bluuebunny/crossref_metadata_2025_split huggingface dataset:
The domestication of plant architecture in African rice
Authors: Hu Min , Lv Shuwei , Wu Wenguang , Fu Yongcai , Liu Fengxia , Wang Bingbing , Li Weiguo , Gu Ping , Cai Hongwei , Sun Chuanqing , Zhu Zuofeng 
Published: March 2018

SummaryPlant architecture is a key agronomical factor determining crop yield and has been a major target of cereal crop domestication. The transition of plant architecture from the prostrate tiller of typical African wild rice (Oryza barthii) to the erect tiller of African cultivated rice (Oryza glaberrima) was a key step during domestication of African rice. Here we show that PROG7 (PROSTRATE GROWTH 7), a zinc‐finger transcription factor gene on chromosome 7, is required for the prostrate growth of African wild rice. Mutations in the promoter region of prog7 reduced the level of gene expression in the tiller base, leading to erect growth in African cultivated rice. Sequence comparison and haplotype analysis show that 90 varieties of cultivated rice from 11 countries carry the same mutations in the prog7 region. A strong signal in a 60‐kb genomic region was detected around the prog7 gene, suggesting that the region was under strong positive selection during the domestication process. Identification of the PROG7 gene provides new insights into the molecular basis of plant architecture in crops and facilitates investigation of the history of domestication of African rice.
Noninvasive prenatal paternity testing using targeted massively parallel sequencing
Authors: Qu Ning‐ , Xie Yifan , Li Haiyan , Liang Hao‐ , Lin Shaobin , Huang Erwen , Gao Jun‐ , Chen Fang‐ , Shi Yanwei , Ou Xueling 
Published: March 2018

BACKGROUNDRecent advances in massively parallel sequencing (MPS) technology have provided efficient methods for noninvasive prenatal paternity testing (NIPAT). However, a well‐accepted protocol has not been established. The present study developed an MPS‐based approach for NIPAT and compared the performance of two recently reported methods for MPS data interpretation.STUDY DESIGN AND METHODSWe selected 1795 unlinked polymorphic single‐nucleotide polymorphisms (SNPs) and performed paternity analysis in 34 real parentage test cases with maternal plasma samples using the Illumina HiSeq platform. Sequencing data were interpreted by the straightforward counting method for the identification of paternal alleles and mathematical algorithms for paternity index (PI) calculation, respectively.RESULTSBased on the sequencing data from each family case, both of the two statistical approaches produced a significant separation between the biological father and 90 unrelated males (p < 0.0001) when sufficient effective loci were attained. Nevertheless, up to 30.82% of real paternal alleles were filtered by a predefined cutoff and resulted in insufficient effective loci, especially in plasma samples with low fetal fraction (approx. 90.60% were filtered). In contrast, the PI calculation model utilized all maternal homozygous SNPs as effective loci (approx. 40% of total SNPs) and successfully identified the correct biological father, with the log‐transformed combined PI (Lg(CPI)) value varying from 68.23 to 158.01 in each family case.CONCLUSIONOur study illustrates that the Bayesian approach represents the better choice in NIPAT data interpretation. Further, the adoption of more informative markers (e.g., tri‐allelic SNPs, tetra‐allelic SNPs, and micro‐haplotypes) or deeper sequencing is recommended for the improvement of the testing efficiency.
Remediation of pharmaceutical contaminated water by use of magnetic functionalized metal organic framework. Physicochemical study of doxycycline adsorption
Authors: Naeimi Shakiba , Faghihian Hossein 
Published: March 2018

