bluuebunny/crossref_metadata_2025 huggingface dataset:
Mobile-Based Technology for Data Management of Students Fieldwork Practices
Authors: Hermanto Nandang , Dzakkiyah Alya Khansa
Published: April 2021

Fieldwork Practices (PKL) is one of the activities in the vocational teaching and learning process which takes place in a direct business environment. The main purpose of implementing PKL is to introduce students to the real work. The implementation of PKL at SMK Ma'arif NU 1 Sumpiuh is carried out for 6 months which is divided into 2 implementation activities, namely 3 months in odd semester and 3 months in even semester. The purpose of this study is to provide a suggestion to facilitate the process of recording PKL student data both in odd and even periods. In addition, the proposed system also provides details on the location of PKL and provides if in the second stage of PKL implementation there are students who change the location. The PKL application has gone through the system functional testing phase and has been running according to the needs of the PKL activity process. The technology used in this study uses a mobile so that all activities both from the school, committee and students can be monitored in real time by all related parties.
Synthesis of triazole-containing ciprofloxacin conjugate and its in silico test as a cytochrome P450 ligand
Authors: Фалетров Ярослав Вячеславович , Глинская Лилия Игоревна , Хорецкий Матвей Сергеевич , Панада Ян Владимирович , Фролова Нина Степановна , Шкуматов Владимир Макарович
Published: April 2021

Cytochromes P450 are hem-containing monooxygenases which catalyse biosynthesis of many compounds playing an essential role in cellular functions as well as degradation of drugs and xenobiotics. Some P450s (e. g., human CYP19 and CYP17, fungal CYP51) are valid target proteins for some drugs. The others P450s are also interesting for pharmacology-related researches. Aiming to design new fluorescent inhibitor of P450s we have synthesised the azole-bearing conjugate of ciprofloxacin (CPF-bab-Z1). To estimate potential of the compound as a ligand for CYPs we performed high-throughput virtual screening (multiple docking calculations) for CPF-bab-Z1 and multiple known 3D structures of P450s. The best affinity for CPF-bab-Z1 (the smallest value of energy of binding is equal -12.5 kcal/mol) were found for protein with PDB code 5esh among 28 structures of CYP51. The calculated pose of CPF-bab-Z1 in the active site of the protein is characterised by cyclopropyl (but not azole) proximity to the heme iron of the CYP51. The data obtained demonstrate perspectives for in vitro investigations of CPF-bab-Z1 with P450s.
Preparation procedure to obtain iron nanopowder under non-isothermal conditions
Authors: Нгуен Тиен Хиеп , Нгуен Ван Минь , Нгуен Мань Хунг , Данчук Виталий Николаевич
Published: April 2021

The kinetics for the procedure of preparing iron nanopowder from α-FeOOH by hydrogen reduction under non-isothermal conditions were studied. The reduction of α-FeOOH nanopowder was shown to occur within the temperature range from 180 to 550 °С, with a maximum specific rate value attained at 500 °С. The activation energy for the reduction process α-FeOOH nanopowder was measured to be ~43 kJ/mol, evidencing a mixed reaction mode. Performing the reduction of α-FeOOH at 500 °С accelerated the process while ensuring the required properties of the product obtained. The Fe nanoparticles thus prepared were of rounded shape, the size ranging from 70 to 100 nm.
Morphological differences in the pancreas of normo- and hypertensive rats after joint exposure of intermittent hypoxia and melatonin
Authors: Yanko Roman V. , Levashov Mikhail I.
Published: April 2021

The morphological changes in the pancreas of normo- and hypertensive rats after combined exposure to intermittent normobaric hypoxia and melatonin were studied. The study was conducted in the autumn on 24 normotensive (Wistar line) and 24 spontaneously hypertensive (SHR line) male rats. Experimental rats were daily exposed to hypoxic gas mixture in special sealed chamber. Hypoxic gas mixture (12 % oxygen in nitrogen) was supplied into this chamber from the membrane gas separator element in the intermittent mode: 15 min deoxygenation/ 15 min reoxygenation for 2 h. Exogenous melatonin was orally administered to experimental animals at 10 h in the morning at a dose of 5 mg / kg once a day. The total duration of the experiment was 28 d. Histological preparations of pancreatic tissue were prepared according to the standard methods. The morphometry of the preparations digital images was performed using the computer program ImageJ. The nature and severity of morphological changes in the pancreas of the experimental spontaneously hypertensive rats (hyperplasia of the nucleolus in the nucleus of exocrinocytes, a decrease in the amount of connective tissue) suggests that the combined effect of intermittent normobaric hypoxia and melatonin increases the activity of the exocrine part of the pancreas. At the same time, the activity of the endocrine part of the pancreas decreases, as evidenced by a decrease in the linear dimensions and area of the Langerhans islets, as well as the number of endocrinocytes contained in them. In Wistar rats, the combined effect of intermittent hypoxia and melatonin leads to the appearance of morphological signs of increased activity of both exocrine and endocrine pancreas functions. Thus, after prolonged combined exposure to intermittent normobaric hypoxia and melatonin, morphological signs of increased exocrine pancreas activity appear in both normotensive and hypertensive rats. At the same time, the activity of the endocrine function of the pancreas in experimental Wistar rats increases, while in SHR rats, on the contrary, decreases.
Properties of expression of protein capside porcine circovirus type 2 in bacterial cells
Authors: Titova Anastasia D. , Kudzin Kirill V. , Prokulevich Vladimir A.
Published: April 2021

