bluuebunny/crossref_metadata_2025 huggingface dataset:
HUKUM PEMBERIAN GANTI KERUGIAN TERHADAP PENUMPANG DALAM KECELAKAAN PESAWAT UDARA SIPIL INDONESIA DAN KEWAJIBAN ASURANSI OLEH MASKAPAI PENERBANGAN BERDASARKAN UNDANG-UNDANG NO.1 TAHUN 2009 TENTANG PENERBANG
Authors: Dewi Anggraeni Rosliana , Gultom Potler
Published: September 2024

Penelitian ini mengkaji tanggung jawab hukum maskapai penerbangan terhadap penumpang dalam kecelakaan pesawat udara sipil di Indonesia, dengan fokus pada kewajiban asuransi yang diatur dalam Undang-Undang No. 1 Tahun 2009 tentang Penerbangan. Seiring dengan pesatnya pertumbuhan industri penerbangan dan meningkatnya permintaan jasa transportasi udara, perlindungan terhadap penumpang menjadi isu yang sangat penting, khususnya terkait dengan ganti rugi atas kerugian yang ditimbulkan oleh kecelakaan pesawat. Penelitian ini bertujuan untuk menganalisis peraturan yang mengatur tanggung jawab maskapai penerbangan serta pelaksanaan ganti rugi bagi penumpang yang mengalami kematian, cedera, atau kerugian lainnya akibat kecelakaan penerbangan. Penelitian ini juga menyoroti peran asuransi dalam mengurangi risiko serta tantangan yang dihadapi dalam penyelesaian klaim, termasuk kendala yang sering kali menyebabkan ketidakpuasan penumpang. Metodologi yang digunakan bersifat deskriptif-analitis dengan pendekatan yuridis normatif, berdasarkan studi peraturan perundang-undangan dan wawasan praktis. Hasil penelitian menunjukkan bahwa meskipun kewajiban asuransi telah diatur, terdapat celah signifikan dalam penegakan klaim ganti rugi penumpang yang sering merugikan mereka. Hal ini menekankan perlunya kerangka hukum yang lebih kuat dan mekanisme yang lebih baik untuk memastikan hak-hak penumpang terlindungi secara memadai, serta agar klaim asuransi dapat diproses secara efisien dan adil.
POSSIBILITIES OF CHATGPT AS A THIRD PARTICIPANT IN A CONFLICT SITUATION BETWEEN SCHOOL STUDENTS
Authors:   Pavlodar Pedagogical University named after Alkey Margulan, Tezekbaev Alibek
Published: September 2024

The article concentrates on the communicative potential of ChatGPT in a conflict speech situation with school student participants. The results of the pragmatic analysis show that ChatGPT has the ability to determine the timing of the involving into dialogue between the main communicators if it is given permission for that by the participants in the process of communication. However, due to his capabilities, it cannot resolve the dispute between communicants on its own; it only offers widespreaded options for resolving the dispute. The final decision will be stayed by the main communicators. Based on ChatGPT responses in examples related to conflict situations among school students, we have identified an algorithm for generating chat remarks in a dispute. It was conducted a number of queries in order to identify the communicative role of ChatGPT, and made an attempt to study its role status as a third participant ‒ a mediator. The theoretical and practical significance of this research is studying the possibility of using ChatGPT in some conflict situations among school students.
Experimental marketing at pondok pesantren Indonesia
Authors: Wahyuni Sri Intan , Kurnia Fitri Melisa , Hayati Syarifatul
Published: September 2024

One of the objectives of this reaserch is to find out how Experiential Marketing is impelented at Pondok Pesantren. Judging from the growth and development experienced by Pondok Pesantren Syafa’aturrasul from 2018 to 2022, public interest continues to increase, so that the number of students at Pondok Pesantren Syafa’aturrasul currently stands at 1500 students. Seeing this potential, the researcher was interested in conducting research on experiential marketing conducted by Pondok Pesantren This research is a qualitative descriptive study using triangulation to test the validity of the data. The data collection techniques are interviews, observation, documentation and questionnaires. Based on data analysis, strategies for implementing experiential marketing, namely in terms of sense, feel, think, act and relate marketing. The result of data analysis show that Pondok Pesantren  implements experiential marketing well.
Pelvic Rocking and Back Rub Can Reduce Back Pain in Third Trimester Pregnant Women
Authors: Rahmadania Elmi , Elly Nur , . Asmawati
Published: September 2024

