bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Authors: Zhang Yinan , Qu Qinfeng , Rao Mingzhen , Zhang Nana , Zhao Yu , Tao Fei 
Published: June 2020

AbstractCurrently, the inspection and supervision of animal ingredients relies primarily upon specific amplification-dependent methods, whose efficiency and accuracy are being seriously challenged by the increasing diversity and complexity of meat products. High-throughput sequencing (HTS) technology was employed to develop an alternative method to detect animal-derived ingredients in meat products. A custom-built database containing 2,354 complete mitochondrial genomic sequences from animals, an identification analysis pipeline based on short-sequence alignment, and a web-based server were built to facilitate this detection. The entire process, including DNA extraction, gene amplification, and sequencing, was established and optimized for both marker gene (part of the CYTB gene)-based detection and total DNA-based detection. Using simulated samples containing various levels of pig, cattle, sheep, chicken, rabbit, and mice ingredients, the detection capability and accuracy of this method were investigated. The results of this study indicated that the method is capable of detecting animal components in meats that are present at levels as low as 1%. Our method was then tested using 28 batches of real meat products such as raw meat slices, raw meat mince, cooked dried meat, cooked meat sausage, and other supermarket samples, with a traditional qPCR method as the control. The results demonstrated an accuracy of 97.65% for the qualitative detection method, which indicate that the developed method is reliable for the detection of animal components. The method is also effective for the identification of unknown food samples containing mixed animal components, which suggests a good future in application.
Identification of the novel polymorphisms and potential genetic features of the prion protein gene (PRNP) in horses, a prion disease-resistant animal
Authors: Kim Yong-Chan , Won Sae-Young , Do Kyoungtag , Jeong Byung-Hoon 
Published: June 2020

AbstractPrion diseases, a protein misfolded disorder (PMD) caused by misfolded prion protein (PrPSc), present in a wide variety of hosts, ranging from ungulates to humans. To date, prion infections have not been reported in horses, which are well-known as prion disease-resistant animals. Several studies have attempted to identify distinctive features in the prion protein of horses compared to prion disease-susceptible animals, without the study on polymorphisms of the horse prion protein gene (PRNP). Since single nucleotide polymorphisms (SNPs) of PRNP in prion disease-susceptible animals are major susceptibility factors, the investigation of SNPs in the horse PRNP gene is important; however, only one study investigated a single horse breed, Thoroughbred. Thus, we investigated genetic polymorphisms and potential characteristics of the PRNP gene in 2 additional horse breeds. To this end, we performed amplicon sequencing of the horse PRNP gene and investigated SNPs in Jeju and Halla horses. We compared genotype, allele and haplotype frequencies among three horse breeds, namely, Thoroughbred, Jeju and Halla horses. In addition, we evaluated the potential influence of the identified nonsynonymous SNPs on the prion protein using PolyPhen-2, PROVEAN, and PANTHER. Furthermore, we measured the aggregation propensity of prion proteins using AMYCO and analyzed linkage disequilibrium (LD) between PRNP and prion-like protein gene (PRND) SNPs. A total of 4 SNPs were found, including two nonsynonymous SNPs (c.301 T > A, c.525 C > A) and three novel SNPs (c.-3A > G, c.301 T > A and c.570 G > A). There were significant differences in genotype, allele and haplotype frequencies among the three horse breeds. The nonsynonymous SNP, c.301 T > A (W101R), was predicted to be benign, deleterious, and possibly damaging by PolyPhen-2, PROVEAN and PANTHER, respectively. In addition, the amyloid propensity of horse prion protein according to 4 haplotypes of nonsynonymous SNPs was predicted to be benign by AMYCO. Finally, we identified weak LD between PRNP and PRND SNPs.
Exact Analytical Model for Bose-Einstein Condensate at Negative Temperature
Authors: Nath Ajay , Bera Jayanta , Ghosh Suranjana , Roy Utpal 
Published: June 2020

