bluuebunny/crossref_metadata_2025_split huggingface dataset:
A deep learning model for predicting next-generation sequencing depth from DNA sequence
Authors: Zhang Jinny X. , Yordanov Boyan , Gaunt Alexander , Wang Michael X. , Dai Peng , Chen Yuan-Jyue , Zhang Kerou , Fang John Z. , Dalchau Neil , Li Jiaming , Phillips Andrew , Zhang David Yu 
Published: July 2021

AbstractTargeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization kinetics, resulting in non-uniform coverage that increases sequencing costs and decreases sequencing sensitivities. Here, we present a deep learning model (DLM) for predicting Next-Generation Sequencing (NGS) depth from DNA probe sequences. Our DLM includes a bidirectional recurrent neural network that takes as input both DNA nucleotide identities as well as the calculated probability of the nucleotide being unpaired. We apply our DLM to three different NGS panels: a 39,145-plex panel for human single nucleotide polymorphisms (SNP), a 2000-plex panel for human long non-coding RNA (lncRNA), and a 7373-plex panel targeting non-human sequences for DNA information storage. In cross-validation, our DLM predicts sequencing depth to within a factor of 3 with 93% accuracy for the SNP panel, and 99% accuracy for the non-human panel. In independent testing, the DLM predicts the lncRNA panel with 89% accuracy when trained on the SNP panel. The same model is also effective at predicting the measured single-plex kinetic rate constants of DNA hybridization and strand displacement.
Dimensional reduction by geometrical frustration in a cubic antiferromagnet composed of tetrahedral clusters
Authors: Okuma Ryutaro , Kofu Maiko , Asai Shinichiro , Avdeev Maxim , Koda Akihiro , Okabe Hirotaka , Hiraishi Masatoshi , Takeshita Soshi , Kojima Kenji M. , Kadono Ryosuke , Masuda Takatsugu , Nakajima Kenji , Hiroi Zenji 
Published: July 2021

AbstractDimensionality is a critical factor in determining the properties of solids and is an apparent built-in character of the crystal structure. However, it can be an emergent and tunable property in geometrically frustrated spin systems. Here, we study the spin dynamics of the tetrahedral cluster antiferromagnet, pharmacosiderite, via muon spin resonance and neutron scattering. We find that the spin correlation exhibits a two-dimensional characteristic despite the isotropic connectivity of tetrahedral clusters made of spin 5/2 Fe3+ ions in the three-dimensional cubic crystal, which we ascribe to two-dimensionalisation by geometrical frustration based on spin wave calculations. Moreover, we suggest that even one-dimensionalisation occurs in the decoupled layers, generating low-energy and one-dimensional excitation modes, causing large spin fluctuation in the classical spin system. Pharmacosiderite facilitates studying the emergence of low-dimensionality and manipulating anisotropic responses arising from the dimensionality using an external magnetic field.
Geometry symmetry-free and higher-order optical bound states in the continuum
Authors: Zhou Qingjia , Fu Yangyang , Huang Lujun , Wu Qiannan , Miroshnichenko Andrey , Gao Lei , Xu Yadong 
Published: July 2021

AbstractGeometrical symmetry plays a significant role in implementing robust, symmetry-protected, bound states in the continuum (BICs). However, this benefit is only theoretical in many cases since fabricated samples’ unavoidable imperfections may easily break the stringent geometrical requirements. Here we propose an approach by introducing the concept of geometrical-symmetry-free but symmetry-protected BICs, realized using the static-like environment induced by a zero-index metamaterial (ZIM). We find that robust BICs exist and are protected from the disordered distribution of multiple objects inside the ZIM host by its physical symmetries rather than geometrical ones. The geometric-symmetry-free BICs are robust, regardless of the objects’ external shapes and material parameters in the ZIM host. We further show theoretically and numerically that the existence of those higher-order BICs depends only on the number of objects. By practically designing a structural ZIM waveguide, the existence of BICs is numerically confirmed, as well as their independence on the presence of geometrical symmetry. Our findings provide a way of realizing higher-order BICs and link their properties to the disorder of photonic systems.
Development of double antibody sandwich ELISA as potential diagnostic tool for rapid detection of Crimean-Congo hemorrhagic fever virus
Authors: Shrivastava Neha , Kumar Jyoti S. , Yadav Pragya , Shete Anita M. , Jain Rajlaxmi , Shrivastava Ambuj , Dash Paban Kumar 
Published: July 2021

