should help clinicians reduce the burden of multiple and toxic therapy; quality of life (QoL) should be at the core of MM management. Patient selection and stratification needs to be reinforced with the help of comprehensive knowledge on conventional risk factors, and supplemented by molecular pathways in the near future in order to provide tailored options and strategies to patients, including the use of monoclonal antibodies. Numerous drugs are on the horizon and the next few years should witness marked improvements in survival, QoL, and safety of MM management.
Preventing Infections in Higher-Risk Myelodysplastic Syndrome Patients Treated with Hypomethylation Agents
Authors: Ofran Yishai
Published: January 2023

Hypomethylation agents became the standard of care for patients with high-risk myelodysplastic syndrome (MDS). While long-term benefits of azacitidine (AZA) and decitabine (DEC) were demonstrated in multiple studies, methods to enhance patients’ safety during therapy with those agents are pending. The causative correlations between drug administration and non-life-threatening complications such as injection-site erythema or gastrointestinal (GI) discomfort are obvious. However, infections, which are the most common life-threatening complication among higher risk MDS patients, are frequent even in those receiving therapy other than hypomethylation agents, including supportive care solely. Therefore, the contribution of hypomethylation therapy to infection risk is difficult to determine. Herein, data regarding infectious complications, their prevalence, risk stratification, and methods of prevention will be reviewed.
Immediate Perinatal Outcome of Mothers with Maternal Near-Miss at Moi Teaching and Referral Hospital, Eldoret, Kenya
Authors: Nding’ori David , Mwangi Winfred , Mishra Pallavi , Odunga Jack
Published: January 2023

Objective: To compare the immediate perinatal outcome of females with maternal near-miss (MNM) morbidity and those without near-miss morbidity in Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya.

Methods: A case-control study was conducted at MTRH. Near-miss cases were identified using World Health Organization (WHO) criteria for near-miss. A consecutive sampling technique was applied to obtain a total of 45 cases and 225 controls. Determinants of near-miss were assessed using a binary logistic regression model. Perinatal outcomes were compared between the near-miss and control.

Results: Severe maternal outcome ratio was 11.4 per 1,000 live births, the MNM ratio was 10.4 per 1,000 live births (95% confidence interval [CI]:7.6–13.9), and MNM mortality ratio was 11.2. The most common condition associated with near-miss was haematological or coagulation dysfunction (64%). Hypertension was the leading underlying cause of near-miss (35%). Factors associated with reduced odds of near-miss were employment (odds ratio: 0.12; 95% CI: 0.03–0.42) and awareness of danger signs (odds ratio: 0.41; 95% CI: 0.19–0.91). Most babies of the near-miss cases were born alive (76%), with median appearance, pulse, grimace, activity, respiration (Apgar) score of 9/10; stillbirth rate was 22%; and median birth weight was 2,700 g. This was similar to the control group with live birth at 77%, a median Apgar score of 9/10, and stillbirth of 23%. There was no statistically significant difference in perinatal outcome between cases and control.

Conclusion: MNM indicators are comparable to the world. The determinants of near-miss are unemployment and lack of awareness of danger signs. There was no difference in perinatal outcome between the cases and control.
The Issue of Local Content in Offshore Renewables: Aspirational, Legally-Binding or Missing the Mark? A Comparative Analysis of the UK and Poland
Authors: Gilbert Daniel , Wood Geoffrey
Published: January 2023

The focus of this article is the evolution of local content law and policy in the context of European renewable energy understood through a critical review of the offshore wind policies of the United Kingdom (UK) and Poland. It includes an analysis of the significance of a nascent local content claim made, in 2021, by the European Commission against a former European Union (EU) Member State, the UK, and its swift resolution out-of-court in 2022.
SOME CLASSES OF RICCATI EQUATIONS INTEGRABLE IN QUADRATURES
Authors: URDALETOVA Anarkul , ZABİNYAKOVA Olga , KYDYRALİEV Syrgak
Published: January 2023

As it is known, the second-order ordinary linear differential equation with variable coefficients is solvable in case if related Riccati equation can be integrated by quadratures. This paper considers establishment of correspondence between such equations by the authors’ method which means the second-order equation representation by a chain of the first-order equations. The algorithm of special Riccati equation solving is demonstrated (coefficients of these Riccati equations satisfy special conditions). One more peculiarity of this paper stands in consideration of exact applicational example – the Riccati equation which describes the magnetotellurics impedance behavior in geological media.
Political History and/as the Future for Undergraduate American Politics Curriculum
Authors: Plencner Joshua , Rank Allison
Published: January 2023