To improve expression of the porcine circovirus type 2 (PCV2) capsid protein in E. coli cells, the corresponding gene was optimized and two variants of the open reading frame were constructed, which encoded the full-sized and shortened capsid proteins as part of the expression vector. Rare codons were replaced, and in the case of a shortened version of the gene, the region corresponding to the N-terminal domain of the protein was deleted. A comparison was made of the expression level of the studied proteins. It was established that the highest level of expression in bacterial cells is achieved by simultaneously optimizing the codons and removing the initial (N-terminal) 108 base pair (bp) portion of the gene, which contains the nuclear localization signal.
The influence of Rose Bengal photosensitizer on the productivity and pigment composition of Haematococcus pluvialis
Authors: Pechenkina Elizaveta I. , Samovich Tatyana V. , Kozel Nikolay V.
Published: April 2021

The stimulation of astaxanthin synthesis in Haematococcus pluvialis cells under high-intensity light in the combined action of Rose Bengal photosensitizer has been established. It was revealed that when Rose Bengal was used as an additional inducer of carotenogenesis in high-intensity light, the dry weight of the Haematococcus and the diameter of the cells in suspension increase compared to the action of only high-intensity light on algae cells. The observed increases in dry weight are significant and reach 40 % excess over control. We suggest that the increase in dry weight, Haematococcus cell diameter and astaxanthin yield when H. pluvialis photosensitizer is added to the incubation medium against the background of high-intensity light is not associated with increased stress (since the used concentrations of Rose Bengal are too small to induce photo-oxidative stress), but the signaling properties of the generated Rose Bengal singlet oxygen, which may be the primary agent in the transduction of a signal that triggers increased synthesis of astaxanthin in H. pluvialis cells.
The prospects of alcohol industry wastes application in photoproduction of hydrogen by the purple bacteria Rhodobacter sphaeroides
Authors: Gabrielyan Lilit S.
Published: April 2021

The possibilities of using various industrial wastes to produce biofuel are currently being considered. It will provide not only novel, efficient and cheap sources of hydrogen (H2), but will also help to solve the problem of waste disposal. The current work presents the prospects of application of alcohol industry wastes, such as distillers grains and brewery spent grains, for production of H2 by the purple bacteria Rhodobacter sphaeroides MDC6522. The data obtained showed the possibility of using distillers grains and brewery spent grains as effective carbon sources for producing H2. It was shown that pre-treatment of wastes, their dilution and neutralization are necessary to ensure the effective bacterial growth and H2 production by R. sphaeroides. The growth rate and H2 yield during the cultivation of bacteria on a 2-fold diluted distillers grains medium increased 2- and 4-fold, respectively, compared with a culture, grown on standard Ormerod medium. At the same time, the growth rate and photoproduction of H2 on a 10-fold diluted brewery spent grains medium were 2-fold higher, in comparison with the control. Thus, the results obtained indicate that these alcohol industry wastes can be used as promising substrates for biohydrogen production.
Complex Treatment of Patients With Chronic Generalized Periodontitis of a Medium Degree of Severity Using the Methods of Osteogygivoplasty With Biocomposite Materials and Guided Tissue Regeneration
Authors: Imanalieva A. , Abaskanova P. , Tursunaliev O. , Bakiev B. , Kuttubaeva K.
Published: April 2021

Improvement of methods of complex treatment of periodontium diseases continues to be an urgent problem of dentistry and requires an interdisciplinary approach. The severity of the course of periodontitis and the severity of destructive phenomena dictates the need to use osteoplastic agents to restore damaged periodontium tissues. It has been proven that the efficiency of membrane technology is significantly increased when membranes and substitute materials are used together. The positive effect of the combined use of Platelet Rich Plasma (PRP — autogenous growth factors), osteoplastic materials, and the method of Guided Tissue Regeneration (GTR) has been confirmed. To increase the efficiency of reconstructive treatment of patients with generalized periodontitis through the combined use of alloplasty, Platelet Rich Plasma, and the method of Guided Tissue Regeneration. Method of testing: clinical, X-ray. For the period 2018–2019, 34 patients with chronic generalized periodontal atrophy of moderate severity were under observation. All patients underwent professional oral hygiene, laser therapy, and antibacterial therapy with rovamycin. 6 patients in complex therapy underwent surgical interventions: osteogingivoplasty with biocomposite materials using GTR auto-allogenic membranes. Bone defects were filled with biocomposite material: hydroxylappatite granules (Polistom, RF) in combination with PRP, on top of an alto plasma membrane isolated from PRP and collagen membrane (Polistom, RF). The immediate and long-term periods of treatment were quite favorable. Control X-ray examination after 12 months showed restoration of a bone defect with an organotypic structure.
FORECASTING THE FUTURE OF ISLAMIC EDUCATIONAL MANAGEMENT STUDY PROGRAM: PROJECTION OF NEEDS FOR LECTURERS
Authors: Purnomo Nurul Hudha
Published: April 2021

