bluuebunny/crossref_metadata_2025 huggingface dataset:
Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria
Authors: Sereika Mantas , Petriglieri Francesca , Jensen Thomas Bygh Nymann , Sannikov Artur , Hoppe Morten , Nielsen Per Halkjær , Marshall Ian P G , Schramm Andreas , Albertsen Mads
Published: January 2023

Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the “saltwater” Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
Cortical-blood vessel assembloids exhibit Alzheimer’s disease phenotypes by activating glia after SARS-CoV-2 infection
Authors: Kong Dasom , Park Ki Hoon , Kim Da-Hyun , Kim Nam Gyo , Lee Seung-Eun , Shin Nari , Kook Myung Geun , Kim Young Bong , Kang Kyung-Sun
Published: January 2023

A correlation between COVID-19 and Alzheimer’s disease (AD) has been proposed recently. Although the number of case reports on neuroinflammation in COVID-19 patients has increased, studies of SARS-CoV-2 neurotrophic pathology using brain organoids have restricted recapitulation of those phenotypes due to insufficiency of immune cells and absence of vasculature. Cerebral pericytes and endothelial cells, the major components of blood-brain barrier, express viral entry receptors for SARS-CoV-2 and response to systemic inflammation including direct cell death. To overcome the limitations, we developed cortical-blood vessel assembloids by fusing cortical organoid with blood vessel organoid to provide vasculature to brain organoids a nd obtained the characteristics of increased expression of microglia and astrocytes in brain organoids. Furthermore, we observed AD pathologies, including β-amyloid plaques, which were affected by the inflammatory response from SARS-CoV-2 infection. These findings provide an advanced platform to investigate human neurotrophic diseases, including COVID-19, and suggest that neuroinflammation caused by viral infection facilitates AD pathology.
Gut microbiota and microbiota-derived metabolites promotes endometriosis
Authors: Chadchan Sangappa B. , Naik Sumanta K. , Popli Pooja , Talwar Chandni , Putluri Satwikreddy , Ambati Chandrasekhar R. , Lint Michael A. , Kau Andrew L. , Stallings Christina L. , Kommagani Ramakrishna
Published: January 2023

Endometriosis is a pathological condition of the female reproductive tract characterized by the existence of endometrium-like tissue at ectopic sites, affecting 10% of women between the age 15 and 49 in the USA. However, currently there is no reliable non-invasive method to detect the presence of endometriosis without surgery and many women find hormonal therapy and surgery as ineffective in avoiding the recurrences. There is a lack of knowledge on the etiology and the factors that contribute to the development of endometriosis. A growing body of recent evidence suggests an association between gut microbiota and endometriosis pathophysiology. However, the direct impact of microbiota and microbiota-derived metabolites on the endometriosis disease progression is largely unknown. To understand the causal role of gut microbiota and endometriosis, we have implemented a novel model using antibiotic-induced microbiota-depleted (MD) mice to investigate the endometriosis disease progression. Interestingly, we found that MD mice showed reduced endometriotic lesion growth and, the transplantation of gut microbiota by oral gavage of feces from mice with endometriosis rescued the endometriotic lesion growth. Additionally, using germ-free donor mice, we indicated that the uterine microbiota is dispensable for endometriotic lesion growth in mice. Furthermore, we showed that gut microbiota modulates immune cell populations in the peritoneum of lesions-bearing mice. Finally, we found a novel signature of microbiota-derived metabolites that were significantly altered in feces of mice with endometriosis. Finally, we found one the altered metabolite, quinic acid promoted the survival of endometriotic epithelial cells in vitro and lesion growth in vivo, suggesting the disease-promoting potential of microbiota-derived metabolites. In summary, these data suggest that gut microbiota and microbiota-derived metabolome contribute to lesion growth in mice, possibly through immune cell adaptations. Of translational significance, these findings will aid in designing non-invasive diagnostics using stool metabolites for endometriosis.
Enhancing the coherence of superconducting quantum bits with electric fields
Authors: Lisenfeld Jürgen , Bilmes Alexander , Ustinov Alexey V.
Published: January 2023

In the endeavor to make quantum computers a reality, integrated superconducting circuits have become a promising architecture. A major challenge of this approach is decoherence originating from spurious atomic tunneling defects at the interfaces of qubit electrodes, which may resonantly absorb energy from the qubit’s oscillating electric field and reduce the qubit’s energy relaxation time T1. Here, we show that qubit coherence can be improved by tuning dominating defects away from the qubit resonance using an applied DC-electric field. We demonstrate a method that optimizes the applied field bias and enhances the average qubit T1 time by 23%. We also discuss how local gate electrodes can be implemented in superconducting quantum processors to enable simultaneous in situ coherence optimization of individual qubits.
City-scale holographic traffic flow data based on vehicular trajectory resampling
Authors: Wang Yimin , Chen Yixian , Li Guilong , Lu Yuhuan , He Zhaocheng , Yu Zhi , Sun Weiwei
Published: January 2023

