bluuebunny/crossref_metadata_2025 huggingface dataset:
The bidirectional associations between sarcopenia-related traits and cognitive performance
Authors: Lu Chun-feng , Liu Wang-shu , Cang Xiao-min , Sun Xin , Wang Xue-qin , Wang Chun-hua , Xu Feng
Published: March 2024

While many studies have sought to explore the degree to which sarcopenia-related traits are associated with cognitive performance, these studies have yielded contradictory results without any clear indication of the causality of such relationships. In efforts to better understand associations between sarcopenia-related traits and cognitive ability, a series of multivariate linear regression assessments were carried out upon datasets derived through the National Health and Nutrition Examination Survey (NHANES). Of these, cognitive performance was assessed by the Digit Symbol Substitution Test (DDST), the Consortium to Establish a Registry for Alzheimer’s Disease Immediate Recall Test (CERAD-IR), Delayed Recall Test (CERAD-DR) and Animal Fluency Test (AFT). Causal relationships between the two were further inferred via a two-sample Mendelian randomization (MR) analysis approach. Sarcopenia-related traits considered in these assessments included walking speed, appendicular skeletal muscle mass (ASM), and hand grip strength (HGS). Walking speed, ASM, and HGS were all significantly independently related to cognitive scores following adjustment for covariates. MR assessments also identified that each 1-SD higher walking speed and appendicular lean mass were causally and respectively associated with a 0.34 [standard error (SE) = 0.09; p < 0.001)] standardized score higher and a 0.07 (SE = 0.01; p < 0.001) standardized score higher cognitive score, whereas a higher hand grip strength was positively associated with a better cognitive performance. Reverse MR assessments also yielded similar findings. These data suggest that lower walking speed, muscle strength, and muscle mass were all closely related to lower cognitive performance irrespective of gender, and that there may be a mutually reinforcing relationship among these variables.
Micro/nanomotors for neuromodulation
Authors: Huang Yulin , Peng Fei
Published: March 2024

This article provides a review of various emerging micro/nanomotors utilized for neural modulation in recent years, with the aim of inspiring readers to explore broader biomedical applications of micro/nanomotors.
Expediting ion migration and stabilizing interface deposition through pre-polarized ion channels for zinc-ion batteries
Authors: Li Gang , Hu Fulong , Chen Jinxiu , Fan Xiaozhong , Xiao Xiong , Ma Longtao , Kong Long
Published: March 2024

A pre-polarized ion channels are constructed to inhibit the tip effect and selectively accelerate ion transport, achieving stable and uniform ion deposition, suppressing dendrite growth and side reaction for long-term Zn striping/plating.
Additive multiple contacts and saturation phenomena in epidemiological models are not detected by R0
Authors: Villavicencio-Pulido José Geiser , Barradas Ignacio , Nila-Luévano Claudia
Published: March 2024

Many infections are transmitted by direct contacts. Usually, one single direct contact is needed to transmit the required minimum infectious load. Most models describe contagions by single contacts using a term of the type mass action law. However, modelling infections that are transmitted after the susceptible individual had contact with several sources of infection requires more than mass action law terms. We call additive multiple contacts those that do not produce infection by themselves, but can produce infection if they happen simultaneously. We are interested in understanding the role played by R0 missing the mark in infections in which the minimum infectious load is reached not only by single contacts but also by additive multiple contacts. We propose different mathematical models describing not only infections by one single contact but also by additive multiple contacts. We show that all models have the same value of R0, but correspond to different epidemiological mechanisms. Two models show contagions by additive multiple contacts and a third one shows reduction of infections by some saturation process which is not captured by R0. This shows that trying to control the epidemics by controlling R0 could be unsufficient or, in some cases, waste resources.
Can the Remaining Coronal Tooth Structure Influence the Mechanical Behavior of Nonpost Full Crowns?
Authors: Pinto Alana Barbosa Alves , Andrade Guilherme Schmitt de , Abu Hasna Amjad , Souza Joyce Rodrigues de , Tribst João Paulo Mendes , Borges Alexandre Luiz Souto
Published: March 2024

Objectives This study investigated the impact of the remaining coronal tooth structure on the mechanical behavior of nonpost (NP) full crowns on endodontically treated maxillary central incisors.

Materials and Methods Forty bovine incisors with NP and 2-mm of ferrule were divided into four groups based on the remaining structure: complete 2-mm ferrule (NP-2), absence of mesial and distal ferrule effect (NP-BL), absence of buccal and lingual ferrule effect (NP-MD), and no ferrule (NP-0). The specimens underwent a stepwise stress fatigue test until fracture occurred, and stress distribution was analyzed using in silico finite element analysis (FEA). Additionally, groups with endodontic posts (P) were simulated in the FEA.

Results The results showed that the survival rates varied among the different groups under oblique loading. The NP-2 group exhibited the highest survival rate, with all samples enduring loads up to 200 N and some surviving up to 520 N. The NP-MD and NP-BL groups had lower survival rates, while the NP-0 group had the poorest survival rate. The predominant failure mode was a nonrepairable root fracture. FEA results indicated no significant difference between groups with and without posts. NP intraradicular restorations on nonweakened roots with a minimum height of 2mm and partial or total ferrule thickness of 1mm offer a promising treatment option.