AbstractCrimean-Congo hemorrhagic fever (CCHF) virus, a highly pathogenic viral agent is responsible for severe fatal hemorrhagic infections in many parts of the world. The early diagnosis of CCHF infection is important for successful clinical management and epidemiological control. The nucleoprotein (NP) of CCHFV being highly conserved and immunogenic is used as early diagnostic marker. In this study, we report a rapid and sensitive double antibody based antigen capture ELISA to detect Crimean-Congo hemorrhagic fever virus (CCHFV). Highly specific polyclonal and monoclonal antibody against NP has been generated and used as capture and detector antibody respectively. The assay was able to detect viral nucleoprotein in different matrices including human serum, ticks and culture supernatant. The detection limit of the developed sandwich ELISA assay was 25 ng of purified antigen. Comparison with a real time RT-PCR revealed its detection limit to be 1000 genome equivalents of CCHFV. Further the assay was comparatively evaluated with a commercial kit employing gamma irradiated CCHFV, revealing a sensitivity and specificity of 100%. This newly developed sandwich ELISA (sELISA) with high sensitivity and specificity could be used as an efficient method for the detection of CCHF virus in humans, ticks and culture supernatant. The assay will be useful as alternate tool for diagnosis of acute infection and is amenable for screening of large scale samples in resource limited settings.
Electrophysiological characterization of a diverse group of sugar transporters from Trichoderma reesei
Authors: Havukainen Sami , Pujol-Giménez Jonai , Valkonen Mari , Westerholm-Parvinen Ann , Hediger Matthias A. , Landowski Christopher P. 
Published: July 2021

AbstractTrichoderma reesei is an ascomycete fungus known for its capability to secrete high amounts of extracellular cellulose- and hemicellulose-degrading enzymes. These enzymes are utilized in the production of second-generation biofuels and T. reesei is a well-established host for their production. Although this species has gained considerable interest in the scientific literature, the sugar transportome of T. reesei remains poorly characterized. Better understanding of the proteins involved in the transport of different sugars could be utilized for engineering better enzyme production strains. In this study we aimed to shed light on this matter by characterizing multiple T. reesei transporters capable of transporting various types of sugars. We used phylogenetics to select transporters for expression in Xenopus laevis oocytes to screen for transport activities. Of the 18 tested transporters, 8 were found to be functional in oocytes. 10 transporters in total were investigated in oocytes and in yeast, and for 3 of them no transport function had been described in literature. This comprehensive analysis provides a large body of new knowledge about T. reesei sugar transporters, and further establishes X. laevis oocytes as a valuable tool for studying fungal sugar transporters.
Levels and health risk assessment of heavy metals in dried fish consumed in Bangladesh
Authors: Rakib Md. Refat Jahan , Jolly Y. N. , Enyoh Christian Ebere , Khandaker Mayeen Uddin , Hossain M. Belal , Akther Shirin , Alsubaie Abdullah , Almalki Abdulraheem S. A. , Bradley D. A. 
Published: July 2021

AbstractAs a cheap source of high-quality protein, healthy fats and essential nutrients, dried fish is a common item in the daily diet of the Bangladesh populace. In this study, ten types of widely consumed dried fish (H. neherius, T. lepturu, P.chinensis, P. affinis, A. mola, P. microdon, I. megaloptera, C. dussumieri, L. calcarifer, and G. chapra) were analyzed for Cr, Mn, Fe, Co, Cu, Zn, Se, Rb, Hg, Pb, Ni and As by using an Energy Dispersive X-ray Fluorescence (EDXRF) technique. The concentration of the studied metals was found in the order Fe > Zn > Hg > Cu > Se > Cr > Mn > Co > Rb > Pb, while As and Ni were below the limit of detection. All fish species showed moderate to high pollution, where the speciesH. NeheriusandP. Chinensisare the most and least polluted ones, respectively. The probable source of contamination is the leaching from the drying pans into the fish samples, atmospheric deposition, anthropogenic contamination, etc. of the water body where these fish were harvested. The calculated hazard index for the general population was below the maximum limiting value (i.e., < 1) except for Hg to children. The carcinogenic risk showed values lower than the acceptable limit for cancer risks (10–6to 10–4). Periodic monitoring of trace metals in the aquatic organisms along with fish is recommended to avoid any unexpected health hazards caused by the toxic heavy metals via fish consumption.
RETRACTED ARTICLE: The role of ascorbic acid combined exposure on Imidacloprid-induced oxidative stress and genotoxicity in Nile tilapia
Authors: El-Garawani Islam M. , Khallaf Elsayed A. , Alne-na-ei Alaa A. , Elgendy Rehab G. , Mersal Gaber A. M. , El-Seedi Hesham R. 
Published: July 2021