AbstractThe presence of pharmaceutical pollutant, doxycycline (DOC) in water and waste streams has negative impact on the environment. In this research, metal organic framework was synthesized and functionalized by potassium nickel ferrocyanide (KNiFC). After characterisation, the functionalized adsorbent was used for removal of DOC from aqueous solutions. The adsorbent containing 80% of KNiFC exhibited the high adsorption capacity of 100 mg/g. The adsorption process was kinetically fast and the equilibration was established within 30 min. The used adsorbent retained 90% of its initial capacity after regeneration. The magnetic susceptibility of the adsorbent measured by VSM technique was 35 emu/g and sufficient for separation of the used adsorbent by external magnetic field. Isotherm models including Langmuir, Freundlich, Tempkin, Redlich‐Peterson, and Sips were applied to correlate the experimental equilibrium data. To evaluate the fitness of the isotherm equations error analysis methods, residual root mean square error and average relative error were used.
Experiences in Physical Education: Exploring the Intersection of Visual Impairment and Maleness
Authors: Haegele Justin A. , Kirk T. Nicole 
Published: March 2018

The purpose of this study was to adopt an explicitly intersectional approach to examine the embodied perspectives of males with visual impairments about physical education. An interpretative phenomenological analysis research approach was used, and six adults (18–33 years) who identified as males with visual impairments acted as participants. The primary sources of data were semistructured, audiotaped, telephone interviews and reflective field notes. Thematic development utilized a four-step interpretative phenomenological analysis-guided analytical process. Based on the data analysis, the following three interrelated themes emerged: (a) “I didn’t feel very integrated”: Noninclusionary experiences based on blindness; (b) “Oh great, where’s my cane now?”: Bullying, blindness, and maleness; and (c) “Okay, just do what you can”: Competitive culture glass ceiling. The themes highlight several issues that have been faced by males with visual impairments, which should be considered by physical education and adapted physical education personnel to enhance the quality of education for this population.
Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells
In Vitro
Authors: Kitano Mitsutaka , Hosmillo Myra , Emmott Edward , Lu Jia , Goodfellow Ian 
Published: March 2018

ABSTRACT

Human norovirus (HuNoV) is a major cause of nonbacterial gastroenteritis worldwide, yet despite its impact on society, vaccines and antivirals are currently lacking. A HuNoV replicon system has been widely applied to the evaluation of antiviral compounds and has thus accelerated the process of drug discovery against HuNoV infection. Rupintrivir, an irreversible inhibitor of the human rhinovirus 3C protease, has been reported to inhibit the replication of the Norwalk virus replicon via the inhibition of the norovirus protease. Here we report, for the first time, the generation of rupintrivir-resistant human Norwalk virus replicon cells
in vitro
. Sequence analysis revealed that these replicon cells contained amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease NS6. The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In summary, using a combination of different approaches, we have demonstrated that, under the correct conditions, mutations in the norovirus protease that lead to the generation of resistant mutants can rapidly occur.
Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain
Authors: Sütterlin Susanne , Téllez-Castillo Carlos J. , Anselem Leticia , Yin Hong , Bray James E. , Maiden Martin C. J. 
Published: March 2018

ABSTRACT

Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently identified as a potential factor contributing to the aggravation of this situation. The present study investigated heavy metal susceptibility and genetic resistance determinants in
Escherichia coli
isolated from clinical urine samples from Sweden, Germany, and Spain. A total of 186 isolates were tested for their sodium arsenite, silver nitrate, and copper(II) sulfate MICs. In addition, 88 of these isolates were subjected to whole-genome sequencing for characterization of their genetic resistance determinants and epidemiology. For sodium arsenite, the isolates could be categorized into a resistant and a nonresistant group based on MIC values. Isolates of the resistant group exhibited the chromosomal
ars
operon and belonged to non-B2 phylogenetic groups; in contrast, within the B2 phylogroup, no
ars
operon was found, and the isolates were susceptible to sodium arsenite. Two isolates also harbored the silver/copper resistance determinant
pco/sil
, and they belonged to sequence types ST10 (phylogroup A) and ST295 (phylogroup C). The ST295 isolate had a silver nitrate MIC of ≥512 mg/liter and additionally produced extended-spectrum beta-lactamases. To our knowledge, this is the first study to describe the distribution of the arsenic resistance
ars
operon within phylogroups of
E. coli
strains isolated from patients with urinary tract infections. The arsenic resistance
ars
operon was present only in all non-B2 clades, which have previously been associated with the environment and commensalism in both humans and animals, while B2 clades lacked the
ars
operon.
In Vitro
Activity of Lefamulin against Sexually Transmitted Bacterial Pathogens
Authors: Paukner Susanne , Gruss Astrid , Jensen Jørgen Skov 
Published: March 2018