Conclusion A complete 2-mm ferrule was found to be the most favorable configuration for NP full crowns. However, maintaining the remaining tissue is crucial, as both combinations with preserved ferrule effect exhibited superior behavior in terms of fatigue and fracture load compared to the group with no ferrule. These findings contribute to understanding the mechanical considerations for NP full crowns and provide insights into treatment planning and design choices in restorative dentistry.
Examination of the Structure and Formation Streptococcus mutans Biofilm Induced by Glucose, Lactose, Soy Protein, and Iron
Authors: Kriswandini Indah Listiana , Budi Hendrik Setia , Justitia Fuadia Mumaiyyiah
Published: March 2024

Objective Streptococcus mutans, the main causative agent of caries, have the ability to form biofilms on the surface of teeth. The availability of nutrients such as glucose, lactose, soy protein, and iron can influence S. mutans in biofilm formation. All four sources of nutrients have been shown to increase the formation of S. mutans biofilms. The purpose of this study was to determine the structure and thickness of S. mutans biofilms induced by glucose, lactose, soy protein, and iron.

Materials and Methods This experimental laboratory study aimed to examine the formation of biofilm structures (chemical elements) and determine the thickness of S. mutans biofilms induced by glucose, lactose, soy protein, and iron. The structures (chemical elements) were examined using scanning electron microscopy-energy-dispersive X-ray (SEM-EDX) analysis. Confocal laser scanning microscopy (CLSM) was used to determine the thickness of S. mutans biofilms with an Olympus FV1000 microscope, and the findings were analyzed using Olympus Fluoview Ver. 4.2a software.

Results It was established that the results of SEM-EDX examination of the structure of S. mutans biofilms induced by glucose had oxygen (O) as the dominant chemical element (30.24 w%); lactose reported oxygen (O) as the dominant element (29.65 w%); soy protein had carbon (C) as the dominant element (34.31 w%); and iron showed oxygen (O) as the dominant element (32.51 w%). The thickness (measured by the CLSM examination) of biofilms induced by glucose, lactose, soy protein, and iron were 17,666, 12,666, 18,000, and 15,666 nm, respectively.

Conclusion The structure of S. mutans biofilms induced by glucose, lactose, and iron contain the following elements in amounts from the highest to lowest: O, C, N, P, and S; the biofilm produced by S. mutans induced by soy protein in amounts from the highest to lowest comprised the elements: C, O, N, S, and P. The S. mutans biofilms induced by soy protein had the maximum thickness, followed by those induced by glucose, iron, and lactose.
Caries Etiology and Preventive Measures
Authors: Meyer Frederic , Schulze zur Wiesche Erik , Amaechi Bennett T. , Limeback Hardy , Enax Joachim
Published: March 2024

Caries is a widespread disease in both children and adults. Caries is caused by the conversion of fermentable carbohydrates by plaque bacteria into acids on the tooth surface. Thus, it is important to focus on sugar reduction and plaque control. For efficient plaque removal/control, state-of-the-art toothpastes contain various active ingredients such as antimicrobial agents (e.g., chlorhexidine, stannous salts, and zinc salts), abrasives (e.g., calcium carbonate, calcium phosphates, and hydrated silica), surfactants (e.g., sodium lauryl sulfate and sodium methyl cocoyl taurate), and natural compounds (e.g., polyphenols and xylitol). Agents with pH-buffering and calcium-releasing properties (e.g., calcium carbonate and calcium phosphates) and biomimetic actives (e.g., hydroxyapatite) reverse the effects of the acids. Additionally, modern toothbrushes (i.e., electric toothbrushes) as well as dental floss and interdental brushes significantly help remove plaque from dental surfaces including interproximal surfaces. In conclusion, modern concepts in caries prevention should focus not only on tooth remineralization alone but also on the control of all the key factors involved in caries development.
Limosilactobacillus reuteri as an Adjuvant in the Treatment of Peri-implant Mucositis in Total Rehabilitation: An Exploratory Study
Authors: Parreira Gonçalo J.G. , de Araújo Nobre Miguel A. , Moreira André G.C.R. , Luís Henrique P.S.
Published: March 2024

Objectives Mechanical debridement is the traditional method for the treatment of peri-implant mucositis (P-im) and its success depends on the patient's correct oral hygiene. It is believed that probiotics may help by their ability to modulate the oral biofilm, resulting in anti-inflammatory and antibacterial plaque action. The aim of this study was to evaluate the adjuvant effect of the probiotic Limosilactobacillus reuteri (LR) in the mechanical treatment of P-im.

Materials and Methods This exploratory study included 29 subjects with implant-supported total rehabilitation and P-im, divided into test (TG) and control (CG) groups, equally subjected to professional mechanical debridement, with the administration of a daily GUM PerioBalance lozenge for 30 days added to the TG. The modified Plaque Index (mPlI) modified Sulcus Bleeding Index (mBI) and pocket depth (PD) were evaluated before the intervention (baseline) and 6 and 10 weeks later.

Statistical Analysis Parametric and nonparametric tests with 5% significance level were used in the statistical analysis, using IBM SPSS Statistics 27.0 software.