The Islamic Educational Management program in IAIN Kediri was established in 2018 so that it requires proper planning to maintain the quality of the study program education. One of the planning steps is to maintain the ratio of the students and the lecturers by projecting the needs for lecturers. The method used in this research model is quantitative methods with the projection method, namely the growth rate and the input output, the parameter numbers used are the input rate and the graduate number, the assumption in this research is target so that the total of students can increase every year. The basic data used is the total of graduates, the total of new students and the total of lecturers. This research results in the number of needs for lecturers in the future. The results of this research reveal that in 2027, the number of lecturers needed for institutional courses will be 16 lecturers, while the number of lecturers for study program courses will increase to 25 lecturers. In 2028, the number of lecturers needed for institutional courses will increase to 18 lecturers, while the number of lecturers for study program courses will be 28 lecturers. Eventually in 2029 the number of lecturers in institutional courses will increase to 20 lecturers, while the number of lecturers needed for study program courses is 30 lecturers.
THE LEARDERSHIP ROLE OF SCHOOL PRINCIPALS IN ONLINE LEARNING DURING THE COVID-19 PANDEMIC
Authors: Rahman Ainur , Subiyantoro Subiyantoro
Published: April 2021

This study aims to describe and analyze the leadership role of school principals in online learning during the Covid-19 pandemic. This study used a qualitative approach with phenomenology. The research site at SD Negeri Krapyak Wetan. The data collection technique is done through interviews, documentation and observation. Data analysis was carried out through data collection, data reduction and ending with drawing conclusions. The results showed that; the role of the principal's leadership in online learning during the Covid-19 pandemic, is; a) Optimizing learning and deliberations with teachers, b) Providing education and training on online learning platforms (online), c) Providing appreciation and motivation to teachers, students and guardians of students, d) Conducting multidirectional coordination and communication.
KNOWLEDGE SHARING MANAGEMENT: STRATEGY FOR IMPROVING THE QUALITY OF HUMAN RESOURCES
Authors: Baharun Hasan , Hefniy Hefniy , Silviani Silviani , Maarif Muhammad Anas , Wibowo Adi
Published: April 2021

This study aims to analyze and understand about analyzing the knowledge sharing strategy carried out by SMA Nurul Jadid, Paiton, Probolinggo in improving the quality of its human resources. This research uses a qualitative approach to the type of case study. Data collection techniques are carried out through interviews, observation, and documentation. Data analysis was carried out through display data, data reduction and conclusion drawing. The results showed that the strategy to improve the quality of human resources through knowledge sharing at SMA Nurul Jadid was carried out through; utilize materials, talk space, knowledge sharing culture, benchmarking best practices.
Археологічні пам’ятки Казанківського району Миколаївської області (за матеріалами А.О. Сікорського)
Authors: Borysova Tetiana , Borysov Artem
Published: April 2021

У статті подається короткий аналіз підйомного матеріалу з археологічних поселень Повисуння, розташованих на території південної частини Казанківського району Миколаївської області, за даними польових щоденників першовідкривача – історика, вчителя Анатолія Олексійовича Сікорського. Обстеження пам’яток здійснювалося впродовж 1960-1980-х років. Зібрані науковцем матеріали в основному зберігаються у фондах Миколаївського обласного краєзнавчого музею та у Березнегуватському районному народному історико-краєзнавчому музеї.
Керамічний комплекс Борисфена періоду ранньої архаїки (за матеріалами колекції В.В. Лапіна)
Authors: Gavrylyuk Nadiya
Published: April 2021

У статті йдеться про керамічний комплекс перших поселенців на о. Березань і визначення ролі ліпного посуду у ньому. Вирішується питання кому належала ліпна кераміка з матеріалів найраніших шарів Борисфену – варварам чи грекам. Джерельною базою статті є матеріал з колекції В.В. Лапіна. Показані перспективи використання статистичних методів у вивченні масового керамічного матеріалу. Показана різниця між керамічними комплексами об’єктів, котрі були створені «до стихійного лиха» та «після стихійного лиха» у межах другої половина VII – початку VI ст. до н.е.
Wildlife-Friendly Livestock Management Promotes Mammalian Biodiversity Recovery on a Semi-Arid Karoo Farm in South Africa
Authors: Schurch Matthew P. E. , McManus Jeannine , Goets Stefan , Pardo Lain E. , Gaynor David , Samuels Igshaan , Cupido Clement , Couldridge Vanessa , Smuts Bool
Published: April 2021

