bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions
Authors: Olavarria Karel , Pijman Yared O. , Cabrera Ricardo , van Loosdrecht Mark C. M. , Wahl S. Aljoscha 
Published: March 2022

AbstractThe coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories.
Histone H2AX promotes metastatic progression by preserving glycolysis via hexokinase-2
Authors: Liu Yue , Li Haojian , Wilson Crystal N. , Bai Hui Jen , Boufraqech Myriem , Weyemi Urbain 
Published: March 2022

AbstractGenomic stability is essential for organismal development, cellular homeostasis, and survival. The DNA double-strand breaks are particularly deleterious, creating an environment prone to cellular transformation and oncogenic activation. The histone variant H2AX is an essential component of the nucleosome responsible for initiating the early steps of the DNA repair process. H2AX maintains genomic stability by initiating a signaling cascade that collectively functions to promote DNA double-strand breaks repair. Recent advances have linked genomic stability to energetic metabolism, and alterations in metabolism were found to interfere with genome maintenance. Utilizing genome-wide transcripts profiling to identify differentially-expressed genes involved in energetic metabolism, we compared control and H2AX-deficient metastatic breast cancer cell lines, and found that H2AX loss leads to the repression of key genes regulating glycolysis, with a prominent effect on hexokinase-2 (HK2). These observations are substantiated by evidence that H2AX loss compromises glycolysis, effect which was reversed by ectopic expression of HK2. Utilizing models of experimental metastasis, we found that H2AX silencing halts progression of metastatic breast cancer cells MDA-MB-231. Most interestingly, ectopic expression of HK2 in H2AX-deficient cells restores their metastatic potential. Using multiple publicly available datasets, we found a significantly strong positive correlation between H2AX expression levels in patients with invasive breast cancer, and levels of glycolysis genes, particularly HK2. These observations are consistent with the evidence that high H2AX expression is associated with shorter distant metastasis-free survival. Our findings reveal a role for histone H2AX in controlling the metastatic ability of breast cancer cells via maintenance of HK2-driven glycolysis.
Self-collected gargle specimen as a patient-friendly sample collection method for COVID-19 diagnosis in a population context
Authors: Utama Revata , Hapsari Rebriarina , Puspitasari Iva , Sari Desvita , Hendrianingtyas Meita , Nurainy Neni 
Published: March 2022

AbstractScaling up SARS-CoV-2 testing and tracing continues to be plagued with the limitation of the sample collection method, which requires trained healthcare workers to perform and causes discomfort to the patients. In response, we assessed the performance and user preference of gargle specimens for qRT-PCR-based detection of SARS-CoV-2 in Indonesia. Inpatients who had recently been diagnosed with COVID-19 and outpatients who were about to perform qRT-PCR testing were asked to provide nasopharyngeal and oropharyngeal (NPOP) swabs and self-collected gargle specimens. We demonstrated that self-collected gargle specimens can be an alternative specimen to detect SARS-CoV-2 and the viral RNA remained stable for 31 days at room temperature storage. The developed method was validated for use on multiple RNA extraction kits and commercially available COVID-19 RT-PCR kits. Our developed method achieved a sensitivity of 91.38% when compared to paired NPOP swab specimens (Ct < 35), with 97.10% of patients preferring the self-collected gargle method.
Rehydration of the sleeping chironomid, Polypedilum vanderplanki Hinton, 1951 larvae from cryptobiotic state up to full physiological hydration (Diptera: Chironomidae)
Authors: Knutelski Stanisław , Harańczyk Hubert , Nowak Piotr , Wróbel Andrzej , Leszczyński Bartosz , Okuda Takashi , Strzałka Kazimierz , Baran Ewelina 
Published: March 2022

AbstractDuring desiccation the Polypedilum vanderplanki larva loses 97% of its body water, resulting in the shutdown of all metabolic and physiological processes. The larvae are able to resume active life when rehydrated. As dehydration process has already been largely understood, rehydration mechanisms are still poorly recognized. X-ray microtomograms and electron scanning microscopy images recorded during the hydration showed that the volume of the larva's head hardly changes, while the remaining parts of the body increase in volume. In the 1H-NMR spectrum, as recorded for active larvae, component characteristic of solid state matter is absent. The spectrum is superposition of components coming from tightly and loosely bound water fraction, as well as from lipids. The value of the c coefficient (0.66 ± 0.02) of the allometric function describing the hydration models means that the increase in the volume of rehydrated larvae over time is linear. The initial phase of hydration does not depend on the chemical composition of water, but the amount of ions affects the further process and the rate of return of larva’s to active life. Diffusion and ion channels play a major role in the permeability of water through the larva's body integument.
ATP13A3 facilitates polyamine transport in human pancreatic cancer cells
Authors: Sekhar Vandana , Andl Thomas , Phanstiel Otto 
Published: March 2022