Results Both treatments resulted in reduced mPlI, mBI, and PD at 6 weeks; while from 6 to 10 weeks there was an increase in mPlI and mBI and maintenance of PD. Compared with baseline, differences were close to statistical significance in the reduction in PD at 10 weeks in the CG (p = 0.018), after Bonferroni correction, and statistically significant in the mPlI at 6 weeks in the CG (p = 0.004) and in the TG (p = 0.002) as well as at 10 weeks in the TG (p = 0.016). Comparing the groups in the postintervention assessments, no statistically significant differences were found.

Conclusion LR adjuvant mechanical treatment of P-im does not show a clear benefit compared with mechanical treatment alone, with both interventions achieving similar clinical results. Further prospective and long-term studies are needed.
Effect of Two Different Intraoral Polishing Systems on Surface Roughness, Color Stability, and Bacterial Accumulation of Zirconia-Reinforced Lithium Silicate Ceramic
Authors: Makkeyah Fatma , Moustafa Dina Mohamed , Bakr Mahmoud M. , Al Ankily Mahmoud
Published: March 2024

Objective The aim of this study was to investigate the effects of two intraoral polishing methods on zirconia-reinforced lithium silicate ceramic after ultrasonic scaling.

Materials and Methods Thirty disc-shaped samples of zirconia-reinforced lithium silicate were constructed. Freshly extracted bovine teeth were collected and cleaned then the discs were cemented into a cavity prepared onto their labial surface. The samples were divided into three groups (10 samples per group); S: Scaling only, SE: Scaling followed by polishing using Eve Diapro lithium disilicate polishers, SD: Scaling followed by polishing using Diatech ShapeGuard ceramic polishing plus kit. The surface roughness was evaluated after scaling and polishing the samples. For color stability, the samples were stored for 12 days at 37°C in an incubator to simulate 1-year consumption of coffee. L*a*b* color parameters were assessed using VITA Easyshade Advance 4.0 before and after the staining procedure and the color difference was measured. Finally, bacterial accumulation was evaluated by incubating the samples with a suspension of Streptococcus mutans ( S. mutans), after that the S. mutans colonies were counted to obtain the values of colony-forming units (CFU). The final overall roughness, change in color and bacterial count were compared between all groups using one-way ANOVA and Tukey's post-hoc analysis. The Pearson correlation coefficient was used to determine the correlation between continuous variables. The cutoff for significance was chosen at p ≤ 0.05.

Results Scaling induced surface roughness of the zirconia-reinforced lithium silicate ceramic was significantly decreased after using both intraoral polishing systems and this was accompanied by a significant decrease in color change and bacterial count.

Conclusion Intraoral polishing techniques can reduce the roughness of the surface of zirconia reinforced lithium silicate restorations induced due to scaling and subsequently reduce the stainability and bacterial accumulation.
Efficacy of Biofilm Removal on the Dental Implant Surface by Sodium Bicarbonate and Erythritol Powder Airflow System
Authors: Pujarern Patr , Klaophimai Arthit , Amornsettachai Parinya , Panyayong Woraphong , Chuenjitkuntaworn Boontharika , Rokaya Dinesh , Suphangul Suphachai
Published: March 2024

Objective Peri-implantitis is a common complication in implant therapy and it is one of the main contributing factors to implant failure. This can be prevented by regular maintenance with mechanical debridement. One of the recent mechanical debridement methods is air abrasion therapy using different abrasive powders. This study aimed to evaluate the two common abrasive powders of different sizes (sodium bicarbonate and erythritol) for their biofilm cleaning efficacy on dental implant surfaces.

Materials and Methods In an in vitro setting, a total of 33 implants were divided into three groups: Group 1 (n =11) = no treatment; group 2 (n = 11) = air abrasion therapy treated group using a sodium bicarbonate powder (AIRFLOW Powder Classic Comfort, EMS Electro Medical Systems, Nyon, Switzerland); and group 3 (n = 11) = air abrasion therapy treated group using an erythritol powder (AIRFLOW Powder Plus, EMS Electro Medical Systems, Nyon, Switzerland). The implants in each group were subjected to biofilm formation, and group 2 and group 3 were treated with air abrasion therapy of two different powders having different sizes with the same settings. The particle sizes were sodium bicarbonate (40 µm) and erythritol (14µm). The surface characteristics of the dental implants in three groups were studied from a digital camera and under the scanning electron microscope at different magnifications. The comparison of biofilm-removal efficacy between the three groups was performed by using a one-way analysis of variance with post-hoc Dunnett's T3 test. A p-value less than 0.05 was chosen to indicate statistical significance.

Results There were no statistical differences (p > 0.05) between the two powder-treated groups for the biofilm cleaning efficacy. However, both groups showed significantly better biofilm-cleaning efficacy than the control group (p < 0.05).

Conclusion This suggests that both powders are effective in removing biofilm from the implant surface under ideal conditions. However, there was no clear distinction between the cleaning potential of the two powders, as both performed in a similar manner.
Experiencing Exclusion among Iranian-Canadian Muslim Women
Authors: Mahmoudi Mohadeseh
Published: March 2024

This case study includes three narratives of Iranian-Canadian Muslim women who describe their experience of visiting natural spaces in Canada. They wear Islamic hijabs and follow Islamic rules, which may cause them to experience natural spaces differently compared to other Canadians. These narratives resulted from a series of interviews I conducted in which I aimed to understand how Iranian Canadians used Canada’s natural environment and the opportunities or challenges they face. Their stories revealed their joy in nature-based leisure and recreation while also unfolding their feelings of social exclusion in some natural settings where dogs were off-leash. In dogs’ off-leash areas, participants encountered serious constraints and exclusion or felt in need of protection from spouses.