Agriculture is an essential production system used to feed the growing human population, but at the same time has become a major driver of biodiversity loss and environmental degradation. Employing production methods that restore degraded landscapes can have a positive impact on biodiversity, whilst improving food production. We assessed how mammalian biodiversity, specifically richness and their relative abundances varied on five Karoo farms in South Africa that had been amalgamated and subjected to a transition from traditional livestock grazing techniques (sporadic rotational grazing and lethal predator control) to wildlife-friendly non-lethal predator management, using human shepherding of livestock under a high-density short-duration grazing regime. We used camera trap data collected over a 4-year period, to measure mammalian species richness, distribution and relative abundance on the wildlife-friendly farm to investigate temporal changes throughout the conversion from traditional farming practices. In the last year of the study (2019) additional cameras were used to provide a spatial comparison of mammalian species on the wildlife-friendly farm to two neighboring farms, a traditional livestock farm using lethal predator controls, and a game farm. We found that mammalian species richness increased year on year resulting in a significant increase of 24% over the duration of the study. Herbivores showed an increase of 33% in the number of species detected over the years, while predator species increased by 8%. The relative abundance and distribution of most species also showed increases as the conversion process took place. For example, 73% of the herbivore species detected throughout the study increased in their relative abundance. Similarly, 67% of all species showed an increase in the number of sites occupied over the years. In the final year of the study the wildlife-friendly farm had more mammalian species compared to the game farm and traditional livestock farm, with the latter two sites having a similar number of species when compared to the commencement of the conversion of the wildlife-friendly site. These broad improvements in mammalian biodiversity demonstrate that livestock production can benefit local mammalian biodiversity through a combination of herder grazing management and wildlife-friendly farming.
Outcomes After Repair of Pulmonary Atresia With Ventricular Septal Defect and Major Aortopulmonary Collateral Arteries: A Tailored Approach in a Developing Setting
Authors: Zou Ming-Hui , Ma Li , Cui Yan-Qing , Wang Huai-Zhen , Li Wen-Lei , Li Jia , Chen Xin-Xin
Published: April 2021

Objectives: Pulmonary atresia with ventricular septal defect and major aortopulmonary collateral arteries (PA/VSD/MAPCAs) is complex and diverse that has led to a variety of treatment strategies. Experience has been largely obtained in the advanced countries. The clinical diversity is greater in China. We evaluated our surgical approaches and outcomes of these patients.

Methods: We reviewed 127 patients undergoing varied surgeries in our center in 2010–2019.

Results: Thirty patients underwent single-stage complete repair by unifocalizing MAPCAs and VSD closure (aged 3.9–131.4 months, median 22) with 3 (10%) early deaths. Ninety-seven underwent the first-stage rehabilitation strategy including systemic-to-pulmonary shunt in 29 (aged 0.5–144 month, median 8), and palliative RV-PA conduit in 68 (aged 2.2–209.6 months, median 14) with 5 (5.2%) early deaths. Eight-one patients (63.8%) eventually achieved complete repair with a median right/left ventricular (RV/LV) pressure ratio of 0.7 (ranged 0.4–1.0). Fourteen patients (11.0%) accepted palliation as final destination. Survival for the entire cohort was 89.5, 85.2, and 76.1% at 1, 5, and 10 years, respectively. Survival for those undergoing complete repair was 88.2 and 76.6% at 1 and 5 year, respectively. RV/LV pressure ratio ≥0.8 was risk factor for mortality (HR10.3, p = 0.003).

Conclusions: Our cohort, the largest from China, had distinctive clinical features with substantially wider age range and higher RV/LV pressure ratio. Using the combined approaches tailored to individual patients, complete repair was achieved in 64% of patients. The early and intermediate outcomes are acceptable compared to many of the previous reports.
The Sonic Hedgehog–Patched–Gli Signaling Pathway Maintains Dental Epithelial and Pulp Stem/Progenitor Cells and Regulates the Function of Odontoblasts
Authors: Ishikawa Yuko , Ida-Yonemochi Hiroko , Saito Kotaro , Nakatomi Mitsushiro , Ohshima Hayato
Published: April 2021

