bluuebunny/crossref_metadata_2025 huggingface dataset:
IMPLEMENTASI KONVERTER BERBASIS SEPIC PADA MODUL SOLAR PANEL DENGAN ALGORITMA FUZZY LOGIC
Authors: Pattria Pattria Dwin Cahyawati , Radianto Donny , Safitri Hari Kurnia
Published: November 2023

Sumber energi matahari merupakan salah satu energi terbarukan yang ramah lingkungan dan dapat dijadikan sebagai energi alternatif. Dengan menggunakan modul solar panel, maka energi matahari dapat diubah menjadi energi listrik. Terdapat dua parameter yang mempengaruhi keluaran modul solar panel yaitu intensitas radiasi matahari dan temperatur yang mengakibatkan keluaran dari modul solar panel tidak stabil. Pada sistem pengisian aki memerlukan keluaran yang stabil pada 14 V, sehingga ketidak stabilan pada keluaran modul solar panel merupakan masalah yang dapat menyebabkan over voltage pada aki. Untuk itu, sistem ini menggunakan konverter berjenis SEPIC yang dapat menaikkan dan menurunkan tegangan. Agar keluaran lebih optimal, maka sistem menggunakan metode fuzzy logic kontrol. Dengan metode dan rangkaian konverter yang digunakan tersebut diharapkan tegangan output pada solar panel akan stabil untuk melakukan pengisian pada aki. Sedangkan waktu pengisian aki yaitu 3 jam dengan tenganan awal sebesar 11.5 V dan tegangan setelah pengisian  sebesar 12.54 V. Pada saat proses pengisian aki, tegangan akan bertambah dan arus akan semakin kecil ketika aki penuh.
Sistem Monitoring Nutrisi dan PH Air pada Tanaman Hidroponik Berbasis Internet of Things (IoT)
Authors: Rivana Rivana Risqi , Made Made Rahmawaty , Edilla  , Jajang Jaenudin
Published: November 2023

Hydroponics is a soilless cultivation method that relies on water and the fulfillment of plant nutritional needs. Nutrient provision is usually done manually, which can be time-consuming. To improve efficiency, an automated system using sensors and an IoT-based application can be implemented. This system utilizes a TDS sensor, pH sensor, and NodeMCU ESP32 to monitor nutrient and pH levels in water. The values are displayed on an LCD screen and sent to the application. If the nutrient content falls below 700 ppm or the pH falls below 5 or above 8, indicating a nutrient deficiency, the nutrient pump can be remotely activated through the application. The pump stops when the nutrient level reaches 1000 ppm or the pH reaches 8. The system provides TDS and pH readings, which have an average error of 3.16% and 2.87%, respectively. This automated system can be used to reading TDS and pH values to assist in providing nutrients to hydroponic plants.
Perancangan Sistem Penggorengan Otomatis Menggunakan Metode PI
Authors: Rifqi Aisyah , Fauziyah Mila , Al Azhar Gillang
Published: November 2023

Ayam goreng tepung atau yang dikenal sebagai ayam crispy ini memiliki banyak penggemar, baik dari kalangan orang dewasa, remaja hingga anak kecil. ayam krispiini pun sudah banyak dijual oleh orang – orang. Namun, kualitas gorengan yang dihasilkan masih belum maksimal. Salah satu penyebab kualitas yang tidak maksimal adalah penggunaan penggorengan yang masih konvensional dan menyebabkan stabilitas panas belum dapat dikontrol dengan baik. Kestabilan panas, waktu penggorengan, dan kualitas minyak goreng merupakan faktor yang mempengaruhi kualitas. Oleh karena itu, diperlukan suatu sistem penggorengan otomatis yang dapat menjaga suhu secara stabil sesuai dengan nilai setpoint guna meningkatkan efektifitas pekerjaan. Dengan menerapkan kontrol PI sebagai metode kontrol suhu, diharapkan kinerja sistem akan meningkat dan memperbaiki sistem reformasi, sehingga sistem dapat merespons perubahan kenaikan suhu lebih cepat dan mampu menjaga suhu tetap stabil. Dengan menggunakan sensor suhu PT100 yang terhubung dengan Arduino UNO untuk membaca besaran suhu pada minyak penggorengan yang nantinya dikontrol dengan menggunakan kontrol PI sebagai metodenya. Nilaidapatkan kontrol PI pada sistem ini menggunakan dan . Dari hasil pengujian menunjukkan bahwa setpoint suhu dan rentang waktu yang tepat untuk mendapatkan hasil kematangan yang baik berbeda-beda tergantung dari bagian ayam yang dimasak. Pada suhu 160℃ dalam selang waktu 12 menit, digunakan pada ayam bagian dada dikarenakan jika dengan waktu yang sama dan suhu terlalu rendah, maka hasil penggorengan akan lebih berminyak dan kurang matang.
Analisa QoS pada MQTT untuk website monitoring dan pengendalian pintu air
Authors: Achmad Vandy , Khumaidi Agus , Adhitya Ryan Yudha , Riananda Dimas Pristovani , Sutrisno Imam
Published: November 2023