Information

© CAB International 2024
Using nanopore sequencing to identify bacterial infection in joint replacements: a preliminary study
Authors: Wilkinson Hollie , McDonald Jamie , McCarthy Helen S , Perry Jade , Wright Karina , Hulme Charlotte , Cool Paul
Published: March 2024

This project investigates if third-generation genomic sequencing can be used to identify the species of bacteria causing prosthetic joint infections (PJIs) at the time of revision surgery. Samples of prosthetic fluid were taken during revision surgery from patients with known PJIs. Samples from revision surgeries from non-infected patients acted as negative controls. Genomic sequencing was performed using the MinION device and the rapid sequencing kit from Oxford Nanopore Technologies. Bioinformatic analysis pipelines to identify bacteria included Basic Local Alignment Search Tool, Kraken2 and MinION Detection Software, and the results were compared with standard of care microbiological cultures. Furthermore, there was an attempt to predict antibiotic resistance using computational tools including ResFinder, AMRFinderPlus and Comprehensive Antibiotic Resistance Database. Bacteria identified using microbiological cultures were successfully identified using bioinformatic analysis pipelines. Nanopore sequencing and genomic classification could be completed in the time it takes to perform joint revision surgery (2–3 h). Genomic sequencing in this study was not able to predict antibiotic resistance in this time frame, this is thought to be due to a short-read length and low read depth. It can be concluded that genomic sequencing can be useful to identify bacterial species in infected joint replacements. However, further work is required to investigate if it can be used to predict antibiotic resistance within clinically relevant timeframes.
Advances in phage–host interaction prediction: in silico method enhances the development of phage therapies
Authors: Nie Wanchun , Qiu Tianyi , Wei Yiwen , Ding Hao , Guo Zhixiang , Qiu Jingxuan
Published: March 2024

Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable therapeutic phages that are capable of infecting pathogens from massive phage databases has been a principal step in phage therapy design. Experimental methods to identify phage–host interaction (PHI) are time-consuming and expensive; high-throughput computational method to predict PHI is therefore a potential substitute. Here, we systemically review bioinformatic methods for predicting PHI, introduce reference databases and in silico models applied in these methods and highlight the strengths and challenges of current tools. Finally, we discuss the application scope and future research direction of computational prediction methods, which contribute to the performance improvement of prediction models and the development of personalized phage therapy.
D3EGFR: a webserver for deep learning-guided drug sensitivity prediction and drug response information retrieval for EGFR mutation-driven lung cancer
Authors: Shi Yulong , Li Chongwu , Zhang Xinben , Peng Cheng , Sun Peng , Zhang Qian , Wu Leilei , Ding Ying , Xie Dong , Xu Zhijian , Zhu Weiliang
Published: March 2024

As key oncogenic drivers in non-small-cell lung cancer (NSCLC), various mutations in the epidermal growth factor receptor (EGFR) with variable drug sensitivities have been a major obstacle for precision medicine. To achieve clinical-level drug recommendations, a platform for clinical patient case retrieval and reliable drug sensitivity prediction is highly expected. Therefore, we built a database, D3EGFRdb, with the clinicopathologic characteristics and drug responses of 1339 patients with EGFR mutations via literature mining. On the basis of D3EGFRdb, we developed a deep learning-based prediction model, D3EGFRAI, for drug sensitivity prediction of new EGFR mutation-driven NSCLC. Model validations of D3EGFRAI showed a prediction accuracy of 0.81 and 0.85 for patients from D3EGFRdb and our hospitals, respectively. Furthermore, mutation scanning of the crucial residues inside drug-binding pockets, which may occur in the future, was performed to explore their drug sensitivity changes. D3EGFR is the first platform to achieve clinical-level drug response prediction of all approved small molecule drugs for EGFR mutation-driven lung cancer and is freely accessible at https://www.d3pharma.com/D3EGFR/index.php.
PANoptosis, an indicator of COVID-19 severity and outcomes
Authors: Yang Qingyuan , Song Wanmei , Reheman Hanizaier , Wang Dan , Qu Jieming , Li Yanan
Published: March 2024

Coronavirus disease 2019 (COVID-19) has been wreaking havoc for 3 years. PANoptosis, a distinct and physiologically relevant inflammatory programmed cell death, perpetuates cytokine storm and multi-organ injuries in COVID-19. Although PANoptosis performs indispensable roles in host defense, further investigation is needed to elucidate the exact processes through which PANoptosis modulates immunological responses and prognosis in COVID-19. This study conducted a bioinformatics analysis of online single-cell RNA sequence (scRNA-seq) and bulk RNA-seq datasets to explore the potential of PANoptosis as an indicator of COVID-19 severity. The degree of PANoptosis in bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) indicated the severity of COVID-19. Single-cell transcriptomics identified pro-inflammatory monocytes as one of the primary sites of PANoptosis in COVID-19. The study subsequently demonstrated the immune and metabolic characteristics of this group of pro-inflammatory monocytes. In addition, the analysis illustrated that dexamethasone was likely to alleviate inflammation in COVID-19 by mitigating PANoptosis. Finally, the study showed that the PANoptosis-related genes could predict the intensive care unit admission (ICU) and outcomes of COVID-19 patients who are hospitalized.
MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning
Authors: Wang Tao , Li Zhen , Zhuo Linlin , Chen Yifan , Fu Xiangzheng , Zou Quan
Published: March 2024