Despite abundant accessible traffic data, researches on traffic flow estimation and optimization still face the dilemma of detailedness and integrity in the measurement. A dataset of city-scale vehicular continuous trajectories featuring the finest resolution and integrity, as known as the holographic traffic data, would be a breakthrough, for it could reproduce every detail of the traffic flow evolution and reveal the personal mobility pattern within the city. Due to the high coverage of Automatic Vehicle Identification (AVI) devices in Xuancheng city, we constructed one-month continuous trajectories of daily 80,000 vehicles in the city with accurate intersection passing time and no travel path estimation bias. With such holographic traffic data, it is possible to reproduce every detail of the traffic flow evolution. We presented a set of traffic flow data based on the holographic trajectories resampling, covering the whole city, including stationary average speed and flow data of 5-minute intervals and dynamic floating car data (FCD).
China’s process-related greenhouse gas emission dataset 1990–2020
Authors: Yu Xiang , Tan Chang
Published: January 2023

China’s industrial process-related Greenhouse Gas (GHG) emissions are growing rapidly and are already equivalent to 13–19% of energy-related emissions in the past three decades. Previous studies mainly focused on emissions from fossil fuel combustion, however, there are a broad range of misconceptions regarding the trend and source of process-related emissions. To effectively implement emission reduction policies, it is necessary to compile an accurate accounting of process-related GHG emissions. However, the incompleteness in scope, unsuitable emission factor, and delay in updates in the current emission inventory have led to inaccurate emission estimates and inefficient mitigation actions. Following the methodology provided by Intergovernmental Panel on Climate Change (IPCC), we constructed a time series inventory of process-related GHG emissions for 15 industrial products from 1990–2020 in China. This emission inventory covers more than 90% of China’s process-related GHG emissions. In our study, emission factors were adjusted to refer to the industrial production process, technology, and raw material structure in China, which has led to increased accuracy of emission accounting. The dataset can help identify the sources of process-related GHG emissions in China and provide a data base for further policy implications.
Buffalo milk and rumen fluid metabolome are significantly affected by green feed
Authors: Neglia G. , Cotticelli A. , Vassetti A. , Matera R. , Staropoli A. , Vinale F. , Salzano A. , Campanile G.
Published: January 2023

The use of green feed for livestock breeding is an important strategy to encounter both the increasing demand for animal derived products and the perceptions of the consumers regarding animal welfare and sustainability. The aim of this study was to compare different feeding strategies in lactating water buffaloes by using a metabolomic approach. The study was carried out on 32 milking buffaloes that were randomly divided into two groups for a total period of 90 days (3 sampling times). DD Group (dry diet) received a standard total mixed ratio (TMR) characterized by dry forages and concentrates; ZG Group (zero grazing) fed an isoenergetic and isoproteic diet obtained using 30% of sorghum as green forage. Samples of milk and rumen fluid were analyzed by liquid chromatography—mass spectrometry (LC–MS) techniques. Data analyses revealed the presence of several differentially accumulated metabolites and among these, ten compounds were putatively identified in milk samples (i.e. l-carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, 2-methylbutyroylcarnitine, 2-hexenoylcarnitine, hexanoylcarnitine, glycerophosphocholine, δ-valerobetaine and γ-butyrobetaine) and four in rumen fluid (3-(2-hydroxyphenyl) propanoate, Indole-3-acrylic acid, oleamide (cis-9,10-octadecenoamide) and 20-carboxy-leukotriene B4). The modulation of these molecules in buffalo milk is significantly related to the green/dry based feeding and some the natural compound detected could be considered as health-promoting nutrients.
Administration of anti-inflammatory M2 macrophages suppresses progression of angiotensin II-induced aortic aneurysm in mice
Authors: Ashida Shinichi , Yamawaki-Ogata Aika , Tokoro Masayoshi , Mutsuga Masato , Usui Akihiko , Narita Yuji
Published: January 2023

Aortic aneurysm (AA) is a vascular disorder characterized pathologically by inflammatory cell invasion and extracellular matrix (ECM) degradation. It is known that regulation of the balance between pro-inflammatory M1 macrophages (M1Ms) and anti-inflammatory M2 macrophages (M2Ms) plays a pivotal role in AA stabilization. We investigated the effects of M2M administration in an apolipoprotein E-deficient (apoE−/−) mouse model in which AA was induced by angiotensin II (ATII) infusion. Mice received intraperitoneal administration of 1 million M2Ms 4 weeks after ATII infusion. Compared with a control group that was administered saline, the M2M group exhibited reduced AA expansion; decreased expression levels of interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and monocyte chemoattractant protein-1 (MCP-1); and a lower M1M/M2M ratio. Moreover, the M2M group exhibited upregulation of anti-inflammatory factors, including IL-4 and IL-10. PKH26-labeled M2Ms accounted for 6.5% of cells in the aneurysmal site and co-expressed CD206. Taken together, intraperitoneal administration of M2Ms inhibited AA expansion by reducing the inflammatory reaction via regulating the M1M/M2M ratio. This study shows that M2M administration might be useful for the treatment of AA.
Vascular malperfusion and abruption are prevalent in placentas from pregnancies with congenital heart disease and not associated with cardiovascular risk
Authors: Altendahl Marie , Mok Thalia , Adimkpayah Ekene , Goldstein Jeffrey , Lin Jeannette , Afshar Yalda
Published: January 2023

