bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of vehicle carbon emissions on horizontal curve road sections
Authors: Dong Yaping , Li Tong , Xu Jinliang
Published: January 2024

The high carbon emissions of vehicles traveling on horizontal curve road sections cannot be ignored. Facing the difficulty of accurately quantifying the carbon emission of driving on horizontal curves and the unknown causes of high carbon emission, this study proposes to construct a carbon emission prediction model applicable to road sections with different planar geometries. The direct and indirect effects of horizontal curve alignment on vehicle carbon emissions are represented in the model in terms of travel stabilization and speed changes, respectively. A lateral force coefficient parameter was introduced into the model to integrate the carbon emission quantification problem for different planar geometry sections. Meanwhile, field tests were conducted to assess the reliability of the model and the research findings. The model reveals that the geometric parameters of horizontal curves that affect carbon emissions are the radius of the circular curve, the superelevation, and the length of the gentle curve. The root causes of high carbon emissions on horizontal curve road sections are curve driving resistance and speed fluctuations. Under the free-flow driving condition of the highway, the maximum curve radius affecting the carbon emissions of passenger cars and trucks is 400 m and 550 m, respectively. The research results can realize the carbon emission quantification of vehicles on the road sections with different plane geometries. Also, it is helpful to control the high carbon emission of vehicles traveling on horizontal curve road sections.
Plant communities and potential phytoremediation species for resource utilization of abandoned drilling mud
Authors: Wang Shuzhuan , Hao Mingde
Published: January 2024

Oil and gas development produces a large amount of abandoned drilling mud, which may be a source of pollution but may also be a potential resource. A quadrat sampling method was used in the Changqing Oilfield to investigate the plant community characteristics inside and outside abandoned drilling mud pits at different completion times. The importance value of plant showed that the natural succession of plant communities in the abandoned drilling mud pool could be divided into three stages: (1) 4–8 years after the completion of the well, Leymus secalinus, Calamagrostis epigeios with the importance values of more than 100, were dominant species in the initial construction stage; (2) 9–13 years after the succession, the intense competition stage of the plant community, although the importance value of plant inside the mud pit had decreased, it was still higher than the importance value of plant outside the mud pool. The importance values of L. secalinus and Artemisia scoparia outside the mud pool were 62.5 and 52.5, while those in the mud pool were 95 and 75, respectively; (3) 23–28 years after the succession, the gradual stabilization stage of the plant community, the importance value of plant was lower than that in the mud pool. Leymus secalinus, C. epigeios and A. scoparia could be used for phytoremediation of abandoned drilling soil for their higher importance values. Changes of Shannon–Wiener index, Pielou index, Community ecological dominance and vegetation biomass showed that the mud pit was suitable for the recovery and growth of the dominant species, improved the diversity of plant communities inside the mud pit compared with the stable plant community outside the mud pit. Abandoned drilling mud increased the content of nitrogen, potassium and trace elements in plants. While the variation coefficient of heavy metal content in plants inside and outside the mud pit was large, but the content of heavy metals in plants was within the normal range. Abandoned drilling mud has the potential for resource utilization on the premise of ensuring soil quality and safety. This study provides information on the comprehensive treatment, resource utilization, disposal economics and environmental safety of abandoned drilling mud.
Juvenile hormone III induction reveals key genes in general metabolism, pheromone biosynthesis, and detoxification in Eurasian spruce bark beetle
Authors: Ramakrishnan Rajarajan , Roy Amit , Hradecký Jaromír , Kai Marco , Harant Karel , Svatoš Aleš , Jirošová Anna
Published: January 2024

Introduction

In recent years, bark beetle Ips typographus, has caused extensive damage to European Norway spruce forests through widespread outbreaks. This pest employs pheromone-assisted aggregation to overcome tree defense, resulting in mass attacks on host spruce. Many morphological and behavioral processes in I. typographus are under the regulation of juvenile hormone III (JH III), including the biosynthesis of aggregation pheromones and associated detoxification monoterpene conjugates.

Objectives and Methods

In this study, we topically applied juvenile hormone III (JH III) and performed metabolomics, transcriptomics, and proteomics in I. typographus both sexes, with focused aims; 1. Highlight the JH III-regulated metabolic processes; 2. Identify pheromone biosynthesis-linked genes; and 3. Investigate JH III’s impact on detoxification conjugates linked to pheromonal components.