Motivation

Accurately predicting molecular metabolic stability is of great significance to drug research and development, ensuring drug safety and effectiveness. Existing deep learning methods, especially graph neural networks, can reveal the molecular structure of drugs and thus efficiently predict the metabolic stability of molecules. However, most of these methods focus on the message passing between adjacent atoms in the molecular graph, ignoring the relationship between bonds. This makes it difficult for these methods to estimate accurate molecular representations, thereby being limited in molecular metabolic stability prediction tasks.

Results

We propose the MS-BACL model based on bond graph augmentation technology and contrastive learning strategy, which can efficiently and reliably predict the metabolic stability of molecules. To our knowledge, this is the first time that bond-to-bond relationships in molecular graph structures have been considered in the task of metabolic stability prediction. We build a bond graph based on ‘atom-bond-atom’, and the model can simultaneously capture the information of atoms and bonds during the message propagation process. This enhances the model’s ability to reveal the internal structure of the molecule, thereby improving the structural representation of the molecule. Furthermore, we perform contrastive learning training based on the molecular graph and its bond graph to learn the final molecular representation. Multiple sets of experimental results on public datasets show that the proposed MS-BACL model outperforms the state-of-the-art model.

Availability and Implementation

The code and data are publicly available at https://github.com/taowang11/MS.
Mice and minipigs with compromised expression of the Alzheimer’s disease gene SORL1 show cerebral metabolic disturbances on hyperpolarized [1-13C]pyruvate and sodium MRI
Authors: Bøgh Nikolaj , Sørensen Charlotte B , Alstrup Aage K O , Hansen Esben S S , Andersen Olav M , Laustsen Christoffer
Published: March 2024

The sortilin-related receptor 1 (SORL1) gene, encoding the cellular endosomal sorting-related receptor with A-type repeats (SORLA), is now established as a causal gene for Alzheimer’s disease. As the latest addition to the list of causal genes, the pathophysiological effects and biomarker potential of SORL1 variants remain relatively undiscovered. Metabolic dysfunction is, however, well described in patients with Alzheimer’s disease and is used as an imaging biomarker in clinical diagnosis settings. To understand the metabolic consequences of loss-of-function SORL1 mutations, we applied two metabolic MRI technologies, sodium (23Na) MRI and MRI with hyperpolarized [1-13C]pyruvate, in minipigs and mice with compromised expression of SORL1. At the age analysed here, both animal models display no conventional imaging evidence of neurodegeneration but show biochemical signs of elevated amyloid production, thus representing the early preclinical disease. With hyperpolarized MRI, the exchange from [1-13C]pyruvate to [1-13C]lactate and 13C-bicarbonate was decreased by 32 and 23%, respectively, in the cerebrum of SORL1-haploinsufficient minipigs. A robust 11% decrease in the sodium content was observed with 23Na-MRI in the same minipigs. Comparably, the brain sodium concentration gradually decreased from control to SORL1 haploinsufficient (−11%) to SORL1 knockout mice (−23%), suggesting a gene dose dependence in the metabolic dysfunction. The present study highlights that metabolic MRI technologies are sensitive to the functional, metabolic consequences of Alzheimer’s disease and Alzheimer’s disease–linked genotypes. Further, the study suggests a potential avenue of research into the mechanisms of metabolic alterations by SORL1 mutations and their potential role in neurodegeneration.
‘It’s nice that we can do that too’: investigating transgender persons' negotiations with identity and community questions in Indian science institutions
Authors: Datta Sayantan
Published: March 2024

In 2014, the Indian Supreme Court passed the landmark NALSA v. Union of India judgment that not only granted transgender persons the right to self-identify their gender but also recognized their right to equitable and accessible education. Further, in 2018, the apex court passed another landmark judgment in the case of Navtej Singh Johar & Ors. v. Union of India, reading down Section 377 of the Indian Penal Code, and, therefore, decriminalizing consensual adult homosexual sex acts. In the backdrop of these landmark judgments – i.e. in post-NALSA and post-377 India – identity and community questions pertaining to transgender, gender non-conforming, and non-binary persons’ access to and presence in educational institutions in India have intensified. Focusing on science institutions, this paper attempts to delineate the ways in which proximal and distal networks of caste-class and gender shape transgender, gender non-conforming, and non-binary persons’ exclusion from and belonging in science collectivities. Further, this paper also investigates how transgender persons’ sense of belonging to certain communities speaks to their shifting epistemic dispositions. Finally, contextualizing transpersons’ negotiations in science communities and individual and collective scales as ‘unstable and hybrid assemblages’, this paper demonstrates the ways in which trans collectives in science institutions radicalize community building and development in these institutional spaces by interrupting dominant institutional cultures and practices.
Precarious life in a heartless world: COVID-19 and the gender transgressive Shivashaktis in Southern India
Authors: Mukherjee Debomita , Rao Archana , Kumar Pushpesh
Published: March 2024