AbstractWe present an exact analytical model of a cigar-shaped Bose-Einstein condensate at negative temperature. This work is motivated by the first experimental discovery of negative temperature in Bose-Einstein condensate by Braun et al. We have considered an external confinement which is a combination of expulsive trap, bi-chromatic optical lattice trap, and linear trap. The present method is capable of providing the exact form of the condensate wavefunction, phase, nonlinearity and gain/loss. One of the consistency conditions is shown to map onto the Schrödinger equation, leading to a significant control over the dynamics of the system. We have modified the model by replacing the optical lattice trap by a bi-chromatic optical lattice trap, which imparts better localization at the central frustrated site, delineated through the variation of condensate fraction. Estimation of temperature and a numerical stability analysis are also carried out. Incorporation of an additional linear trap introduces asymmetry and the corresponding temporal dynamics reveal atom distillation at negative temperature.
Increased immunocompetence and network centrality of allogroomer workers suggest a link between individual and social immunity in honeybees
Authors: Cini Alessandro , Bordoni Adele , Cappa Federico , Petrocelli Iacopo , Pitzalis Martina , Iovinella Immacolata , Dani Francesca Romana , Turillazzi Stefano , Cervo Rita 
Published: June 2020

AbstractThe significant risk of disease transmission has selected for effective immune-defense strategies in insect societies. Division of labour, with individuals specialized in immunity-related tasks, strongly contributes to prevent the spread of diseases. A trade-off, however, may exist between phenotypic specialization to increase task efficiency and maintenance of plasticity to cope with variable colony demands. We investigated the extent of phenotypic specialization associated with a specific task by using allogrooming in the honeybee, Apis mellifera, where worker behaviour might lower ectoparasites load. We adopted an integrated approach to characterize the behavioural and physiological phenotype of allogroomers, by analyzing their behavior (both at individual and social network level), their immunocompetence (bacterial clearance tests) and their chemosensory specialization (proteomics of olfactory organs). We found that allogroomers have higher immune capacity compared to control bees, while they do not differ in chemosensory proteomic profiles. Behaviourally, they do not show differences in the tasks performed (other than allogrooming), while they clearly differ in connectivity within the colonial social network, having a higher centrality than control bees. This demonstrates the presence of an immune-specific physiological and social behavioural specialization in individuals involved in a social immunity related task, thus linking individual to social immunity, and it shows how phenotypes may be specialized in the task performed while maintaining an overall plasticity.
Tryptophan, a non-canonical melanin precursor: New L-tryptophan based melanin production by Rubrivivax benzoatilyticus JA2
Authors: Ahmad Shabbir , Mohammed Mujahid , Mekala Lakshmi Prasuna , Chintalapati Sasikala , Chintalapati Venkata Ramana 
Published: June 2020

AbstractMelanins are chemically diverse ubiquitous pigments found across the life forms synthesizedviadifferent biochemical pathways mainly from L-tyrosine or acetyl CoA. Though few reports suggest the possibility of tryptophan-based melanin synthesis, however, such tryptophan-based melanin and its biosynthesis remained a biochemical riddle. Here we report tryptophan-based melanin production by bacterium,Rubrivivax benzoatilyticusJA2. Aerobic cultures of strain JA2 produced brown pigment when grown on L-tryptophan-containing media. Purified pigment showed typical physico-chemical properties of melanin. Further, extensive spectroscopic studies revealed that pigment is an amorphous, indole-type polymer with stable free radical centers. Further, hydrolysis of the brown pigment revealed the presence of indole moiety, confirming the indolic nature of the pigment. Demonstration ofin vitroandin vivopigment synthesis directly from L-tryptophan or hydroxytryptophan confirms tryptophan-based melanin synthesis in strain JA2. Interestingly, canonical melanin biosynthetic inhibitors did not affect the pigment synthesis indicating possible non-canonical tryptophan-based melanin biosynthesis in strain JA2. Further, the exometabolite profiling and precursor feeding studies suggests that L-tryptophan converted to hydroxytryptophan/hydroxyindoles and their subsequent polymerization lead to the formation of melanin. The current study sheds light on biosynthetic diversity of melanins and L-tryptophan can be a potential precursor for melanin synthesis in life forms.
Doping Dependent Magnetic Behavior in MBE Grown GaAs1-xSbx Nanowires
Authors: Kumar Raj , Liu Yang , Li Jia , Iyer Shanthi , Reynolds Lewis 
Published: June 2020