This study aimed to elucidate the role of the Sonic hedgehog (Shh)–Patched (Ptch)–Gli signaling pathway in maintaining dental epithelial and pulp stem/progenitor cells and regulating the function of odontoblasts. Doxycycline (dox)-inducible histone 2B (H2B)–green fluorescent protein (GFP) transgenic mice ingested dox at prenatal embryonic days 14.5 or 15.5 and their offspring were collected from postnatal day 1 (P1) to week 3 (P3W). Immunohistochemistry for Gli1, Ptch1, and Ptch2 andin situhybridization forShhandPtch1were conducted. Mandibular incisors of postnatal day 2 H2B-GFP transgenic and wild-type mice were cultivated in a nutrient medium with Shh antibody for 4 days and subsequently processed for immunohistochemistry for Sox2. In molars, dense H2B-GFP-label-retaining cells (H2B-GFP-LRCs) were densely distributed throughout the dental pulp during P1 to postnatal week 2 (P2W) and decreased in number by postnatal P3W, whereas the number of dense H2B-GFP-LRCs in the subodontoblastic layer increased in number at P2W. Gli1+and Pthc1+cells were distributed throughout the enamel organ and dental pulp, including the odontoblast and subodontoblastic layers.ShhmRNA was expressed in the inner enamel epithelium and shifted into odontoblasts after dentin deposition.Ptch1mRNA was expressed in the inner enamel epithelium and cuspal pulpal tissue on P1 and decreased in intensity from postnatal week 1 to P3W. In incisors, the apical bud contained H2B-GFP-LRCs, Gli1+cells, and Ptch1+cells. The addition of Shh antibody to explants induced a decrease in the number of Sox2+cells due to the increase in apoptotic cells in the apical bud. Thus, the Shh–Ptch–Gli signaling pathway plays a role in maintaining quiescent adult stem cells and regulating the function of odontoblasts.
Can Inhibin B Reflect Ovarian Reserve of Healthy Reproductive Age Women Effectively?
Authors: Wen Jingyi , Huang Kecheng , Du Xiaofang , Zhang Hanwang , Ding Ting , Zhang Cuilian , Ma Wenmin , Zhong Ying , Qu Wenyu , Liu Yi , Li Zhiying , Deng Song , Luo Aiyue , Jin Yan , Zhang Jinjin , Wang Shixuan
Published: April 2021

Objective

The reference range and potential value of inhibin B are still unclear and controversial. This study aimed to define the variation trend of inhibin B in healthy women with age and explore its value in the reflection of ovarian reserve.

Methods

A total of 2524 healthy reproductive age women from eight medical institutes nationwide were recruited. The variation tendency of inhibin B with age was primarily established in the first group of 948 women and validated in another 605. We evaluated the relationship between inhibin B and classic ovarian reserve and function markers. The potency of inhibin B in predicting AFC <5-7 was also estimated and compared with FSH.

Results

The nomogram showed that serum levels of inhibin B rapidly decreased after the age of 40. Inhibin B was positively correlated with AMH (R = 0.57, P < 0.001), AFC (R = 0.34, P < 0.001) and testosterone (R = 0.10, P = 0.002), and negatively correlated with FSH (R = -0.41, P < 0.001) and LH (R = -0.20, P < 0.001) and FSH/LH (R=-0.18, P < 0.001), while no correlation was found with PRL. Unexpectedly, Inhibin B (AUC = 0.74, P < 0.001 for the establishment population; AUC = 0.78, P < 0.001 for the validation population) had a slightly higher value than FSH (AUC = 0.71, P < 0.001 for the establishment population; AUC = 0.72, P < 0.001 for the validation population) in diagnosing AFC <5-7.

Conclusions

For healthy reproductive age women, the decline of inhibin B can reflect decreased ovarian reserve effectively, having a good consistency with AMH and AFC. More importantly, inhibin B had an advantage in predicting AFC <5-7 compared with FSH, which suggested the potential of inhibin B in predicting ovarian response. These results will be helpful to the clinical application of inhibin B in the evaluation of female ovarian reserve and the assessment of their reproductive capacity. Trial registration: http://clinicaltrials.gov; NCT02294500.
Germline Structural Variations in Cancer Predisposition Genes
Authors: Pócza Tímea , Grolmusz Vince Kornél , Papp János , Butz Henriett , Patócs Attila , Bozsik Anikó
Published: April 2021

In addition to single nucleotide variations and small-scale indels, structural variations (SVs) also contribute to the genetic diversity of the genome. SVs, such as deletions, duplications, amplifications, or inversions may also affect coding regions of cancer-predisposing genes. These rearrangements may abrogate the open reading frame of these genes or adversely affect their expression and may thus act as germline mutations in hereditary cancer syndromes. With the capacity of disrupting the function of tumor suppressors, structural variations confer an increased risk of cancer and account for a remarkable fraction of heritability. The development of sequencing techniques enables the discovery of a constantly growing number of SVs of various types in cancer predisposition genes (CPGs). Here, we provide a comprehensive review of the landscape of germline SV types, detection methods, pathomechanisms, and frequency in CPGs, focusing on the two most common cancer syndromes: hereditary breast- and ovarian cancer and gastrointestinal cancers. Current knowledge about the possible molecular mechanisms driving to SVs is also summarized.
Single-Cell RNA Sequencing Analysis of the Immunometabolic Rewiring and Immunopathogenesis of Coronavirus Disease 2019
Authors: Qi Furong , Zhang Wenbo , Huang Jialu , Fu Lili , Zhao Jinfang
Published: April 2021

