bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baseline proteomics characterisation of the emerging host biomanufacturing organism Halomonas bluephagenesis
Authors: Russell Matthew , Currin Andrew , Rowe William , Chen Guo-Qiang , Barran Perdita , Scrutton Nigel S. 
Published: August 2022

AbstractDespite its greener credentials, biomanufacturing remains financially uncompetitive compared with the higher carbon emitting, hydrocarbon-based chemical industry. Replacing traditional chassis such as E. coli with novel robust organisms, are a route to cost reduction for biomanufacturing. Extremophile bacteria such as the halophilic Halomonas bluephagenesis TD01 exemplify this potential by thriving in environments inherently inimical to other organisms, so reducing sterilisation costs. Novel chassis are inevitably less well annotated than established organisms. Rapid characterisation along with community data sharing will facilitate adoption of such organisms for biomanufacturing. The data record comprises a newly sequenced genome for the organism and evidence via LC-MS based proteomics for expression of 1160 proteins (30% of the proteome) including baseline quantification of 1063 proteins (27% of the proteome), and a spectral library enabling re-use for targeted LC-MS proteomics assays. Protein data are annotated with KEGG Orthology, enabling rapid matching of quantitative data to pathways of interest to biomanufacturing.
Identification of small molecules targeting homoserine acetyl transferase from Mycobacterium tuberculosis and Staphylococcus aureus
Authors: Chaudhary Deepika , Singh Avantika , Marzuki Mardiana , Ghosh Abhirupa , Kidwai Saqib , Gosain Tannu Priya , Chawla Kiran , Gupta Sonu Kumar , Agarwal Nisheeth , Saha Sudipto , Kumar Yashwant , Thakur Krishan Gopal , Singhal Amit , Singh Ramandeep 
Published: August 2022

AbstractThere is an urgent need to validate new drug targets and identify small molecules that possess activity against both drug-resistant and drug-sensitive bacteria. The enzymes belonging to amino acid biosynthesis have been shown to be essential for growth in vitro, in vivo and have not been exploited much for the development of anti-tubercular agents. Here, we have identified small molecule inhibitors targeting homoserine acetyl transferase (HSAT, MetX, Rv3341) from M. tuberculosis. MetX catalyses the first committed step in L-methionine and S-adenosyl methionine biosynthesis resulting in the formation of O-acetyl-homoserine. Using CRISPRi approach, we demonstrate that conditional repression of metX resulted in inhibition of M. tuberculosis growth in vitro. We have determined steady state kinetic parameters for the acetylation of L-homoserine by Rv3341. We show that the recombinant enzyme followed Michaelis–Menten kinetics and utilizes both acetyl-CoA and propionyl-CoA as acyl-donors. High-throughput screening of a 2443 compound library resulted in identification of small molecule inhibitors against MetX enzyme from M. tuberculosis. The identified lead compounds inhibited Rv3341 enzymatic activity in a dose dependent manner and were also active against HSAT homolog from S. aureus. Molecular docking of the identified primary hits predicted residues that are essential for their binding in HSAT homologs from M. tuberculosis and S. aureus. ThermoFluor assay demonstrated direct binding of the identified primary hits with HSAT proteins. Few of the identified small molecules were able to inhibit growth of M. tuberculosis and S. aureus in liquid cultures. Taken together, our findings validated HSAT as an attractive target for development of new broad-spectrum anti-bacterial agents that should be effective against drug-resistant bacteria.
Machine learning in point-of-care automated classification of oral potentially malignant and malignant disorders: a systematic review and meta-analysis
Authors: Ferro Ashley , Kotecha Sanjeev , Fan Kathleen 
Published: August 2022