AbstractIntrinsic and Te-doped GaAsSb nanowires with diameters ~100–120 nm were grown on a p-type Si(111) substrate by molecular beam epitaxy (MBE). Detailed magnetic, current/voltage and low-energy electron energy loss spectroscopy measurements were performed to investigate the effect of Te-doping. While intrinsic nanowires are diamagnetic over the temperature range 5–300 K, the Te-doped nanowires exhibit ferromagnetic behavior with the easy axis of magnetism perpendicular to the longitudinal axis of the nanowire. The temperature dependence of coercivity was analyzed and shown to be in agreement with a thermal activation model from 50–350 K but reveal more complex behavior in the low temperature regime. The EELS data show that Te doping introduced a high density of states (DOS) in the nanowire above the Fermi level in close proximity to the conduction band. The plausible origin of ferromagnetism in these Te-doped GaAsSb nanowires is discussed on the basis of d0 ferromagnetism, spin ordering of the Te dopants and the surface-state-induced magnetic ordering.
Metabolic reprogramming associated with progression of renal ischemia reperfusion injury assessed with hyperpolarized [1-13C]pyruvate
Authors: Nielsen Per Mose , Qi Haiyun , Bertelsen Lotte Bonde , Laustsen Christoffer 
Published: June 2020

AbstractAcute kidney injury is a major clinical challenge affecting as many as 1 percent of all hospitalized patients. Currently it is not possible to accurately stratify and predict the outcome of the individual patient. Increasing evidence supports metabolic reprogramming as a potential target for new biomarkers. Hyperpolarized [1-13C]pyruvate imaging is a promising new tool for evaluating the metabolic status directly in the kidneys. We here investigate the prognostic potential of hyperpolarized [1-13C]pyruvate in the setting of acute kidney injury in a rodent model of ischemia reperfusion. A significant correlation was found between the intra-renal metabolic profile 24 hours after reperfusion and 7 days after injury induction, as well as a correlation with the conventional plasma creatinine biomarker of renal function and markers of renal injury. This leads to a possible outcome prediction of renal function and injury development from a metabolic profile measured in vivo. The results support human translation of this new technology to renal patients as all experiements have been performed using clinical MRI equipment.
Targeted metabolomic analysis of serum amino acids in the adult Fontan patient with a dominant left ventricle
Authors: Michel Miriam , Dubowy Karl-Otto , Entenmann Andreas , Karall Daniela , Adam Mark Gordian , Zlamy Manuela , Odri Komazec Irena , Geiger Ralf , Niederwanger Christian , Salvador Christina , Müller Udo , Laser Kai Thorsten , Scholl-Bürgi Sabine 
Published: June 2020

AbstractGrowing interest lies in the assessment of the metabolic status of patients with a univentricular circulation after Fontan operation, especially in changes of amino acid metabolism. Using targeted metabolomic examinations, we investigated amino acid metabolism in a homogeneous adult Fontan-patient group with a dominant left ventricle, seeking biomarker patterns that might permit better understanding of Fontan pathophysiology and early detection of subtle ventricular or circulatory dysfunction. We compared serum amino acid levels (42 analytes; AbsoluteIDQ p180 kit, Biocrates Life Sciences, Innsbruck, Austria) in 20 adult Fontan patients with a dominant left ventricle and those in age- and sex-matched biventricular controls. Serum concentrations of asymmetric dimethylarginine, methionine sulfoxide, glutamic acid, and trans-4-hydroxyproline and the methionine sulfoxide/methionine ratio (Met-SO/Met) were significantly higher and serum concentrations of asparagine, histidine, taurine, and threonine were significantly lower in patients than in controls. Met-SO/Met values exhibited a significant negative correlation with oxygen uptake during exercise. The alterations in amino acid metabolome that we found in Fontan patients suggest links between Fontan pathophysiology, altered cell energy metabolism, oxidative stress, and endothelial dysfunction like those found in biventricular patients with congestive heart failure. Studies of extended amino acid metabolism may allow better understanding of Fontan pathophysiology that will permit early detection of subtle ventricular or circulatory dysfunction in Fontan patients.
ROS-Mediated Apoptotic Cell Death of Human Colon Cancer LoVo Cells by Milk δ-Valerobetaine
Authors: D’Onofrio Nunzia , Cacciola Nunzio Antonio , Martino Elisa , Borrelli Francesca , Fiorino Ferdinando , Lombardi Assunta , Neglia Gianluca , Balestrieri Maria Luisa , Campanile Giuseppe 
Published: June 2020