Pintu air merupakan sistem yang digunakan untuk mengatur ketinggian air, mengalirkan air untuk diolah PDAM dan mengatur pengendalian debit air agar tidak terjadi banjir. Namun, pada pintu air jagir wonokromo, sistem yang digunakan adalah panel kendali yang dikendalikan oleh operator. Oleh karena itu penulis membuat website agar sistem menjadi lebih efisien. Website ini dapat memantau ketingian air, posisi pintu air dan mengirim data untuk mengendalikan pintu air dari pc. Dengan menggunakan sistem ini, sistem pengendalian akan bekerja dengan lebih optimal. Pengujian QoS yang telah dilakukan menunjukkan performa yang bagus dari sisi delay, throughput, jitter dan packet loss. Berdasarkan pengujian delay mencapai 53.53 ms dan masuk ke dalam kategori bagus. Pengujian throughput mencapai 220 Kb/s dan dapat dikategorikan dalam indeks 4 atau sangat bagus. Pengujian jitter mencapai 0.17 ms dan masuk ke dalam kategori sedang. Sedangkan pengujian packet loss mencapai 0.24 % dan dapat dikategorikan dalam indeks 4 atau sangat bagus. Pengujian mengenai performa jaringan berdasarkan QoS(Quality of Service) tersebut terbukti meningkatkan performa operator dalam monitoring dan pengendalian pintu air.
Implementasi Metode K- Nearest Neighbor Pada Penelitian Sistem Otomasi Pemberian Pakan Ikan Nila Bioflok
Authors: Nurul Achmadiah Mas , Rifai Muhamad , Maulidan Ammar
Published: November 2023

Salah satu program ketahanan pangan dan pemberdayaan masyarakat yang berada di desa Oro-Oro Ombo Kota Batu merupakan budidaya ikan nila bioflok. Ikan nila merupakan komoditas ikan bernilai ekonomi tinggi hal tersebut berdampak pada harga pakan ikan yang cukup tinggi. Efisiensi pakan merupakan strategi untuk mengatasi masalah kelebihan pakan dan jumlah flok yang terlalu banyak karena pakan yang berlebih tersebut akan diurai oleh mikroorganisme yang mengakibatkan pertumbuhan bakteri sangat cepat dan menyebabkan adanya persaingan oksigen antara ikan dan bakteri, dengan cara pemberian pakan seminimal mungkin akan tetapi pertumbuhan ikan tidak terhambat. Sistem ini bekerja dengan cara membaca jumlah flok menggunakan tabung lmhof dan membaca kadar ph air kemudian data akan diproses oleh arduino untuk mengatur jumlah pakan yang akan di berikan. Proses klasifikasi dilakukan dengan menggunakan metode k-nearest neighbor dengan training data. Implementasi metode K-Nearest Neighbor pada penelitian sistem otomasi pemberian pakan ikan nila bioflok sudah berhasil diterapkan dengan pemberian pakan secara terukur supaya mendapatkan efisiensi yang baik dengan persentase 28% dan penghematan biaya pakan sebesar Rp.63.000,00.
Desain permodelan dan simulasi Field Oriented Control (FOC) menggunakan motor BLDC
Authors: Nurul Achmadiah Mas , Rosyidin Arif anwar , Pracoyo Agus , Siradjuddin Indrazno , Permatasari Dinda Ayu , Azhar Gillang Al
Published: November 2023

Motor brushless DC (BLDC) mulai popular digunakan pada kendaraan listrik dibandingkan motor induksi. Hal ini dikarenakan beberapa keunggulan motor BLDC seperti efisiensi daya yang lebih tinggi, dimensi yang lebih kecil jika dibandingkan dengan motor lain yang memiliki daya yang sama. Beberapa metode telah diterapkan pada motor BLDC diantaranya adalah trapezoidal commutation dan field oriented control (FOC). Dari kedua metode tersebut, FOC lebih unggul dalam meminimalisir ripple torsi dan dalam hal efisiensi daya terutama pada saat motor pada kecepatan rendah, tetapi FOC memerlukan sensor yang lebih banyak dan algortitma yang lebih rumit. Dengan memperhatikan hal tersebut maka penelitian ini akan berfokus pada permodelan dan simulasi motor BLDC menggunakan metode Field Oriented Control (FOC). Aplikasi dari penelitian ini adalah pada swerve drive. aplikasi penelitian ini adalah pada Swerve drive. Swerve drive, juga dikenal sebagai holonomic drive atau swerve and steer drive, adalah jenis sistem penggerak roda yang digunakan dalam robot atau kendaraan untuk memberikan kemampuan manuver tingkat tinggi. Sistem ini memungkinkan kendaraan untuk bergerak dalam berbagai arah dengan mudah dan presisi, termasuk berbelok dalam tempat dengan radius yang sangat kecil. Metode ini sering digunakan dalam robotika, terutama dalam konteks perlombaan robot dan aplikasi yang membutuhkan manuver yang canggih. Swerve drive terdiri dari 2 motor yang masing-masing fungsinya adalah untuk steering dan driving untuk pergerakaannya sehingga dibutuhkan sebuah kontroller agar perputaran motor sesuai dengan set point yang telah ditentukan. hasil dari metode ini adalah, error berkurang sebesar 2% dan pada steering mengurangi error sebesar 0,7%. Selain itu kontroler juga dapat memperbaiki respon dari driving dan steering sehingga dapat memperbaiki performa dari alat penelitian ini..
The different outcomes in the elderly with subclinical hypothyroidism diagnosed by age-specific and non-age-specific TSH reference intervals: a prospectively observational study protocol
Authors: Zhang Xueqi , Li Yang , Jin Jing , Wang Huangman , Zhao Bozun , Wang Songwen , Shan Zhongyan , Teng Weiping , Teng Xiaochun
Published: November 2023