ABSTRACT

The pleuromutilin antibiotic lefamulin demonstrated
in vitro
activity against the most relevant bacterial pathogens causing sexually transmitted infections (STI), including
Chlamydia trachomatis
(MIC
50/90
, 0.02/0.04 mg/liter;
n
= 15), susceptible and multidrug-resistant
Mycoplasma genitalium
(MIC range, 0.002 to 0.063 mg/liter;
n
= 6), and susceptible and resistant
Neisseria gonorrhoeae
(MIC
50/90
, 0.12/0.5 mg/liter;
n
= 25). The results suggest that lefamulin could be a promising first-line antibiotic for the treatment of STI, particularly in populations with high rates of resistance to standard-of-care antibiotics.
Improvement of Bartonella henselae DNA Detection in Cat Blood Samples by Combining Molecular and Culture Methods
Authors: Drummond Marina Rovani , Lania Bruno Grosselli , Diniz Pedro Paulo Vissotto de Paiva , Gilioli Rovilson , Demolin Daniele Masselli Rodrigues , Scorpio Diana Gerardi , Breitschwerdt Edward B. , Velho Paulo Eduardo Neves Ferreira 
Published: March 2018

ABSTRACT

Bartonella
spp. are bacteria of worldwide distribution that cause asymptomatic to fatal infections in animals and humans. The most common zoonotic species is
Bartonella henselae
, for which cats are the major natural reservoir host. To better understand
Bartonella
sp. diagnostic limitations, we determined the frequency of bloodstream infection in 112 cats by comparing and combining the results of multiple conventional and nested PCRs from blood and liquid culture samples. Using liquid culture conventional PCR,
Bartonella
sp. DNA was amplified from 27.7% of samples (31/112) compared to 90.2% of samples (101/112) by combining nested PCR from blood and liquid culture, indicating that PCR testing of more than one type of sample provides better sensitivity than a standalone PCR and that bloodstream infection is very frequent among cats in southeastern Brazil. This study reinforces the need for multistep testing for
Bartonella
sp. infection to prevent false-negative diagnostic results, even in reservoir hosts such as cats that typically maintain higher bacteremia levels.
Exacerbated Apoptosis of Cells Infected with Infectious Bursal Disease Virus upon Exposure to Interferon Alpha
Authors: Cubas-Gaona Liliana L. , Diaz-Beneitez Elisabet , Ciscar Marina , Rodríguez José F. , Rodríguez Dolores 
Published: March 2018

ABSTRACT

Infectious bursal disease virus (IBDV) belongs to the
Birnaviridae
family and is the etiological agent of a highly contagious and immunosuppressive disease (IBD) that affects domestic chickens (
Gallus gallus
). IBD or Gumboro disease leads to high rates of morbidity and mortality of infected animals and is responsible for major economic losses to the poultry industry worldwide. IBD is characterized by a massive loss of IgM-bearing B lymphocytes and the destruction of the bursa of Fabricius. The molecular bases of IBDV pathogenicity are still poorly understood; nonetheless, an exacerbated cytokine immune response and B cell depletion due to apoptosis are considered main factors that contribute to the severity of the disease. Here we have studied the role of type I interferon (IFN) in IBDV infection. While IFN pretreatment confers protection against subsequent IBDV infection, the addition of IFN to infected cell cultures early after infection drives massive apoptotic cell death. Downregulation of double-stranded RNA (dsRNA)-dependent protein kinase (PKR), tumor necrosis factor alpha (TNF-α), or nuclear factor κB (NF-κB) expression drastically reduces the extent of apoptosis, indicating that they are critical proteins in the apoptotic response induced by IBDV upon treatment with IFN-α. Our results indicate that IBDV genomic dsRNA is a major viral factor that contributes to the triggering of apoptosis. These findings provide novel insights into the potential mechanisms of IBDV-induced immunosuppression and pathogenesis in chickens.