This paper outlines our response to fundamental challenges confronting undergraduate political science education. While enrollments in the political science major have declined at many institutions, including our own, we believe a structured APD approach offers an opportunity to capitalize on the wave of youth activism as well as the turbulent moment in contemporary politics by framing our major as the place where students can go to learn more about how we reached this particular political moment, think about what it takes and means to make change in a thoughtful, meaningful way, and equip themselves with the tools to interpret both the rhetorical and institutional contexts in which they hope to make this change while also overcoming some of the hurdles posed by the distribution model that remains the prevalent structure of many political science undergraduate programs.
Why Should We Care? Teaching Emotional Competency to Support Engaged Citizenship
Authors: Sweet-Cushman Jennie , Mathews-Schultz Lanethea
Published: January 2023

This paper introduces the notion of emotional competency as a key component of democratic citizenship and suggests a variety of ways to help students become emotionally competent citizens in undergraduate courses on American government. We offer several teaching strategies designed to foster students’ capacities to recognize their own processes of political socialization; to see politics as an extension of personal and collective values; to connect trends in political behavior to differential access to resources and varied identities and, thereby, to foster greater understanding and tolerance for difference; and to understand how, when, and why emotional cues shape and constrain political action.
Confronting Core Issues: A Critical Test of Attitude Polarization
Authors: Velez Yamil , Liu Patrick
Published: January 2023

A long-standing debate in the political psychology literature considers whether individuals update their beliefs and attitudes in the direction of evidence or grow more confident in their convictions when confronted with counter-attitudinal arguments and information. Though recent studies have shown that instances of the latter tendency, which scholars have termed attitude polarization and "belief backfire, are rarely observed in settings involving hot-button issues or viral misinformation, we know surprisingly little about how participants respond to information directly targeting deeply held attitudes, a key condition for triggering attitude polarization according to theories of motivated reasoning. To address this gap, we develop a tailored experimental design that measures participants' positions regarding their most important issues and randomly assigns them to different mixtures of personalized pro-attitudinal and counter-attitudinal information using the large language model GPT-3. We fail to recover evidence consistent with attitude polarization.
Raising the Stakes on a Political Science Major Field Test: Evidence from a New Capstone Course
Authors: Phillips John
Published: January 2023

Using a major field test (MFT) is a common method of program assessment. For accurate assessment to take place, however, students must be sufficiently motivated to perform. This paper studies a change in major requirements that associates a major field test to a grade in a capstone course, when it previously counted for nothing. After controlling for possibly confounding factors, a modest but robust treatment effect was found. Adding stakes also appears to cause MFT scores to correlate more strongly with other measures of student learning, which suggests more accurate assessment.
Urban Politics and Historic Importance of Black Neighborhoods: Examination of Titusville Neighborhood in Birmingham Alabama
Authors: Moak Stacy
Published: January 2023

This paper presents analysis of an Urban Politics course linked with an Art Studio course in which students participated in community engagement in an historically Black neighborhood to produce digital stories.
Showing the Other Side: What Kinds of Empathy Should Political Science Teach?
Authors: Brown Colin , Kaufman Chelsea
Published: January 2023

In 2006, then-Senator Barack Obama implored undergraduates at Northwestern to cultivate empathy, and called on the country to address its “empathy deficit.” Empathy is being taken seriously in politics and political science—but what exactly do we mean by empathy? This paper reviews the uses of “empathy” in the political science and teaching and learning literatures in order to identify which of many possible definitions we really mean when we as educators say that we wish to develop empathy as a skill. We identify several different conceptualizations of empathy in the political science and related literatures. We also begin to consider the question of where we go from here—if empathy is a necessary skill for democracy, how exactly can we as educators help our students to develop it?
Terrorism-Related Topic In The Language Of Fake News In Indonesia
Authors: Tonny Dian Effendi Ahmet Yiğitalp Tulga ,
Published: January 2023

he discussion on the relations between terrorism and social media mainly focuses on social media's role in spreading the terrorism ideology and recruiting the member of the terrorist group. However, social media has also become means to share fake news related to terrorism. Considering the relationship between fake news and terrorism, the primary purpose of this study is to examine the content, language used, and emotion of fake news about terrorism in Indonesia. It also reveal what kind of language used in fake news to manipulate the public and what emotions it appeals to. We analyzed fake news about terrorism in Indonesia using quantitative text analysis methods, such as sentiment analysis and dictionary-based analysis methods with R statistical software. We created two dictionaries covering the religious and violence words, and fake news was examined under these two dictionaries. For reliability, we applied the "Split-half test" to the results and we reached similar results. This study shows that ISIS, Aceh, and terrorist action in Sulawesi are three dominant topics in fake news. Second, the language on fake news is mostly about terrorism and violence to create fear in society. Third, violence and religious language are equal in the language of misleading content. We interpreted the results obtained with the traditional fear of crime theory. We then discussed the major results of this research and made effort to explain reasons behind our research results. The study has a limitation because of the small number of fake news. Future studies may overcome this limitation by selecting multiple countries as cases or increasing the date range of fake news. The dictionary-based method we used in this study is relatively new for the literature and provides the opportunity to analyze fake news content effectively. Our results using the Dictionary-based method can provide valuable clues for policymakers in the counter-terrorism field.
Implantable biomedical materials for treatment of bone infection
Authors: Shuaishuai Wang , Tongtong Zhu , Dapeng Wang , Mingran Zhang , Xukai Wang , Yue Yu , Hengliang Dong , Guangzhi Wu , Minglei Zhang
Published: January 2023