Results

Numerous gene families were enriched after JH III treatment, including genes associated with catalytic and oxidoreductase activity, esterases, phosphatases, and membrane transporters. Sex-specific enrichments for reproduction-related and detoxification genes in females and metabolic regulation genes in males were observed. On the protein level were enriched metal ion binding and transferase enzymes in male beetles. After JHIII treatment, mevalonate pathway genes, including terminal isoprenyl diphosphate synthase (IPDS), were exclusively 35- folds upregulated in males, providing evidence of de novo biosynthesis of pheromone components 2-methyl-3-buten-2-ol and ipsdienol. In addition, cytochrome P450 genes likely involved in the biosynthesis of cis/trans-verbenol, detoxification, and formation of ipsdienol, were 3-fold upregulated in the male gut. The increase in gene expression correlated with the heightened production of the respective metabolites. Detoxification conjugates, verbenyl oleate in the beetle fat body and verbenyl diglycosides in the gut, were induced by JHIII application, which confirms the hormone regulation of their formation. The JH III induction also increased the gene contigs esterase and glycosyl hydrolase up to proteins from male gut tissue. The esterase was proposed to release pheromone cis-verbenol in adult males by breaking down verbenyl oleate. The correlating analyses confirmed a reduction in the abundance of verbenyl oleate in the induced male beetle.

Conclusion

The data provide evidence of JH III’s regulatory role in the expression of genes and enzymes related to fundamental beetle metabolism, pheromone biosynthesis, and detoxification in Ips typographus.
Hereditary deafness carrier screening in 9,993 Chinese individuals
Authors: Liu Yanqiu , Wang Lei , Yuan Lanlai , Li Yaqing , Chen Zhengshi , Yang Bicheng , Wang Daqing , Sun Yu
Published: January 2024

Background: Preconception or prenatal carrier screening plays an important role in reproductive decision-making, but current research on hereditary deafness is limited. This study aimed to investigate the carrier frequencies of common deafness genes in the Chinese population who underwent carrier screening and to follow up on pregnancy outcomes in high-chance couples.

Methods: Individual females or couples in preconception or early pregnancy were recruited from two hospitals in China. Carrier screening for common deafness genes in the Chinese population, including the GJB2 and SLC26A4 genes, was performed using next-generation sequencing technology. Genetic counseling was provided to subjects before and after testing.

Results: Of the 9,993 subjects screened, the carrier rate was 2.86% for the GJB2 gene and 2.63% for the SLC26A4 gene. The variant with the highest carrier frequency in GJB2 was c.235delC (1.89%), and c.919–2A>G (1.08%) in SLC26A4. Of the six high-chance couples, four made alternative reproductive decisions (three with prenatal diagnosis and one with preimplantation genetic testing), with consequent termination of the birth of two affected fetuses.

Conclusion: These findings confirmed the clinical utility of preconception or prenatal carrier screening for hereditary deafness.
Age-related exacerbation of lung damage after trauma is associated with increased expression of inflammasome components
Authors: Zhou Yuzhuo , Meng Fanshuai , Köhler Kernt , Bülow Jasmin Maria , Wagner Alessa , Neunaber Claudia , Bundkirchen Katrin , Relja Borna
Published: January 2024

Background

Trauma, a significant global cause of mortality and disability, often leads to fractures and hemorrhagic shock, initiating an exaggerated inflammatory response, which harms distant organs, particularly the lungs. Elderly individuals are more vulnerable to immune dysregulation post-trauma, leading to heightened organ damage, infections, and poor health outcomes. This study investigates the role of NF-κB and inflammasomes in lung damage among aged mice post-trauma.

Methods

Twelve male C57BL/6J mice underwent hemorrhagic shock and a femoral fracture (osteotomy) with external fixation (Fx) (trauma/hemorrhage, THFx), while another 12 underwent sham procedures. Mice from young (17-26 weeks) and aged (64-72 weeks) groups (n=6) were included. After 24h, lung injury was assessed by hematoxylin-eosin staining, prosurfactant protein C (SPC) levels, HMGB1, and Muc5ac qRT-PCR. Gene expression of Nlrp3 and Il-1β, and protein levels of IL-6 and IL-1β in lung tissue and bronchoalveolar lavage fluid were determined. Levels of lung-infiltrating polymorphonuclear leukocytes (PMNL) and activated caspase-3 expression to assess apoptosis, as well as NLRP3, ASC, and Gasdermin D (GSDMD) to assess the expression of inflammasome components were analyzed via immunostaining. To investigate the role of NF-κB signaling, protein expression of phosphorylated and non-phosphorylated p50 were determined by western blot.

Results

Muc5ac, and SPC as lung protective proteins, significantly declined in THFx versus sham. THFx-aged exhibited significantly lower SPC and higher HMGB1 levels versus THFx-young. THFx significantly increased activated caspase-3 versus both sham groups, and THFx-aged had significantly more caspase-3 positive cells versus THFx-young. IL-6 significantly increased in both sham and THFx-aged groups versus corresponding young groups. THFx significantly enhanced PMNL in both groups versus corresponding sham groups. This increase was further heightened in THFx-aged versus THFx-young. Expression of p50 and phosphorylated p50 increased in all aged groups, and THFx-induced p50 phosphorylation significantly increased in THFx-aged versus THFx-young. THFx increased the expression of inflammasome markers IL-1β, NLRP3, ASC and GSDMD versus sham, and aging further amplified these changes significantly.