IMPORTANCE
IBDV infection represents an important threat to the poultry industry worldwide. IBDV-infected chickens develop severe immunosuppression, which renders them highly susceptible to secondary infections and unresponsive to vaccination against other pathogens. The early dysregulation of the innate immune response led by IBDV infection and the exacerbated apoptosis of B cells have been proposed as the main factors that contribute to virus-induced immunopathogenesis. Our work contributes for the first time to elucidating a potential mechanism driving the apoptotic death of IBDV-infected cells upon exposure to type I IFN. We provide solid evidence about the critical importance of PKR, TNF-α, and NF-κB in this phenomenon. The described mechanism could facilitate the early clearance of infected cells, thereby aiding in the amelioration of IBDV-induced pathogenesis, but it could also contribute to B cell depletion and immunosuppression. The balance between these two opposing effects might be dramatically affected by the genetic backgrounds of both the host and the infecting virus strain.
Herpesvirus Evasion of Natural Killer Cells
Authors: De Pelsmaeker Steffi , Romero Nicolas , Vitale Massimo , Favoreel Herman W. 
Published: March 2018

ABSTRACTNatural killer (NK) cells play an important role in the host response against viral infections and cancer development. They are able to kill virus-infected and tumor cells, and they produce different important cytokines that stimulate the antiviral and antitumor adaptive immune response, particularly interferon gamma. NK cells are of particular importance in herpesvirus infections, which is illustrated by systemic and life-threatening herpesvirus disease symptoms in patients with deficiencies in NK cell activity and by the myriad of reports describing herpesvirus NK cell evasion strategies. The latter is particularly obvious for cytomegaloviruses, but increasing evidence indicates that most, if not all, members of the herpesvirus family suppress NK cell activity to some extent. This review discusses the different NK cell evasion strategies described for herpesviruses and how this knowledge may translate to clinical applications.
Domains of the Hepatitis B Virus Small Surface Protein S Mediating Oligomerization
Authors: Suffner Sascha , Gerstenberg Nadine , Patra Maria , Ruibal Paula , Orabi Ahmed , Schindler Michael , Bruss Volker 
Published: March 2018

ABSTRACT
During hepatitis B virus (HBV) infections, subviral particles (SVP) consisting only of viral envelope proteins and lipids are secreted. Heterologous expression of the small envelope protein S in mammalian cells is sufficient for SVP generation. S is synthesized as a transmembrane protein with N-terminal (TM1), central (TM2), and hydrophobic C-terminal (HCR) transmembrane domains. The loops between TM1 and TM2 (the cytosolic loop [CL]) and between TM2 and the HCR (the luminal loop [LL]) are located in the cytosol and the endoplasmic reticulum (ER) lumen, respectively. To define the domains of S mediating oligomerization during SVP morphogenesis, S mutants were characterized by expression in transiently transfected cells. Mutation of 12 out of 15 amino acids of TM1 to alanines, as well as the deletion of HCR, still allowed SVP formation, demonstrating that these two domains are not essential for contacts between S proteins. Furthermore, the oligomerization of S was measured with a fluorescence-activated cell sorter (FACS)-based Förster resonance energy transfer (FRET) assay. This approach demonstrated that the CL, TM2, and the LL independently contributed to S oligomerization, while TM1 and the HCR played minor roles. Apparently, intermolecular homo-oligomerization of the CL, TM2, and the LL drives S protein aggregation. Detailed analyses revealed that the point mutation C65S in the CL, the mutation of 13 out of 19 amino acids of TM2 to alanine residues, and the simultaneous replacement of all 8 cysteine residues in the LL by serine residues blocked the abilities of these domains to support S protein interactions. Altogether, specific domains and residues in the HBV S protein that are required for oligomerization and SVP generation were defined.