AbstractThe purpose of this study is to provide an increased understanding of the molecular mechanisms responsible for mammalian polyamine transport, a process that has been a long-standing ‘black box’ for the polyamine field. Here, we describe how ATP13A3, a P-type ATPase, functions as a polyamine transporter in response to different polyamine stimuli and polyamine-targeted therapies in highly proliferating pancreatic cancer cells. We assessed the expression, cellular localization and the response of the human ATP13A3 protein to polyamine treatments in different pancreatic cancer cell lines using Western blot and immunofluorescence microscopy. Using CRISPR mutagenesis and radiolabeled polyamine uptake assays, we investigated the role of ATP13A3 protein in polyamine transport. Highly metastatic cancer cells with high polyamine import express higher levels of the full-length ATP13A3 compared to cells with slow proliferation and low import activity. Highlighting its role in polyamine trafficking, the localization of ATP13A3 is altered in the presence of polyamine stimuli and polyamine-targeted therapies in these cells. Using CRISPR mutagenesis, we demonstrate that the first membrane-associated domain of this protein is critical and indispensable for its function as a spermidine and spermine transporter in cells. Further analysis of existing databases revealed that pancreatic cancer patients with high expression of ATP13A3 have decreased overall survival consistent with the role of intracellular polyamines in supporting tumor growth. Our studies shed light on the mysterious polyamine transport process in human cells and clearly establishes ATP13A3 as an intrinsic component of the spermidine and spermine transport system in humans.
Development of a fibrin-mediated gene delivery system for the treatment of cystinosis via design of experiment
Authors: Graceffa Valeria 
Published: March 2022

AbstractCystinosis is a rare disease, caused by a mutation in the gene cystinosin and characterised by the accumulation of cystine crystals. Advantages of biomaterial-mediated gene delivery include reduced safety concerns and the possibility to cure organs that are difficult to treat using systemic gene transfer methods. This study developed novel fibrin hydrogels for controlled, localised gene delivery, for the treatment of cystinosis. In the first part, fabrication parameters (i.e., DNA, thrombin, and aprotinin concentrations) were optimised, using a Design of Experiment (DOE) methodology. DOE is a statistical engineering approach to process optimisation, which increases experimental efficiency, reduces the number of experiments, takes into consideration interactions between different parameters, and allows the creation of predictive models. This study demonstrated the utility of DOE to the development of gene delivery constructs. In the second part of the study, primary fibroblasts from a patient with cystinosis were seeded on the biomaterials. Seeded cells expressed the recombinant CTNS and showed a decrease in cystine content. Furthermore, conditioned media contained functional copies of the recombinant CTNS. These were taken up by monolayer cultures of non-transfected cells. This study described a methodology to develop gene delivery constructs by using a DOE approach and ultimately provided new insights into the treatment of cystinosis.
Metabolite profile of African horned cucumber (Cucumis metuliferus E. May. Ex Naudin) fruit grown under differing environmental conditions
Authors: Maluleke Mdungazi Knox. 
Published: March 2022

AbstractPlant metabolites are known as biological compounds that are essential to the growth and development of a plant and have a direct impact on yield and biochemical constituents of plants. For this study, the objective was to conduct primary metabolomics analysis using liquid chromatography mass spectrometry. African horned cucumber fruits were harvested from plants grown under pots experiment (greenhouse, shade net and open field), soil types (loamy soil and sandy loam) and three water stress levels (no water stress-100%—3L, moderate water stress-75%—2L, and severe water stress-35%—1L) during 2017/18 and 2018/19 seasons. Results showed that the treatment of no water stress combined with sandy loam under shade net environment, significantly increased asparagine content from 10 × 106to 80 × 106peak intensity. The treatment of no water stress, in combination with sandy loam soil under open field environment increased 4-hydroxyproline from 10 × 106to 90 × 106peak intensity compared to other treatments. It can be deduced that the treatment combination of (no water stress and moderate water stress) and all soil types, under greenhouse environment increased most metabolites content of the fruit when compared to other treatments. Therefore, it subsequently has potential to affect fruit quality such as taste and other biochemical constituents.
Decreased thalamic monoamine availability in drug-induced parkinsonism
Authors: Oh Yoon-Sang , Yoo Sang-Won , Lyoo Chul Hyoung , Kim Joong-Seok 
Published: March 2022