Introduction

Subclinical hypothyroidism (SCH) is a common endocrine disorder characterized by elevated thyroid-stimulating hormone (TSH) levels and normal free thyroxine (FT4) levels. The overdiagnosis and overtreatment of SCH in elderly patients have become concerns as TSH levels naturally increase with age. Studies have shown that many elderly patients with SCH can recover without treatment, and the administration of levothyroxine (L-T4) does not improve their prognosis. Therefore, It is necessary to establish age-specific reference ranges for TSH in elderly individuals to aid in clinical decision-making and prevent overdiagnosis.

Methods

This is a multicenter prospective study that focuses on Chinese elderly patients with SCH who have TSH levels below 10 mU/L. After obtaining the informed consent of the patients, their initial diagnosis information will be registered, and they will be asked to fill out questionnaires such as the Montreal Cognitive Assessment-Basic (MoCA-B), Hamilton Depression Scale (HAMD), Hypothyroidism Symptom Questionnaire (SRQ), frail scale(FRAIL), fatigue scale, and EQ-5D. In addition, thyroid function tests, blood lipid analysis, carotid artery ultrasound, and thyroid ultrasound examinations will be conducted. Patients will also be grouped according to FT4 levels, the changes in FT4 and its relationship with TSH can also be described. For patients over 80 years old, a decrease in FT4 will be used as an endpoint event, while for patients between 60-80 years old, TSH levels greater than or equal to 10mIU/L or a decline in FT4 will be used as the endpoint event. The TSH reference intervals of the general and elderly populations will be used to calculate medical costs associated with multiple follow-ups of patients, and a social-economic analysis will also be conducted.

Discussion

This study will prospectively observe elderly patients with SCH who are screened using both age-specific and non-age-specific TSH reference ranges for the elderly population. We will compare the results of elderly patients diagnosed with SCH using different reference ranges and analyze their association with FT4 to identify meaningful SCH patients and reduce over diagnosis and over treatment of elderly SCH.

Ethics

The Medical Science Research Ethics Committee of the First Affiliated Hospital of China Medical University approved this study (ID: AF-SOP-07-1.1-01). The results will be published in an open-access journal.

Clinical trial registration

https://www.chictr.org.cn/, identifier ChiCTR2300070831.
Proteome profiling identifies circulating biomarkers associated with hepatic steatosis in subjects with Prader-Willi syndrome
Authors: Pascut Devis , Giraudi Pablo J. , Banfi Cristina , Ghilardi Stefania , Tiribelli Claudio , Bondesan Adele , Caroli Diana , Minocci Alessandro , Grugni Graziano , Sartorio Alessandro
Published: November 2023

Introduction

Prader-Willi syndrome (PWS) is a rare genetic disorder characterized by loss of expression of paternal chromosome 15q11.2-q13 genes. Individuals with PWS exhibit unique physical, endocrine, and metabolic traits associated with severe obesity. Identifying liver steatosis in PWS is challenging, despite its lower prevalence compared to non-syndromic obesity. Reliable biomarkers are crucial for the early detection and management of this condition associated with the complex metabolic profile and cardiovascular risks in PWS.

Methods

Circulating proteome profiling was conducted in 29 individuals with PWS (15 with steatosis, 14 without) using the Olink Target 96 metabolism and cardiometabolic panels. Correlation analysis was performed to identify the association between protein biomarkes and clinical variables, while the gene enrichment analysis was conducted to identify pathways linked to deregulated proteins. Receiver operating characteristic (ROC) curves assessed the discriminatory power of circulating protein while a logistic regression model evaluated the potential of a combination of protein biomarkers.

Results

CDH2, CTSO, QDPR, CANT1, ALDH1A1, TYMP, ADGRE, KYAT1, MCFD, SEMA3F, THOP1, TXND5, SSC4D, FBP1, and CES1 exhibited a significant differential expression in liver steatosis, with a progressive increase from grade 1 to grade 3. FBP1, CES1, and QDPR showed predominant liver expression. The logistic regression model, -34.19 + 0.85 * QDPR*QDPR + 0.75 * CANT1*TYMP - 0.46 * THOP1*ALDH1A, achieved an AUC of 0.93 (95% CI: 0.63-0.99), with a sensitivity of 93% and specificity of 80% for detecting steatosis in individuals with PWS. These biomarkers showed strong correlations among themselves and were involved in an interconnected network of 62 nodes, related to seven metabolic pathways. They were also significantly associated with cholesterol, LDL, triglycerides, transaminases, HbA1c, FLI, APRI, and HOMA, and showed a negative correlation with HDL levels.