Conclusion

This study’s findings suggest that the aging process exacerbates the excessive inflammatory response and damage to the lung following trauma. The underlying mechanisms are associated with enhanced activation of NF-κB and increased expression of inflammasome components.
DNAJC8: a prognostic marker and potential therapeutic target for hepatocellular carcinoma
Authors: Zhang Zhibo , Ju Mingxiu , Tang Zhongming , He Zhen , Hua Shengni
Published: January 2024

Background

Hepatocellular carcinoma (HCC) is the most common type of liver cancer, accounting for ~90% of the total cases. DnaJ heat shock protein family member C8 (DNAJC8), belonging to the heat shock protein 40 (HSP40) family, is known to regulate cancer biology function. However, the role of DNAJC8 on HCC development remains unknown.

Methods

The Cancer Genome Atlas, GTEx, cBioPortal, and Human Protein Atlas were used to analyze the expression and clinical significance of DNAJC8 in HCC. Two HCC cell lines, MHCC-97H and Huh-7, were utilized to determine the biological function of DNAJC8.

Results

DNAJC8 expression was upregulated in HCC tissues and correlated with poor clinical prognosis. It was closely related to spliceosome, nucleocytoplasmic transport, and cell cycle and might be involved in the formation of tumor immunosuppressive microenvironment. Knockdown of DNAJC8 severely inhibited HCC cell proliferation and induced apoptosis.

Conclusion

Our study demonstrate that DNAJC8 functions as an oncogene in HCC and hence may be used as a potential therapeutic target and prognostic marker for HCC.
Hydrothermal activity fuels microbial sulfate reduction in deep and distal marine settings along the Arctic Mid Ocean Ridges
Authors: Roerdink Desiree L. , Vulcano Francesca , Landro Jan-Kristoffer , Moltubakk Karen E. , Babel Hannah R. , Jørgensen Steffen Leth , Baumberger Tamara , Økland Ingeborg E. , Reeves Eoghan P. , Thorseth Ingunn H. , Reigstad Laila J. , Strauss Harald , Steen Ida H.
Published: January 2024

Microbial sulfate reduction is generally limited in the deep sea compared to shallower marine environments, but cold seeps and hydrothermal systems are considered an exception. Here, we report sulfate reduction rates and geochemical data from marine sediments and hydrothermal vent fields along the Arctic Mid Ocean Ridges (AMOR), to assess the significance of basalt-hosted hydrothermal activity on sulfate reduction in a distal deep marine setting. We find that cored marine sediments do not display evidence for sulfate reduction, apart from low rates in sediments from the Knipovich Ridge. This likely reflects the overall limited availability of reactive organic matter and low sedimentation rates along the AMOR, except for areas in the vicinity of Svalbard and Bear Island. In contrast, hydrothermal samples from the Seven Sisters, Jan Mayen and Loki’s Castle vent fields all demonstrate active microbial sulfate reduction. Rates increase from a few 10s to 100s of pmol SO42- cm-3 d-1 in active high-temperature hydrothermal chimneys, to 10s of nmol SO42- cm-3 d-1 in low-temperature barite chimneys and up to 110 nmol cm-3 d-1 in diffuse venting hydrothermal sediments in the Barite field at Loki’s Castle. Pore fluid and sediment geochemical data suggest that these high rates are sustained by organic compounds from microbial mats and vent fauna as well as methane supplied by high-temperature hydrothermal fluids. However, significant variation was observed between replicate hydrothermal samples and observation of high rates in seemingly inactive barite chimneys suggests that other electron donors may be important as well. Sediment sulfur isotope signatures concur with measured rates in the Barite field and indicate that microbial sulfate reduction has occurred in the hydrothermal sediments since the recent geological past. Our findings indicate that basalt-hosted vent fields provide sufficient electron donors to support microbial sulfate reduction in high- and low-temperature hydrothermal areas in settings that otherwise show very low sulfate reduction rates.
Whole-genome survey reveals interspecific differences in genomic characteristics and evolution of Pampus fish
Authors: Zhao Xiang , Zheng Tianlun , Song Na , Qu Yinquan , Gao Tianxiang
Published: January 2024

