bluuebunny/crossref_metadata_2025 huggingface dataset:
Psydrax multiflora sp. nov. (Rubiaceae) from Palawan, Philippines
Authors: Arriola Axel H. , Cobangkiat Adrienne B. , Alejandro Grecebio Jonathan D.
Published: January 2017

Psydrax multiflora, a new species of Vanguerieae collected in the Palawan, Luzon Island, Philippines is herein described and illustrated. Morphological observation showed that P. multilfora approaches three Malesian Psydrax species, namely P. amplifolia, P. nitida and P. puberula. However, P. multiflora can be delineated from these three by its caudate leaf apex, 20–30‐flowered umbellate inflorescences and broadly triangular corolla lobes.
Patients’ and Physicians’ Perceptions Regarding the Benefits of Atrial Fibrillation Ablation
Authors: BADIN AUROA , PARR ALAN R. , BANGA SANDEEP , WIGANT REBECCA R. , BAMAN TIMIR S.
Published: January 2017

Background

It is unclear whether patients and physicians understand that atrial fibrillation ablation (AFA) has been shown to only improve symptomology and not reduce morbidity or mortality.

Methods

Note that 177 of 445 (40%) consecutive patients referred to an electrophysiology clinic for atrial fibrillation (AF) management responded anonymously to our survey via mail. Note that 105 of 656 (15%) physicians responded to our survey via email. Comparisons among groups were conducted using χ2 test for categorical variables. Odds ratios and 95% confidence intervals were estimated by using a multivariate logistic regression model.

Results

Almost half of patients and physicians believed AF ablation (AFA) would eliminate the need for anticoagulation (43% vs. 44%, P > 0.05) while the majority of both groups believed AFA would improve survival (58% vs. 67%, P = 0.308). The great majority of both groups believed AFA would decrease stroke rates (89% vs. 80%, P = 0.106). When comparing noncardiologists (n = 86) to cardiologists (n = 19), noncardiologists were more likely to believe that an AFA would eliminate the need for anticoagulation 49% vs. 21% (X = 4.9, P = 0.04), improve survival 80% vs. 11% (X = 30.2, P < 0.001), and decrease stroke 87% vs. 44% (X = 15.6, P < 0.001), respectively.

Conclusions

The perceived benefit of AFA by patients and physicians is not supported by the medical literature. It is the responsibility of the electrophysiology community to educate patients and referring physicians regarding the true benefits of AFA. In addition, our study displays the great need for long‐term clinical trials examining the impact AFA has on morbidity and mortality.
Genome‐wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China
Authors: Sun Congwei , Zhang Fuyan , Yan Xuefang , Zhang Xiangfen , Dong Zhongdong , Cui Dangqun , Chen Feng
Published: January 2017

Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield‐related traits in series of genome‐wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high‐quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length‐related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height‐related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield‐related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length‐ and plant height‐related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield‐related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield‐related traits and valuable genetic loci for marker‐assisted selection in Chinese wheat breeding programme.
Nutritional status and feeding problems in pediatric attention deficit–hyperactivity disorder
Authors: Sha'ari Norsuhaila , Manaf Zahara Abdul , Ahmad Mahadir , Rahman Fairuz Nazri Abd
Published: January 2017

Background

Children with attention deficit–hyperactivity disorder (ADHD) may be at risk of nutrient deficiency due to the inability to sit through meals. This comparative cross‐sectional study was therefore carried out to determine the nutritional status and feeding problems of ADHD children aged 4–12 years.

Methods

Sociodemographic data, anthropometric measurements and 3 day dietary intake record were collected from 54 ADHD children and 54 typical development (TD) children. The Behavioral Pediatrics Feeding Assessment Scale was used to assess feeding problems.

Results

Mean subject age was 8.6 ± 2.1 years. On anthropometric assessment, 11.1% of the ADHD children had wasting, while 1.9% had severe wasting. In contrast, none of the TD children had wasting. Approximately 5.6% of the ADHD children had stunting, as compared with 3.7% of the TD children, while none of the TD children had severe stunting compared with 3.7% of the ADHD children. More than half of the ADHD children had mid‐upper arm circumference (MUAC) below the 5th percentile, indicating undernutrition, compared with only 35.2% of TD children. More than one‐third of the ADHD children had feeding problems compared with 9.3% of TD children. There was a significant negative relationship between the ADHD children's feeding problems and bodyweight (r = −0338, P = 0.012), body mass index (r = −0322, P = 0.017) and MUAC (r = −0384, P = 0.004).