IMPORTANCE
The small hepatitis B virus envelope protein S has the intrinsic ability to direct the morphogenesis of spherical 20-nm subviral lipoprotein particles. Such particles expressed in yeast or mammalian cells represent the antigenic component of current hepatitis B vaccines. Our knowledge about the steps leading from the initial, monomeric, transmembrane translation product of S to SVP is very limited, as is our information on the structure of the complex main epitope of SVP that induces the formation of protective antibodies after vaccination. This study contributes to our understanding of the oligomerization process of S chains during SVP formation and shows that the cytoplasmic loop, one membrane-embedded domain, and the luminal loop of S independently drive S-S oligomerization.
Off-label use of tacrolimus in children with Henoch-Schönlein purpura nephritis: a pilot study
Authors: Zhang Dong-Feng , Hao Guo-Xiang , Li Chun-Zhen , Yang Yan-Jun , Liu Fu-Juan , Liu Ling , Yuan Xiao-Ying , Li Rui-Hong , Dong Lei , Dong Qian , Jacqz-Aigrain Evelyne , Zhao Wei 
Published: March 2018

BackgroundTacrolimus is used off-label in the treatment of Henoch-Schönlein purpura nephritis (HSPN) in children, with limited evidence-based data. Based on clinical empirical experience and mechanism of action, tacrolimus might be promoted as treatment for childhood HSPN. The objectives of this pilot study were to assess its effectiveness and safety, and to explore the potential impact of CYP3A5 genotype.MethodsChildren with HSPN receiving tacrolimus as empirical treatment were included in this prospective, observational study. Effectiveness was classified as complete remission, partial remission or non-response. General safety data analyses during and after study drug exposure included adverse events, reasons for discontinuation, deaths, laboratory data and vital signs. Trough concentration was determined using high-performance liquid chromatography with tandem mass spectrometry. Pharmacogenetic analysis was performed on the CYP3A5 gene.ResultsA total of 20 patients with a mean age of 7.5 (SD 2.1) years participated in the whole process of the study. Twelve patients reached complete remission and eight patients reached partial remission at the end of 6-month treatment. No patients discontinued tacrolimus treatment due to adverse events, and no drug-related adverse events were shown to have a causal association with tacrolimus therapy. Dose-adjusted trough concentration was significantly higher in children with CYP3A5*1 allele as compared with patients with CYP3A5*3/*3 genotype (170.7±100.9 vs 79.8±47.4 (ng/mL)/(mg/kg)).ConclusionThis pilot study showed that tacrolimus might be an effective and well-tolerated drug for the treatment of HSPN in children. CYP3A5 polymorphism had a significant impact on tacrolimus concentration.
National, regional and global mortality due to alcoholic cardiomyopathy in 2015
Authors: Manthey Jakob , Probst Charlotte , Rylett Margaret , Rehm Jürgen 
Published: March 2018

Objectives(1) A comprehensive mortality assessment of alcoholic cardiomyopathy (ACM) and (2) examination of under-reporting using vital statistics data.MethodsA modelling study estimated sex-specific mortality rates for each country, which were subsequently aggregated by region and globally. Input data on ACM mortality were obtained from death registries for n=91 countries. For n=99 countries, mortality estimates were predicted using aggregate alcohol data from WHO publications. Descriptive additional analyses illustrated the scope of under-reporting.ResultsIn 2015, there were an estimated 25 997 (95% CI 17 385 to 49 096) global deaths from ACM. This translates into 6.3% (95% CI 4.2% to 11.9%) of all global deaths from cardiomyopathy being caused by alcohol. There were large regional variations with regard to mortality burden. While the majority of ACM deaths were found in Russia (19 749 deaths, 76.0% of all ACM deaths), for about one-third of countries (n=57) less than one ACM death was found. Under-reporting was identified for nearly every second country with civil registration data. Overall, two out of three global ACM deaths might be misclassified.ConclusionsThe variation of ACM mortality burden is greater than for other alcohol-attributable diseases, and partly may be the result of stigma and lack of detection. Misclassification of ACM fatalities is a systematic phenomenon, which may be caused by low resources, lacking standards and stigma associated with alcohol-use disorders. Clinical management may be improved by including routine alcohol assessments. This could contribute to decrease misclassifications and to provide the best available treatment for affected patients.