Pampus belongs to the Perciformes, Stromateoidei, and Stromateidae and are widely distributed throughout the Indian Ocean and the Western Pacific. In this study, we employed next-generation sequencing to generate comprehensive genomic data for Pampus punctatissimus and Pampus echinogaster and subsequently compared the obtained genomic information with the published data of Pampus argenteus. P. echinogaster was identified to be the largest genome size (602 Mb), heterozygosity (1.38%), and repetitive sequence ratio (33.06%), while similar genome sizes between P. punctatissimus (540 Mb) and P. argenteus (550 Mb) were observed. A total of 402,921 and 628,298 SSRs were identified for P. punctatissimus and P. echinogaster, respectively. Additionally, 1,876, 638, and 394 single-copy homologous genes were identified from P. punctatissimus, P. echinogaster, and P. argenteus, respectively. The KEGG enrichment results of the unique single-copy genes to the three species were significantly different in genetic information processing, protein processing, and metabolic functions. The complete mitochondrial genomes of P. punctatissimus and P. echinogaster were successfully assembled, and the resulting phylogenetic relationships align with the currently reported taxonomic status of species in the Stromateoidei. Additionally, population size analysis using PSMC revealed that P. punctatissimus experienced one bottleneck effect, while P. echinogaster underwent two bottleneck events during the Pleistocene Glacial Epoch.
PcASTA in Procambarus clarkii, a novel astaxanthin gene affecting shell color
Authors: Chen Xiajun , Chen Jing , Huang Long , Wu Benli , Wu Cangcang , He Jixiang , Bai Zhiyi
Published: January 2024

The color of crayfish (Procambarus clarkii) shells not only affects their value, but also has a significant impact on individual size. Astaxanthin is a common carotenoid that has been found in many studies to have different functions, including regulating body color formation. In this study, the levels of different carotenoids were detected using high performance liquid chromatography (HPLC) and found a significant correlation between astaxanthin content and shell color. An astaxanthin gene (PcASTA) was identified from P. clarkii, and it was expressed in tissues of crayfish with dark-red shells and green shells. The highest expression levels of PcASTA were found in the hepatopancreas, followed by the muscle. The expression of PcASTA in all tissues of red shell crayfish was higher than that of green shell crayfish, indicating that PcASTA may be involved in shell color formation in crayfish. Moreover, high water temperature and feeding β-carotene can lead to an increase in tissue expression of PcASTA and astaxanthin content in crayfish shells. The findings indicate that PcASTA may affect shell color in P. clarkii by being involved in astaxanthin synthesis and transformation.
Predicting environmental biodegradability using initial rates: mineralization of cellulose, guar and their semisynthetic derivatives in wastewater and soil
Authors: Hart-Cooper William M. , Kalla Nabeel , Klamczynski Artur , Torres Lennard , Glenn Gregory M. , Cunniffe Julia , Johnson Kaj , Orts William J.
Published: January 2024

Microplastic pollution is a growing concern, and natural materials are being increasingly sought as plastic alternatives. Semisynthetic biopolymers occupy a grey area between natural and synthetic materials and are often presented as green alternatives to conventional plastic. They can be water-soluble or insoluble, and are ubiquitous in commercial products as thickeners, films, filters, viscosity modifiers and coatings. This work compares the mineralization kinetics of cellulose, guar and several of their commercialized derivatives using a simple pseudo first-order kinetic model to extrapolate half-lives and lifetimes, while identifying the levers that influence the mineralization rates of these ubiquitous materials. Industrial composting rates were consistently faster than those of wastewater. While partially substituted biopolymers exhibited measurable degradation, kinetic analysis revealed this effect could be entirely accounted for by the fraction of unsubstituted biopolymer. Surprisingly, the initial rates of highly substituted biopolymers exhibited persistence on par with conventional plastics over the experimental durations studied.
The fractured lens: a controversial revision of the International Classification of Primary Care
Authors: Soler Jean K. , Buono Nicola , Cardillo Elena , Frese Thomas , Vinker Shlomo , Ungan Mehmet
Published: January 2024

Background

The International Classification of Primary Care (ICPC) has represented the international standard reduction for measuring the content of primary care for over 30 years. In the process of its third revision, its authors, the Wonca International Classification Committee (WICC), delegated a major part of the technical work to a purposely formed Consortium. However, in the process of such revision, standard classification principles and rules have been inconsistently applied with the result that ICPC-3 has been published with major errors and an inconsistent structure.

Objectives

To formally describe and critically appraise the revision process of ICPC-3.

Methods

The formal review of ICPC-3 performed by an expert group within WICC and commissioned by the Executive Council of Wonca Europe is presented in abridged form.

Results

ICPC-3 as currently presented introduces major departures from formal classification principles and rules, besides other major errors and inconsistencies, all of which are listed and described.