This paper attempts to understand and narrate the experiences of Shivashaktis, a gender transgressive community from Southern India, during the COVID-19 pandemic. The Shivashaktis’ gender transgressions and embodied ritual power allow them to intercede between the human and the divine. This secures them religious sanction and legitimacy and offers a source of income for them. They are engaged in several livelihood practices that are associated with ritual practices such as performing oracles, laggams (deity marriages), joggu, etc. Their embeddedness in heterosexual family structures, however, hinder their access to benefits that are allocated for the transgender community through the state and non-state policy programmes. During the pandemic, with the state-announced lockdown across the nation, and particularly in Telangana, Shivashaktis were pushed further into precarity, burdened by economic, psychological and community disruptions. Within this context, the paper critically engages with the impact of COVID-19 that brought the entire relational world of the gender transgressive Shivashaktis to collapse rigorously, affecting their livelihood and sense of being and belonging in the world.
National Unified Renal Translational Research Enterprise: Idiopathic Nephrotic Syndrome (NURTuRE-INS) study
Authors: Colby Elizabeth , Hayward Samantha , Benavente Melissa , Robertson Fiona , Bierzynska Agnieszka , Osborne Amy , Parmesar Kevon , Afzal Maryam , Chapman Tracey , Ullah Fatima , Davies Elaine , Nation Michael , Cook Wendy , Johnson Tim , Andag Uwe , Radresa Olivier , Skroblin Philipp , Bayerlova Michaela , Unwin Robert , Vuilleumier Nicolas , Banks Rosamonde E , Braddon Fiona , Koziell Ania , Taal Maarten W , Welsh Gavin I , Saleem Moin A
Published: March 2024

Background

Idiopathic nephrotic syndrome (INS) is a heterogenous disease and current classification is based on observational responses to therapies or kidney histology. The National Unified Renal Translational Research Enterprise (NURTuRE)-INS cohort aims to facilitate novel ways of stratifying INS patients to improve disease understanding, therapeutics and design of clinical trials.

Methods

NURTuRE-INS is a prospective cohort study of children and adults with INS in a linked biorepository. All recruits had at least one sampling visit collecting serum, plasma, urine and blood for RNA and DNA extraction, frozen within 2 hours of collection. Clinical histology slides and biopsy tissue blocks were also collected.

Results

A total of 739 participants were recruited from 23 centres to NURTuRE-INS, half of whom were diagnosed in childhood [n = 365 (49%)]. The majority were white [n = 525 (71%)] and the median age at recruitment was 32 years (interquartile range 12–54). Steroid-sensitive nephrotic syndrome (SSNS) was the most common clinical diagnosis [n = 518 (70%)]. Of patients diagnosed in childhood who underwent a kidney biopsy, for SSNS (n =103), 76 demonstrated minimal change disease (MCD), whereas for steroid-resistant nephrotic syndrome (n =80), 21 had MCD. Almost all patients diagnosed in adulthood had a kidney biopsy [n = 352 (94%)]; 187 had MCD and 162 had focal segmental glomerulosclerosis.

Conclusions

NURTuRE-INS is a prospective cohort study with high-quality biosamples and longitudinal data that will assist research into the mechanistic stratification of INS. Samples and data will be available through a Strategic Access and Oversight Committee.
Seasonal impacts on gut microbial composition of the Eastern subterranean termite (Blattodea: Rhinotermitidae)
Authors: Sapkota Rajani , Nakatsu Cindy H , Scharf Michael E
Published: March 2024

Termite hindguts are inhabited by symbionts that help with numerous processes, but changes in the gut microbiome due to season can potentially impact the physiology of termites. This study investigated the impact of seasonal changes on the composition of bacteria and protozoa in the termite gut. Termites were obtained monthly from May to October 2020 at a location in the central United States that typically experiences seasonal air temperatures ranging from < 0 to > 30 °C. The guts of 10 termites per biological replication were dissected and frozen within 1 day after collections. DNA was extracted from the frozen gut tissues and used for termite 16S rRNA mitochondrial gene analysis and bacterial 16S rRNA gene sequence surveys. Phylogenetic analysis of termite 16S rRNA gene sequences verified that the same colony was sampled across all time points. On processing bacterial 16S sequences, we observed alpha (observed features, Pielou’s evenness, and Shannon diversity) and beta diversity (unweighted Unifrac, Bray-Curtis, and Jaccard) metrics to vary significantly across months. Based on the analysis of the composition of microbiomes with bias correction (ANCOM-BC) at the genus level, we found several significant bacterial taxa over collection months. In addition, Spearman correlation analysis demonstrated that 41 bacterial taxa were significantly correlated (positively and negatively) with average soil temperature. These results from a single termite colony suggest termite microbial communities go through seasonal changes in relative abundance related to temperature, although other seasonal effects cannot be excluded. Further investigations are required to conclusively define the consistency of microbial variation among different colonies with season.
Noncontiguous operon atlas for the Staphylococcus aureus genome
Authors: Iturbe Pablo , Martín Alvaro San , Hamamoto Hiroshi , Marcet-Houben Marina , Galbaldón Toni , Solano Cristina , Lasa Iñigo
Published: March 2024