Abstractδ-Valerobetaine (δVB) is a constitutive milk metabolite with antioxidant and anti-inflammatory activities. Here, we tested the antineoplastic properties of milk δVB on human colorectal cancer cells. CCD 841 CoN (non-tumorigenic), HT-29 (p53 mutant adenocarcinoma) and LoVo (APC/RAS mutant adenocarcinoma) cells were exposed to 3 kDa milk extract, δVB (2 mM) or milk+δVB up to 72 h. Results showed a time- and dose-dependent capability of δVB to inhibit cancer cell viability, with higher potency in LoVo cells. Treatment with milk+δVB arrested cell cycle in G2/M and SubG1 phases by upregulating p21, cyclin A, cyclin B1 and p53 protein expressions. Noteworthy, δVB also increased necrosis (P < 0.01) and when used in combination with milk it improved its activity on live cell reduction (P < 0.05) and necrosis (P < 0.05). δVB-enriched milk activated caspase 3, caspase 9, Bax/Bcl-2 apoptotic pathway and reactive oxygen species (ROS) production, whereas no effects on ROS generation were observed in CCD 841 CoN cells. The altered redox homeostasis induced by milk+δVB was accompanied by upregulation of sirtuin 6 (SIRT6). SIRT6 silencing by small interfering RNA blocked autophagy and apoptosis activated by milk+δVB, unveiling the role of this sirtuin in the ROS-mediated apoptotic LoVo cell death.
Weak correlations between cerebellar tests
Authors: Löwgren Karolina , Bååth Rasmus , Rasmussen Anders 
Published: June 2020

AbstractEyeblink conditioning, finger tapping, and prism adaptation are three tasks that have been linked to the cerebellum. Previous research suggests that these tasks recruit distinct but partially overlapping parts of the cerebellum, as well as different extra-cerebellar networks. However, the relationships between the performances on these tasks remain unclear. Here we tested eyeblink conditioning, finger tapping, and prism adaptation in 42 children and 44 adults and estimated the degree of correlation between the performance measures. The results show that performance on all three tasks improves with age in typically developing school-aged children. However, the correlations between the performance measures of the different tasks were consistently weak and without any consistent directions. This reinforces the view that eyeblink conditioning, finger tapping, and prism adaptation rely on distinct mechanisms. Consequently, performance on these tasks cannot be used separately to assess a common cerebellar function or to make general conclusions about cerebellar dysfunction. However, together, these three behavioral tasks have the potential to contribute to a nuanced picture of human cerebellar functions during development.
Clinical and ultrasound variables for early diagnosis of septic acute kidney injury in bitches with pyometra
Authors: Gasser Beatriz , Uscategui Ricardo Andres Ramirez , Maronezi Marjury Cristina , Pavan Letícia , Simões Ana Paula Rodrigues , Martinato Fernanda , Silva Priscila , Crivellenti Leandro Zuccolotto , Feliciano Marcus Antônio Rossi 
Published: June 2020

AbstractThe aetiology of septic acute kidney injury (AKI) is not completely elucidated. Early identification of AKI in septic patients is considered to improve survival rate since it allows rapid treatment onset. We evaluated clinical, haematological, urinary, B-mode, spectral Doppler, and contrast-enhanced ultrasound variables in 20 bitches with pyometra as sepsis models and 12 healthy controls. All animals with pyometra presented some degree of renal damage on histological examination; however, sequential organ failure assessment (SOFA) classified only 40% cases with sepsis. AKI derived from systemic infection was identified in 57% of cases with hypoperfusion and in 22% with inflammation, being an affection of multifactorial origin. Among the evaluated parameters, urinary protein/creatinine ratio >0.15, serum albumin <2.94 mg/dL, time-averaged minimum velocity <21.5 cm/s, renal length/aorta diameter ratio >5.93, pulsatility index >1.53, haematocrit <45%, time-averaged maximum velocity <45.7 cm/s, haemoglobin <16 g/dL, leukocytes >12.53 × 103/uL, and cortical contrast peak intensity <69%, in the order of accuracy, are significant indicators of septic AKI with an accuracy >80%. Thus, AKI is a very prevalent condition in septic patients, derived mainly from changes in renal perfusion and inflammation. Additionally, reviewing the SOFA score parameters is suggested to identify renal failure.
Essential factors involved in the precise targeting and insertion of telomere-specific non-LTR retrotransposon, SART1Bm
Authors: Nichuguti Narisu , Fujiwara Haruhiko 
Published: June 2020