The treatment of bone infections has always been difficult. The emergence of drug-resistant bacteria has led to a steady decline in the effectiveness of antibiotics. It is also especially important to fight bacterial infections while repairing bone defects and cleaning up dead bacteria to prevent biofilm formation. The development of biomedical materials has provided us with a research direction to address this issue. We aimed to review the current literature, and have summarized multifunctional antimicrobial materials that have long-lasting antimicrobial capabilities that promote angiogenesis, bone production, or “killing and releasing.” This review provides a comprehensive summary of the use of biomedical materials in the treatment of bone infections and a reference thereof, as well as encouragement to perform further research in this field.
Drug delivery systems based on polyethylene glycol hydrogels for enhanced bone regeneration
Authors: Sun Shouye , Cui Yutao , Yuan Baoming , Dou Minghan , Wang Gan , Xu Hang , Wang Jingwei , Yin Wen , Wu Dankai , Peng Chuangang
Published: January 2023

Drug delivery systems composed of osteogenic substances and biological materials are of great significance in enhancing bone regeneration, and appropriate biological carriers are the cornerstone for their construction. Polyethylene glycol (PEG) is favored in bone tissue engineering due to its good biocompatibility and hydrophilicity. When combined with other substances, the physicochemical properties of PEG-based hydrogels fully meet the requirements of drug delivery carriers. Therefore, this paper reviews the application of PEG-based hydrogels in the treatment of bone defects. The advantages and disadvantages of PEG as a carrier are analyzed, and various modification methods of PEG hydrogels are summarized. On this basis, the application of PEG-based hydrogel drug delivery systems in promoting bone regeneration in recent years is summarized. Finally, the shortcomings and future developments of PEG-based hydrogel drug delivery systems are discussed. This review provides a theoretical basis and fabrication strategy for the application of PEG-based composite drug delivery systems in local bone defects.
In-situ Sr isotope disequilibrium in plagioclases from Late Cenozoic basalts in Leiqiong area: Evidence for the role of the Hainan plume and mantle metasomatism due to a paleo-subduction event
Authors: Chen Shuang-Shuang , Wu Duo-Yang , Gao Rui , Cheng Qiuming , Liu Jia-Qi
Published: January 2023

The origin of the EM2 (enriched mantle 2)-type reservoir beneath the Southeast Asia is controversial. In this study, we present new in-situ major and trace element (olivine, clinopyroxene, and plagioclase), and Sr isotopic compositions (plagioclase) for Leiqiong basaltic rocks to explain the potential source of Leiqiong EM2-like reservoir. Leiqiong olivines show the normal zoning textures with in-situ trace element heterogeneity, Leiqiong plagioclases exhibit the complex zoning textures with in-situ87Sr/86Sr isotopic disequilibria. It likely suggests the contribution to an individual crystal by the incorporation of heterogeneous components. The olivine and plagioclase phenocrysts, and the calculated Leiqiong clinopyroxene-equilibrium melts show the features of OIB-type enriched compositions associated with the plume, likely indicating the presence of Hainan mantle plume. The clear disequilibrium of 87Sr/86Sr isotopic ratios among bulk-rock, plagioclase phenocryst, and groundmass likely indicates the isotopically heterogeneous mantle source and the influence of the recycled subduction-related H2O-enriched oceanic fluid/melts carried by the deep Hainan plume. Leiqiong olivines are crystallized by the incorporation of pyroxenitic mantle source, but different from those from olivine-rich peridotitic mantle lithology, likely due to the reaction between eclogite-derived silicate melts (recycled oceanic crust) and peridotite.
Significant fibrosis assessed by liver biopsy among Chinese bariatric surgery patients: A prospective cross-sectional study
Authors: Huang Yongsheng , Dong Shiliang , Wang Cunchuan , Dong Zhiyong , Chen Wenhui
Published: January 2023

Background

Fibrosis stages affect clinical prognoses related to nonalcoholic fatty liver disease (NAFLD). However, data on the prevalence and clinical features of significant fibrosis are scarce in Chinese bariatric surgery patients. We aimed to investigate the prevalence of significant fibrosis in bariatric surgery patients and to identify its predictors.