Background: Back pain is the most common complaint among third-trimester pregnant women.
Objective: The purpose of this study was to determine the effect of pelvic rocking and backrub on the intensity of back pain in third-trimester pregnant women.
Methodology: This type of research is a quasi-experiment with a control group. The sample size was 52 third-trimester pregnant women who participated in the antenatal care program at the community health center in Bengkulu City. The sample was divided into the intervention group and the control group, each of 26 pregnant women. The sampling technique used purposive sampling. The instrument used to measure back pain is the numerical rating scale (NRS). The intervention group was given a combination of pelvic rocking and backrub while the control group was given pelvic tilt. Both groups were given treatment once for four consecutive days. The pain intensity has been evaluated on the first day (pre-test) and the fourth day of the post test. The data analysis used is the Mann-Whitney U test.
Results: There is a significant difference in the decreased pain scale before and after treatment between the intervention group 4.19 with (P-value = 0.000) and the control group 2.38 (P-value = 0.002).
Conclusion: Pelvic rocking and backrub are effective techniques to lower back pain intensity in pregnant women in their trimester.

Keywords: Backrub, Pregnant women, Back pain, Pelvic rocking, Pelvic tilt
The Influence of Leadership and Organizational Culture on Employee Performance Mediated by Interpersonal Communication
Authors: Sugiyanto Eko , Ekowati Sri , Finthariasari Meilaty , Harini Ririn , Yuniarti Rina , Pitra Ahmad
Published: September 2024

The purpose of this research is to answer and solve the research problems outlined above, including the following: to analyze the influence of leadership, organizational culture, and interpersonal communication on employee performance; the impact of leadership on employee performance; the effect of organizational culture on employee performance; and the role of interpersonal communication in mediating the relationship between leadership and organizational culture on employee performance. In this research, the method used is quantitative. The population used in this study consisted of all Civil Servants in South Bengkulu Regency, totaling 5,617 individuals. Based on the results of the sample calculation, the minimum sample size to be used in this study is 365 samples. The research concludes that leadership has a positive effect on interpersonal communication, organizational culture positively affects interpersonal communication and interpersonal communication influences employee performance. Additionally, leadership and organizational culture also have a positive impact on employee performance, and interpersonal communication can mediate this relationship.
Bio-Synthesis of AgNPs and MnNPs of Philodendron giganteum Herbal Extract and catalysis’s activity
Authors: V Lokhande Manohar , R. Kokate Priyaka , M. Sapkale Khushi , M. Tendulkar Mitali , Gond Ankita , Parkar Akansha , Redkar Snehal , Dighe Tejal , Gurav Gaurang , P Shukla Piyush
Published: September 2024

We are presenting our successful bio-synthesis of silver nanoparticles (AgNPs) and manganese nanoparticles (MnNPs) using aqueous extracts from the leaves of P. giganteum, a plant native to India. The aqueous extract from P. giganteum serves as a bio-reductant, facilitating the conversion of Ag⁺ to Ag⁰ during incubation in a dark environment. UV–Vis characterization revealed surface plasmon resonance peaks for AgNPs in the wavelength range of 410–460nm. Scanning electron microscopy energy-dispersive X-ray spectrometry (SEM-EDS) confirmed the agglomeration and spherical shapes of AgNPs and MnNPs with diameters ranging from 18-54nm. The TEM and X-ray diffraction shows that both the nanoparticle is crystalline in nature and AgNPs particles are fcc crystalline in nature. The outstanding catalytic activity of AgNPs was demonstrated by employing the reduction of 4-nitrophenol to 4-aminophenol.
Gall Bladder Stones – Treated by Spiritual Healing by Rajyoga
Authors: Dr. Suraj Kumar Brahma Kumar , Kumar Jogander Singh Brahma , Nayak Dr. Chaya , Gupta Ritika
Published: September 2024