Conclusion

The biomarkers identified in this study offer the potential for improved patient stratification and personalized therapeutic protocols.
Aging dysregulates neutrophil extracellular trap formation in response to HIV in blood and genital tissues
Authors: Moreno de Lara Laura , Werner Alexandra , Borchers Anna , Carrillo-Salinas Francisco J. , Marmol Wendelin , Parthasarathy Siddharth , Iyer Vidya , Vogell Alison , Illanes Diego , Abadía-Molina Ana C. , Ochsenbauer Christina , Wira Charles R. , Rodriguez-Garcia Marta
Published: November 2023

Women acquire HIV through sexual transmission, with increasing incidence in women >50 years old. Identifying protective mechanisms in the female genital tract (FGT) is important to prevent HIV-acquisition in women as they age. Human genital and blood neutrophils inactivate HIV by releasing neutrophil extracellular traps (NETs), an innate protective mechanism against HIV-infection. However, how NET formation is triggered by HIV in different tissues and whether this mechanism is affected by aging remain unknown. We demonstrate that the mechanisms that trigger NET release in response to HIV are different in blood and genital tissues, and that NET release decreases with aging. In blood neutrophils, HIV stimulation independently activated calcium pathways and endosomal TLR8, but aging reduced calcium responses, resulting in delayed NET release. In contrast, calcium responses were absent in genital neutrophils and NET release was triggered preferentially through TLR8 activation, but aging impaired this pathway. HIV induced NET formation through non-lytic pathways in blood and FGT neutrophils, except for a small subset of NETs that incorporated annexin V and lactoferrin predominantly in blood, suggesting proinflammatory and lytic NET release. Our findings demonstrate that blood neutrophils cannot model genital neutrophil responses which has important implications to understanding protection against HIV acquisition.
Liquid Biopsy in Organ Damage: small extracellular vesicle chip-based assessment of polytrauma
Authors: Wang Bingduo , Wöhler Aliona , Greven Johannes , Salzmann Rebekka J. S. , Keller Cindy M. , Tertel Tobias , Zhao Qun , Mert Ümit , Horst Klemens , Lupu Ludmila , Huber-Lang Markus , van Griensven Martijn , Mollnes Tom Erik , Schaaf Sebastian , Schwab Robert , Strassburg Christian P. , Schmidt-Wolf Ingo G. H. , Giebel Bernd , Hildebrand Frank , Lukacs-Kornek Veronika , Willms Arnulf G. , Kornek Miroslaw T.
Published: November 2023

Background

Despite major advances in medicine, blood-borne biomarkers are urgently needed to support decision-making, including polytrauma. Here, we assessed serum-derived extracellular vesicles (EVs) as potential markers of decision-making in polytrauma.

Objective

Our Liquid Biopsy in Organ Damage (LiBOD) study aimed to differentiate polytrauma with organ injury from polytrauma without organ injury. We analysed of blood-borne small EVs at the individual level using a combination of immunocapture and high-resolution imaging.

Methods

To this end, we isolated, purified, and characterized small EVs according to the latest Minimal Information for Studies of Extracellular Vesicles (MISEV) guidelines from human blood collected within 24 h post-trauma and validated our results using a porcine polytrauma model.

Results

We found that small EVs derived from monocytes CD14+ and CD14+CD61+ were significantly elevated in polytrauma with organ damage. To be precise, our findings revealed that CD9+CD14+ and CD14+CD61+ small EVs exhibited superior performance compared to CD9+CD61+ small EVs in accurately indicating polytrauma with organ damage, reaching a sensitivity and a specificity of 0.81% and 0.97%, respectively. The results in humans were confirmed in an independent porcine model of polytrauma.

Conclusion

These findings suggest that these specific types of small EVs may serve as valuable, non-invasive, and objective biomarkers for assessing and monitoring the severity of polytrauma and associated organ damage.
Measuring the impact of monoclonal antibody therapies
Authors: Lim Ka Keat , Ng Kenrick , Balachandran Sathiyaa , Russell Mark D. , Boalch Amy , Sinclair Alasdair , Coker Bolaji , Vinnakota Krishna , Mansoor Rashid , Douiri Abdel , Marks Lara V. , Sacks Steven
Published: November 2023

Objective

Monoclonal antibody (Mab) treatments have significantly improved the quality and quantity of life, but they are some of the most expensive treatments, resulting in a degree of hesitancy to introduce new Mab agents. A system for estimating the effect of Mab drugs, in general, would optimally inform health strategy and fully realize how a single scientific discovery can deliver health benefits. We evaluated such a method with several well-established Mab regimens.

Methods

We selected five different Mab regimens in oncology and rheumatology in England. We carried out two systematic literature reviews and meta-analyses to assess health outcomes (Health Assessment Questionnaire-Disability Index for rheumatoid arthritis; overall mortality for melanoma) from real-world data and compared them to the outcomes from randomized control trials (RCTs). We applied economic modeling to estimate the net monetary benefits for health outcomes for the estimated patient population size for each Mab regimen.

Results

Meta-analyses of 27 eligible real-world data (RWD) sets and 26 randomized controlled trial (RCT) sets found close agreement between the observed and expected health outcomes. A Markov model showed the net positive monetary benefit in three Mab regimens and the negative benefit in two regimens. However, because of limited access to NHS data, the economic model made several assumptions about the number of treated patients and the cost of treatment to the NHS, the accuracy of which may affect the estimation of the net monetary benefit.