Methods

We prospectively enrolled the patients performing intra-operative liver biopsies during bariatric surgery from a bariatric surgery center in a university hospital between May 2020 and January 2022. Anthropometric characteristics, co-morbidities, laboratory data and pathology reports were collected and analyzed. The performance of non‐invasive models was evaluated.

Results

Of 373 patients, 68.9%% had non-alcoholic steatohepatitis (NASH) and 60.9% exhibited fibrosis. Significant fibrosis was present in 9.1% of patients, advanced fibrosis in 4.0%, and cirrhosis in 1.6%. Multivariate logistic regression showed that increasing age (odds ratio [OR], 1.06; p=0.003), presence of diabetes (OR, 2.62; p=0.019), elevated c- peptide (OR, 1.26; p=0.025) and elevated aspartate aminotransferase (AST) (OR, 1.02; p=0.004) were independent predictors of significant fibrosis. The non-invasive models, AST to Platelet ratio (APRI), Fibrosis‐4 (FIB-4), and Hepamet fibrosis scores (HFS) provided greater accuracy for predicting significant fibrosis, compared to the NAFLD Fibrosis Score (NFS) and BARD score.

Conclusion

More than two-thirds of bariatric surgery patients had NASH and the prevalence of significant fibrosis was high. Elevated levels of AST and c- peptide, advanced age and diabetes indicated a higher risk of significant fibrosis. Non-invasive models, APRI, FIB-4 and HFS can be used to identify significant liver fibrosis in bariatric surgery patients.
Soft-masks guided faster region-based convolutional neural network for domain adaptation in wind turbine detection
Authors: Xu Yang , Luo Xiong , Yuan Manman , Huang Bohao , Malof Jordan M.
Published: January 2023

Wind turbine generator system plays a fundamental role in electricity generation in industry 4.0, and wind turbines are usually distributed separately and in poor locations. Unmanned Aerial Vehicles (UAV) which could overcome the above challenges are deployed to collect photographs of wind turbines, could be used for predictive maintenance of wind turbines and energy management. However, identifying meaningful information from huge amounts of photographs taken by drones is a challenging task due to various scales, different viewpoints, and tedious manual annotation. Besides, deep neural networks (DNN) are dominant in object detection, and training DNN requires large numbers of accurately labeled training data, and manual data annotation is tedious, inefficient, and error-prone. Considering these issues, we generate a synthetic UAV-taken dataset of wind turbines, which provides RGB images, target bounding boxes, and precise pixel annotations as well. But directly transferring the model trained on the synthetic dataset to the real dataset may lead to poor performance due to domain shifts (or domain gaps). The predominant approaches to alleviate the domain discrepancy are adversarial feature learning strategies, which focus on feature alignment for style (e.g., color, texture, illumination, etc.) gaps without considering the content (e.g., densities, backgrounds, and layout scenes) gaps. In this study, we scrutinize the real UAV-taken imagery of wind turbines and develop a synthetic generation method trying to simulate the real ones from the aspects of style and content. Besides, we propose a novel soft-masks guided faster region-based convolutional neural network (SMG Faster R-CNN) for domain adaptation in wind turbine detection, where the soft masks help to extract highly object-related features and suppress domain-specific features. We evaluate the accuracy of SMG Faster R-CNN on the wind turbine dataset and demonstrate the effectiveness of our approach compared with some prevalent object detection models and some adversarial DA models.
Downscaling global land-use/cover change scenarios for regional analysis of food, energy, and water subsystems
Authors: Yourek Matt , Liu Mingliang , Scarpare Fabio V. , Rajagopalan Kirti , Malek Keyvan , Boll Jan , Huang Maoyi , Chen Min , Adam Jennifer C.
Published: January 2023