This is a case report of female reported of gall stones indicated for surgery. Therapy of spiritual healing with positive energy and vibrations was applied to her with proper healthy routine with asanas, pranayama and meditation, and she healed without any surgery. A plan with four therapies was applied on her, she uses to meditate and do Rajyoga for an hour everyday. She used to charge the water with positive energy to drink that is pure, and healing happened and eat energized food with these thoughts as they say “Jaisa ann waisa mann”.
Niosomal-based Drug Delivery System: A Novel Target Strategy for the Treatment of Arthritis
Authors: A. Mandal Priyanka , N. Dhoble Nilakshi , Padole Nitin , Dhapke Pankaj , R. Baheti Jagdish
Published: September 2024

Arthritis is one or more joints that are swollen and sore. Joint stiffness and pain are the primary symptoms of arthritis, and they usually get worse with age. The two most common types of arthritis are osteoarthritis and rheumatoid arthritis. The firm, slick substance called cartilage, which covers the ends of bones where they meet to create joints, deteriorates as a result of osteoarthritis. The illness known as rheumatoid arthritis occurs when the body's immune system targets the joints, starting with the joint lining. Niosomal drug delivery system is one of the best examples of great evolution in drug delivery technology. The main composition of niosomes is cholesterol and non-ionic surfactants which act as penetration enhancers. Cholesterol also stabilizes the niosomes membrane. The idea of incorporating drugs into niosomes reduces the toxicity and side effects of the drugs and directs them toward a specific site. Niosomes appear to be a well-preferred drug delivery system over other dosage forms as niosomes are mostly stable in nature and economic. This study describes a more effective and efficient strategy to deliver the drug via the transdermal route at the affected joint area for a prolonged period to treat effectively the inflammation and other associated symptoms or progression of cartilage degradation associated with arthritis.
A Survey of Medicinal Plants on Acharya Prafulla Chandra College Campus
Authors:   Department of Botany, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India., Sarkar Bhanumati , Polley Sangram ,   Department of Zoology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India., Halder Nikhil Chandra ,   Department of Botany, Uluberia College, Uluberia, Howrah, West Bengal, Pin–711315, India., Biswas Goutam ,   Department of Zoology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India., Das Nilanjan ,   Department of Zoology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India., Ganguly Snigdha ,   Department of Zoology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India., Madhu Nithar Ranjan ,   Department of Zoology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata-700131, West Bengal, India.
Published: September 2024

A survey of medicinal plants was undertaken on the campus of Acharya Prafulla Chandra College in New Barrackpore, Kolkata, West Bengal, India. The study included in-depth field visits and observations of the surrounding outdoor spaces as well as the medicinal plant garden. The well-organized recording of the plant species by the research work means that the traditional knowledge is conserved and the basis for further scientific research is laid. The medicinal garden is made by going to the field to find and categorize plant species, talking with the old aged Kaviraj all over West Bengal to get their opinions and a review of the existing literature to put the findings into perspective with the help of the Government of West Bengal, Department of Higher Education, Science & Technology and Biotechnology (Science & Technology Branch and Biotechnology Branch). The study is designed to list the different species of medicinal flora that are identified in the conventional knowledge, traditional application and pharmacological properties. One hundred fourteen (114) different species of medical plants were recorded in the designated medicinal plant garden. The medicinal properties of the plants that were recorded included anti-bacterial, anti-cancer, anti-diabetic, anti-viral, anti-fungal, antidote, anthelminthic, and anti-analgesic qualities. These properties were found to be efficacious in treating a variety of ailments, including colds, coughs, ulcers, diarrhea, skin conditions, and snakebite. This survey draws attention to the possibility that, in the ensuing decades, some species may become endangered on college campuses. Thus, the campus can be considered a great source for both education and medicinal aspects. The purpose of this survey’s results is to offer Acharya Prafulla Chandra College students insightful information on the medicinal plants on campus. It also highlights the significance of conservation efforts in maintaining these bioresources for therapeutic purposes. Furthermore, the survey research also covers the conservation status of these plants and proposes methods for their sustainable use and protection.
Autism-related dietary preferences mediate autism-gut microbiome associations
Authors: Yap Chloe
Published: September 2024

There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.
Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically underappreciated)
Authors: Eisen Jonathan
Published: September 2024

Panel discussion with Jonathan Eisen, Clara Belzer, and Rick Bushman, chaired by Nicola Segata, following Jonathan Eisen's Keynote talk Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically underappreciated)
Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2’-fucosyllactose utilization can be facilitated by co-existing species
Authors: Lou Clare
Published: September 2024