Conclusion

Almost half of the ADHD children had suboptimal nutrition compared with 11.1% of the TD children. It is imperative to screen ADHD children for nutritional status and feeding problems to prevent negative health impacts later on.
FRET in a Synthetic Flavin‐ and Bilin‐binding Protein
Authors: Simon Julian , Losi Aba , Zhao Kai‐Hong , Gärtner Wolfgang
Published: January 2017

The last decade has seen development and application of a large number of novel fluorescence‐based techniques that have revolutionized fluorescence microscopy in life sciences. Preferred tags for such applications are genetically encoded fluorescent proteins (FP), mostly derivatives of the green fluorescent protein (GFP). Combinations of FPs with wavelength‐separated absorption/fluorescence properties serve as excellent tools for molecular interaction studies, for example, protein–protein complexes or enzyme–substrate interactions, based on the FRET phenomenon (Förster resonance energy transfer). However, alternatives are requested for experimental conditions where FP proteins or FP couples are not or less efficiently applicable. We here report as a “proof of principle” a specially designed, non‐naturally occurring protein (LG1) carrying a combination of a flavin‐binding LOV‐ and a photochromic bilin‐binding GAF domain and demonstrate a FRET process between both chromophores.
An Automated Model-Order Reduction Method for Automatic Transmissions
Authors: Ranogajec Vanja , Deur Joško
Published: January 2017

New generation of torque converter automatic transmissions (AT) includes a large number of gears for improved fuel economy and vehicle performance, which leads to exponentially increasing number of shift types and shift events. In order to facilitate various numerical/simulation analyses of AT dynamics, shift control optimization, and control strategy design, a full-order AT model is usually reduced by eliminating state variables related to locked clutches in particular gears or shifts. The paper proposes an automated model-order reduction method for an arbitrary, user-specified clutch state, and demonstrates its application on an example of ten-speed AT. The method is based on determining the locked-clutch torque variables and their substitution into the full-order state-space model input vector, as well as finding a linear relation between the reduced-order and full-order model state-space variables.
Nonlinear Model Predictive Control of Axial Piston Pumps
Authors: Zeman Paul , Kemmetmüller Wolfgang , Kugi Andreas
Published: January 2017

Variable displacement axial piston units are the core components of many hydrostatic and hydraulic hybrid drive trains. Therein, the fast and accurate control of the swash plate angle, utilizing the full possible dynamics of the displacement system, is essential for a good performance of the overall drive train. This paper describes the development, implementation, and the experimental validation of a control strategy for the swash plate angle based on nonlinear model predictive control (NMPC). A tailored mathematical model, which serves as the basis for the NMPC, is described in the first part of the paper. Two versions of NMPC, an indirect and a direct method, are compared with respect to their numerical complexity and their capability of handling input and state constraints. An observer strategy, which is designed to obtain the nonmeasurable states and varying parameters of the system, completes the overall control strategy. To reduce the negative influence of stick–slip friction, the concept of dithering is applied in the experimental implementation. The differences of the NMPC methods are analyzed by simulation studies and experiments. Finally, the experimental results, using an industrial electronic control unit (ECU), prove the practical feasibility and the improved control accuracy and robustness in comparison to classical (nonlinear) control strategies.
Design of Repetitive-Control System With Input Dead Zone Based on Generalized Extended-State Observer
Authors: Wu Min , Yu Pan , Chen Xin , She Jinhua
Published: January 2017

This paper concerns a repetitive-control system with an input-dead-zone (IDZ) nonlinearity. First, the expression for the IDZ is decomposed into a linear term and a disturbance-like one that depends on the parameters of the dead zone. A function of the system-state error is used to approximate the combination of the disturbancelike term and an exogenous disturbance. The estimate is used to compensate for the overall effect of the IDZ and the exogenous disturbance. Next, the state-feedback gains are obtained from a linear matrix inequality that contains two tuning parameters for adjusting control performance; and the pole assignment method is employed to design the gain of a state observer. Then, two stability criteria are used to test the stability of the closed-loop system. The method is simple, employing neither an inverse model of the plant nor an adaptive control technique. It is also robust with regard to the different parameters of the IDZ, uncertainties in the plant, and the exogenous disturbance. Finally, two numerical examples demonstrate the effectiveness of this method and its advantages over others.
Sound field reconstruction using compressed modal equivalent point source method
Authors: Bi Chuan-Xing , Liu Yuan , Xu Liang , Zhang Yong-Bin
Published: January 2017