Integrated assessment models (IAMs) capture synergies between human development and natural ecosystems that have important implications for the food-energy-water (FEW) nexus. However, their lack of fine-scale representation of water regulatory structure and landscape heterogeneity impedes their application to FEW impact studies in water-limited basins. To address this limitation, we developed a framework for studying effects of global change on regional outcomes for food crops, bioenergy, hydropower, and instream flows. We applied the new methodology to the Columbia River Basin (CRB) as a case study. The framework uses the Demeter land-use and land-cover change (LULCC) downscaling tool, which we updated so that water rights are spatially integrated in the land allocation process. We downscaled two LULCC scenarios (SSP2-RCP 4.5 and SSP5-RCP 8.5) under three levels of irrigation expansion: no expansion (historical extent), moderate expansion (all land presently authorized by a water right is irrigated), and maximum expansion (new water rights are granted to cover all irrigable land). The downscaled scenarios were evaluated using a hydrology-cropping systems model and a reservoir model coupled in a linear fashion to quantify changes in food and bioenergy crop production, hydropower generation, and availability of instream flows for fish. The net changes in each sector were partitioned among climate, land use, and irrigation-expansion effects. We found that climate change alone resulted in approximately 50% greater production of switchgrass for bioenergy and 20% greater instream flow deficits. In the irrigation-expansion scenarios, the combination of climate change and greater irrigated extent increased switchgrass production by 76% to 256% at the cost of 42% to 165% greater instream flow deficits and 0% to 8% less hydropower generation. Therefore, while irrigation expansion increased bioenergy crop productivity, it also exacerbated seasonal water shortages, especially for instream use. This paper provides a general framework for assessing benchmark scenarios of global LULCC in terms of their regional FEW subsystem outcomes.
Does ESG always improve corporate performance? Evidence from firm life cycle perspective
Authors: Gao Shang , Meng Fanchen , Wang Wenshuai , Chen Wenxin
Published: January 2023

In this study, drawing on firm life cycle theory, we focus on the corporate performance of Environmental, Social, and Governance (ESG) engagement via financial stress and consider the moderate effect of transparency, financial slack, and environmental uncertainty. The industry-year fixed effects panel regression analysis is executed based on the data including 11,742 firm-year observations for 1,486 Chinese A-share listed companies from 2010 to 2020. The results show that ESG performance can significantly improve corporate performance at all life cycle stages, especially when the corporate is in the growth stage. Moreover, the mechanism analysis shows that the financial risk mediates the relation between ESG performance and corporate performance for the corporates in the growth and maturity stages. The association between ESG and corporate performance is more pronounced when corporate information disclosure quality is high. Moreover, financial slack moderates and undermine the association between ESG and corporate performance in the maturity stages. Similarly, for the maturity and decline stages of corporate, environmental uncertainty moderates and undermines the association between ESG and corporate performance. Besides offering scientific evidence for the role of ESG ratings in relieving financial pressure and promoting corporate performance in growth and maturity stages, the results can also inform the regulators and/or investors of the benefit of engaging in corporates sustainability transition, which has implications for both the success of the regulatory regime and the advancement of long-term investment philosophy.
Forest regeneration pathways in contrasting deforestation patterns of Amazonia
Authors: Alencar Lucas , Escada Maria Isabel Sobral , Camargo José Luís Campana
Published: January 2023

Secondary vegetation is increasingly recognized as a key element for biodiversity conservation and carbon stocks in human-modified landscapes. Contrasting deforestation patterns should lead to distinct patterns of forest regeneration, but this relationship is yet to be unveiled for long-term studies. Using Landsat data from 1985–2015, we analyzed the surface area, spatial distribution, and age of secondary vegetation in Fishbone and Geometric patterns of deforestation. Additionally, we investigated to which extent secondary vegetation reduces forest patch isolation at the landscape level across time. We found the Fishbone pattern to consistently have more secondary vegetation over time than the Geometric pattern, despite having the same size of the deforested area. However, the Fishbone pattern showed more secondary vegetation area with less than 5 years old, while the Geometric pattern showed more area with secondary vegetation with more than 30 years old. Regarding spatial distribution, we found secondary vegetation to be more spread across the entire landscape at the Fishbone pattern and to consistently reduce forest patch isolation across time. This is congruent with the land use typically found in Geometric (industrial cropping and ranching) and Fishbone (fallow agriculture with small-scale ranching) patterns. These findings indicate that the Fishbone pattern of deforestation produces a more biodiversity-friendly landscape structure than the Geometric pattern. On the other hand, older secondary vegetation found in the Geometric deforestation pattern could indicate more carbon stocked in those landscapes. Future public policies of land use and occupation should consider better landscape planning and management to overcome this duality and create synergies between biodiversity conservation and secondary vegetation carbon stock.
Integrative analysis of the expression profiles of whole coding and non-coding RNA transcriptomes and construction of the competing endogenous RNA networks for chronic obstructive pulmonary disease
Authors: Feng Xueyan , Dong Hui , Li Beibei , Yu Liang , Zhu Jinyuan , Lou Caili , Zhang Jin
Published: January 2023