Human milk oligosaccharides (HMOs) ensure proper infant gut microbiome establishment. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigated microbiome responses to 2'-fucosyllactose (2’FL), a prevalent HMO and infant formula additive, by establishing individualized microbiomes using fecal samples from three different infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2’FL. Using metagenomic data, we predicted that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2’FL breakdown, thus critical for B. breve’s growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2’FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrated that HMO utilization can vary with an individual’s microbiome.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.03.10.532136v1
Achieving pan-microbiome biological insights via the dbBact knowledge base
Authors: Shental Noam
Published: September 2024

Microbiome 16S rRNA studies have examined diverse habitats, including oceans, soil, plants, animals, and large cross-sectional human studies. However, finding commonalities between different experiments, habitats, or conditions is very difficult due to technical issues related to using different primer pairs and relying on taxonomy for scientific reporting. Hence, grosso modo, the 16S rRNA microbiome literature has not been integrated into a collaborative body of knowledge. It often comprises effectively isolated studies, where researchers may be completely unaware of commonalities between their findings and those in other studies, especially across different niches or habitats. In the past five years, we have created dbBact (www.dbbact.org), a knowledge base, to bridge this gap and lay the groundwork for gaining core pan-microbiome insights. Briefly, amplicon sequence variants (ASVs) from datasets of published papers are manually analyzed, and bacterial sequences associated with experimental conditions are uploaded to dbBact, together with ontology-based characterizations (e.g., “the abundance of sequence ACTGGA… was higher in fecal samples of horses with colitis compared to healthy controls in California”). To date, dbBact contains data from more than 1000 published studies across diverse habitats, spanning  370,000 unique 16S rRNA ASVs, with approximately 1,500,000 sequence-to-phenotype associations. We demonstrated how dbBact provides many types of novel hypotheses that cannot be formulated by standard methods (Amir et al., Nucleic Acids Research, 2023). We will show how dbBact may be (1) applied as part of microbiome research in any niche; (2) allow a new type of meta-analysis; and (3) be harnessed to answer ecological questions.

Link to publication: https://academic.oup.com/nar/article/51/13/6593/7199329?login=true
Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease
Authors: Salamzade Rauf
Published: September 2024

Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes.

Link to OA paper: https://journals.asm.org/doi/10.1128/spectrum.03578-22
Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity
Authors: Peng Ye
Published: September 2024

Childhood obesity is linked to maternal smoking during pregnancy. Gut microbiota may partially mediate this association and could be potential targets for intervention; however, its role is understudied. We included 1,592 infants from the Canadian Healthy Infants Longitudinal Development Cohort. Data on environmental exposure and lifestyle factors were collected prenatally and throughout the first three years. Weight outcomes were measured at one and three years of age. Stool samples collected at 3 and 12 months were analyzed by sequencing the V4 region of 16S rRNA to profile microbial compositions and magnetic resonance spectroscopy to quantify the metabolites. We showed that quitting smoking during pregnancy did not lower the risk of offspring being overweight. However, exclusive breastfeeding until the third month of age may alleviate these risks. We also reported that maternal smoking during pregnancy significantly increased Firmicutes abundance and diversity. We further revealed that Firmicutes diversity mediates the elevated risk of childhood overweight and obesity linked to maternal prenatal smoking. This effect possibly occurs through excessive microbial butyrate production. These findings add to the evidence that women should quit smoking before their pregnancies to prevent microbiome-mediated childhood overweight and obesity risk, and indicate the potential obesogenic role of excessive butyrate production in early life.