Congenital heart disease (CHD) in pregnancy is associated with an increased risk of adverse maternal, obstetric, and neonatal outcomes, plausibly through mechanisms involving abnormal placental development and function. This retrospective study aims to elucidate how maternal CHD influences placental health. Demographic and clinical information were collected via electronic medical record review, and placentas underwent histopathological evaluation. Fifty-three singleton pregnancies were included: 35 participants (66%) were classified as lower cardiovascular risk (modified World Health Organization Classification (mWHO) I, II, II-III), and 18 (34%) were classified as higher cardiovascular risk (mWHO III, IV). 12 participants (23%) had a fetus with small for gestational age (SGA). Maternal vascular malperfusion (53%) and placental abruption (11.6%) were common in this cohort, with prevalence above baseline risk. Participants at higher cardiovascular risk had higher rates of SGA (p = 0.04), subchorionic hematomas (p = 0.01) and birth weight:placental weight < 10th percentile (p = 0.04), but did not differ in rates of maternal vascular malperfusion (p = 0.15) compared to those at lower cardiovascular risk. In pregnancies with maternal CHD, SGA and histologic evidence of maternal vascular malperfusion and placental abruption were common, though patients at higher cardiovascular risk did not show evidence of worsened placental health compared to those at lower risk.
Citrulline and kynurenine to tryptophan ratio: potential EED (environmental enteric dysfunction) biomarkers in acute watery diarrhea among children in Bangladesh
Authors: Das Rina , Haque Md. Ahshanul , Sobi Rukaeya Amin , Sultana Al-Afroza , Khan Murad Alam , Gazi Amran , Mahfuz Mustafa , Nahar Baitun , Bardhan Pradip Kumar , Ahmed Tahmeed
Published: January 2023

Two emerging biomarkers of environmental enteric dysfunction (EED) include plasma citrulline (CIT), and the kynurenine (KYN): tryptophan (TRP)/ (KT) ratio. We sought to investigate the plasma concentration of CIT and KT ratio among the children having dehydrating diarrhea and examine associations between concentrations of CIT and KT ratio with concurrent factors. For this analysis, we used cross-sectional data from a total of 102, 6–36 months old male children who suffered from non-cholera acute watery diarrhea and had some dehydration admitted to an urban diarrheal hospital, in Bangladesh. CIT, TRP, and KYN concentrations were determined at enrollment from plasma samples using ELIZA. At enrollment, the mean plasma CIT concentration was 864.48 ± 388.55 µmol/L. The mean plasma kynurenine, tryptophan concentrations, and the KT ratio (× 1000) were 6.93 ± 3.08 µmol/L, 33.44 ± 16.39 µmol/L, and 12.12 ± 18.10, respectively. With increasing child age, KYN concentration decreased (coefficient: − 0.26; 95%CI: − 0.49, − 0.04; p = 0.021); with increasing lymphocyte count, CIT concentration decreased (coef.: − 0.01; 95% CI: − 0.02,0.001, p = 0.004); the wasted child had decreased KT ratio (coef.: − 0.6; 95% CI: − 1.18, − 0.02; p = 0.042) after adjusting for potential covariates. The CIT concentration was associated with blood neutrophils (coef.: 0.02; 95% CI: 0.01, 0.03; p < 0.001), lymphocytes (coef.: − 0.02; 95% CI: − 0.03, − 0.02; p < 0.001) and monocyte (coef.: 0.06; 95% CI: 0.01, 0.11; p = 0.021); KYN concentration was negatively associated with basophil (coef.: − 0.62; 95% CI: − 1.23, − 0.01; p = 0.048) after adjusting for age. In addition, total stool output (gm) increased (coef.: 793.84; 95% CI: 187.16, 1400.52; p = 0.011) and also increased duration of hospital stay (hour) (coef.: 22.89; 95% CI: 10.24, 35.54; p = 0.001) with increasing CIT concentration. The morphological changes associated with EED may increase the risk of enteric infection and diarrheal disease among children. Further research is critically needed to better understand the complex mechanisms by which EED biomarkers may impact susceptibility to dehydrating diarrhea in children.
Diagnosis and treatment patterns among patients with newly diagnosed Helicobacter pylori infection in the United States 2016–2019
Authors: Shah Shailja , Cappell Katherine , Sedgley Robert , Pelletier Corey , Jacob Rinu , Bonafede Machaon , Yadlapati Rena
Published: January 2023