Conclusion

RCT results reliably inform the real-world experience of Mab treatments. Calculation of the net monetary benefit by the algorithm described provides a valuable overall measure of the health impact, subject to the accuracy of data inputs. This study provides a compelling case for building a comprehensive, systematized, and accessible database and related analytics, on all Mab treatments within health services.
Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods
Authors: Protasov Evgenii , Nonoh James O. , Kästle Silva Joana M. , Mies Undine S. , Hervé Vincent , Dietrich Carsten , Lang Kristina , Mikulski Lena , Platt Katja , Poehlein Anja , Köhler-Ramm Tim , Miambi Edouard , Boga Hamadi I. , Feldewert Christopher , Ngugi David K. , Plarre Rudy , Sillam-Dussès David , Šobotník Jan , Daniel Rolf , Brune Andreas
Published: November 2023

Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
Cellulose and JbKOBITO 1 mediate the resistance of NaHCO3-tolerant chlorella to saline-alkali stress
Authors: Qiu Jiale , Zhang Jie , Zhao Huihui , Wu Cuiping , Jin Caoliang , Hu Xiangdong , Li Jian , Cao Xiuling , Liu Shenkui , Jin Xuejiao
Published: November 2023

Carbonate stress has profound impacts on both agricultural and industrial production. Although a number of salinity-tolerant genes have been reported and applied in plants, there is a lack of research on the role of cell wall-related genes in resistance to carbonate. Likewise, in industry, current strategies have not been able to more effectively address the conflict between stress-induced microalgal biofuel accumulation and microalgal growth inhibition. It is of great significance to study the adaptation mechanism of carbonate-tolerant organisms and to explore related genes for future genetic modification. In this study, the role of the cell wall in the NaHCO3-tolerant chlorella JB17 was investigated. We found that JB17 possesses a relatively thick cell wall with a thickness of 300–600 nm, which is much higher than that of the control chlorella with a thickness of about 100 nm. Determination of the cell wall polysaccharide fractions showed that the cellulose content in the JB17 cell wall increased by 10.48% after NaHCO3 treatment, and the decrease in cellulose levels by cellulase digestion inhibited its resistance to NaHCO3. Moreover, the saccharide metabolome revealed that glucose, rhamnose, and trehalose levels were higher in JB17, especially rhamnose and trehalose, which were almost 40 times higher than in control chlorella. Gene expression detection identified an up-regulated expressed gene after NaHCO3 treatment, JbKOBITO1, overexpression of which could improve the NaHCO3 tolerance of Chlamydomonas reinhardtii. As it encodes a glycosyltransferase-like protein that is involved in cellulose synthesis, the strong tolerance of JB17 to NaHCO3 may be partly due to the up-regulated expression of JbKOBITO 1 and JbKOBITO 1-mediated cellulose accumulation. The above results revealed a critical role of cellulose in the NaHCO3 resistance of JB17, and the identified NaHCO3-tolerance gene will provide genetic resources for crop breeding in saline-alkali soils and for genetic modification of microalgae for biofuel production.
A mechanism-based pathway toward administering highly active N-phage cocktails
Authors: Smith Nicholas M. , Nguyen Thomas D. , Chin Wai Hoe , Sanborn Jacob T. , de Souza Harriet , Ho Brian M. , Luong Tiffany , Roach Dwayne R.
Published: November 2023

Bacteriophage (phage) therapy is being explored as a possible response to the antimicrobial resistance public health emergency. Administering a mixture of different phage types as a cocktail is one proposed strategy for therapeutic applications, but the optimal method for formulating phage cocktails remains a major challenge. Each phage strain has complex pharmacokinetic/pharmacodynamic (PK/PD) properties which depend on the nano-scale size, target-mediated, self-dosing nature of each phage strain, and rapid selection of resistant subpopulations. The objective of this study was to explore the pharmacodynamics (PD) of three unique and clinically relevant anti-Pseudomonas phages after simulation of dynamic dosing strategies. The Hollow Fiber Infection Model (HFIM) is an in vitro system that mimics in vivo pharmacokinetics (PK) with high fidelity, providing an opportunity to quantify phage and bacteria concentration profiles over clinical time scales with rich sampling. Exogenous monotherapy-bolus (producing max concentrations of Cmax = 7 log10 PFU/mL) regimens of phages LUZ19, PYO2, and E215 produced Pseudomonas aeruginosa nadirs of 0, 2.14, or 2.99 log10 CFU/mL after 6 h of treatment, respectively. Exogenous combination therapy bolus regimens (LUZ19 + PYO2 or LUZ19 + E215) resulted in bacterial reduction to <2 log10 CFU/mL. In contrast, monotherapy as a continuous infusion (producing a steady-state concentration of Css,avg = 2 log10PFU/mL) was less effective at reducing bacterial densities. Specifically, PYO2 failed to reduce bacterial density. Next, a mechanism-based mathematical model was developed to describe phage pharmacodynamics, phage–phage competition, and phage-dependent adaptive phage resistance. Monte Carlo simulations supported bolus dose regimens, predicting lower bacterial counts with bolus dosing as compared to prolonged phage infusions. Together, in vitro and in silico evaluation of the time course of phage pharmacodynamics will better guide optimal patterns of administration of individual phages as a cocktail.
Alterations via inter-regional connective relationships in Alzheimer’s disease
Authors: Ren Xiaomei , Dong Bowen , Luan Ying , Wu Ye , Huang Yunzhi ,   the Alzheimer's Disease Neuroimaging Initiative
Published: November 2023