Although immune dysfunction is a key feature of coronavirus disease 2019 (COVID-19), the metabolism-related mechanisms remain elusive. Here, by reanalyzing single-cell RNA sequencing data, we delineated metabolic remodeling in peripheral blood mononuclear cells (PBMCs) to elucidate the metabolic mechanisms that may lead to the progression of severe COVID-19. After scoring the metabolism-related biological processes and signaling pathways, we found that mono-CD14+cells expressed higher levels of glycolysis-related genes (PKM, LDHAandPKM) and PPP-related genes (PGDandTKT) in severe patients than in mild patients. These genes may contribute to the hyperinflammation in mono-CD14+cells of patients with severe COVID-19. The mono-CD16+cell population in COVID-19 patients showed reduced transcription levels of genes related to lysine degradation (NSD1, KMT2E, andSETD2) and elevated transcription levels of genes involved in OXPHOS (ATP6V1B2,ATP5A1,ATP5E, andATP5B), which may inhibit M2-like polarization. Plasma cells also expressed higher levels of the OXPHOS geneATP13A3in COVID-19 patients, which was positively associated with antibody secretion and survival of PCs. Moreover, enhanced glycolysis or OXPHOS was positively associated with the differentiation of memory B cells into plasmablasts or plasma cells. This study comprehensively investigated the metabolic features of peripheral immune cells and revealed that metabolic changes exacerbated inflammation in monocytes and promoted antibody secretion and cell survival in PCs in COVID-19 patients, especially those with severe disease.
Epigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b
Authors: Sidwell Tom , Rothenberg Ellen V.
Published: April 2021

The transcription factor Bcl11b is critically required to support the development of diverse cell types, including T lymphocytes, type 2 innate lymphoid cells, neurons, craniofacial mesenchyme and keratinocytes. Although in T cell development its onset of expression is tightly linked to T-lymphoid lineage commitment, the Bcl11b protein in fact regulates substantially different sets of genes in different lymphocyte populations, playing strongly context-dependent roles. Somewhat unusually for lineage-defining transcription factors with site-specific DNA binding activity, much of the reported chromatin binding of Bcl11b appears to be indirect, or guided in large part by interactions with other transcription factors. We describe evidence suggesting that a further way in which Bcl11b exerts such distinct stage-dependent functions is by nucleating changes in regional suites of epigenetic modifications through recruitment of multiple families of chromatin-modifying enzyme complexes. Herein we explore what is - and what remains to be - understood of the roles of Bcl11b, its cofactors, and how it modifies the epigenetic state of the cell to enforce its diverse set of context-specific transcriptional and developmental programs.
Challenges in Current Coral Reef Protection – Possible Impacts of UV Filters Used in Sunscreens, a Critical Review
Authors: Moeller Mareen , Pawlowski Sascha , Petersen-Thiery Mechtild , Miller Ingo B. , Nietzer Samuel , Heisel-Sure Yannik , Kellermann Matthias Y. , Schupp Peter J.
Published: April 2021

Coral reefs are highly endangered ecosystems. The identification and quantification of potential stress factors are essential to protect them. UV filters from sunscreens that are introduced to coral reef areas are considered as one of these stressors and their impact on corals needs to be further investigated. Even though UV filters are functionally similar, their structural features are very diverse. Their impact on limnic organisms have also been shown to be highly variable ranging from no or low to high toxicity. It is therefore to be expected that their effect on corals also differs significantly and that each compound has to be evaluated individually. The demand for conclusive benchmarks and guidelines from policy makers and the public over the past years shows the necessity for an objective literature review on the effects of various UV filters on scleractinian corals. Here, we review the present literature, summarize the data on the different UV filters and discuss the different approaches, advantages and limitations of the studies. However, the methods used in the latter studies vary greatly. They differ in many aspects such as species and life stage used, field and laboratory approaches, with exposure times ranging from hours to weeks. Some studies include analytics and measure the actual test concentration, others only provide nominal concentrations. The lack of standardized methods renders comparisons between studies futile. Additionally, most UV filters have only been investigated in a single or a few studies of different quality. Reliable thresholds are therefore impossible to draw on the basis of currently available studies. Nevertheless, certain UV filters repeatedly showed comparable toxicity in both freshwater and marine species tested. Yet, existing differences in results from coral tests emphasize the need for a standardized testing method comparable to those established for other aquatic organisms in order to allow for a more conclusive assessment. In this review, we describe what a scientifically sound testing proposal should include in order to obtain reliable and reproducible data, which ultimately should result in an internationally organized standardized ring test trial. Such standardized toxicity tests would enable validation of coral toxicity data related to UV filters, but also testing of other types of compounds that are known to be introduced and effect coral reefs, thus helping to identify significant stressors and enabling objective policy decisions.
Artisanal and Aboriginal Subsistence Whaling in Saint Vincent and the Grenadines (Eastern Caribbean): History, Catch Characteristics, and Needs for Research and Management
Authors: Fielding Russell , Kiszka Jeremy J.
Published: April 2021