AbstractImidacloprid (Imid), a systemic neonicotinoid insecticide, is broadly used worldwide. It is reported to contaminate aquatic systems. This study was proposed to evaluate oxidative stress and genotoxicity of Imid on Nile tilapia (Oreochromis niloticus) and the protective effect of ascorbic acid (Asc). O. niloticus juveniles (30.4 ± 9.3 g, 11.9 ± 1.3 cm) were divided into six groups (n = 10/replicate). For 21 days, two groups were exposed to sub-lethal concentrations of Imid (8.75 ppm, 1/20 of 72 h-LC50 and 17.5 ppm, 1/10 of 72 h-LC50); other two groups were exposed to Asc (50 ppm) in combination with Imid (8.75 and 17.5 ppm); one group was exposed to Asc (50 ppm) in addition to a group of unexposed fish which served as controls. Oxidative stress was assessed in the liver where the level of enzymatic activities including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) in addition to mRNA transcripts and, Lipid peroxidation (LPO) were evaluated. Moreover, mitotic index (MI) and comet assay were performed, in addition, the erythrocytic micronucleus (MN), and nuclear abnormalities (NA) were observed to assess genotoxicity in fish. Imid exposure induced significant (p ˂ 0.05) changes in the antioxidant profile of the juveniles' liver by increasing the activities and gene expression of SOD, CAT and GPX as well as elevating the levels of LPO. DNA strand breaks in gill cells, erythrocytes and hepatocytes along with erythrocytic MN and NA were also significantly elevated in Imid-exposed groups. MI showed a significant (p ˂ 0.05) decrease associated with Imid exposure. Asc administration induced a significant amelioration towards the Imid toxicity (8.75 and 17.5 ppm). A significant protective potency against the genotoxic effects of Imid was evidenced in Asc co-treated groups. Collectively, results highlight the importance of Asc as a protective agent against Imid-induced oxidative stress and genotoxicity in O. niloticus juveniles.
Metabolic factors and the risk of Dupuytren’s disease: data from 30,000 individuals followed for over 20 years
Authors: Rydberg Mattias , Zimmerman Malin , Löfgren Jin Persson , Gottsäter Anders , Nilsson Peter M. , Melander Olle , Dahlin Lars B. 
Published: July 2021

AbstractDupuytren’s disease (DD) is a fibroproliferative disorder affecting the palmar fascia of the hand. Risk factors include diabetes mellitus (DM), whereas a high body mass index (BMI) is associated with a lower prevalence of DD. The aim of this study was to further elucidate risk and protective factors for the development of DD using longitudinal population-based data from the Malmö Diet and Cancer Study (MDCS). During 1991–1996, the inhabitants aged 46–73 years in the city of Malmö, Sweden were invited to participate in the population-based MDCS (41% participation rate). Data on incident DD were retrieved from Swedish national registers. Associations between DM, alcohol consumption, BMI, and serum apolipoprotein A1 (ApoA1) and apolipoprotein B (ApoB) at baseline were analysed in multivariable Cox regression models adjusted for known confounders. Among 30,446 recruited participants, 347 men and 194 women were diagnosed with DD during a median follow-up time of 23 years. DM (men HR 2.23; 95% CI 1.50–3.30, women HR 2.69; 95% CI 1.48–4.90) and alcohol consumption (men HR 2.46; 95% CI 1.85–3.27, women HR 3.56; 95% CI 1.95–6.50) were independently associated with incident DD in the Cox regression models. Furthermore, inverse associations with incident DD were found for obesity among men, and ApoB/ApoA1 ratio among both sexes. DM and excess alcohol consumption constituted major risk factors for the development of DD. Furthermore, an inverse association between obesity among men and DD, and also between ApoB/ApoA1 ratio and DD was found in both sexes.
Investigation of energy metabolic dynamism in hyperthermia-resistant ovarian and uterine cancer cells under heat stress
Authors: Kanamori Taisei , Miyazaki Natumi , Aoki Shigeki , Ito Kousei , Hisaka Akihiro , Hatakeyama Hiroto 
Published: July 2021