Disruptions in the inter-regional connective correlation within the brain are believed to contribute to memory impairment. To detect these corresponding correlation networks in Alzheimer’s disease (AD), we conducted three types of inter-regional correlation analysis, including structural covariance, functional connectivity and group-level independent component analysis (group-ICA). The analyzed data were obtained from the Alzheimer’s Disease Neuroimaging Initiative, comprising 52 cognitively normal (CN) participants without subjective memory concerns, 52 individuals with late mild cognitive impairment (LMCI) and 52 patients with AD. We firstly performed vertex-wise cortical thickness analysis to identify brain regions with cortical thinning in AD and LMCI patients using structural MRI data. These regions served as seeds to construct both structural covariance networks and functional connectivity networks for each subject. Additionally, group-ICA was performed on the functional data to identify intrinsic brain networks at the cohort level. Through a comparison of the structural covariance and functional connectivity networks with ICA networks, we identified several inter-regional correlation networks that consistently exhibited abnormal connectivity patterns among AD and LMCI patients. Our findings suggest that reduced inter-regional connectivity is predominantly observed within a subnetwork of the default mode network, which includes the posterior cingulate and precuneus regions, in both AD and LMCI patients. This disruption of connectivity between key nodes within the default mode network provides evidence supporting the hypothesis that impairments in brain networks may contribute to memory deficits in AD and LMCI.
Modulation of prefrontal couplings by prior belief-related responses in ventromedial prefrontal cortex
Authors: Wang Bin A. , Drammis Sabrina , Hummos Ali , Halassa Michael M. , Pleger Burkhard
Published: November 2023

Humans and other animals can maintain constant payoffs in an uncertain environment by steadily re-evaluating and flexibly adjusting current strategy, which largely depends on the interactions between the prefrontal cortex (PFC) and mediodorsal thalamus (MD). While the ventromedial PFC (vmPFC) represents the level of uncertainty (i.e., prior belief about external states), it remains unclear how the brain recruits the PFC-MD network to re-evaluate decision strategy based on the uncertainty. Here, we leverage non-linear dynamic causal modeling on fMRI data to test how prior belief-dependent activity in vmPFC gates the information flow in the PFC-MD network when individuals switch their decision strategy. We show that the prior belief-related responses in vmPFC had a modulatory influence on the connections from dorsolateral PFC (dlPFC) to both, lateral orbitofrontal (lOFC) and MD. Bayesian parameter averaging revealed that only the connection from the dlPFC to lOFC surpassed the significant threshold, which indicates that the weaker the prior belief, the less was the inhibitory influence of the vmPFC on the strength of effective connections from dlPFC to lOFC. These findings suggest that the vmPFC acts as a gatekeeper for the recruitment of processing resources to re-evaluate the decision strategy in situations of high uncertainty.
Impact of omega-3 fatty acids supplementation on the gene expression of peroxisome proliferator activated receptors-γ, α and fibroblast growth factor-21 serum levels in patients with various presentation of metabolic conditions: a GRADE assessed systematic review and dose–response meta-analysis of clinical trials
Authors: Ahmadi Amirhossein Ramezani , Shirani Fatemeh , Abiri Behnazi , Siavash Mansoor , Haghighi Sasan , Akbari Mojtaba
Published: November 2023

There is some debate about the effects of omega-3 fatty acids on the regulation of adipose tissue related genes. This systematic review and meta-analysis aimed to evaluate the effects of omega-3 fatty acids supplementation on the gene expression of peroxisome proliferator activated receptors (PPAR-α and PPAR-γ) and serum fibroblast growth factor-21 (FGF-21) levels in adults with different presentation of metabolic conditions. To identify eligible studies, a systematic search was conducted in the Cochrane Library of clinical trials, Medline, Scopus, ISI Web of Science, and Google Scholar up to April 2022. Eligibility criteria included a clinical trial design, omega-3 fatty acids supplementation in adults, and reporting of at least one of the study outcomes. Effect sizes were synthesized using either fixed or random methods based on the level of heterogeneity. Fifteen studies met the inclusion criteria. Omega-3 fatty acids supplementation significantly increased the PPAR-γ (10 studies) and PPAR-α (2 studies) gene expression compared to the control group (WMD: 0.24; 95% CI: 0.12, 0.35; p < 0.001 and 0.09; 95% CI: 0.04, 0.13; p < 0.001, respectively). Serum FGF-21 (8 studies) levels exhibited no significant change following omega-3 fatty acids supplementation (p = 0.542). However, a dose–response relationship emerged between the dose of omega-3 fatty acids and both PPAR-γ gene expression and serum FGF-21 levels. Overall, this study suggests that omega-3 fatty acids supplementation may have positive effects on the regulation of adipose tissue related genes in patients with various presentation of metabolic condition. Further research is needed to validate these findings and ascertain the effectiveness of this supplementation approach in this population.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?, CRD42022338344.
Metabolomic and lipidomic studies on the intervention of taurochenodeoxycholic acid in mice with hyperlipidemia
Authors: Cui Na , Zhang Wensen , Su Fazhi , Zhang Zhihong , Li Biao , Peng Donghui , Sun Yanping , Zeng Yuanning , Yang Bingyou , Kuang Haixue , Wang Qiuhong
Published: November 2023