Link to OA paper: https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2323234
Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing
Authors: Marquet Mike
Published: September 2024

Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes, and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (higher than 90%), decreasing the overall microbial resolution. Nanopore’s adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation.
Genetic Diversity of the Chlorhexidine Resistance in Cultivable Bacteria Isolated from a Medical Intensive Care Unit Environment
Authors: Weng Sherlyn
Published: September 2024

The emergence of resistance to biocides is a critical concern in healthcare settings, severely limiting our ability to prevent infection. Chlorhexidine is one of the most widely used disinfectants in the medical intensive care units (MICU) since the 1950s . It is usually applied onto the skin of the patients and health care providers and acts against a wide range of bacteria by disrupting the cell membrane of the bacterial cell wall. However, studies have shown that the exposure to sub-lethal chlorhexidine concentrations may enhance resistance in species well known for emerging antibiotic resistance . To understand the genomic diversity of chlorhexidine tolerance in a high-priority environment, we surveyed an MICU for cultivable organisms demonstrating chlorhexidine resistance and performed whole genome sequencing on selected isolates. We collected 219 swab samples from different locations (e.g. nurse calls, keyboards, bed rails, etc) over two sampling events. The samples were then subjected to cultivation, morphological characterization and selective media screening, resulting in 1415 isolates, of which 308 isolates (21.8%) were able to grow on agar containing 18.75 µg/mL chlorhexidine digluconate. We take a comparative genomics approach to identifying genes related to chlorhexidine resistance by comparing genomes of the same species with different chlorhexidine susceptibility. Future work will focus on testing cross-resistance between chlorhexidine and clinically relevant antibiotics in the collected isolates. As the hospital microbiome can serve as a source of antibiotic-resistant bacteria, contributing to hospital-acquired infections, the genetic characterization of chlorhexidine-resistant organisms at environmental locations within the MICU has important implications for disinfection and patient safety, as well as advancing our basic understanding of resistance to this widely used disinfectant.
Widespread within-person adaptation in the human gut microbiome
Authors: Zhang Anni
Published: September 2024

Gut microbiota plays an essential role in regulating human health. How host environment drives microbial evolution was studied in some bacterial species, however, some studies concluded long-term purifying selection while others demonstrated evidence of adaptation. To address this problem, we broadly investigated the within-person evolution of 64 gut commensal species in healthy subjects. We found that most (24 of 27) species with sufficient genetic variation underwent recent adaptation, evidenced by parallel evolution (PE). This finding was supported by three lines of evidence on PE mutations (significantly more than expected, significantly higher dN/dS, significant enrichment of truncations). Moreover, signal transduction pathways underwent the strongest and most widespread positive selection. One striking example is an HTH-type transcriptional regulator (msmR) regulating carbohydrate transportation that underwent widespread PE in six species across 28 people, potentially driven by host diet changes. We resolved the previous debate of gut microbiota evolution showing widespread within-host adaptation, and identified adaptive mutations to guide precise microbiome manipulations.
Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1
Authors: Degraeve Alexandra Louise
Published: September 2024

Background. Following solid organ transplantation, tacrolimus (TAC) is an essential drug in the immunosuppressive strategy. Its use constitutes a challenge due to its narrow therapeutic index and its high inter- and intra- pharmacokinetic (PK) variability. As the contribution of the gut microbiota to drug metabolism is now emerging, it might be explored as one of the factors explaining TAC PK variability. Herein, we studied the contribution of the gut microbiota to TAC PK, using a combination of in vivo and in vitro models. Results. TAC oral administration was performed in mice. Compared to controls, mice with a lower intestinal microbial load due to antibiotics administration exhibit a 33% reduction in TAC whole blood exposure and a lower inter-individual variability. This reduction in TAC levels was strongly correlated with higher expression of the efflux transporter ABCB1 (also known as the p-glycoprotein (P-gp) or the multidrug resistance protein 1 (MDR1)) in the small intestine. Conventionalization of germ-free mice confirmed the ability of the gut microbiota to downregulate ABCB1 expression in a site-specific fashion. The functional inhibition of ABCB1 in vivo by zosuquidar formally established the implication of this efflux transporter in the modulation of TAC PK by the gut microbiota. Furthermore, we showed that polar bacterial metabolites could recapitulate the transcriptional regulation of ABCB1 by the gut microbiota, without affecting its functionality. Finally, whole transcriptome analyses pinpointed, among others, the Constitutive Androstane Receptor (CAR) as a transcription factor likely to mediate the impact of the gut microbiota on ABCB1 transcriptional regulation. Conclusions. We highlight for the first time how the modulation of ABCB1 expression by bacterial metabolites results in changes in TAC PK, affecting not only blood levels but also the inter-individual variability. More broadly, considering the high number of drugs with unexplained PK variability transported by ABCB1, our work is of clinical importance and paves the way for incorporating the gut microbiota in prediction algorithms for dosage of such drugs.