AbstractDrug-induced parkinsonism (DIP) is caused by a dopamine receptor blockade and is a major cause of misleading diagnosis of Parkinson’s disease (PD). Striatal dopamine activity has been investigated widely in DIP; however, most studies with dopamine transporter imaging have focused on the clinical characteristics and prognosis. This study investigated differences in striatal subregional monoamine availability among patients with DIP, normal controls, and patients with early PD. Thirty-five DIP patients, the same number of age-matched PD patients, and 46 healthy controls were selected for this study. Parkinsonian motor status was examined. Brain magnetic resonance imaging and positron emission tomography with 18F-N-(3-fluoropropyl)-2beta-carbon ethoxy-3beta-(4-iodophenyl) nortropane were performed, and the regional standardized uptake values were analyzed with a volume-of-interest template and compared among the groups. The groups were evenly matched for age, but there were numerically more females in the DIP group. Parkinsonian motor symptoms were similar in the DIP and PD groups. Monoamine availability in the thalamus of the DIP group was lower than that of the normal controls and similar to that of the PD group. In other subregions (putamen, globus pallidus, and ventral striatum), monoamine availability in the DIP group and normal controls did not differ and was higher than that in the PD group. This difference compared to healthy subject suggests that low monoamine availability in the thalamus could be an imaging biomarker of DIP.
Potentially preventable hospital readmissions after patients’ first stroke in Taiwan
Authors: Chiou Ling-Jan , Lang Hui-Chu 
Published: March 2022

AbstractReadmission is an important indicator of the quality of care. The purpose of this study was to explore the probabilities and predictors of 30-day and 1-year potentially preventable hospital readmission (PPR) after a patient’s first stroke. We used claims data from the National Health Insurance (NHI) from 2010 to 2018. Multinomial logistic regression was used to assess the predictors of 30-day and 1-year PPR. A total of 41,921 discharged stroke patients was identified. We found that hospital readmission rates were 15.48% within 30-days and 47.25% within 1-year. The PPR and non-PPR were 9.84% (4123) and 5.65% (2367) within 30-days, and 30.65% (12,849) and 16.60% (6959) within 1-year, respectively. The factors of older patients, type of stroke, shorter length of stay, higher Charlson Comorbidity Index (CCI), higher stroke severity index (SSI), regional hospital, public and private hospital, and hospital in the lower urbanized area were associated significantly with the 30-day PPR. In addition, the factors of male, hospitalization year, and monthly income were associated significantly with 1-year PPR. The ORs of long-term PPR showed a decreasing trend since implementing the national health insurance post-acute care (PAC) program in 2014 and a dramatic drop in 2018 after the government expanded the long-term care plan-LTC 2.0 in 2017. The results showed that better discharge planning, implementing post-acute care programs and long-term care plan-LTC 2.0 may benefit the care of stroke patients and help reduce long-term readmission in Taiwan.
Rotational symmetry engineered, polarization and incident angle-insensitive, perfect metamaterial absorber for X and Ku band wireless applications
Authors: Hannan Saif , Islam Mohammad Tariqul , Almalki Sami H. A. , Faruque Mohammad Rashed Iqbal , M M. Salaheldeen , Islam Md. Shabiul 
Published: March 2022

AbstractIn this paper, a square enclosed split-maze shaped metamaterial absorber is proposed for X and Ku band wireless applications. Two square metal enclosures were introduced around the split-maze structure to make it rotational symmetric and thus insensitive to cross-polarization. The proposed absorber has shown maximum absorptions at 9.33 GHz, 12.83 GHz, 13.86 GHz, and 15.61 GHz with single negative value of permittivity. The absorber is insensitive to the incident angle of applied EM waves for normal and oblique incidence up to 180 degrees. In addition, it was proved co- & cross-polarization insensitive due to the symmetric structure of the patch. A comprehensive equivalent circuit analysis was done to explain the fundamental EM behaviour of the metamaterial structure, and the circuit outputs coincided with the simulation results. Finally, the metamaterial was measured for both unit cell, and the array after fabrication and simulation results were validated. The proposed MMA is suitable for wireless applications in devices, especially for sensing, EM energy harvesting, EM coupling reduction, and antenna gain enhancement purposes.
Immunity elicitors for induced resistance against the downy mildew pathogen in pearl millet
Authors: Lavanya Senapathyhally Nagaraju , Niranjan-Raj Sathyanarayana , Jadimurthy Ragi , Sudarsan Sujesh , Srivastava Rakesh , Tarasatyavati C. , Rajashekara H. , Gupta Vijai Kumar , Nayaka Siddaiah Chandra 
Published: March 2022