AbstractMachine learning (ML) algorithms are becoming increasingly pervasive in the domains of medical diagnostics and prognostication, afforded by complex deep learning architectures that overcome the limitations of manual feature extraction. In this systematic review and meta-analysis, we provide an update on current progress of ML algorithms in point-of-care (POC) automated diagnostic classification systems for lesions of the oral cavity. Studies reporting performance metrics on ML algorithms used in automatic classification of oral regions of interest were identified and screened by 2 independent reviewers from 4 databases. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed. 35 studies were suitable for qualitative synthesis, and 31 for quantitative analysis. Outcomes were assessed using a bivariate random-effects model following an assessment of bias and heterogeneity. 4 distinct methodologies were identified for POC diagnosis: (1) clinical photography; (2) optical imaging; (3) thermal imaging; (4) analysis of volatile organic compounds. Estimated AUROC across all studies was 0.935, and no difference in performance was identified between methodologies. We discuss the various classical and modern approaches to ML employed within identified studies, and highlight issues that will need to be addressed for implementation of automated classification systems in screening and early detection.
Longitudinal follow-up of the asthma status in a French–Canadian cohort
Authors: Lavoie Marie-Eve , Meloche Jolyane , Boucher-Lafleur Anne-Marie , Bégin Paul , Morin Charles , Boulet Louis-Philippe , Madore Anne-Marie , Laprise Catherine 
Published: August 2022

AbstractAsthma affects 340 million people worldwide and varies in time. Twenty years ago, in Canada, the Saguenay–Lac-Saint-Jean asthma family cohort was created to study the genetic and environmental components of asthma. This study is a follow-up of 125 participants of this cohort to explore the appearance, persistence, and progression of asthma over 10–20 years. Participants answered a clinical standardized questionnaire. Lung function was assessed (forced expiratory volume in 1 s, forced vital capacity, bronchial reversibility, and methacholine bronchoprovocation), skin allergy testing was performed, blood samples were obtained (immunoglobulin E, white blood cell counts) and phenotypes were compared between recruitment and follow-up. From the participants without asthma at recruitment, 12% developed a phenotype of adult-onset asthma with the presence of risk factors, such as atopy, high body mass index, and exposure to smoking. A decrease of PC20 values in this group was observed and a decrease in the FEV1/FVC ratio in all groups. Also, 7% of individuals with asthma at recruitment developed chronic obstructive pulmonary disease, presenting risk factors at recruitment, such as moderate-to-severe bronchial hyperresponsiveness, exposure to smoking, and asthma. This study allowed a better interpretation of the evolution of asthma. Fine phenotypic characterization is the first step for meaningful genetic and epigenetic studies.
Energy consumption, CO2 emissions and electricity costs of lighting for commercial buildings in Southeast Asia
Authors: Hong Wan Yun , Rahmat Bibi Nurmuslihah Ni’matullah Nura’l 
Published: August 2022

AbstractBuilding energy intensity (BEI) has been used to assess a building’s overall energy performance. However, the energy performance, CO2 footprint and electricity costs due to lighting in buildings are currently required to assist relevant authorities to develop, revise and implement energy-efficient lighting policies that are effective and acceptable for the country. This work presents an estimation approach for lighting in commercial buildings in Southeast Asia and its decarbonisation pathway for benchmarking. Application of this approach to a selected library in Brunei Darussalam showed that an energy-efficient light-emitting diode (LED) lighting system would make the building greener. We projected reductions in lighting energy consumption by 6.7 times (3.98 kWh/m2/year), its associated CO2 emissions by 8 times (0.59 kg CO2/m2/year) and electricity costs by 8.7 times (B$7.07/m2/year) by 2050 if existing lamps in the library are retrofitted with LED lamps.
Pollinator and floral odor specificity among four synchronopatric species of Ceropegia (Apocynaceae) suggests ethological isolation that prevents reproductive interference
Authors: Kidyoo Aroonrat , Kidyoo Manit , McKey Doyle , Proffit Magali , Deconninck Gwenaëlle , Wattana Pichaya , Uamjan Nantaporn , Ekkaphan Paweena , Blatrix Rumsaïs 
Published: August 2022