The accuracy, resolution, and economic cost of near-field acoustic holography (NAH) are highly dependent on the number of spatial sampling points. Generally, higher accuracy and resolution require more spatial sampling points, which may increase the workload of measurement or the hardware cost. Compressive sensing (CS) is able to solve the underdetermined problems by utilizing the sparsity of signals, and thus it can be applied to NAH to reduce the number of spatial sampling points but at the same time provide a high-resolution reconstruction image. Based on the CS theory, this paper proposes a compressed modal equivalent point source method (CMESM). In the method, a sparse basis that is obtained from the eigen-decomposition of the power resistance matrix is introduced to compress the equivalent point source strengths, and the ℓ1–norm minimization is used to promote sparse solutions. Both numerical simulation and experimental results demonstrate the validity of the proposed CMESM and show its advantage over the existing methods when the number of spatial sampling points is reduced.
The discovery of a conjugate system of faults in the Wharton Basin intraplate deformation zone
Authors: Singh Satish C. , Hananto Nugroho , Qin Yanfang , Leclerc Frederique , Avianto Praditya , Tapponnier Paul E. , Carton Helene , Wei Shengji , Nugroho Adam B. , Gemilang Wishnu A. , Sieh Kerry , Barbot Sylvain
Published: January 2017

A conjugate system of faults (shear and reactivated fracture zones) accommodates intraplate deformation in the Wharton Basin.
Density functional theory is straying from the path toward the exact functional
Authors: Medvedev Michael G. , Bushmarinov Ivan S. , Sun Jianwei , Perdew John P. , Lyssenko Konstantin A.
Published: January 2017

Whither the density in DFT calculations?

The continuing development of density functional theory (DFT) has greatly expanded the size and complexity of molecules amenable to computationally tractable simulation. The conventional metric of success for new functionals has been the accuracy of their calculated energies. Medvedev
et al.
examined how well these functionals calculate electron density across a series of neutral and cationic atoms (see the Perspective by Hammes-Schiffer). Although historically the accuracies of energy and density have improved in tandem, certain recent functionals have sacrificed fidelity to the true density.

Science
, this issue p.
49
; see also p.
28
A supramolecular assembly mediates lentiviral DNA integration
Authors: Ballandras-Colas Allison , Maskell Daniel P. , Serrao Erik , Locke Julia , Swuec Paolo , Jónsson Stefán R. , Kotecha Abhay , Cook Nicola J. , Pye Valerie E. , Taylor Ian A. , Andrésdóttir Valgerdur , Engelman Alan N. , Costa Alessandro , Cherepanov Peter
Published: January 2017

High-resolution insights into the intasome

An essential step in the life cycle of lentiviruses such as HIV-1 is when viral DNA integrates into the host genome, establishing a permanent infection of the host cell. The viral integrase enzyme catalyzes this process and is a major drug target. During viral integration, integrase binds the ends of viral DNA, forming a higher-order structure called the intasome. Passos
et al.
and Ballandras-Colas
et al.
used cryo—electron microscopy to solve the structures of the intasomes from HIV-1 and maedi-visna virus (ovine lentivirus), respectively. These structures reveal how integrase self-associates to form a functional intasome and help resolve previous conflicting models of intasome assembly.

Science
, this issue p.
89
, p.
93
A global view of meiotic double-strand break end resection
Authors: Mimitou Eleni P. , Yamada Shintaro , Keeney Scott
Published: January 2017

Recombination revealed by mapping tails

Meiosis is a specialized double cell division that generates haploid gametes from diploid parent cells. Meiotic recombination between homologous chromosomes ensures the proper segregation of chromosomes to the daughter cells. Mimitou
et al.
carried out a genome-wide survey of resection of the ends of DNA double strand breaks in yeast. Resection generates single-stranded tails that are vital for meiotic recombination. The Tel1 kinase promoted initiation of resection. Nucleosomes, which normally package DNA, needed to be disassembled to allow rapid and efficient resection.

Science, this issue p.
40
Additive manufacturing of hydrogel-based materials for next-generation implantable medical devices
Authors: Chin Sau Yin , Poh Yukkee Cheung , Kohler Anne-Céline , Compton Jocelyn T. , Hsu Lauren L. , Lau Kathryn M. , Kim Sohyun , Lee Benjamin W. , Lee Francis Y. , Sia Samuel K.
Published: January 2017

Wirelessly controlled, tailored, integrated biocompatible devices with moving components are used for drug delivery.
Spermine and Spermidine Alter Gene Expression and Antigenic Profile of Borrelia burgdorferi
Authors: Lin Ying-Han , Romo Jesus A. , Smith Trever C. , Reyes Ann N. , Karna S. L. Rajasekhar , Miller Christine L. , Van Laar Tricia A. , Yendapally Raghunandan , Chambers James P. , Seshu J.
Published: January 2017