Conclusion

Major changes in ICPC-3 defy categorisation and conceptualisation standards. ICPC-3 now represents an untested departure from international standard presentations, without a formal academic base. The direct inclusion of measures of functioning in a classification of reasons for encounter and health problems fails to address the dichotomy of these domains, the boundaries of and relationships between which are not satisfactorily resolved by the system. Analysis of ICPC-3 data will require the development and implementation of alternative, as yet undefined, models of the relationships between disease and health. By including different domains without resolving ambiguity, and by splitting function from other body systems, ICPC-3 becomes an internally fractured instrument.
Translation of the working alliance inventory short revised into Italian using a Delphi procedure and a forward-backward translation
Authors: Buono Nicola , Sassier Béatrice , Thulesius Hans , Hoffman Robert , Nabbe Patrice , Petek Davorina , Le Reste Jean Yves
Published: January 2024

Introduction

Enhancing treatment adherence, especially for chronic diseases, can be achieved through therapeutic alliance, potentially elevating the quality of care. An instrument to evaluate the therapeutic alliance could be beneficial in routine clinical settings, educational environments, and extensive research efforts at national and European levels. In this study, we translated therapist and patient versions of the Working Alliance Inventory Short Revised (WAI-SR) into Italian.

Methodology

An email-based Delphi method was employed for the English-to-Italian translation, incorporating a forward-backward process. The initial translation team comprised two Italian family physicians proficient in English, a linguist, and a psychiatrist. The forward translation was then reviewed by 18 Italian family physicians through a Delphi process and was subjected to a backward translation by two Italian English teachers. A cultural correspondence was subsequently identified to adjust translations within a national and international framework.

Results

All 18 experts fully engaged in the Delphi process, and consensus was achieved by the second Delphi round. A cultural check checked for discrepancies regarding linguistic consistency with other translations and found no difference.

Conclusion

This Italian translation of the WAI-SR is expected to support Italian family physicians aiming to enhance their clinical practice and therapeutic outcomes. It could also be a valuable tool for Italian medical students to foster therapeutic relationships and improve their communication skills.
Clinical application of CT-based radiomics model in differentiation between laryngeal squamous cell carcinoma and squamous cell hyperplasia
Authors: Cui Fengzhi , Khodrog Osama A. , Liu Wei , Liu Jianhua , Yuan Qinghai
Published: January 2024

Objective

To evaluate the clinical application of the CT-based radiomics prediction model for discriminating SCC and SCH.

Methods

A total of 254 clinical samples were selected from 291 patients with larynx-occupying lesions who underwent primary surgery. All lesions were validated via histopathological examination at The Second Hospital of Jilin University between June 2004 and December 2019. All patients were randomly allocated to the training (n = 177) and validation (n = 77) cohorts. After the acquisition of CT images, manual 3D tumor segmentation was performed using the CT images of the arterial, venous, and non-contrast phases via ITK-SNAP software. Subsequently, radiomics features were extracted using A.K. software. Based on the above features, three different diagnostic models (CTN, CTA+CTV, and CTN+CTA+CTV) were constructed to classify squamous cell carcinoma (SCC) and squamous cell hyperplasia (SCH). Additionally, receiver operating characteristic (ROC) and decision curve analysis (DCA) curves were measured to evaluate the diagnostic characteristics and clinical safety of the proposed three prognostic models.

Results

In the radiomic prediction Model 1 (CTN), the area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the training cohorts in differentiating SCC and SCH were 0.883, 0.785, 0.645, 1.000, 1.000, and 0.648, while in the testing cohorts, these values were 0.852, 0.792, 0.66, 1.000, 1.000, and 0.652, respectively. In the radiomic prediction Model 2 (CTA+CTV), the AUC, accuracy, sensitivity, specificity, PPV, and NPV values of the training cohorts were 0.965, 0.91, 0.916, 0.9, 0.933, and 0.875, respectively, while in the testing cohorts, the corresponding values were 0.902, 0.805, 0.851, 0.733, 0.833, and 0.759, respectively. In the radiomic prediction Model 3(CTN+CTA+CTV), the AUC, accuracy, sensitivity, specificity, PPV, and NPV values of the training cohorts were 0.985, 0.944, 0.953, 0.929, 0.953, and 0.929, while in the testing cohorts, the corresponding values were 0.965, 0.857, 0.894, 0.8, 0.875, and 0.828, respectively.

Conclusion

The radiomic prediction Model 3, based on the arterial-venous-plain combined scan phase of CT, achieved promising diagnostic performance, expected to be regarded as a preoperative imaging tool in classifying SCC and SCH to guide clinicians to develop individualized treatment programs.
Description of the vaginal microbiota in nulliparous ewes during natural mating and pregnancy: preliminary signs of the male preputial microbiota modulation
Authors: Barba Marta , Toquet Marion , García-Roselló Empar , Gomis Jesús , Quereda Juan J. , González-Torres Pedro , Carbonetto Belén , Gómez-Martín Ángel
Published: January 2024