Approximately 36% of the United States (US) population is infected with Helicobacter pylori (HP), a known major risk factor for peptic ulcer disease and gastric cancer. HP eradication reduces the rate of complications; however, the benefits are undermined by rising rates of HP eradication treatment failure. This real-world observational cohort analysis aims to describe HP diagnostic and treatment patterns among insured patients in the US. Using diagnoses, lab results, and treatment patterns, we identified adults (18+) with new diagnoses of HP in the Veradigm Health Insights EHR Database linked to Komodo claims data (1/1/2016–12/31/2019). Patients were required to have ≥ 12 months of data pre-/post-index. We captured patient characteristics, HP-related diagnostic testing, and the use of US guideline-recommended HP eradication regimens. HP eradication rates following first-line eradication treatment were measured among patients with available lab results. Overall, 31.8% of the 60,593 included patients did not receive guideline-recommended treatment. Among the 68.2% (41,340) with first-line treatment, 80.2% received clarithromycin-based triple therapy, and 6.6% received bismuth quadruple therapy. Of the 4569 patients with a repeated course of eradication therapy, 53.4% received the same regimen as their first-line, the majority (90.7%) of whom received two rounds of clarithromycin-based triple therapy. Among the 2455 patients with results of HP non-serology testing following first-line treatment, the 180-day eradication rate was 80.2% overall, with differences based on treatments and demographics. This study highlights gaps between guideline-recommended HP management and real-world patterns, underscoring the need to improve HP testing, treatment, and follow-up practices.
Modeling community COVID-19 transmission risk associated with U.S. universities
Authors: Uelmen J. A. , Kopsco H. , Mori J. , Brown W. M. , Smith R. L.
Published: January 2023

The ongoing COVID-19 pandemic is among the worst in recent history, resulting in excess of 520,000,000 cases and 6,200,000 deaths worldwide. The United States (U.S.) has recently surpassed 1,000,000 deaths. Individuals who are elderly and/or immunocompromised are the most susceptible to serious sequelae. Rising sentiment often implicates younger, less-vulnerable populations as primary introducers of COVID-19 to communities, particularly around colleges and universities. Adjusting for more than 32 key socio-demographic, economic, and epidemiologic variables, we (1) implemented regressions to determine the overall community-level, age-adjusted COVID-19 case and mortality rate within each American county, and (2) performed a subgroup analysis among a sample of U.S. colleges and universities to identify any significant preliminary mitigation measures implemented during the fall 2020 semester. From January 1, 2020 through March 31, 2021, a total of 22,385,335 cases and 374,130 deaths were reported to the CDC. Overall, counties with increasing numbers of university enrollment showed significantly lower case rates and marginal decreases in mortality rates. County-level population demographics, and not university level mitigation measures, were the most significant predictor of adjusted COVID-19 case rates. Contrary to common sentiment, our findings demonstrate that counties with high university enrollments may be more adherent to public safety measures and vaccinations, likely contributing to safer communities.
Preliminary comparison of the modified extraperitoneal free-PORT single incision technique and transabdominal multi-incision robot-assisted laparoscopic radical prostatectomy
Authors: Ren Shangqing , Ou Yong , Wang Yaoqian , Wei Yi , Luo Cheng , Yang Bo , Yuan Jiazheng , Lv Qian , Zhou Fang , Chen Zhengjun , Nie Yu , Lin Jie , Wu Yilei , Yang Bo , Fan Shida , Wang Dong
Published: January 2023

To compare the clinical efficacy of an innovative modified single-incision technique without special extraperitoneal PORT with that of transperitoneal multi-incision robot-assisted laparoscopic radical prostatectomy and to explore the feasibility and safety of the former. A retrospective analysis was performed on 259 patients who received robot-assisted laparoscopic radical prostatectomy in the Robot Minimally Invasive Center of Sichuan Provincial People's Hospital between September 2018 and August 2021. Among them were 147 cases involving extraperitoneal single incision with no special PORT (Group A) and 112 cases involving multiple incisions by the transperitoneal method (Group B). Differences in age, PSA level, Gleason score, prostate volume, body mass index, clinical stage, lower abdominal operation history, and lymph node dissection ratio between the two groups were not statistically significant (P > 0.05). All operations were performed by the same operator. In this study, all 259 operations were completed successfully, and there was no conversion. There was no significant difference in transperitoneal blood loss, postoperative hospital stay, positive rate of incision margin, indwelling time of urinary catheter, satisfaction rate of immediate urine control, satisfaction rate of urine control 3 months after operation, positive rate of postoperative lymph node pathology or postoperative pathological stage between the two groups (P > 0.05). There were significant differences in operation time, postoperative exhaust time and incision length (P < 0.05). The modified extraperitoneal nonspecial PORT single-incision technique is safe and feasible for robot-assisted laparoscopic radical prostatectomy, and its curative effect is similar to that of transperitoneal multi-incision RARP. It has the advantages of a short operation time, less impact on the gastrointestinal tract and a more beautiful incision. The long-term effect of treatment needs to be further confirmed by prospective studies.
Second-life battery systems for affordable energy access in Kenyan primary schools
Authors: Kebir Nisrine , Leonard Alycia , Downey Michael , Jones Bernie , Rabie Khaled , Bhagavathy Sivapriya Mothilal , Hirmer Stephanie A.
Published: January 2023