Bacteria synchronize the expression of genes with related functions by organizing genes into operons so that they are cotranscribed together in a single polycistronic messenger RNA. However, some cellular processes may benefit if the simultaneous production of the operon proteins coincides with the inhibition of the expression of an antagonist gene. To coordinate such situations, bacteria have evolved noncontiguous operons (NcOs), a subtype of operons that contain one or more genes that are transcribed in the opposite direction to the other operon genes. This structure results in overlapping transcripts whose expression is mutually repressed. The presence of NcOs cannot be predicted computationally and their identification requires a detailed knowledge of the bacterial transcriptome. In this study, we used direct RNA sequencing methodology to determine the NcOs map in the Staphylococcus aureus genome. We detected the presence of 18 NcOs in the genome of S. aureus and four in the genome of the lysogenic prophage 80α. The identified NcOs comprise genes involved in energy metabolism, metal acquisition and transport, toxin–antitoxin systems, and control of the phage life cycle. Using the menaquinone operon as a proof of concept, we show that disarrangement of the NcO architecture results in a reduction of bacterial fitness due to an increase in menaquinone levels and a decrease in the rate of oxygen consumption. Our study demonstrates the significance of NcO structures in bacterial physiology and emphasizes the importance of combining operon maps with transcriptomic data to uncover previously unnoticed functional relationships between neighbouring genes.
Interplay between gut microbiota and the master iron regulator, hepcidin, in the pathogenesis of liver fibrosis
Authors: Ahmadi Badi Sara , Bereimipour Ahmad , Rohani Pejman , Khatami Shohreh , Siadat Seyed Davar
Published: March 2024

Introduction: There is a proven role for hepcidin and the composition of gut microbiota and its derivatives in the pathophysiology of liver fibrosis. Area covered: This review focuses on the literature search regarding the effect of hepcidin and gut microbiota on regulating liver physiology. We presented the regulating mechanisms of hepcidin expression and discussed the possible interaction between gut microbiota and hepcidin regulation. Furthermore, we investigated the importance of the hepcidin gene in biological processes and bacterial interactions using bioinformatics analysis. Expert Opinion: One of the main features of liver fibrosis is iron accumulation in hepatic cells, including hepatocytes. This accumulation can induce an oxidative stress response, inflammation, and activation of hepatic stellate cells. Hepcidin is a crucial regulator of iron by targeting ferroportin expressed on hepatocytes, macrophages, and enterocytes. Various stimuli, such as iron load and inflammatory signals, control hepcidin regulation. Furthermore, a bidirectional relationship exists between iron and the composition and metabolic activity of gut microbiota. We explored the potential of gut microbiota to influence hepcidin expression and potentially manage liver fibrosis, as the regulation of iron metabolism plays a crucial role in this context.
Lipidomic Profiling of Kidney Cortical Tubule Segments Identifies Lipotypes with Physiological Implications
Authors: Cheval Lydie , Poindessous Virginie , Sampaio Julio L , Crambert Gilles , Pallet Nicolas
Published: March 2024

A detailed knowledge of the lipid composition of components of nephrons is crucial for understanding physiological processes and the development of kidney diseases. However, the lipidomic composition of kidney tubular segments is unknown. We manually isolated the proximal convoluted tubule (PCT), the cortical thick ascending limb of Henle’s loop, and the cortical collecting duct from 5 lean and obese mice and subjected the samples to shotgun lipidomics analysis by high-resolution mass spectrometry acquisition. Across all samples, more than 500 lipid species were identified, quantified, and compared. We observed significant compositional differences among the 3 tubular segments, which serve as true signatures. These intrinsic lipidomic features are associated with a distinct proteomic program that regulates highly specific physiological functions. The distinctive lipidomic features of each of the 3 segments are mostly based on the relative composition of neutral lipids, long-chain polyunsaturated fatty acids, sphingolipids, and ether phospholipids. These features support the hypothesis of a lipotype assigned to specific tubular segments. Obesity profoundly impacts the lipotype of PCT. In conclusion, we present a comprehensive lipidomic analysis of 3 cortical segments of mouse kidney tubules. This valuable resource provides unparalleled detail that enhances our understanding of tubular physiology and the potential impact of pathological conditions.
Application of insecticide dusts for the management of Indian meal moth (Lepidoptera: Pyralidae) wandering larvae under laboratory conditions
Authors: Pan Xiaodan , Wang Changlu
Published: March 2024

The Indian meal moth, Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae), is a very common stored-product pest. The mature larvae wander around searching for suitable places to pupate, offering an opportunity to control this pest. We evaluated the efficacy of 5 insecticide dusts: Alpine (0.25% dinotefuran, 95% diatomaceous earth [DE]), CimeXa (92.1% amorphous silica gel), DX13 (100% DE), Tempo (1% cyfluthrin), and Tri-Die (1% pyrethrin, 10% piperonyl butoxide, 40% amorphous silica) against P. interpunctella wandering larvae by allowing larvae to pass 1-inch treated band, expose to treated vinyl tiles for 5 min, and expose to treated harborage (with or without the presence of an untreated harborage). A commercially treated harborage product (Nattaro band) served as a positive control in the exposure to the treated harborage test. Tempo was significantly more effective than other insecticide dusts in the 1-inch band and forced exposure tests but caused only 44% and 54% larvae mortality in the 2 tests. In contrast, CimeXa, Tri-Die, and Tempo caused 84%–89% mortality when the larvae were provided with treated harborages. When both treated and untreated harborages were present, Tempo caused a significantly higher mortality and a lower percentage of emerged adults from larvae than Tri-Die, but not significantly more than CimeXa. Deploying Tempo or CimeXa-treated harborages and/or applying insecticide dust directly into the wall crevices, perimeters of the floor, shipping pallets, and other areas where P. interpunctella larvae hide could be an effective method for the management of the wandering stage of P. interpunctella larvae in storage facilities.
Effects of deploying ethanol lures in tandem with generic pheromone lures for attraction of cerambycid beetles in field bioassays
Authors: Rice Marlin E , Zou Yunfan , Millar Jocelyn G , Hanks Lawrence M
Published: March 2024