AbstractPossession of flowers that trap fly pollinators is a conservative trait within the genus Ceropegia, in which pollination systems can be generalized or highly specialized. However, little is known about the role of plant–pollinator interactions in the maintenance of species boundaries. This study examined the degree of plant–pollinator specialization and identified the parameters responsible for specificity among four co-occurring Ceropegia species with overlapping flowering times. All investigated plant species were functionally specialized on pollination by Chloropidae and/or Milichiidae flies and each Ceropegia species was, in turn, ecologically highly specialized on only two pollinating fly morphospecies, though one plant species appeared more generalist. Species-specific fly attraction was due to the differences between plant species in floral scents, floral morphology, colour patterns, and presence of other functional structures, e.g., vibratile trichomes, which were shown to contribute to pollinator attraction in one study species. The combination of these olfactory and visual cues differentially influenced pollinator preferences and thus hindered heterospecific visitation. Furthermore, a pollinator exchange experiment also highlighted that species integrity is maintained through efficient ethological isolation (pollinator attraction). The mechanical isolation mediated by the fit between floral morphology and size and/or shape of fly pollinators appears less pronounced here, but whether or not the morphological match between male (pollinium) and female (guide rails) reproductive organs can impede hybridization remains to be investigated.
Accelerated marsh erosion following the Deepwater Horizon oil spill confirmed, ameliorated by planting
Authors: Zengel Scott , Nixon Zachary , Weaver Jennifer , Rutherford Nicolle , Bernik Brittany M. , Michel Jacqueline 
Published: August 2022

AbstractMultiple studies have examined the effects of the Deepwater Horizon oil spill on coastal marsh shoreline erosion. Most studies have concluded that the spill increased shoreline erosion (linear retreat) in oiled marshes by ~ 100–200% for at least 2–3 years. However, two studies have called much of this prior research into question, due to potential study design flaws and confounding factors, primarily tropical cyclone influences and differential wave exposure between oiled (impact) and unoiled (reference) sites. Here we confirm that marsh erosion in our field experiment was substantially increased (112–233%) for 2 years in heavily oiled marsh after the spill, likely due to vegetation impacts and reduced soil shear strength attributed to the spill, rather than the influences of hurricanes or wave exposure variation. We discuss how our findings reinforce prior studies, including a wider-scale remote sensing analysis with similar study approach. We also show differences in the degree of erosion among oil spill cleanup treatments. Most importantly, we show that marsh restoration planting can drastically reduce oiled marsh erosion, and that the positive influences of planting can extend beyond the immediate impact of the spill.
Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells
Authors: Denisova Oxana V. , Merisaari Joni , Kaur Amanpreet , Yetukuri Laxman , Jumppanen Mikael , von Schantz-Fant Carina , Ohlmeyer Michael , Wennerberg Krister , Aittokallio Tero , Taipale Mikko , Westermarck Jukka 
Published: August 2022

AbstractTherapeutic resistance to kinase inhibitors constitutes a major unresolved clinical challenge in cancer and especially in glioblastoma. Multi-kinase inhibitors may be used for simultaneous targeting of multiple target kinases and thereby potentially overcome kinase inhibitor resistance. However, in most cases the identification of the target kinases mediating therapeutic effects of multi-kinase inhibitors has been challenging. To tackle this important problem, we developed an actionable targets of multi-kinase inhibitors (AToMI) strategy and used it for characterization of glioblastoma target kinases of staurosporine derivatives displaying synergy with protein phosphatase 2A (PP2A) reactivation. AToMI consists of interchangeable modules combining drug-kinase interaction assay, siRNA high-throughput screening, bioinformatics analysis, and validation screening with more selective target kinase inhibitors. As a result, AToMI analysis revealed AKT and mitochondrial pyruvate dehydrogenase kinase PDK1 and PDK4 as kinase targets of staurosporine derivatives UCN-01, CEP-701, and K252a that synergized with PP2A activation across heterogeneous glioblastoma cells. Based on these proof-of-principle results, we propose that the application and further development of AToMI for clinically applicable multi-kinase inhibitors could provide significant benefits in overcoming the challenge of lack of knowledge of the target specificity of multi-kinase inhibitors.
Scale robust point matching‐Net: End‐to‐end scale point matching using Lie group
Authors: Wang Xin , Ding Hui , Zhao Guangwei , Peng Yaxin , Shen Chaomin 
Published: August 2022