Bile acids are the main component of animal bile and are directly involved in the metabolic process of lipids in vivo. Taurochenodeoxycholic acid (TCDCA) is the primary biologically active substance in bile acids and has biological functions such as antioxidant, antipyretic, anti-inflammatory, and analgesic activities and improves immunity. In the present study, we assessed the impact of TCDCA on hyperlipidemia development in mouse models. Mice were fed a high-fat diet (HFD) to induce hyperlipidemia and orally administered different doses of TCDCA orally for 30 days. Then, indicators such as triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) in mice were detected. Using HE and ORO staining techniques, the morphology of the mice’s liver tissue was detected. Based on metabolomic and lipidomic analyses, we determined the mechanism of TCDCA in treating hyperlipidemia. The results showed that TCDCA had a significant ameliorating effect on dietary hyperlipidemia. In addition, it exerted therapeutic effects through glycerophospholipid metabolism.
Efficacy and underlying mechanisms of berberine against lipid metabolic diseases: a review
Authors: Cai Yajie , Yang Qiaoning , Yu Yanqiao , Yang Furong , Bai Ruina , Fan Xiaodi
Published: November 2023

Lipid-lowering therapy is an important tool for the treatment of lipid metabolic diseases, which are increasing in prevalence. However, the failure of conventional lipid-lowering drugs to achieve the desired efficacy in some patients, and the side-effects of these drug regimens, highlight the urgent need for novel lipid-lowering drugs. The liver and intestine are important in the production and removal of endogenous and exogenous lipids, respectively, and have an important impact on circulating lipid levels. Elevated circulating lipids predisposes an individual to lipid deposition in the vascular wall, affecting vascular function. Berberine (BBR) modulates liver lipid production and clearance by regulating cellular targets such as cluster of differentiation 36 (CD36), acetyl-CoA carboxylase (ACC), microsomal triglyceride transfer protein (MTTP), scavenger receptor class B type 1 (SR-BI), low-density lipoprotein receptor (LDLR), and ATP-binding cassette transporter A1 (ABCA1). It influences intestinal lipid synthesis and metabolism by modulating gut microbiota composition and metabolism. Finally, BBR maintains vascular function by targeting proteins such as endothelial nitric oxide synthase (eNOS) and lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1). This paper elucidates and summarizes the pharmacological mechanisms of berberine in lipid metabolic diseases from a multi-organ (liver, intestine, and vascular system) and multi-target perspective.
Construction of EMT related prognostic signature for kidney renal clear cell carcinoma, through integrating bulk and single-cell gene expression profiles
Authors: Huang Qi , Li Feiyu , Liu Li , Xu Rui , Yang Tao , Ma Xiaoyun , Zhang Hongmei , Zhou Yan , Shao Yongxiang , Wang Qiaofeng , Xi Haifeng , Ding Yancai
Published: November 2023

Introduction: Kidney renal clear cell carcinoma (KIRC), as a main type of malignant kidney cancers, has a poor prognosis. Epithelial-mesenchymal transformation (EMT) exerts indispensable role in tumor progression and metastasis, including in KIRC. This study aimed to mine more EMT related details and build prognostic signature for KIRC.

Methods: The KIRC scRNA-seq data and bulk data were downloaded from GEO and TCGA databases, respectively. The cell composition in KIRC was calculated using CIBERSORT. Univariate Cox regression analysis and LASSO Cox regression analysis were combined to determine the prognostic genes. Gene set variation analysis and cell-cell communication analysis were conducted to obtain more functional information. Additionally, functional analyses were conducted to determine the biological roles of si-LGALS1 in vitro.

Results: We totally identified 2,249 significant differentially expressed genes (DEGs) in KIRC samples, meanwhile a significant distinct expression pattern was found in KIRC, involving Epithelial Mesenchymal Transition pathway. Among all cell types, significantly higher proportion of epithelial cells were observed in KIRC, and 289 DEGs were identified in epithelial cells. After cross analysis of all DEGs and 970 EMT related genes, SPARC, TMSB10, LGALS1, and VEGFA were optimal to build prognostic model. Our EMT related showed good predictive performance in KIRC. Remarkably, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process.

Conclusion: A novel powerful EMT related prognostic signature was built for KIRC patients, based on SPARC, TMSB10, LGALS1, and VEGFA. Of which, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process.
Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.)
Authors: Lin Ying-Chen , Mansfeld Ben N. , Tang Xuemei , Colle Marivi , Chen Feifan , Weng Yiqun , Fei Zhangjun , Grumet Rebecca
Published: November 2023

Phytophthora fruit rot (PFR) caused by the soilborne oomycete pathogen, Phytophthora capsici, can cause severe yield loss in cucumber. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to PFR using multiple genomic approaches and populations. Two types of resistances have been identified: age-related resistance (ARR) and young fruit resistance. ARR occurs at 12-16 days post pollination (dpp), coinciding with the end of exponential fruit growth. A major QTL for ARR was discovered on chromosome 3 and a candidate gene identified based on comparative transcriptomic analysis. Young fruit resistance, which is observed during the state of rapid fruit growth prior to commercial harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance were also performed on a cucumber core collection representing > 96% of the genetic diversity of the USDA cucumber germplasm. Several SNPs overlapped with the QTL identified from QTL-seq analysis on biparental populations. In addition, novel SNPs associated with the resistance were identified from the germplasm. The resistant alleles were found mostly in accessions from India and South Asia, the center of diversity for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.
Functional physical training improves fitness and cognitive development in 4~5 years old children
Authors: Hao Lei , Fan Yongzhao , Zhang Xiaojuan , Rong Xiangjiang , Sun Youping , Liu Kun
Published: November 2023

Background

Development of physical and cognitive function is very critical in 4~5 years children. It has been addressed in this research if the 18 weeks of specific functional training with or without cognitive training can be effective on improving fitness and cognitive development in 4~5 years preschool children.