Male cerambycid beetles of the large subfamilies Cerambycinae and Lamiinae produce aggregation-sex pheromones that attract both sexes. The pheromones of many species are conserved among both closely related species (e.g., congeners) and more distantly related species (e.g., different subfamilies), including those endemic to different continents. This parsimony in pheromone structures suggests that multiple species may be attracted to traps baited with blends of pheromones, and such blends are finding use in delineating geographic ranges of native species and in surveillance programs for incursions of exotic species. Here, we present the results of a field experiment conducted at multiple sites in Iowa that tested the effects of deploying ethanol lures in tandem with a 6-component blend of common pheromone components for cerambycine and lamiine species and a 5-component blend that specifically targeted lamiines. Eight cerambycine species showed significant treatment effects, most of which were attracted to the 6-component blend, and ethanol increased attraction for half of these species. Two cerambycine species were attracted only by ethanol. Seven lamiine species were attracted by the lamiine-specific blend, alone or when combined with ethanol, and 3 of these species also were attracted to the 6-component blend. Taken together, these findings provide further evidence that carefully crafted blends of pheromones can be used to monitor the presence or abundance of multiple cerambycid species. Ethanol either increased the number of beetles attracted by pheromones or had no effect, so there is no apparent downside to deploying ethanol lures in combination with pheromones.
Epithelioid hemangioendothelioma—its history, clinical features, molecular biology and current therapy
Authors: Tsuchihashi Kenji , Baba Eishi
Published: March 2024

Epithelioid hemangioendothelioma (EHE) is a remarkably rare tumor arising from endothelial cells that is classified as a vascular tumor in the WHO classification. The tumor is predominantly characterized by the presence of fusion genes, such as WWTR1-CAMTA1 or YAP1-TFE3, with a minority of cases exhibiting other rare fusion genes. EHE exhibits a broad age of onset, typically presenting at ~50 years, but it is not uncommon in pediatric populations. It manifests in a variety of organs, including the liver, lung, soft tissue and bone. Initial multiple-organ involvement is also observed. The tumor’s biological behavior and prognosis vary substantially based on the primary site of manifestation. From a therapeutic perspective, initial active surveillance might be considered in selected cases, although surgical intervention remains the mainstay of treatment, especially for localized single-organ involvement. Chemotherapy is administered to patients with progressive unresectable tumors. Recent advances in the biological analysis of EHE fusion genes have elucidated their diverse functions. Additionally, next-generation sequencing has facilitated the identification of other mutations beyond the fusion genes. These continuous efforts to understand the biology of the fusion genes themselves and/or the dysregulated signaling by fusion genes are expected to lead to the development of novel therapeutic strategies for EHE. This article aims to provide a comprehensive review of EHE, encompassing its historical context, clinical manifestations, molecular biology and the current state of treatment.
Early enteral nutrition and mobilization following head and neck surgery with free flap reconstruction
Authors: Yamamoto Takuya , Shinozaki Takeshi , Nishiya Yukio , Okano Wataru , Tomioka Toshifumi , Matsuura Kazuto , Furuse Kiichi , Oshima Azusa , Higashino Takuya , Hayashi Ryuichi
Published: March 2024

Background

Perioperative management methods that reduce surgery-associated invasiveness and improve the quality of postoperative recovery are being promoted as enhanced recovery after surgery programs in various areas. Early enteral nutrition and mobilization are essential elements for enhanced recovery after surgery; however, their safety and feasibility are unclear in head and neck surgery with free tissue transfer reconstruction. This study aimed to clarify these uncertainties.

Methods

This is a retrospective before–after study. From 2018 to 2022, 187 and 173 patients received conventional management on or before April 2020 and early management on or after May 2020, respectively. The conventional management and early management groups received enteral nutrition and mobilization on postoperative days 2 and 1, respectively. The primary outcome for safety assessment was the incidence of complications. The secondary outcome was the compliance rate of conventional management or early management for feasibility assessment and the length of hospital stay.

Results

The clinical tumour–node–metastasis stage and American Society of Anesthesiologists physical status showed significant differences between the groups. In multivariable analysis, the early management group demonstrated a significantly lower incidence of treatment-required complication classified Clavien–Dindo Grade 2 and above (odds ratio = 0.57; 95% confidence interval = 0.31–0.92) and lower wound infection (odds ratio = 0.53; 95% confidence interval = 0.31–0.92). The early management group had lower compliance rate than the conventional management group; however, no statistically significant difference was observed (79.8% vs. 85.0%, P = 0.21).

Conclusion

Early management is safe and feasible following head and neck surgery with free tissue transfer reconstruction. It could reduce the complication rate and is considered a useful postoperative management method.