Whaling has been a contentious international environmental issue for decades and carries complex ecological and socioeconomic implications. In Saint Vincent and the Grenadines (SVG), a small archipelagic nation located in the Eastern Caribbean, present-day whaling traces its origin to local interaction with American-based whalers during the nineteenth and early twentieth centuries. When American whaling in the region ceased, local shore-based whaling arose to fill the niche and to exploit the remaining, though diminished, stocks of large whales, as well as stocks of small cetaceans that the American whalers had not targeted as heavily. After a period of expansion throughout the late nineteenth and early twentieth centuries, which saw shore-whaling operations established on at least 11 islands in the region, Eastern Caribbean whaling experienced a period of attrition, during which most local whaling operations ceased. Two operations, both based in SVG, continue regularly today. This paper reviews the past and present status of whaling activities in SVG from the literature and using recent data collected from 2007 to 2017 through logbook data, interview surveys, and ethnographic observations. Small cetacean captures have been documented since 1949, and at least 15 species of odontocetes have been captured (primarily delphinids). From 1949 to 2017, a total of 13,856 small cetacean captures has been recorded, including 5,896 short-finned pilot whales (Globicephala macrorhynchus), 109 killer whales (Orcinus orca), and 7,851 other small cetaceans. Small cetacean catch records are largely incomplete and total catch estimates could not be attempted. Reliable abundance estimates do not exist. Consistent records for the take of large whales are only available for the period 1986–2020, during which 45 humpback whales (Megaptera novaeangliae) and 2 Bryde’s whales (Balaenoptera edeni) were taken. Additionally, 8 sperm whale (Physeter macrocephalus) captures were reported from 1967 and 1974. We also review whaling practices, existing national policy on whaling, management techniques outside of formal policy regimes, research needs, and future management perspectives. Future monitoring and management of whaling activities in SVG are strongly needed to assess the sustainability of small cetacean exploitation.
Electrochemical Double-Layer Capacitor Containing Mixtures of Ionic Liquid, Lithium Salt, and Organic Solvent as an Electrolyte
Authors: Li Xiangyuan , Li Hao , Feng Rui , He Long , Lu Hai
Published: April 2021

A modified ionic liquid (IL)-based electrolyte, with conventional carbonates as the support solvent and lithium salt as the additive, was designed for a high-voltage electrochemical double-layer capacitor (EDLC). It is found that the employment of carbonate solvents enhances the ionic conductivity and decreases the viscosity of the electrolyte. At the same time, the addition of lithium salt plays a key role in the stabilization of the operating potential window and the modification of the passivation layer on the electrode. As a result, increased specific capacitance, improved cycle stability, and rate capability are demonstrated in the EDLC with an EMI-BF4/LiPF6/PC/DMC electrolyte at the upper voltage of 3 V, in contrast to that with pure IL and IL/carbonate mixture. This study primarily stresses the combination effect of Li salt and organic solvent in an IL electrolyte system for constructing advanced 3 V-class EDLC with excellent overall performance.
Performance Evaluation of BD Phoenix NMIC-413 Antimicrobial Susceptibility Testing Panel for Imipenem, Meropenem, and Ertapenem Against Clinical Carbapenem-Resistant and Carbapenem-Susceptible Enterobacterales
Authors: Zhang Jingjia , Jia Peiyao , Zhu Ying , Zhang Ge , Xu Yingchun , Yang Qiwen
Published: April 2021

Purpose: The infection of carbapenem-resistant Enterobacterales (CRE) has become a major clinical and healthcare problem worldwide. The screening methods of CRE have been extensively developed but still need improving [e.g., tests with accurate and simple minimum inhibitory (MICs)]. In this study, the performance of the BD Phoenix NMIC-413 AST panel was evaluated against clinical CRE and carbapenem-susceptible Enterobacterales (CSE) in China. The panel was first evaluated in the Chinese clinical lab.

Methods: Antimicrobial susceptibility testing of 303 clinical Enterobacterales isolates were conducted by broth microdilution (BMD), Phoenix NMIC-413 AST panel, and disk diffusion method for imipenem, ertapenem, and meropenem. Considering BMD is a gold standard, essential agreement (EA), categorical agreement (CA), minor error (MIE), major error (ME), and very major error (VME) were determined according to CLSI guidelines. CA and EA > 90%, ME <3%, and VME <1.5% were considered as acceptable criteria. Polymerase chain reaction and sanger sequencing were performed to determine the β-lactamase genotypes of CRE isolates.