AbstractTelomere length maintenance is essential for most eukaryotes to ensure genome stability and integrity. A non-long terminal repeat (LTR) retrotransposon, SART1Bm, targets telomeric repeats (TTAGG)n of the silkworm Bombyx mori and is presumably involved in telomere length maintenance. However, how many telomeric repeats are required for its retrotransposition and how reverse transcription is initiated at the target site are not well understood. Here, using an ex vivo and trans-in vivo recombinant baculovirus retrotransposition system, we demonstrated that SART1Bm requires at least three (TTAGG) telomeric repeats and a longer poly(A) tail for its accurate retrotransposition. We found that SART1Bm retrotransposed only in the third (TTAGG) tract of three repeats and that the A residue of the (TTAGG) unit was essential for its retrotransposition. Interestingly, SART1Bm also retrotransposed into telomeric repeats of other species, such as human (TTAGGG)n repeats, albeit with low retrotransposition efficiency. We further showed that the reverse transcription of SART1Bm occurred inaccurately at the internal site of the 3′ untranslated region (UTR) when using a short poly(A) tail but at the accurate site when using a longer poly(A) tail. These findings promote our understanding of the general mechanisms of site-specific retrotransposition and aid the development of a site-specific gene knock-in tool.
Effects of nitrogen deposition and litter layer management on soil CO2, N2O, and CH4 emissions in a subtropical pine forestland
Authors: Fan Jianling , Luo Ruyi , McConkey Brian G. , Ziadi Noura 
Published: June 2020

AbstractForestland soils play vital role in regulating global soil greenhouse gas (GHG) budgets, but the interactive effect of the litter layer management and simulated nitrogen (N) deposition on these GHG flux has not been elucidated clearly in subtropical forestland. A field trial was conducted to study these effects by using litter removal method under 0 and 40 kg N ha−1 yr−1 addition in a subtropical forestland in Yingtan, Jiangxi Province, China. Soil CO2 emission was increased by N addition (18–24%) but decreased by litter removal (24–32%). Litter removal significantly (P < 0.05) decreased cumulative N2O emission by 21% in treatments without N addition but only by 10% in treatments with 40 kg N ha−1 yr−1 addition. Moreover, litter-induced N2O emission under elevated N deposition (0.094 kg N2O-N ha−1) was almost the same as without N addition (0.088 kg N2O-N ha−1). Diffusion of atmospheric CH4 into soil was facilitated by litter removal, which increased CH4 uptake by 55%. Given that the increasing trend of atmospheric N deposition in future, which would reduce litterfall in subtropical N-rich forest, the effect of surface litter layer change on soil GHG emissions should be considered in assessing forest GHG budgets and future climate scenario modeling.
Epididymal proteins Binder of SPerm Homologs 1 and 2 (BSPH1/2) are dispensable for male fertility and sperm motility in mice
Authors: Eskandari-Shahraki Marzieh , Prud’homme Bruno , Bergeron Francis , Manjunath Puttaswamy 
Published: June 2020

AbstractThe binder of sperm family of proteins has been reported to be indispensable for sperm maturation and capacitation. However, their physiological functions in fertility have only been studied in vitro. CRISPR/Cas9 genome editing was utilized to generate double knockout (DKO) mice by simultaneously targeting the two murine binder of sperm genes, Bsph1 and Bsph2. To confirm that the homologous genes and proteins were completely eliminated in the DKO mice, different methods such as reverse transcription polymerase chain reaction, digital droplet-polymerase chain reaction and liquid chromatography tandem mass spectrometry were applied. Bsph1/2 DKO male mice were bred by intercrossing. Compared to wild type counterparts, male Bsph1/2 null mice, lacking BSPH1/2 proteins, were fertile with no differences in sperm motility and sperm count. However, the weights of male pups were significantly increased in Bsph1/2 double knockout mice in a time dependent manner spanning days 6 and 21, as well as 6 weeks of age. No change was detected in the weights of female pups during the same period. Taken together, these data indicate that BSPH1/2 proteins are dispensable for male fertility in mice but may influence growth.