As the world transitions to net zero, energy storage is becoming increasingly important for applications such as electric vehicles, mini-grids, and utility-scale grid stability. The growing demand for storage will constrain raw battery materials, reduce the availability of new batteries, and increase the rate of battery retirement. As retired batteries are difficult to recycle into components, to avoid huge amounts of battery waste, reuse and repurposing options are needed. In this research, we explore the feasibility of using second-life batteries (which have been retired from their first intended life) and solar photovoltaics to provide affordable energy access to primary schools in Kenya. Based on interviews with 12 East African schools, realistic system sizes were determined with varying solar photovoltaic sizes (5–10 kW in 2.5 kW increments) and lithium-ion battery capacities (5–20 kWh in 5 kWh increments). Each combination was simulated under four scenarios as a sensitivity analysis of battery transportation costs (i.e., whether they are sourced locally or imported). A techno-economic analysis is undertaken to compare new and second-life batteries in the resulting 48 system scenarios in terms of cost and performance. We find that second-life batteries decrease the levelized cost of electricity by 5.6–35.3% in 97.2% of scenarios compared to similar systems with new batteries, and by 41.9–64.5% compared to the cost of the same energy service provided by the utility grid. The systems with the smallest levelized cost of electricity (i.e., 0.11 USD/kWh) use either 7.5 kW or 10 kW of solar with 20 kWh of storage. Across all cases, the payback period is decreased by 8.2–42.9% using second-life batteries compared to new batteries; the system with the smallest payback period (i.e., 2.9 years) uses 5 kW solar and 5 kWh storage. These results show second-life batteries to be viable and cost-competitive compared to new batteries for school electrification in Kenya, providing the same benefits while reducing waste.
Energy landscapes from cryo-EM snapshots: a benchmarking study
Authors: Dsouza Raison , Mashayekhi Ghoncheh , Etemadpour Roshanak , Schwander Peter , Ourmazd Abbas
Published: January 2023

Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.
Utilisation of exome sequencing for muscular disorders in Thai paediatric patients: diagnostic yield and mutational spectrum
Authors: Summa Sarinya , Ittiwut Chupong , Kulsirichawaroj Pimchanok , Paprad Tanitnun , Likasitwattanakul Surachai , Sanmaneechai Oranee , Boonsimma Ponghatai , Suphapeetiporn Kanya , Shotelersuk Vorasuk
Published: January 2023

Muscular dystrophies and congenital myopathies are heterogeneous groups of inherited muscular disorders. An accurate diagnosis is challenging due to their complex clinical presentations and genetic heterogeneity. This study aimed to determine the utilisation of exome sequencing (ES) for Thai paediatric patients with muscular disorders. Of 176 paediatric patients suspected of genetic/inherited myopathies, 133 patients received a molecular diagnosis after performing conventional investigations, single gene testing, and gene panels. The remaining 43 patients from 42 families could be classified into three groups: Group 1, MLPA-negative Duchenne muscular dystrophy (DMD) with 9 patients (9/43; 21%), Group 2, other muscular dystrophies (MD) with 18 patients (18/43; 42%) and Group 3, congenital myopathies (CM) with 16 patients (16/43; 37%). All underwent exome sequencing which could identify pathogenic variants in 8/9 (89%), 14/18 (78%), and 8/16 (50%), for each Group, respectively. Overall, the diagnostic yield of ES was 70% (30/43) and 36 pathogenic/likely pathogenic variants in 14 genes were identified. 18 variants have never been previously reported. Molecular diagnoses provided by ES changed management in 22/30 (73%) of the patients. Our study demonstrates the clinical utility and implications of ES in inherited myopathies.
A study of management decisions to adopt emission reduction measures in heavy industry in an emerging economy
Authors: Panjaitan Togar Wiliater Soaloon , Dargusch Paul , Wadley David , Aziz Ammar Abdul
Published: January 2023

Heavy industry can face challenges in choosing applicable climate change mitigation measures due to a lack of technical background and practical guidance. A better understanding of these determinants is needed to design region-specific climate policies that most effectively enable more ‘successful’ low carbon transitions. Set in an emerging economy, this study aims to understand the determinants which underlie investment decision-making in greenhouse gas reduction. It relies on empirical research using an exploratory case study method in the leading cement company in Indonesia. The results show four key determinants influencing (constraining) adoption were (1) the primacy of profit-seeking objectives in operational planning and development; (2) the availability of sources (clinker substitutes and alternative energy fuels); (3) the limited access to cash capital; and (4) the complexity in implementing emissions reduction projects. The inquiry also compares determinants in an emerging and developed country to provide a comparative perspective on emissions management in manufacturing. It appears that firms from the industrial sector in emerging economies have investment strategies that are largely characterised by activities that accentuate achieving financial benefits or best value for money or cost savings in a short time frame, or ‘short-termism’. Currently, greenhouse gas emissions management activities tend to be second-preference strategies for firms in emerging economies, at least in the industrial manufacturing sector.
Deformable cardiac surface tracking by adaptive estimation algorithms
Authors: Tuna E. Erdem , Franson Dominique , Seiberlich Nicole , Çavuşoğlu M. Cenk
Published: January 2023