The vaginal microbiota plays a key role in animals’ health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams’ prepuce were the same as in the ewes’ vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram’s preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes’ vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe’s reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.
Unveiling Curvularia tuberculata-induced leaf anomalies in Rhododendron ferrugineum: implications in cultural-ecological conservation and harnessing microbial intervention in socio-economic advancement
Authors: Dhar Juhita , Hazra Aishee , Patra Riddhisha , Kumar Varun , Subramaniyan Vetriselvan , Kumarasamy Vinoth , Mitra Arup Kumar , Sayed Amany A. , Aleya Lotfi , El-Demerdash Fatma M. , Almutairi Mikhlid H. , Akash Shopnil , Abdel-Daim Mohamed M. , Kant Achal , Dhara Bikram
Published: January 2024

Introduction

The research focuses on Rhododendron ferrugineum L., Nepal’s national flower and Uttarakhand’s state tree, thriving in high-altitude mountain ecosystems.

Methodology and Result

A study conducted in Himachal Pradesh (Latitude: N 31° 6’ 2.0088”, Longitude: E 77° 10’ 29.9136”) identified leaf anomalies resembling rust-like manifestations in R. ferrugineum. These anomalies were traced back to the pathogenic fungus Curvularia tuberculata, marking the first documented case of its impact on R. ferrugineum in India.

Discussion

This discovery emphasizes the need for vigilant monitoring, disease management research, and conservation efforts to protect the cultural and ecological significance of this iconic shrub. Beyond its immediate findings, the study introduces a novel dimension to Indian flora by associating C. tuberculata with R. ferrugineum, historically linked to monocotyledonous crops. The research methodology combines traditional microscopic examination with advanced genomic sequencing and phylogenetic analysis, enhancing pathogen identification accuracy.

Future prospect

In a broader context, this research aligns with the United Nations Sustainable Development Goals (SDGs) by highlighting the importance of environmental preservation, conservation, and sustainable management. It underscores the intricate interplay between biodiversity, cultural heritage, and the need for holistic solutions. Overall, this study calls for proactive measures to protect R. ferrugineum’s cultural and ecological heritage and emphasizes the significance of interdisciplinary approaches in addressing emerging ecological threats.
Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis
Authors: Esposito Roberta , Federico Serena , Sonnessa Michele , Reddel Sofia , Bertolino Marco , Ruocco Nadia , Zagami Giacomo , Giovine Marco , Pozzolini Marina , Guida Marco , Zupo Valerio , Costantini Maria
Published: January 2024

The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.
Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities
Authors: Li Maoping , Wang Suqin , Zhong Liang , Heděnec Petr , Tan Zhaoxian , Wang Rong , Chen Xinyang , Zhang Yan , Tang Bingmin , Zhou Huakun , Qu Jiapeng
Published: January 2024

Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host–bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray–Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments—only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.
Stimbiotic supplementation and xylose-rich carbohydrates modulate broiler’s capacity to ferment fibre
Authors: Davies Claire , González-Ortiz Gemma , Rinttilä Teemu , Apajalahti Juha , Alyassin Mohammad , Bedford Michael R.
Published: January 2024

Stimbiotics are a new category of feed additives that can increase fibre fermentability by stimulating fibre-degrading microbiota in the gut. The aim of this study was to test, ex vivo, if the microbiota of broilers fed a stimbiotic are better able to ferment different xylose-rich substrates in an ileal and a caecal environment. The ileal and caecal contents from broiler chickens fed a stimbiotic or from a control group were used as an inoculum in the ex vivo fermentation experiment. Different xylose-rich substrates including monomeric xylose (XYL), XOS with DP 2 to 6 (XOS), short DP XOS of 2 to 3 (sDP-XOS), long DP XOS of 4 to 6 (lDP-XOS) and de-starched wheat bran (WB), were added to each ileal and caecal inoculum in fermentation vessels. Total gas, short-chain fatty acids (SCFA) production, bacterial quantification, and carbohydrate utilisation were monitored for 9 h post-inoculation. No significant interactions were observed in any of the parameters measured in either the ileal or caecal contents (p > 0.05). Stimbiotic ileal inocula resulted in higher total gas (p < 0.001) and volatile fatty acid (VFA) (p < 0.001) production, increased numbers of Lactobacillus spp. (p < 0.001), and decreased numbers of Enterococcus spp. (p < 0.01) after 9 h regardless of the xylose-rich substrate added. Stimbiotic caecal inocula resulted in a higher ratio of VFA to branched-chain fatty acids (BCFAs) by up to +9% (p < 0.05). Ileal microbiota were found to preferentially metabolise WB, while caecal microbiota favoured XOS substrates, particularly lDP-XOS. These results indicate that stimbiotics can promote the abundance of lactic acid bacteria involved in the establishment of fibre-degrading bacteria and VFA content in the gut, which could have beneficial effects on broiler performance. Further, ileal and caecal microbiota differ in their utilisation of different substrates which may impact the effectiveness of different stimbiotic products.
Aabrm1-mediated melanin synthesis is essential to growth and development, stress adaption, and pathogenicity in Alternaria alternata
Authors: Li Rong , Li Yongcai , Xu Wenyi , Liu Wenjuan , Xu Xiaobin , Bi Yang , Prusky Dov
Published: January 2024