The pathogenesis of Chronic Obstructive Pulmonary Disease (COPD) is implicated in airway inflammation, oxidative stress, protease/anti-protease and emphysema. Abnormally expressed non-coding RNAs (ncRNAs) play a vital role in regulation of COPD occurrence and progression. The regulatory mechanisms of the circRNA/lncRNA-miRNA-mRNA (competing endogenous RNA, ceRNA) networks might facilitate our cognition of RNA interactions in COPD. This study aimed to identified novel RNA transcripts and constructed the potential ceRNA networks of COPD patients. Total transcriptome sequencing of the tissues from patients with COPD (COPD) (n = 7) and non-COPD control subjects (Normal) (n = 6) was performed, and the expression profiles of differentially expressed genes (DEGs), including mRNAs, lncRNAs, circRNAs, and miRNAs, were analyzed. The ceRNA network was established based on the miRcode and miRanda databases. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and Gene set variation analysis (GSVA) were implemented for functional enrichment analysis of DEGs. Finally, CIBERSORTx was extracted to analyze the relevance between hub genes and various immune cells.The Starbase and JASPAR databases were used to construct hub-RNA binding proteins (RBPs) and lncRNA-transcription factor (TF) interaction networks. A total of 1,796 mRNAs, 2,207 lncRNAs, and 11 miRNAs showed differentially expression between the lung tissue samples from the normal and COPD groups. Based on these DEGs, lncRNA/circRNA-miRNA-mRNA ceRNA networks were constructed respectively. In addition, ten hub genes were identified. Among them, RPS11, RPL32, RPL5, and RPL27A were associated with the proliferation, differentiation, and apoptosis of the lung tissue. The biological function revealed that TNF–α via NF–kB and IL6/JAK/STAT3 signaling pathways were involved in COPD. Our research constructed the lncRNA/circRNA-miRNA-mRNA ceRNA networks, filtrated ten hub genes may regulate the TNF-α/NF-κB, IL6/JAK/STAT3 signally pathways, which indirectly elucidated the post-transcriptional regulation mechanism of COPD and lay the foundation for excavating the novel targets of diagnosis and treatment in COPD.
Screening for diagnostic targets in tuberculosis and study on its pathogenic mechanism based on mRNA sequencing technology and miRNA-mRNA-pathway regulatory network
Authors: Yang Yue , Fu Yujuan , Sheng Siyu , Ji Chunlei , Pu Xinyi , Xu Guangyu
Published: January 2023

Purpose

Tuberculosis is common infectious diseases, characterized by infectivity, concealment and chronicity, and the early diagnosis is helpful to block the spread of tuberculosis and reduce the resistance of Mycobacterium tuberculosis to anti-tuberculosis drugs. At present, there are obvious limitations in the application of clinical detection methods used for the early diagnosis of tuberculosis. RNA sequencing (RNA-Seq) has become an economical and accurate gene sequencing method for quantifying transcripts and detecting unknown RNA species.

Methods

A peripheral blood mRNA sequencing was used to screen the differentially expressed genes between healthy people and tuberculosis patients. A protein-protein interaction (PPI) network of differentially expressed genes was constructed through Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The potential diagnostic targets of tuberculosis were screened by the calculation of degree, betweenness and closeness in Cytoscape 3.9.1 software. Finally, the functional pathways and the molecular mechanism of tuberculosis were clarified in combination of the prediction results of key gene miRNAs, and by Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia Genes and Genomes (KEGG) pathway annotation analysis.

Results

556 Differential genes of tuberculosis were screened out by mRNA sequencing. Six key genes (AKT1, TP53, EGF, ARF1, CD274 and PRKCZ) were screened as the potential diagnostic targets for tuberculosis by analyzing the PPI regulatory network and using three algorithms. Three pathways related to the pathogenesis of tuberculosis were identified by KEGG pathway analysis, and two key miRNAs (has-miR-150-5p and has-miR-25-3p) that might participate in the pathogenesis of tuberculosis were screened out by constructing a miRNA-mRNA pathway regulatory network.

Conclusion

Six key genes and two important miRNAs that could regulate them were screened out by mRNA sequencing. The 6 key genes and 2 important miRNAs may participate in the pathogenesis of infection and invasion of Mycobacterium tuberculosis through herpes simplex virus 1 infection, endocytosis and B cell receptor signaling pathways.
AFM negatively regulates the infiltration of monocytes to mediate sepsis-associated acute kidney injury
Authors: Guo Caiyun , Fan Youling , Cheng Jiurong , Deng Yingdong , Zhang Xiangsheng , Chen Yanna , Jing Huan , Li Wenjun , Liu Pei , Xie Jiaqi , Ning Wenjun , Chen Hongtao , Zhou Jun
Published: January 2023

Background

Sepsis is organ dysfunction due to the host’s deleterious response to infection, and the kidneys are one of the organs damaged in common sepsis. Sepsis-associated acute kidney injury (SA-AKI) increases the mortality in patients with sepsis. Although a substantial volume of research has improved the prevention and treatment of the disease, SA-SKI is still a significant clinical concern.

Purpose

Aimed to use weighted gene co-expression network analysis (WGCNA) and immunoinfiltration analysis to study SA-AKI-related diagnostic markers and potential therapeutic targets.