This study presents a particle filter based framework to track cardiac surface from a time sequence of single magnetic resonance imaging (MRI) slices with the future goal of utilizing the presented framework for interventional cardiovascular magnetic resonance procedures, which rely on the accurate and online tracking of the cardiac surface from MRI data. The framework exploits a low-order parametric deformable model of the cardiac surface. A stochastic dynamic system represents the cardiac surface motion. Deformable models are employed to introduce shape prior to control the degree of the deformations. Adaptive filters are used to model complex cardiac motion in the dynamic model of the system. Particle filters are utilized to recursively estimate the current state of the system over time. The proposed method is applied to recover biventricular deformations and validated with a numerical phantom and multiple real cardiac MRI datasets. The algorithm is evaluated with multiple experiments using fixed and varying image slice planes at each time step. For the real cardiac MRI datasets, the average root-mean-square tracking errors of 2.61 mm and 3.42 mm are reported respectively for the fixed and varying image slice planes. This work serves as a proof-of-concept study for modeling and tracking the cardiac surface deformations via a low-order probabilistic model with the future goal of utilizing this method for the targeted interventional cardiac procedures under MR image guidance. For the real cardiac MRI datasets, the presented method was able to track the points-of-interests located on different sections of the cardiac surface within a precision of 3 pixels. The analyses show that the use of deformable cardiac surface tracking algorithm can pave the way for performing precise targeted intracardiac ablation procedures under MRI guidance. The main contributions of this work are twofold. First, it presents a framework for the tracking of whole cardiac surface from a time sequence of single image slices. Second, it employs adaptive filters to incorporate motion information in the tracking of nonrigid cardiac surface motion for temporal coherence.
Cross-domain few-shot learning based on pseudo-Siamese neural network
Authors: Gong Yuxuan , Yue Yuqi , Ji Weidong , Zhou Guohui
Published: January 2023

Cross-domain few-shot learning is one of the research highlights in machine learning. The difficulty lies in the accuracy drop of cross-domain network learning on a single domain due to the differences between the domains. To alleviate the problem, according to the idea of contour cognition and the process of human recognition, we propose a few-shot learning method based on pseudo-Siamese convolution neural network. The original image and the sketch map are respectively sent to the branch network in the pre-training and meta-learning process. While maintaining the original image features, the contour features are separately extracted as branch for training at the same time to improve the accuracy and generalization of learning. We conduct cross-domain few-shot learning experiments and good results have been achieved using mini-ImageNet as source domain, EuroSAT and ChestX as the target domains. Also, the results are qualitatively analyzed using a heatmap to verify the feasibility of our method.
Influence of water exchange rates on toxicity and bioaccumulation of hydrophobic organic chemicals in sediment toxicity tests
Authors: Hiki Kyoshiro , Fischer Fabian Christoph , Nishimori Takahiro , Endo Satoshi , Watanabe Haruna , Yamamoto Hiroshi
Published: January 2023

Water exchange conditions significantly affected the overlying water concentrations, but did not affect the pore water concentrations, survival, and bioaccumulation in the freshwater amphipod.
Changes in physiological profiles and co-occurrence patterns of soil microbial community following exposure to nanoceria and ionic cerium
Authors: Hong Jie , Jia Siying , Wei Lan , Wu Minhua , Chen Feng , He Feng , Ogundele Olamide R. , Rico Cyren M.
Published: January 2023

Soil microbial toxicity is an important topic for understanding the environmental risk of cerium oxide nanoparticles (nanoceria).
Generating water/MeOH-soluble and luminescent polymers by grafting 2,6-bis(1,2,3-triazol-4-yl)pyridine (btp) ligands onto a poly(ethylene-alt-maleic anhydride) polymer and cross-linking with terbium(iii)
Authors: Hegarty Isabel N. , Henwood Adam F. , Bradberry Samuel J. , Gunnlaugsson Thorfinnur
Published: January 2023

The synthesis of two new green emitting polymers, made by reacting the btp ligand 1 with the commercially available P(E-alt-MA) polymer and cross-linking with Tb(iii), is described.
Determination of enantiomeric excess and diastereomeric excess via optical methods. Application to α-methyl-β-hydroxy-carboxylic acids
Authors: Moor Sarah R. , Howard James R. , Herrera Brenden T. , McVeigh Matthew S. , Marini Federico , Keatinge-Clay Adrian T. , Anslyn Eric V.
Published: January 2023

Characterization of chiral molecules in solution is paramount for measuring reaction success.
Synthetic aspects of 1,4- and 1,5-benzodiazepines usingo-phenylenediamine: a study of past quinquennial
Authors: Teli Sunita , Teli Pankaj , Soni Shivani , Sahiba Nusrat , Agarwal Shikha
Published: January 2023

This paper presents recent evolutions in the synthetic aspects of 1,5- and 1,4-benzodiazepines usingo-phenylenediamine as a precursor and provides an up-to-date review of recent findings (2018–2022).
Cycling stability of Fe2O3 nanosheets as supercapacitor sheet electrodes enhanced by MgFe2O4 nanoparticles
Authors: Guo Guanlun , Su Qiwei , Zhou Wei , Wei Mingrui , Wang Yun
Published: January 2023