Results: Three hundred and three isolates included 195 CREs and 108 CSEs were enrolled according to the BMD-MIC values of three carbapenems. Tested CREs showing 100 blaKPC−2-positive organisms, 31 blaIMP-positive organisms, 28 blaNDM-positive organisms, 5 blaVIM-positive organisms, 2 both blaIMP and blaVIM-positive organisms, 2 blaOXA−48-positive organisms, and 27 isolates without carbapenemase genes. For the Phoenix NMIC-413 method, CA and EA rates >93%, MIE rates <5%, ME rates <1.75%, and VME rates were 0%, across the three drugs. For the disk diffusion method, the CA rates for three drugs were all >93%, while the MIE and ME rates were all <5 and <3%, respectively. VME rate was 3.28% for imipenem, exceeded the cut-off value specified by CLSI M52, 0 and 0.56% for ertapenem and meropenem, separately.

Conclusion: Based on the genomic data, the detection of CRE and CSE was more reliable using the BD Phoenix NMIC-413 panel compared to the BMD and disk approaches. Therefore, our study supports the use of BD Phoenix NMIC-413 panel as a suitable alternative to BMD for the detection of carbapenem resistant isolates in a clinical setting.
Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information
Authors: Droste Julian , Rückert Christian , Kalinowski Jörn , Hamed Mohamed Belal , Anné Jozef , Simoens Kenneth , Bernaerts Kristel , Economou Anastassios , Busche Tobias
Published: April 2021

Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5′-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5′ untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5′-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5′-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.
Evaluation of Phenolic Root Exudates as Stimulants of Saptrophic Fungi in the Rhizosphere
Authors: Clocchiatti Anna , Hannula S. Emilia , van den Berg Marlies , Hundscheid Maria P. J. , de Boer Wietse
Published: April 2021

The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.
Alleviation of Salinity Stress in Peanut by Application of Endophytic Bacteria
Authors: Pal Kamal K. , Dey Rinku , Sherathia Dharmesh N. , Devidayal  , Mangalassery Shamsudheen , Kumar Arvind , Rupapara Rupal B. , Mandaliya Mona , Rawal Priya , Bhadania Roshani A. , Thomas Manesh , Patel Mili B. , Maida Priyanka , Nawade Bhagwat D. , Ahmad Suhail , Dash Pitabas , Radhakrishnan T.
Published: April 2021

The development of salinity affects 7% of the world’s land surface, acting as a major constraint to crop productivity. This study attempted to use the co-evolving endophytes of peanut to alleviate salinity stress and enhance the yield of peanut. Diverse and different tissue colonizing endophytes were isolated from peanut and screenedin vitroby seed germination bioassay imposing gradients of salinity, with two cultivars TG37A (susceptible) and GG2 (moderately resistant), in potted conditions using saline irrigation water. Finally, nine endophytes capable of producing IAA and ACC-deaminase, promoting root growth and yield in potted conditions were selected for further evaluation in field conditions. They were evaluated with saline water (1.5–2.0 dS/m) in saline soil with susceptible cultivar TG37A. Simultaneously, three endophytes (Bacillus firmusJ22N;Bacillus tequilensisSEN15N; andBacillussp. REN51N) were evaluated with two cultivars, GG2 and TG37A, during rainy and post-rainy seasons with elevated salinity. The application of endophytes likeBacillus firmusJ22N andBacillussp. REN51N enhanced the pod and haulm yield of peanuts by 14–19% across cultivars, salinity, and seasons. In addition, there was significant modulation in parameters like relative water content; production of enzymes like superoxide dismutase (SOD), glutathione reductase (GR), catalase (CAT), ascorbate peroxidase (APX), lipid peroxidase (POD), and H2O2content in leaf; and uptake of potassium. The activities of the enzymes involved in scavenging reactive oxygen species (ROS) increased with salinity, and further increased with endophytes likeBacillus firmusJ22N,Bacillus tequilensisSEN15N, andBacillussp. REN51N. There was an enhanced accumulation of proline, reduced level of phenol and H2O2, and enhanced uptake of potassium with the inoculation of endophytes. This improved scavenging capacity of plants by endophytic modulation of ROS scavengers, uptake of K, production of ACC deaminase and IAA, root and biomass growth, modulation in relative water content, and enhanced accumulation of osmoprotectant might be the reasons of alleviation of salinity stress. Endophytes could have alleviated salinity stress in peanuts, indicating the mechanisms and potential of peanuts at the field level. These endophytes could be applied to bring agricultural sustainability to salinity-affected areas in the future. Furthermore, few genera viz.Kocuria,Brevundimonas,Agrococcus,Dietzia, andKytococcuswere observed in peanut tissue for the first time.
Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas
Authors: Mavrodi Olga V. , McWilliams Janiece R. , Peter Jacob O. , Berim Anna , Hassan Karl A. , Elbourne Liam D. H. , LeTourneau Melissa K. , Gang David R. , Paulsen Ian T. , Weller David M. , Thomashow Linda S. , Flynt Alex S. , Mavrodi Dmitri V.
Published: April 2021

Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of thePseudomonas fluorescensgroup andBrachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates ofB. distachyonand demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for thePseudomonasstrains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation ofP. fluorescensto the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.