Methods

Immunoinfiltration analysis was performed on SA-AKI expression datasets from the Gene Expression Synthesis (GEO) database. A weighted gene co-expression network analysis (WGCNA) analysis was performed on immune invasion scores as trait data, and modules associated with immune cells of interest were identified as hub modules. Screening hub geneset in the hub module using protein-protein interaction (PPI) network analysis. The hub gene was identified as a target by intersecting with significantly different genes screened by differential expression analysis and validated using two external datasets. Finally, the correlation between the target gene, SA-AKI, and immune cells was verified experimentally.

Results

Green modules associated with monocytes were identified using WGCNA and immune infiltration analysis. Differential expression analysis and PPI network analysis identified two hub genes (AFM and GSTA1). Further validation using additional AKI datasets GSE30718 and GSE44925 showed that AFM was significantly downregulated in AKI samples and correlated with the development of AKI. The correlation analysis of hub genes and immune cells showed that AFM was significantly associated with monocyte infiltration and hence, selected as a critical gene. In addition, Gene single-enrichment analysis (GSEA) and PPI analyses results showed that AFM was significantly related to the occurrence and development of SA-AKI.

Conclusions

AFM is inversely correlated with the recruitment of monocytes and the release of various inflammatory factors in the kidneys of AKI. AFM can be a potential biomarker and therapeutic target for monocyte infiltration in sepsis-related AKI.
Protective role of colitis in inflammatory arthritis via propionate-producing Bacteroides in the gut
Authors: Shon Hoh-Jeong , Kim Yu-Mi , Kim Kyeong Seog , Choi Jin-Ouk , Cho Sang-Hyun , An Sujin , Park Se-Hyeon , Cho Yong-Joon , Park Joo-Hong , Seo Sang-Uk , Cho Joo-Youn , Kim Wan-Uk , Kim Donghyun
Published: January 2023

Objectives

To investigate whether and how inflammatory disease in the intestine influences the development of arthritis, considering that organ-to-organ communication is associated with many physiological and pathological events.

Methods

First, mice were given drinking water containing dextran sodium sulfate (DSS) and then subjected to inflammatory arthritis. We compared the phenotypic symptoms between the cohoused and separately-housed mice. Next, donor mice were divided into DSS-treated and untreated groups and then cohoused with recipient mice. Arthritis was then induced in the recipients. The fecal microbiome was analyzed by 16S rRNA amplicon sequencing. We obtained type strains of the candidate bacteria and generated propionate-deficient mutant bacteria. Short-chain fatty acids were measured in the bacterial culture supernatant, serum, feces, and cecum contents using gas chromatography-mass spectrometry. Mice fed with candidate and mutant bacteria were subjected to inflammatory arthritis.

Results

Contrary to expectations, the mice treated with DSS exhibited fewer symptoms of inflammatory arthritis. Intriguingly, the gut microbiota contributes, at least in part, to the improvement of colitis-mediated arthritis. Among the altered microorganisms, Bacteroides vulgatus and its higher taxonomic ranks were enriched in the DSS-treated mice. B. vulgatus, B. caccae, and B. thetaiotaomicron exerted anti-arthritic effects. Propionate production deficiency further prevented the protective effect of B. thetaiotaomicron on arthritis.

Conclusions

We suggest a novel relationship between the gut and joints and an important role of the gut microbiota as communicators. Moreover, the propionate-producing Bacteroides species examined in this study may be a potential candidate for developing effective treatments for inflammatory arthritis.
Application of quantitative proteomics to discover biomarkers for tick resistance in cattle
Authors: Raza Ali , Schulz Benjamin L. , Nouwens Amanda , Naseem Muhammad Noman , Kamran Muhammad , Mantilla Valdivieso Emily F. , Kerr Edward D. , Constantinoiu Constantin , Jonsson Nicholas N. , James Peter , Tabor Ala E.
Published: January 2023

Introduction

Breeding for tick resistance is a sustainable alternative to control cattle ticks due to widespread resistance to acaricidal drugs and the lack of a protective vaccine. The most accurate method used to characterise the phenotype for tick resistance in field studies is the standard tick count, but this is labour-intensive and can be hazardous to the operator. Efficient genetic selection requires reliable phenotyping or biomarker(s) for accurately identifying tick-resistant cattle. Although breed-specific genes associated with tick resistance have been identified, the mechanisms behind tick resistance have not yet been fully characterised.

Methods

This study applied quantitative proteomics to examine the differential abundance of serum and skin proteins using samples from naïve tick-resistant and -susceptible Brangus cattle at two-time points following tick exposure. The proteins were digested into peptides, followed by identification and quantification using sequential window acquisition of all theoretical fragment ion mass spectrometry.