AbstractPearl millet (Pennisetum glaucum (L.) R. Br.) is a globally important cereal whose production is severely constrained by downy mildew caused by Sclerospora graminicola (Sacc.). In this study, immunity eliciting properties of 3,5-dichloroanthranilic acid (DCA), Cell Wall Glucan (CWG), Lipopolysaccharide (LPS), and Glycinebetaine (GB) was deciphered through enzymatic and protein studies based on elicitor treatment activated defense mechanisms. Glycinebetaine, LPS, CWS and DCA elicited enzyme activities and gene expression of the defense enzymes, such as β-1,3-glucanase, phenylalanine ammonia lyase (PAL), peroxidase (POX), polyphenol oxidase (PPO), lipoxygenase (LOX) and defense protein hydroxyproline-rich glycoproteins (HRGPs). However, the speed and the extent of elicitation differed. High levels of enzyme activities and gene expression in elicitor-treated P. glaucum positively correlated with the increased downy mildew resistance. A very rapid and large changes in elicitor-treated seedlings, in contrast to the delayed, smaller changes in the untreated susceptible control seedlings suggests that the rate and magnitude of defense gene expression are important for effective manifestation of defense against pathogen. As compared to other elicitors and control, GB promoted increase in enzyme activities and gene expression, implicating that GB is a promising elicitor of downy mildew resistance in P. glaucum.
Transmissibility of hand, foot, and mouth disease in 97 counties of China
Authors: Zhang Wei , Rui Jia , Cheng Xiaoqing , Deng Bin , Zhang Hesong , Huang Lijing , Zhang Lexin , Zuo Simiao , Li Junru , Huang XingCheng , Su Yanhua , Zhao Benhua , Niu Yan , Li Hongwei , Hu Jian-li , Chen Tianmu 
Published: March 2022

AbstractHand, foot, and mouth disease (HFMD) is a serious disease burden in the Asia–Pacific region, including China. This study calculated the transmissibility of HFMD at county levels in Jiangsu Province, China, analyzed the differences of transmissibility and explored the possible influencing factors of its transmissibility. We built a mathematical model for seasonal characteristics of HFMD, estimated the effective reproduction number (Reff), and compared the incidence rate and transmissibility in different counties using non-parametric tests, rapid cluster analysis and rank-sum ratio in 97 counties in Jiangsu Province from 2015 to 2020. The average daily incidence rate was between 0 and 4 per 100,000 people in Jiangsu Province from 2015–2020. The Quartile of Reff in Jiangsu Province from 2015 to 2020 was 1.54 (0.49, 2.50). Rugao District and Jianhu District had the highest transmissibility according to the rank-sum ratio. Reff generally decreased in 2017 and increased in 2018 in most counties, and the median level of Reff was the lowest in 2017 (P < 0.05). The transmissibility was different in 97 counties in Jiangsu Province. The reasons for the differences may be related to the climate, demographic characteristics, virus subtypes, vaccination, hygiene and other infectious diseases.
Unusual clinical manifestations and predominant stopgain ATM gene variants in a single centre cohort of ataxia telangiectasia from North India
Authors: Rawat Amit , Tyagi Rahul , Chaudhary Himanshi , Pandiarajan Vignesh , Jindal Ankur Kumar , Suri Deepti , Gupta Anju , Sharma Madhubala , Arora Kanika , Bal Amanjit , Madaan Priyanka , Saini Lokesh , Sahu Jitendra Kumar , Ogura Yumi , Kato Tamaki , Imai Kohsuke , Nonoyama Shigeaki , Singh Surjit 
Published: March 2022

AbstractGermline ATM gene variations result in phenotypic heterogeneity characterized by a variable degree of disease severity. We retrospectively collected clinical, genetic, and immunological data of 26 cases with A-T. Clinical manifestations included oculocutaneous telangiectasia (100%), ataxia (100%), fever, loose stools or infection (67%), cerebellar atrophy (50%), nystagmus (8%), dysarthria (15.38%), and visual impairment (8%). Genetic analysis confirmed ATM gene variations in 16 unrelated cases. The most common type of variation was stopgain variants (56%). Immunoglobulin profile indicated reduced IgA, IgG, and IgM in 94%, 50%, and 20% cases, respectively. T cell lymphopenia was observed in 80% of cases among those investigated. Unusual presentations included an EBV-associated smooth muscle tumour located in the liver in one case and Hyper IgM syndrome-like presentation in two cases. Increased immunosenescence was observed in T-cell subsets (CD4+CD57+ and CD8+CD57+). T-cell receptor excision circles (TRECs) were reduced in 3/8 (37.50%) cases.
Mass COVID-19 patient screening using UvsX and UvsY mediated DNA recombination and high throughput parallel sequencing
Authors: Palmieri Dario , Javorina Amanda , Siddiqui Jalal , Gardner Anne , Fries Anthony , Chapleau Richard R. , Starr Clarise , Fishel Richard , Miles Wayne O. 
Published: March 2022

AbstractThe Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A percentage of patients develop coronavirus disease 2019 (COVID-19) after infection, whose symptoms include fever, cough, shortness of breath and fatigue. Acute and life-threatening respiratory symptoms are experienced by 10–20% of symptomatic patients, particularly those with underlying medical conditions. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic/pre-symptomatic individuals. A number of molecular assays are currently used to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening of COVID-19 that may be modified for application to any infectious or non-infectious genome.