Scytalone dehydratase (brm1) is one of the key enzymes in 1, 8-dihydroxynaphthalene (DHN) melanin synthesis, which mediates melanin biosythesis and regulates cell biological process of plant fungi, but its function in Alternaria alternata, the causal agent of pear black spot, is unclear. Brm1 in A. alternata was cloned, identified, and named as Aabrm1. An Aabrm1-deletion mutant was generated and revealed that the deletion of Aabrm1 leads to a significant decrease in melanin production and forms orange colony smooth spores. In addition, the deletion of Aabrm1 gene impaired infection structure information and penetration. The external stress resistance of ΔAabrm1 was significantly weakened, and, in particular, it is very sensitive to oxidative stress, and the contents of H2O2 and O2.- in ΔAabrm1 were significantly increased. Virulence of ΔAabrm1 was reduced in non-wound-inoculated pear leaves but not changed in wound-inoculated pear fruit. These results indicated that Aabrm1-mediated melanin synthesis plays an important role in the pathogenicity of A. alternata.
Classification of clinically actionable genetic mutations in cancer patients
Authors: Shahzad Muhammad , Rafi Muhammad , Alhalabi Wadee , Minaz Ali Naz , Anwar Muhammad Shahid , Jamal Sara , Barket Ali Muskan , Alqurashi Fahad Abdullah
Published: January 2024

Personalized medicine in cancer treatment aims to treat each individual’s cancer tumor uniquely based on the genetic sequence of the cancer patient and is a much more effective approach compared to traditional methods which involve treating each type of cancer in the same, generic manner. However, personalized treatment requires the classification of cancer-related genes once profiled, which is a highly labor-intensive and time-consuming task for pathologists making the adoption of personalized medicine a slow progress worldwide. In this paper, we propose an intelligent multi-class classifier system that uses a combination of Natural Language Processing (NLP) techniques and Machine Learning algorithms to automatically classify clinically actionable genetic mutations using evidence from text-based medical literature. The training data set for the classifier was obtained from the Memorial Sloan Kettering Cancer Center and the Random Forest algorithm was applied with TF-IDF for feature extraction and truncated SVD for dimensionality reduction. The results show that the proposed model outperforms the previous research in terms of accuracy and precision scores, giving an accuracy score of approximately 82%. The system has the potential to revolutionize cancer treatment and lead to significant improvements in cancer therapy.
A MALDI-TOF mass spectrometry-based method for detection of copy number variations in BRCA1 and BRCA2 genes
Authors: Zhou Hongjun , He Xin , Zhao Jiadong , Mei Zhu , Zhang Xiayan , Yuan Wen , Dong Hui
Published: January 2024

Background: Identifying germline mutations in BRCA1 and BRCA2 genes (BRCAs) would benefit the carriers in multiple aspects. In addition to single-nucleotide variations and small indels, copy number variations (CNVs) is also an indispensable component of identifiable mutations in BRCAs. A sensitive, rapid and throughput-flexible method to detect CNVs would be preferred to meet the rising clinical requirements for BRCAs testing.

Methods: We developed a MALDI-TOF-MS-based method (MS assay) which included three steps: first, multiplex end-point PCR followed by a single base extension reaction; second, automated analyte transfer and data acquisition; third, data analysis. We applied MS assay to detect CNVs in BRCAs in 293 Chinese patients with ovarian or pancreatic cancer. All the samples were examined by targeted next-generation sequencing (TS) simultaneously. Samples were further cross-validated by multiplex ligation-dependent probe amplification (MLPA) if the results from MS assay and TS were inconsistent. Long range PCR was then applied to identify the exact breakpoints in BRCAs.

Results: MS assay introduced highly multiplexed panels to detect CNVs of BRCAs semi-quantitatively. Simplified on-board data analysis was available for MS assay and no complex bioinformatics was needed. The turnaround time of MS assay was less than 8 hours with a hands-on time of only 40 min. Compared to TS, MS assay exhibited higher sensitivity (100% vs. 75%) and was more flexible in throughput, with the reagent cost per sample remaining constant no matter how many samples were examined per assay. A total of eight CNVs in BRCAs were detected from the 293 samples, and the molecular breakpoints were successfully identified in five samples through long-range PCR followed by Sanger sequencing.