Link to OA paper: http://dx.doi.org/10.1186/s40168-023-01578-y
Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits
Authors: Shiroma Hirotsugu
Published: September 2024

Accumulating evidence indicates that the gut microbiome and metabolites are associated with colorectal cancer (CRC). However, the influence of surgery for CRC treatment on the gut microbiome and metabolites and how it relates to CRC risk in postoperative CRC patients remain partially understood. Here, we collected 170 fecal samples from 85 CRC patients pre- and approximately 1 year postsurgery and performed shotgun metagenomic sequencing and capillary electrophoresis-time of flight mass spectrometry (CE-TOFMS)-based metabolomics analyses to characterize alterations between pre- and postsurgery. We determined that the relative abundance of 114 species was altered postsurgery (P lower than 0.005). CRC-associated species, such as Fusobacterium nucleatum, were decreased postsurgery. On the other hand, Clostridium scindens, carcinogenesis-associated deoxycholate (DCA)-producing species, and its biotransformed genes (bai operon) were increased postsurgery. The concentration of 60 fecal metabolites was also altered postsurgery (P lower than 0.005). Two bile acids, cholate and DCA, were increased postsurgery. We developed methods to estimate postoperative CRC risk based on the gut microbiome and metabolomic compositions using a random forest machine-learning algorithm that classifies large adenoma or early-stage CRC and healthy controls from publicly available data sets. We applied methods to preoperative samples and then compared the estimated CRC risk between the two groups according to the presence of large adenoma or tumors 5 years postsurgery (P lower than 0.05). Overall, our results show that the gut microbiome and metabolites dynamically change from pre- to postsurgery. In postoperative CRC patients, potential CRC risk derived from gut microbiome and metabolites still remains, which indicates the importance of follow-up assessments.

Link to OA paper: https://journals.asm.org/doi/10.1128/msystems.00018-22
Reporting guidelines for human microbiome research: the STORMS checklist
Authors: Mirzayi Chloe
Published: September 2024

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called Strengthening The Organization and Reporting of Microbiome Studies (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Link to OA paper: https://www.nature.com/articles/s41591-021-01552-x
Variation and transmission of the human gut microbiota across multiple familial generations
Authors: Colomer Mireia Vallès
Published: September 2024

Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother–daughter pairs, decreasing with increasing daughter’s age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.

Link to the OA paper: https://www.nature.com/articles/s41564-021-01021-8
Microbial diversity in aquaculture ecosystems: insights into insect-based feed formulation for sustainable fish farming
Authors: Bruno Antonia
Published: September 2024

Aquaculture, an ancient practice deeply rooted in traditional knowledge, has experienced a recent surge in growth, presenting sustainability challenges. Sustainable aquaculture hinges on several factors, including the well-being of farmed fish, water quality, and feeds. A crucial step toward enhancing sustainability in aquaculture is the transition from fishmeal to alternative protein sources. Extensive research has focused on assessing innovative feed formulations, particularly their impact on the fish gut microbiome. However, limited studies have investigated the microbiome of the aquaculture built environment and host-environment microbiome interactions.
Here, we explored the aquaculture ecosystem microbiome when insect-based novel feed formulations are administered. Using 16S rRNA gene metabarcoding, we conducted a comprehensive analysis of microbiomes across water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples.
Our results showed that overall, water and the aquaculture built environment were characterised by an astounding microbial diversity.
Core microbiome analysis unveiled a highly reduced core shared among all sample sources, in both the control and novel feed test groups.
Network analysis demonstrated sample clustering based on sample source, with no significant variations tied to the feed formulation. Consequently, the different diets did not appear to impact the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. For a more detailed examination of the feed's contribution, we conducted a differential abundance analysis, revealing distinct enrichment/depletion of specific taxa when comparing the control to the insect-based diet group.
The results of this study highlight how the aquaculture environment is a unique source of microbes, able to colonise fish. Omic exploration of the water-fish interface exposes patterns that are otherwise undetected: subtle but significant differences in the abundance of specific taxa are exerted by feed. A comprehensive grasp of aquaculture ecosystems as holobiomes is vital to design the built environment and modulate the microbial communities that are hosted for sustainable aquaculture.
Different Effects of Mineral Versus Vegetal Granular Activated Carbon Filters on the Microbial Community Composition of a Drinking Water Treatment Plant
Authors: Bruno Antonia
Published: September 2024