AbstractPoint cloud matching is an important procedure in a variety of computer vision tasks. Traditional point cloud matching methods have made great progress, while neural network‐based approaches are becoming a trend, powered by their strong capabilities of feature extraction. Existing point matching neural networks, however, mainly focus on the rigid transformation. More complex transformations should also be considered in many scenarios. In this regard, the authors extend the rigid registration to non‐rigid cases and propose a network called the Scale Robust Point Matching (SRPM)‐Net for scale point matching. This robust structure‐preserving network is implemented by incorporating Lie group parametrisation. It is conducted by Lie group linearisation representation with the constraints of parameters under the corresponding basis of Lie algebra. SRPM‐Net preserves the structure of the solution and avoids degeneration. The contributions of this paper lie in two aspects: Most importantly, SRPM‐Net provides an extendable framework for handling complicated transformations. Secondly, it introduces a new feature learning module, which better preserves the shape structure by aggregating the high‐dimensional feature and calculating the normal vector of point cloud surface automatically. Experimental results show that SRPM‐Net is more robust and accurate than existing traditional and recent deep learning methods under various situations.
Prediction method of residual life of transformer oil‐paper insulation based on Wiener random process improved by strong tracking filter
Authors: Zhao Hongshan , Chang Jieying , Qu Yuehan 
Published: August 2022

AbstractIn order to solve the problems of oil‐paper insulation deterioration of oil‐immersed power transformers, including the instability of performance degradation quantity at the early stage, non‐linear deterioration process and uncertainty of life prediction, an improved Wiener stochastic process based on strong tracking filter (STF) is proposed to predict the remaining life of transformer oil‐paper insulation in this paper. Firstly, in order to grasp the dynamic process from healthy state to current deterioration state, a deterioration model is established based on Wiener random process. Secondly, in order to improve the accuracy, the initial values of model parameters are estimated based on expectation maximization (EM) algorithm, then with the increase of monitoring data, model parameters are updated by using STF algorithm, and the probability density function of remaining life is derived to predict the remaining life of oil‐paper insulation. Finally, the accuracy of the proposed method is verified by using furfural content as performance degradation index and accelerated thermal aging experimental data. Compared with the Bayesian–Wiener algorithm, the MSE of the proposed algorithm is reduced to 0.2138 and its MAPE is reduced more than 4%. Besides, the proposed method has the advantages of strong robustness and low uncertainty of residual life prediction.
Spontaneous Downbeat Nystagmus in Anti-GAD-Antibody-Associated Paraneoplastic Syndrome
Authors: Shivaram Sumanth , Tallapalli Ashok V. Reddy , Gupta Manisha , Nashi Saraswati , Kulkarni Girish B. , Alladi Suvarna 
Published: August 2022

Abstract
Spontaneous downbeat nystagmus and ocular flutter are rare clinical signs. Such findings are commonly related to cerebellar pathology, predominantly ischemia. In a significant percentage of patients, the cause may not be found. If these signs are associated with ataxia, cognitive decline, and seizure, anti-glutamic acid decarboxylase-associated neurological syndrome must be suspected. Background history of tumor has to be enquired. Treatment with immune modulation helps in partial recovery of such cases.
Ictal Blinking in Hepatic Encephalopathy Pre- and Post-Liver Transplant: Report of Eight Patients
Authors: Koul Roshan , Maiwall Rakhi , Alam Seema , Pamecha Vineynder , Tevethia Harsh Vardhan , Sarin Shiv K. 
Published: August 2022