AbstractDespite progress in the use of hyperthermia in clinical practice, the thermosensitivity of cancer cells is poorly understood. In a previous study, we found that sensitivity to hyperthermia varied between ovarian and uterine cancer cell lines. Upon hyperthermia, glycolytic enzymes decreased in hyperthermia-resistant SKOV3 cells. However, the mechanisms of glycolysis inhibition and their relationship with thermoresistance remain to be explored. In this study, metabolomic analysis indicated the downregulation of glycolytic metabolites in SKOV3 cells after hyperthermia. Proteomic and pathway analyses predicted that the ubiquitin pathway was explicitly activated in resistant SKOV3 cells, compared with hyperthermia-sensitive A2780 cells, and STUB1, a ubiquitin ligase, potentially targeted PKM, a glycolytic rate-limiting enzyme. PKM is degraded via ubiquitination upon hyperthermia. Although glycolysis is inactivated by hyperthermia, ATP production is maintained. We observed that oxygen consumption and mitochondrial membrane potential were activated in SKOV3 cells but suppressed in A2780 cells. The activation of mitochondria could compensate for the loss of ATP production due to the suppression of glycolysis by hyperthermia. Although the physiological significance has not yet been elucidated, our results demonstrated that metabolomic adaptation from the Warburg effect to mitochondrial oxidative phosphorylation could contribute to thermoresistance in ovarian and uterine cancer cells.
Cultivation of Kabul Dhingri (Pleurotus eryngii) mushroom by standardizing protocols in subtropical zones of world
Authors: Deora Akansha , Sharma S. S. , Kumari Poonam , Dahima Vinita , Kumar Suresh , Rohith M. 
Published: July 2021

AbstractThe study is of great relevance with present day pandemic era where mushrooms have immunity enhancing properties and they convert agro-wastes into protein rich food. India is having a youth population of about 750 million and mushroom cultivation has good potential to contribute in national income as well as enhanced immunity. The key aspects undertaken during research were the spawn production, cultivation methodology, and the suitability of various factors affecting the production and yield attributes of Pleurotus eryngii under ambient conditions in subtropical areas. Study includes yield enhancing substrate, sterilization method, spawn and substrate quantity in the growing of King Oyster i.e. Pleurotus eryngii in subtropical zones. Paddy straw was found to be the best substrate giving the highest biological efficiency and producing maximum number of fruiting bodies which is otherwise burnt by farmers in India and it is a major cause of air pollution. Whereas, maize straw showed fastest spawn run and pin head emergence out of six tested substrates and supplements. But, due to the unavailability of paddy straw in this region, the other straws resulting in optimum yields are to be recommended. Chemical steeping of substrate with chlorine water at 0.4% + carbendazim at 2% + dichlorovos at 0.1% of water used for soaking showed best results in terms of biological efficiency whereas, water and aerated steam treatment of substrate at 85 °C-90°C for about 60–90 min supported the results in leaching of nutrients and thus, biological efficiency gets lower. Out of four spawn rates used, spawn rate of 5% was found significantly best resulting in maximum biological efficiency, fastest mycelial run, primordial initiation and highest average fruit body weight. All the experiments were found statistically significant except the experiment that was performed for evaluating the optimum quantity of substrate for bag preparation. There was not much difference in the obtained yields with respect to increase in the amounts of substrate. So, growing this mushroom from the obtained best results will result in better production with higher income even for the marginal farmers in subtropical zones of world.
Observing the silent world under COVID-19 with a comprehensive impact analysis based on human mobility
Authors: Wang Shaobin , Tong Yun , Fan Yupeng , Liu Haimeng , Wu Jun , Wang Zheye , Fang Chuanglin 
Published: July 2021

AbstractSince spring 2020, the human world seems to be exceptionally silent due to mobility reduction caused by the COVID-19 pandemic. To better measure the real-time decline of human mobility and changes in socio-economic activities in a timely manner, we constructed a silent index (SI) based on Google’s mobility data. We systematically investigated the relations between SI, new COVID-19 cases, government policy, and the level of economic development. Results showed a drastic impact of the COVID-19 pandemic on increasing SI. The impact of COVID-19 on human mobility varied significantly by country and place. Bi-directional dynamic relationships between SI and the new COVID-19 cases were detected, with a lagging period of one to two weeks. The travel restriction and social policies could immediately affect SI in one week; however, could not effectively sustain in the long run. SI may reflect the disturbing impact of disasters or catastrophic events on the activities related to the global or national economy. Underdeveloped countries are more affected by the COVID-19 pandemic.
Skin tolerant inactivation of multiresistant pathogens using far-UVC LEDs
Authors: Glaab Johannes , Lobo-Ploch Neysha , Cho Hyun Kyong , Filler Thomas , Gundlach Heiko , Guttmann Martin , Hagedorn Sylvia , Lohan Silke B. , Mehnke Frank , Schleusener Johannes , Sicher Claudia , Sulmoni Luca , Wernicke Tim , Wittenbecher Lucas , Woggon Ulrike , Zwicker Paula , Kramer Axel , Meinke Martina C. , Kneissl Michael , Weyers Markus , Winterwerber Ulrike , Einfeldt Sven 
Published: July 2021

AbstractMultiresistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) cause serious postoperative infections. A skin tolerant far-UVC (< 240 nm) irradiation system for their inactivation is presented here. It uses UVC LEDs in combination with a spectral filter and provides a peak wavelength of 233 nm, with a full width at half maximum of 12 nm, and an irradiance of 44 µW/cm2. MRSA bacteria in different concentrations on blood agar plates were inactivated with irradiation doses in the range of 15–40 mJ/cm2. Porcine skin irradiated with a dose of 40 mJ/cm2 at 233 nm showed only 3.7% CPD and 2.3% 6-4PP DNA damage. Corresponding irradiation at 254 nm caused 11–14 times higher damage. Thus, the skin damage caused by the disinfectant doses is so small that it can be expected to be compensated by the skin's natural repair mechanisms. LED-based far-UVC lamps could therefore soon be used in everyday clinical practice to eradicate multiresistant pathogens directly on humans.
Homogeneous 2D and 3D alignment of cardiomyocyte in dilated cardiomyopathy revealed by intravital heart imaging
Authors: Masuyama Kiyoshi , Higo Tomoaki , Lee Jong-Kook , Matsuura Ryohei , Jones Ian , Bakal Chris , Higo Shuichiro , Morimoto Sachio , Miyagawa Shigeru , Sawa Yoshiki , Sakata Yasushi 
Published: July 2021

AbstractIn contrast to hypertrophic cardiomyopathy, there has been reported no specific pattern of cardiomyocyte array in dilated cardiomyopathy (DCM), partially because lack of alignment assessment in a three-dimensional (3D) manner. Here we have established a novel method to evaluate cardiomyocyte alignment in 3D using intravital heart imaging and demonstrated homogeneous alignment in DCM mice. Whilst cardiomyocytes of control mice changed their alignment by every layer in 3D and position twistedly even in a single layer, termed myocyte twist, cardiomyocytes of DCM mice aligned homogeneously both in two-dimensional (2D) and in 3D and lost myocyte twist. Manipulation of cultured cardiomyocyte toward homogeneously aligned increased their contractility, suggesting that homogeneous alignment in DCM mice is due to a sort of alignment remodelling as a way to compensate cardiac dysfunction. Our findings provide the first intravital evidence of cardiomyocyte alignment and will bring new insights into understanding the mechanism of heart failure.
Optimized procedures for testing plasma metanephrines in patients on hemodialysis
Authors: Pamporaki Christina , Prejbisz Aleksander , Małecki Robert , Pistrosch Frank , Peitzsch Mirko , Bishoff Steffen , Mueller Petra , Meyer Iris , Reimann Doreen , Hanus Katarzyna , Januszewicz Andrzej , Bornstein Stefan R. , Parmentier Simon , Kunath Carola , Lenders Jacques W. M. , Eisenhofer Graeme , Passauer Jens 
Published: July 2021

AbstractDiagnosis of pheochromocytomas and paragangliomas in patients receiving hemodialysis is troublesome. The aim of the study was to establish optimal conditions for blood sampling for mass spectrometric measurements of normetanephrine, metanephrine and 3-methoxytyramine in patients on hemodialysis and specific reference intervals for plasma metanephrines under the most optimal sampling conditions. Blood was sampled before and near the end of dialysis, including different sampling sites in 170 patients on hemodialysis. Plasma normetanephrine concentrations were lower (P < 0.0001) and metanephrine concentrations higher (P < 0.0001) in shunt than in venous blood, with no differences for 3-methoxytyramine. Normetanephrine, metanephrine and 3-methoxytyramine concentrations in shunt and venous blood were lower (P < 0.0001) near the end than before hemodialysis. Upper cut-offs for normetanephrine were 34% lower when the blood was drawn from the shunt and near the end of hemodialysis compared to blood drawn before hemodialysis. This study establishes optimal sampling conditions using blood from the dialysis shunt near the end of hemodialysis with optimal reference intervals for plasma metanephrines for the diagnosis of pheochromocytomas/paragangliomas among patients on hemodialysis.