Conclusion: Our results suggested that MS assay might be an effective method in primary screening for CNVs in genes such as BRCAs, especially when short turnaround time and/or high sensitivity is a top priority.
Generation of human TMEM16F-specific affibodies using purified TMEM16F
Authors: Kim Eunyoung , Bang Jinho , Sung Ji Hye , Lee Jonghwan , Shin Dae Hwan , Kim Sunghyun , Lee Byoung-Cheol
Published: January 2024

Introduction: TMEM16 family proteins are involved in a variety of functions, including ion transport, phospholipid scrambling, and the regulation of membrane proteins. Among them, TMEM16F has dual functions as a phospholipid scramblase and a nonselective ion channel. TMEM16F is widely expressed and functions in platelet activation during blood clotting, bone formation, and T cell activation. Despite the functional importance of TMEM16F, the modulators of TMEM16F function have not been sufficiently studied.

Method: In this study, we generated TMEM16F-specific affibodies by performing phage display with brain-specific TMEM16F (hTMEM16F) variant 1 purified from GnTi− cells expressing this variant in the presence of digitonin as a detergent. Purified human TMEM16F protein, which was proficient in transporting phospholipids in a Ca2+-dependent manner in proteoliposomes, was coated onto plates and then the phage library was added to fish out TMEM16F-binding affibodies. For the validation of interaction between affibodies and TMEM16F proteins, ELISA, bio-layer interferometry, and size exclusion chromatography were conducted.

Results and Discussion: As a result, the full sequences of 38 candidates were acquired from 98 binding candidates. Then, we selected 10 candidates and purified seven of them from E. coli expressing these candidates. Using various assays, we confirmed that two affibodies bound to human TMEM16F with high affinity. These affibodies can be useful for therapeutical and diagnostic applications of TMEM16F-related cancer and neurodegenerative diseases. Future studies will be required to investigate the effects of these affibodies on TMEM16F function.
Computational analysis of RNA methyltransferase Rv3366 as a potential drug target for combating drug-resistant Mycobacterium tuberculosis
Authors: Nazim Tasmin , Kumar Vipul , Ahmed Faraz , Ehtesham Nasreen Z. , Hasnain Seyed E. , Sundar Durai , Grover Sonam
Published: January 2024

Mycobacterium tuberculosis (M.tb) remains a formidable global health threat. The increasing drug resistance among M.tb clinical isolates is exacerbating the current tuberculosis (TB) burden. In this study we focused on identifying novel repurposed drugs that could be further investigated as potential anti-TB drugs. We utilized M.tb RNA methyltransferase Rv3366 (spoU) as a potential drug target due to its imperative activity in RNA modification and no structural homology with human proteins. Using computational modeling approaches the structure of Rv3366 was determined followed by high throughput virtual screening of Food and Drug Administration (FDA) approved drugs to screen potential binders of Rv3366. Molecular dynamics (MD) simulations were performed to assess the drug-protein binding interactions, complex stability and rigidity. Through this multi-step structure-based drug repurposing workflow two promising inhibitors of Rv3366 were identified, namely, Levodopa and Droxidopa. This study highlights the significance of targeting M.tb RNA methyltransferases to combat drug-resistant M.tb. and proposes Levodopa and Droxidopa as promising inhibitors of Rv3366 for future pre-clinical investigations.
Effects of remote combine exercise-music training on physical and cognitive performance in patients with Alzheimer’s disease: a randomized controlled trial
Authors: Shokri Ghazaleh , Mohammadian Fatemeh , Noroozian Maryam , Amani-Shalamzari Sadegh , Suzuki Katsuhiko
Published: January 2024

Introduction

This study aimed to investigate the effects of combined remote music and exercise training on the cognitive, psychological, and physical function of patients with Alzheimer’s disease (AD).

Methods

Forty-one AD patients were randomly allocated to three groups, including control (C), training (T), and training with music (TM) groups. Participants were evaluated by cognitive and performance test batteries before and after the interventions. Both experimental groups performed 36 remote workouts in 3 months online via WhatsApp video call individually with the trainer. Training included simple and varied movements of all physical indicators. The number of sets began with two sets and progressively increased to one set every month, 5–10 repetitions per set. The overload was applied by reducing the break between sets every week. The TM group performed the same exercises while listening to Mozart and traditional Iranian songs.

Results

We observed a significant main, group, time, and interaction effect on Romberg (ηp2:0.72), 30 s chair sit and stand (ηp2:0.75), and walking on steppe test (ηp2:0.63). Furthermore, there was a significant main time and interaction effect on push-ups (ηp2:0.43), sit and reach (ηp2:0.64), and MMSE (ηp2:0.76). In all variables, two experimental groups demonstrated substantial improvements than the C group (p < 0.01). In addition, the TM group (27.8%) showed a significant improvement compared to the C group (−6.4%) and the T group (12.2%) in MMSE.

Conclusion

Combined remote training with listening to music as adjuvant treatment is an appropriate item to improve the cognitive and physical performance of Alzheimer’s patients, especially during the COVID-19 pandemic.