AbstractObjective Seizures are reported in 20 to 30% of cases with chronic liver disease in association with hepatic encephalopathy. Majority of these are focal seizures. Ictal blinking is reported first time in these patients pre- and post-liver transplant.Methods From November 2018 to October 2021, retrospective data was analyzed in patients with end-stage liver disease and hepatic encephalopathy, both pre- and post-liver transplant.Results Eight patients had ictal blinking, four were pre-transplant and four post-transplant. Five patients (four after liver transplant and one pre-transplant) were seizure free, three died of liver disease and multiorgan dysfunction, and one did not follow-up.Conclusion Ictal blinking in relation to liver disease and hepatic encephalopathy is reported, often missed and requires short duration antiepileptic medications.
Use of an Autologous Bone Graft Derived from Three Caudal Vertebrae for Reconstruction in a Dog with Radioulnar Atrophic Nonunion and Osteomyelitis
Authors: Goto Masato , Ikeda Hitoshi 
Published: August 2022

AbstractThis case report describes the case of a 4-year-old toy poodle who underwent reconstruction using an autologous caudal vertebral graft for nonunion and osteomyelitis of a left radioulnar fracture. Radial reconstruction was performed 14 days after the removal of existing implants. Three autologous caudal vertebrae mounted onto a titanium T-plate were used to fill the radial bone defect. Rehabilitation was initiated 3 weeks after surgery. By the fifth week after surgery, the dog showed weight bearing on the affected limb. One year after the reconstruction surgery, revision surgery for replacing all implants was performed due to increased radiolucency of the graft. The dog remained clinically stable, and radiographic bone union was complete 3 years and 2 months after the first surgery. An autologous caudal vertebral graft was successfully used for the treatment of a large radial defect in a dog suffering from atrophic nonunion. Clinical improvement was prompt, and the long-term functional outcome was satisfactory.
Ontogeny and anatomy of Bouteloua (Poaceae: Chloridoideae) species display a basipetal branch formation and a novel modified leaf structure in grasses
Authors: Cuellar-Garrido Luis Fernando , Ruiz-Sanchez Eduardo , Vargas-Ponce Ofelia , Whipple Clinton J 
Published: August 2022

Abstract

Background and Aims
Shoot ontogenesis in grasses follows a transition from a vegetative phase into a reproductive phase. Current studies provide insight into how branch and spikelet formation occur during the reproductive phase. However, these studies do not explain all the complex diversity of grass inflorescence forms and are mostly focused on model grasses. Moreover, truncated inflorescences of the non-model grass genus Urochloa (Panicoideae) with formation of primary branches have basipetal initiation of branches. Bouteloua species (Chloridoideae) are non-model grasses that form truncated inflorescences of primary branches with apical vestiges of uncertain homology at the tips of branching events and sterile florets above the lowermost fertile floret. Sterile florets are reduced to rudimentary lemmas composed of three large awns diverging from an awn column. Conflict about the awn column identity of this rudimentary lemma is often addressed in species descriptions of this genus. We test if Bouteloua species can display basipetal initiation of branches and explore the identity of vestiges and the awn column of rudimentary lemmas.

Methods
We surveyed the inflorescence ontogeny and branch/awn anatomy of Bouteloua species and compared results with recent ontogenetic studies of chloridoids.

Key Results
Bouteloua arizonica has florets with basipetal maturation. Branches display basipetal branch initiation and maturation. Branch vestiges are formed laterally by meristems during early branching events. The spikelet meristem forms the awn column of rudimentary lemmas. Vestiges and sterile floret awns have anatomical similarities to C4 leaves.

Conclusions
Basipetal initiation of branches is a novel feature for Chloridoideae grasses. Branch vestiges are novel vegetative grass structures. Sterile floret awn columns are likely to be extensions of the rachilla.
Phenotypic and transcriptomic responses of the shade-grown species Panax ginseng to variable light conditions
Authors: Zhang Yu-Xin , Niu Yu-Qian , Wang Xin-Feng , Wang Zhen-Hui , Wang Meng-Li , Yang Ji , Wang Yu-Guo , Zhang Wen-Ju , Song Zhi-Ping , Li Lin-Feng 
Published: August 2022

Abstract

Background and Aims
Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear.

Methods
We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species.

Key Results
Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions.

Conclusions
Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.