Methods

A total of 126 preschool children in the 4~5 age range were selected as participants and randomly assigned to one of four groups: the control group (C), the functional physical training group (P), the cognitive training group (CT), and the functional physical training combined with cognitive training group (PCT).

Results

The results revealed significant pre/post differences in body height and weight among all four groups of children. Furthermore, there was no significant difference in physical fitness between the C group and the CT group after the intervention. However, the children in the P group and the PCT group showed significant improvements in three indicators including standing long jump, continuous jump, and 10-meter shuttle running. Additionally, the children in P group, CT group, and the PCT group demonstrated significant improvement in simple reaction time, attention, and spatial memory. No significant cognitive improvement was found in C group.

Conclusion

Functional physical training with or without cognitive intervention can promote both physical fitness and cognitive development in children aged 4~5 years. Cognitive training alone can significantly improve cognitive function but not physical. Therefore, functional physical training can be used alone to improve the physical and cognitive abilities for aged 4~5 years old children.
Evaluation of the Italian version of the elderly mobility scale in older hospitalized patients
Authors: Nicolai Moreno , Casoni Elisa , Bertino Emanuela , David Letizia , Polverigiani Chiara , Mallucci Federica , Fioretti Paola , Leonzi Sara , Bevilacqua Roberta , Barbarossa Federico , Maranesi Elvira , Baccini Marco , Barboni Ilaria , Riccardi Giovanni R.
Published: November 2023

Introduction

Reliable and valid assessment tools are needed to evaluate and predict physical function in older hospitalized patients. The aim of this study is to develop the Italian version of the Elderly Mobility Scale (I-EMS) and to evaluate its validity and inter-rater reliability for use with geriatric inpatients.

Methods

The study consists of two phases: (i) translation, where EMS version 2 was translated into Italian by two teams, each comprising 2 bilingual physiotherapists; translations were back translated by 2 native English speakers, and a committee of 2 physiotherapists and 1 physician refined the initial I-EMS version, which was pilot-tested for clarity in a group of ten experienced geriatric physiotherapists; (ii) an observational study assessed I-EMS metrics (reliability, validity) in older Italian inpatients at IRCCS INRCA (Ancona, Italy) between September 2022 and April 2023.

Results

No statistically significant differences were found between the scores of individual items and the total score assigned by different raters. The ICC for total I-EMS was 0.951, SEM was 1.10 and MDC95 was 3.06. The absolute agreement and weighted kappa for individual items ranged 80.32–100% and 8.2–1, respectively. The validity of I-EMS was supported by a significant (p < 0.05) correlation with the Barthel Index (r = 0.827 and 0.834 for the I-EMS administered by rater A and rater B, respectively).

Conclusion

I-EMS showed good internal consistency and inter-rater reliability, and confirmed construct validity with respect to BI. Therefore, it can safely be used as an assessment tool for hospitalized Italian geriatric patients.

Clinical trial registration

[ClinicalTrials.gov], [NCT05806242].
Fungal diversity and drug susceptibility of the oral mycobiome of domestic dogs
Authors: Esquivel Brooke D. , Rouse Salcido Elisa M. , Schweiker Allison M. , Holder Brandon L. , KuKanich Butch , KuKanich Kate S. , White Theodore C.
Published: November 2023

The purpose of this study was to characterize the variety and diversity of the oral mycobiome of domestic dogs and to identify the commensal and potentially pathogenic fungi present. Two hundred fifty-one buccal swabs from domestic dogs were obtained and struck onto a chromogenic fungal growth medium that distinguishes between fungal species based on colony color and morphology. After isolating and harvesting single colonies, genomic DNA was extracted from pure cultures. PCR was used to amplify a fungal-specific variable rDNA region of the genome, which was then sent for sequencing. Sequencing results were input into the NCBI BLAST database to identify individual components of the oral mycobiome of tested dogs. Of the 251 dogs swabbed, 73 had cultivable fungi present and 10 dogs had multiple fungal species isolated. Although the dogs did not show signs of oral infections at the time, we did find fungal species that cause pathogenicity in animals and humans. Among fungal isolates, Malassezia pachydermatis and species from the genus Candida were predominant. Following fungal isolate identification, antifungal drug susceptibility tests were performed on each isolate toward the medically important antifungal drugs including fluconazole, ketoconazole, and terbinafine. Drug susceptibility test results indicated that a large number of isolates had high MIC values for all three drugs. Exploring the oral mycobiome of dogs, as well as the corresponding drug susceptibility profiles, can have important implications for canine dental hygiene, health, and medical treatment. Identifying the microorganisms within the canine mouth can illustrate a common pathway for fungal pathogens of One Health concern to spread from our canine companions to humans.