Drinking water quality and safety is strictly regulated and constantly monitored, but little is known about the microorganisms inhabiting drinking water treatment plants (DWTPs). This lack of knowledge prevents optimization of designs and operational controls. Here we investigated the drinking water microbial community harbored by a groundwater-derived DWTP, involving mineral and vegetal granular activated carbon filters (GACs). We used 16S rRNA gene sequencing to analyze water microbiome variations through the potabilization process, considering (i) different GAC materials and (ii) time from GAC regeneration. Our results revealed the predominance of Cand. Patescibacteria, uncultivable bacteria with limited metabolic capacities and small genomes, from source to downstream water. Microbial communities clustered per sampling date, with the noteworthy exception of groundwater samples. If the groundwater microbiome showed no significant variations over time, the community structure of water downstream GACs (both mineral and vegetal) seemed to be affected by time from GAC regeneration. Looking at a finer scale, different GAC material affected microbiome assembly over time with significant variation in the relative abundances of specific taxa. The significance of our research is in identifying the environmental microorganisms intrinsic of deep groundwater and the community shift after the perturbations induced by potabilization processes. Which microorganisms colonize different GACs and become abundant after GACs regeneration and over time is a first step toward advanced control of microbial communities, improving drinking water safety and management of operational costs.

Link to OA paper: https://www.frontiersin.org/articles/10.3389/fevo.2021.615513/full
Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis
Authors: Holman Johanna M
Published: September 2024

Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, affordable, and safe for managing symptoms. Ongoing research has identified inactive compounds in broccoli sprouts, like glucoraphanin, and that mammalian gut microbiota play a role in metabolizing it to the anti-inflammatory sulforaphane. The objectives were to identify biogeographic location of participating microbiota and correlate that to health outcomes. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 40-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, fecal lipocalin, and sequenced bacterial communities from the contents and mucosa in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet while receiving DSS performed better than mice fed the control diet while receiving DSS for all disease parameters, including significantly more weight gain (2-way ANOVA, p lower than 0.05), lower Disease Activity Index scores (2-way ANOVA, p lower than 0.001), and higher bacterial richness in all gut locations (linear regression model, p lower than 0.01 for all locations measured). Bacterial communities were assorted by gut location except in the mice receiving the control diet and DSS treatment (Beta-diversity, ANOVA, p lower than 0.05 for each). Importantly, our results suggested that broccoli sprout feeding completely abrogated the effects of DSS on gut microbiota, as bacterial communities were similar between mice receiving broccoli sprouts with and without DSS. Spatially resolved microbial communities provide greater insight when investigating host-microbe interactions. Here, we show that a 10% broccoli sprout diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis.

Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.01.27.522641v2
Rapid and accurate identification of ribosomal RNA sequences using deep learning
Authors: Deng Zhi Luo
Published: September 2024

Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences do not include polyadenylation, these cannot be easily removed in library preparation, requiring their post-hoc removal with computational techniques to accelerate and improve downstream analyses. Here we describe RiboDetector, a novel software based on a Bi-directional Long Short-Term Memory (BiLSTM) neural network, which rapidly and accurately identifies rRNA reads from transcriptomic, metagenomic, metatranscriptomic, noncoding RNA, and ribosome profiling sequence data. Compared with state-of-the-art approaches, Ribodetector can produce one order of magnitude fewer misclassifications. Importantly, the few false positives of RiboDetector on the benchmark dataset were not enriched in certain Gene Ontology (GO) terms, suggesting a low bias for downstream functional profiling. RiboDetector also demonstrated a remarkable generalization ability for detecting novel rRNA sequences divergent from the training data with sequence identities of less than 90%. On a personal computer, RiboDetector can process 40M reads in less than 6 minutes, which is about 50 times faster in GPU mode and about 15 times in CPU mode than other methods.