Results

Resistant naïve cattle had a suite of proteins associated with immune response, blood coagulation and wound healing that were significantly (adjusted P < 10- 5) more abundant compared with susceptible naïve cattle. These proteins included complement factors (C3, C4, C4a), alpha-1-acid glycoprotein (AGP), beta-2-glycoprotein-1, keratins (KRT1 & KRT3) and fibrinogens (alpha & beta). The mass spectrometry findings were validated by identifying differences in the relative abundance of selected serum proteins with ELISA. The proteins showing a significantly different abundance in resistant cattle following early and prolonged tick exposures (compared to resistant naïve) were associated with immune response, blood coagulation, homeostasis, and wound healing. In contrast, susceptible cattle developed some of these responses only after prolonged tick exposure.

Discussion

Resistant cattle were able to transmigrate immune-response related proteins towards the tick bite sites, which may prevent tick feeding. Significantly differentially abundant proteins identified in this research in resistant naïve cattle may provide a rapid and efficient protective response to tick infestation. Physical barrier (skin integrity and wound healing) mechanisms and systemic immune responses were key contributors to resistance. Immune response-related proteins such as C4, C4a, AGP and CGN1 (naïve samples), CD14, GC and AGP (post-infestation) should be further investigated as potential biomarkers for tick resistance.
Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids
Authors: Walaas Gunnar Andreas , Gopalakrishnan Shreya , Bakke Ingunn , Skovdahl Helene Kolstad , Flatberg Arnar , Østvik Ann Elisabet , Sandvik Arne Kristian , Bruland Torunn
Published: January 2023

Background

The epithelium in the colonic mucosa is implicated in the pathophysiology of various diseases, including inflammatory bowel diseases and colorectal cancer. Intestinal epithelial organoids from the colon (colonoids) can be used for disease modeling and personalized drug screening. Colonoids are usually cultured at 18-21% oxygen without accounting for the physiological hypoxia in the colonic epithelium (3% to <1% oxygen). We hypothesize that recapitulating the in vivo physiological oxygen environment (i.e., physioxia) will enhance the translational value of colonoids as pre-clinical models. Here we evaluate whether human colonoids can be established and cultured in physioxia and compare growth, differentiation, and immunological responses at 2% and 20% oxygen.

Methods

Growth from single cells to differentiated colonoids was monitored by brightfield images and evaluated with a linear mixed model. Cell composition was identified by immunofluorescence staining of cell markers and single-cell RNA-sequencing (scRNA-seq). Enrichment analysis was used to identify transcriptomic differences within cell populations. Pro-inflammatory stimuli induced chemokines and Neutrophil gelatinase-associated lipocalin (NGAL) release were analyzed by Multiplex profiling and ELISA. Direct response to a lower oxygen level was analyzed by enrichment analysis of bulk RNA sequencing data.

Results

Colonoids established in a 2% oxygen environment acquired a significantly larger cell mass compared to a 20% oxygen environment. No differences in expression of cell markers for cells with proliferation potential (KI67 positive), goblet cells (MUC2 positive), absorptive cells (MUC2 negative, CK20 positive) and enteroendocrine cells (CGA positive) were found between colonoids cultured in 2% and 20% oxygen. However, the scRNA-seq analysis identified differences in the transcriptome within stem-, progenitor- and differentiated cell clusters. Both colonoids grown at 2% and 20% oxygen secreted CXCL2, CXCL5, CXCL10, CXCL12, CX3CL1 and CCL25, and NGAL upon TNF + poly(I:C) treatment, but there appeared to be a tendency towards lower pro-inflammatory response in 2% oxygen. Reducing the oxygen environment from 20% to 2% in differentiated colonoids altered the expression of genes related to differentiation, metabolism, mucus lining, and immune networks.

Conclusions

Our results suggest that colonoids studies can and should be performed in physioxia when the resemblance to in vivo conditions is important.
γδ T cells and their clinical application in colon cancer
Authors: Corsale Anna Maria , Di Simone Marta , Lo Presti Elena , Dieli Francesco , Meraviglia Serena
Published: January 2023

In recent years, research has focused on colorectal cancer to implement modern treatment approaches to improve patient survival. In this new era, γδ T cells constitute a new and promising candidate to treat many types of cancer because of their potent killing activity and their ability to recognize tumor antigens independently of HLA molecules. Here, we focus on the roles that γδ T cells play in antitumor immunity, especially in colorectal cancer. Furthermore, we provide an overview of small-scale clinical trials in patients with colorectal cancer employing either in vivo activation or adoptive transfer of ex vivo expanded γδ T cells and suggest possible combinatorial approaches to treat colon cancer.