Compounding of Fe2O3 with MgFe2O4, leading to morphological changes and synergistic effects, resulting in significantly improved cycling stability of supercapacitor sheet electrode.
Evaluating methods to create protein functionalized catanionic vesicles
Authors: Zayka Paul , Parr Brendan , Robichaud Hannah , Hickey Skyler , Topping Amber , Holt Elizabeth , Watts David B. E. , Soto Nicholas , Stein Daniel C. , DeShong Philip , Hurley Matthew
Published: January 2023

A novel method to covalently attach proteins to the surface of catanionic surfactant vesicles is described.
Influence of deposition temperature on microstructure and gas-barrier properties of Al2O3 prepared by plasma-enhanced atomic layer deposition on a polycarbonate substrate
Authors: Ren Yueqing , Sun Xiaojie , Chen Lanlan , Wei Hui , Feng Bo , Chen Jingyun
Published: January 2023

Temperature dependence of the structural evolution of plasma-enhanced atomic layer deposited Al2O3 film and the PC substrate.
Preparation of highly stable and ultrasmooth chemically grafted thin films of chitosan
Authors: Garreau Cyrielle , Chiappisi Leonardo , Micciulla Samantha , Morfin Isabelle , Trombotto Stéphane , Delair Thierry , Sudre Guillaume
Published: January 2023

A simple and easily scalable procedure is presented for the grafting of ultra-smooth and stable chitosan films, with thicknesses ranging from a few tens of nanometers to several microns.
Long-term plasticity of astrocytic phenotypes and their control by neurons in health and disease
Authors: Wardlaw Kyle S. , Hardingham Giles E.
Published: January 2023

The brain is a complex organ even when viewed from a cell biological perspective. Neuronal networks are embedded in a dense milieu of diverse and specialised cell types, including several types of vascular, immune, and macroglial cells. To view each cell as a small cog in a highly complex machine is itself an oversimplification. Not only are they functionally coupled to enable the brain to operate, each cell type’s functions are themselves influenced by each other, in development, maturity, and also in disease. Astrocytes are a type of macroglia that occupy a significant fraction of the human forebrain. They play a critical role in sustaining functional neuronal circuits across the lifespan through myriad homeostatic functions including the maintenance of redox balance, ionic gradients, neurotransmitter clearance, and bioenergetic support. It is becoming apparent that astrocytes’ capacity to carry out these and other neurosupportive roles is not fixed, but is regulated by signals coming from the neurons themselves, both in the healthy brain but also in response to neuron-derived disease pathology. Here, we review mechanisms by which neurons control the properties of astrocytes long term in order to alter their homeostatic capacity both in development and maturity. Our working hypothesis is that these signals are designed to change and maintain the homeostatic capacity of local astrocytes to suit the needs of nearby neurons. Knowledge of the external signals that can control core aspects of a healthy astrocytic phenotype are being uncovered, raising the question as to whether this knowledge can be harnessed to promote astrocyte-mediated neurosupport in brain disorders.
Mucin utilization by gut microbiota: recent advances on characterization of key enzymes
Authors: Raba Grete , Luis Ana S.
Published: January 2023

The gut microbiota interacts with the host through the mucus that covers and protects the gastrointestinal epithelium. The main component of the mucus are mucins, glycoproteins decorated with hundreds of different O-glycans. Some microbiota members can utilize mucin O-glycans as carbons source. To degrade these host glycans the bacteria express multiple carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases, sulfatases and esterases which are active on specific linkages. The studies of these enzymes in an in vivo context have started to reveal their importance in mucin utilization and gut colonization. It is now clear that bacteria evolved multiple specific CAZymes to overcome the diversity of linkages found in O-glycans. Additionally, changes in mucin degradation by gut microbiota have been associated with diseases like obesity, diabetes, irritable bowel disease and colorectal cancer. Thereby understanding how CAZymes from different bacteria work to degrade mucins is of critical importance to develop new treatments and diagnostics for these increasingly prevalent health problems. This mini-review covers the recent advances in biochemical characterization of mucin O-glycan-degrading CAZymes and how they are connected to human health.
Identification of large equivalent width dusty galaxies at 4 < z < 6 from sub-millimetre colours
Authors: Burgarella D. , Theulé P. , Buat V. , Gouiran L. , Turco L. , Boquien M. , Bakx T. J. L. C. , Inoue A. K. , Fudamoto Y. , Sugahara Y. , Zavala J.
Published: January 2023

Context. Infrared (IR), sub-millimetre (sub-mm), and millimetre (mm) databases contain a huge quantity of high-quality data. However, a large part of these data are photometric, and they are thought not to be useful to derive quantitative information on the nebular emission of galaxies.

Aims. The aim of this project is first to identify galaxies at z ≳ 4–6 and in the epoch of reionisation from their sub-millimetre colours. We also aim to show that the colours can be used to try and derive physical constraints from photometric bands when accounting for the contribution from the IR fine structure lines to these photometric bands.

Methods. We modelled the flux of IR fine structure lines with CLOUDY and added them to the dust continuum emission with CIGALE. Including (or not) emission lines in the simulated spectral energy distribution (SED) modifies the broad-band emission and colours.