RiboDetector is available under a GPL v3.0 license at https://github.com/hzi-bifo/RiboDetector.
THE BOOK AS A COGNITIVE TOOL IN "AN INVENTORY OF LOSSES" BY J. SHALANSKY
Authors: SIAMCHONAK L.
Published: September 2024

The article gives a brief characteristic of the work of modern German author Judith Schalansky, analyses the composition and problematics of her narrative book "An Inventory of Losses". The author's graphic design finds in the decoration of the book, helping to comprehensively expose the declared theme of loss as an integral part of life, are noted. It is concluded that the stories presented in the book with all their genre diversity are united both by a common theme and associative threads by means of cross-cutting images and motives.
THE PRINCIPLES OF NOMINATION IN THE BRISTOL GODONYMIC SYSTEM
Authors: PRYSHCHEPA M.
Published: September 2024

This article is the first study in which a multilateral analysis of the system of names of inner-city linear objects of Bristol has been carried out, general and particular principles of their names have been identified, and the motivational model of the city's place names has been analyzed. In the work in the corpus of Bristol urbanonyms, in accordance with the lexical and semantic model developed by onomast A.M. Mezenko, the basic principles of the nomination of objects according to their connection with a person, relation to other objects, natural and qualitative characteristics, connection with abstract concepts are highlighted. These principles are implemented through various signs, on the basis of which thematic groups are formed. From the point of view of the frequency of use of godonyms, the most common are the principles of nomination for the connection of linear objects with humans and their natural and qualitative properties (34.0%, 31.9%, respectively). The prevailing principle of the nomination for human relations includes six thematic groups, of which the dominant ones in terms of number and diversity are names motivated by the surnames of landowners and homeowners, and memorial ones.
POSITIVE FEMALE IMAGE IN GEOFFREY CHAUCER`S WRITINGS
Authors: SMULKEVICH A.
Published: September 2024

The present article studies the writings of the XIVth century English poet Geoffrey Chaucer as correlated with such literary phenomenon as «querelle des femmes», that stated female perfection. The poet disproves all traditional accusations against women in unfaithfulness and infidelity, slander, unreason by means of using examples from legends and history and using courtly canon to make ideal the image of the beloved, capable to simultaneously function as a wise adviser, a friend and a faithful spouse. G. Chaucer tends to explore the essence of Love as Universal law that can transform both men and women into such people who are ready to sacrifice their life for their beloved. According to the poet a woman is created to balance a man in such a way as to keep him from wrath, superstitions and injustice. This idea leads to the deduction that the poet expected women`s influence spread beyond private, family sphere. G. Chaucer considered that his main task was to warn both men (especially old, silly, greedy husbands) and women (gullible women should not become victims for unfaithful, deceitful men who can betray) against negative love situations. In connection to this, he called to apply empiric approach basing on experience accumulation through reading ancient sources and their critical comprehension, the example of which he provides in his own analysis of inconsistency in the wise Solomon`s actions and statements.
Discrimination and Access to Healthcare for People with Disabilities: An Integrative Literature Review
Authors: Silva Francisco Nalberth Santos , Sousa Maria Eduarda Carvalho , Lourenço Caroline Evaristo , Paiva Antônia Valéria Pereira , Monteiro Thais Correia , Grimaldi Monaliza Ribeiro Mariano
Published: September 2024

Introduction: People with disabilities face many challenges on a daily basis. Despite legislative advances and inclusion policies, discrimination against people with disabilities persists in various areas of life, including access to health services. Aim: This study aims to conduct an integrative literature review to investigate the factors associated with discrimination faced by people with disabilities in health services. Materials and Methods: The search was conducted in February 2024 in the IBECS, Lilacs, BDEnf, Medline (PubMed), Scopus, and Web of Science databases. The health descriptors (DeCS) “people with disabilities,” “social discrimination,” and “health services” were used. Original articles available in full, from the last five years, and in any language were included. The exclusion criteria were duplicate articles and those that did not answer the guiding question. Results: A total of 162 records were identified, from which 17 studies were selected, resulting in a final sample of 10 articles. The main factors associated with the discriminatory experiences faced by people with disabilities when accessing and using the health system were “stigmatization,” “negligence,” “prejudice,” and “access difficulties.” Conclusions: Significant drivers of discrimination were identified, including financial barriers, lack of training for health professionals, and other gaps that generate prejudice, stigmatization, and neglect. It is essential to implement public policies to ensure service accessibility, provide financial assistance for people with disabilities, establish training programs for health professionals, and conduct more research on this subject.