Results. The introduction of the lines allows us to identify strong star forming galaxies at z ≳ 4–6 from the [log10(PSW250μm)/(PMW350μm) versus log10(LABOCA870μm)/(PLW500μm)] colour-colour diagram. By comparing the relevant models to each observed galaxy colour, we are able to roughly estimate the fluxes of the lines and the associated nebular parameters. This method allows us to identify a double sequence in a plot built from the ionisation parameter and the gas metallicity.

Conclusions. The HII and photodissociation region fine structure lines are an essential part of the SEDs. It is important to add them when modelling the spectra, especially at z ≳ 4–6, where their equivalent widths can be large. Conversely, we show that we can extract some information on strong-IR fine structure lines and on the physical parameters related to the nebular emission from IR colour-colour diagrams.
Two-Step Progressive Transcrestal Sinus Augmentation Using a 4.5 mm Unloaded Implant as a “Temporary Implant” in Highly Atrophic Ridge: Case Report
Authors: Anitua Eduardo
Published: January 2023

Severe atrophic posterior maxillary ridge (residual bone height < 3 mm) could be a challenging situation to place dental implants. Several treatment options have been proposed, but some of them may require advanced surgical skills to achieve best results. In this article, we present a novel and easier technique to allow implant placing in localized areas of severe atrophy. In a first step, a 4.5-length extra-short (unloaded) implant is placed after a transcrestal maxillary sinus floor augmentation (MSFA). After the gained apical bone consolidation, this “temporary implant” is atraumatically removed and a longer and wider definitive implant is placed to support the definitive single restoration. The case of a 45-year-old female treated with this approach is also presented. The patient suffered a severe resorption in the upper right molar area after a tooth extraction. Four months after the “temporary implant” placement and MSFA grafting with plasma rich in growth factors and autologous bone, 3 mm of dense apical bone gain could be observed. In a second surgical time, the 4.5 mm-length “temporary implant” was removed, and a 5.5 mm-length “definitive implant” was placed. This second implant was placed in a denser type 1 (1,000 Hounsfield Unit) new formed apical bone. Four months later, the implant was loaded with a screw-retained crown over a transepithelial (intermediate abutment). After 1-year follow-up, the implant was in health and no mechanical or biological complications were noticed. The satisfactory results of this case encourage the realization of new studies to elucidate its reproducibility.
Evaluation of Tension and Deformation in a Mandibular Toronto Bridge Anchored on Three Fixtures Using Different Framework Materials, Abutment Systems, and Loading Conditions: A FEM Analysis
Authors: Grande Francesco , Cesare Pozzan Mario , Mochi Zamperoli Edoardo , Gianoli Camilla Martina , Mollica Francesco , Catapano Santo
Published: January 2023

Objective The aim of this study was to investigate by finite element method analysis the behaviour of a three-implant mandible Toronto framework made by three different materials, with two abutment systems and two loading conditions.

Materials and Methods Three implants were virtually inserted in a mandible model in positions 3.6, 4.1, and 4.6. Three prosthetic framework bars with the same design and dimension (4.8 × 5.5 mm) were projected. The variables introduced in the computer model were the framework materials (glass fiber reinforced resin, Co-Cr, TiAl6V4), the abutment systems (Multi-Unit-Abutment [MUA]/OT-Bridge), and the loading conditions (500 N vertical load on all the framework area and 400 N on a 7-mm distal cantilever). The computer was programmed with physical properties of the materials as derived from the literature. Maximum tension and deformation values for each variable were registered at framework, screws, and abutment level and then compared.

Results Metal frameworks Cr-Co and TiAl6V4 resulted in lower deformation than glass fiber-reinforced resin frameworks while presenting higher tension values. The OT-Bridge exhibited lower maximum tension and deformation values than the MUA system. The first loading condition reached higher tension and deformation values than the second and it resulted in more uniformly distributed load on all the framework area, especially with the OT-Bridge system.

Conclusion More rigid materials and OT-Bridge system decrease the deformation on the prosthetic components. Tension stresses are more uniformly distributed with glass fiber-reinforced resin, in the OT-Bridge system and avoiding cantilever loading.
A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome
Authors: Sidebottom Ashley M.
Published: January 2023

Over the past 20 years, the study of microbial communities has benefited from simultaneous advancements across several fields resulting in a high-resolution view of human consortia. Although the first bacterium was described in the mid-1600s, the interest in community membership and function has not been a focus or feasible until recent decades. With strategies such as shotgun sequencing, microbes can be taxonomically profiled without culturing and their unique variants defined and compared across phenotypes. Approaches such as metatranscriptomics, metaproteomics, and metabolomics can define the current functional state of a population through the identification of bioactive compounds and significant pathways. Prior to sample collection in microbiome-based studies it is critical to evaluate the requirements of downstream analyses to ensure accurate processing and storage for generation of high data quality. A common pipeline for the analysis of human samples includes approval of collection protocols and method finalization, patient sample collection, sample processing, data analysis, and visualization. Human-based microbiome studies are inherently challenging but with the application of complementary multi-omic strategies there is an unbounded potential for discovery.