Borrelia burgdorferi
, the agent of Lyme disease, responds to numerous host-derived signals to alter adaptive capabilities during its enzootic cycle in an arthropod vector and mammalian host. Molecular mechanisms that enable
B. burgdorferi
to detect, channel, and respond to these signals have become an intense area of study for developing strategies to limit transmission/infection. Bioinformatic analysis of the borrelial genome revealed the presence of polyamine transport components (PotA, PotB, PotC, and PotD), while homologs for polyamine biosynthesis were conspicuously absent. Although
potABCD
is cotranscribed, the level of PotA was elevated under
in vitro
growth conditions mimicking unfed ticks compared to the level in fed ticks, while the levels of PotD were similar under the aforementioned conditions in
B. burgdorferi
. Among several polyamines and polyamine precursors, supplementation of spermine or spermidine in the borrelial growth medium induced synthesis of major regulators of gene expression in
B. burgdorferi
, such as RpoS and BosR, with a concomitant increase in proteins that contribute to colonization and survival of
B. burgdorferi
in the mammalian host. Short transcripts of
rpoS
were elevated in response to spermidine, which was correlated with increased protein levels of RpoS. Transcriptional analysis of
rpoZ
and
B. burgdorferi
rel
(

rel
Bbu

;
bb0198
) in the presence of spermidine revealed the interplay of multiple regulatory factors in
B. burgdorferi
gene expression. The effect of spermidine on the levels of select borrelial proteins was also influenced by serum factors. These studies suggest that multiple host-derived signals/nutrients and their transport systems contribute to
B. burgdorferi
adaptation during the vector and vertebrate host phases of infection.
Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S-transferase supergene family
Authors: La Roche S D , Leisinger T
Published: January 2017

The nucleotide sequence of a cloned 2.8-kilobase-pair BamHI-PstI fragment containing dcmA, the dichloromethane dehalogenase structural gene from Methylobacterium sp. strain DM4, was determined. An open reading frame with a coding capacity of 287 amino acids (molecular weight, 37,430) was identified as dcmA by its agreement with the N-terminal amino acid sequence, the total amino acid composition, and the subunit size of the purified enzyme. Alignment of the deduced dichloromethane dehalogenase amino acid sequence with amino acid sequences of the functionally related eucaryotic glutathione S-transferases revealed three regions containing highly conserved amino acid residues and indicated that dcmA is a member of the glutathione S-transferase supergene family. The 5' terminus of in vivo dcmA transcripts was determined by nuclease S1 mapping to be 82 base pairs upstream of the GTG initiation codon of dcmA. Despite a putative promoter sequence with high resemblance to the Escherichia coli -10 and -35 consensus sequences, located at an appropriate distance from the transcription start point, dcmA was only marginally expressed in E. coli. The strong induction of dichloromethane dehalogenase in Methylobacterium sp. by dichloromethane was abolished by deleting the 1.3-kilobase-pair upstream region of dcmA. Plasmid constructs devoid of this region directed expression of dichloromethane dehalogenase at a constitutively induced level.
cobA function is required for both de novo cobalamin biosynthesis and assimilation of exogenous corrinoids in Salmonella typhimurium
Authors: Escalante-Semerena J C , Suh S J , Roth J R
Published: January 2017

Salmonella typhimurium is able to synthesize cobalamin (B12) under anaerobic growth conditions. The previously described cobalamin biosynthetic mutations (phenotypic classes CobI, CobII, and CobIII) map in three operons located near the his locus (minute 41). A new class of mutant (CobIV) defective in B12 biosynthesis was isolated and characterized. These mutations map between the cysB and trp loci (minute 34) and define a new genetic locus, cobA. The anaerobic phenotype of cobA mutants suggests an early block in corrin ring formation; mutants failed to synthesize cobalamin de novo but did so when the corrin ring is provided as cobyric acid dicyanide or as cobinamide dicyanide. Under aerobic conditions, cobA mutants were unable to convert either cobyric acid dicyanide or cobinamide dicyanide to cobalamin but could use adenosylcobyric acid or adenosylcobinamide as a precursor; this suggests that the mutants are unable to adenosylate exogenous corrinoids. To explain the anaerobic CobI phenotype of a cobA mutant, we propose that the cobA gene product catalyzes adenosylation of an early intermediate in the de novo B12 pathway and also adenosylates exogenous corrinoids. Under anaerobic conditions, a substitute function, known to be encoded in the main Cob operons, is induced; this substitute function can adenosylate exogenous cobyric acid and cobinamide but not the early biosynthetic intermediate. The cobA gene of S. typhimurium appears to be functionally equivalent to the btuR gene of Escherichia coli.
A tetracycline efflux gene on Bacteroides transposon Tn4400 does not contribute to tetracycline resistance
Authors: Speer B S , Salyers A A
Published: January 2017

Previously, we demonstrated that the Bacteroides transposon Tn4351, which confers tetracycline resistance only on aerobically grown Escherichia coli, carries a gene that codes for a tetracycline-inactivating enzyme (B. S. Speer and A. A. Salyers, J. Bacteriol. 170:1423-1429, 1988). However, Park et al. (B. H. Park, M. Hendricks, M. H. Malamy, F. P. Tally, and S. B. Levy, Antimicrob. Agents Chemother. 31:1739-1743, 1987) showed that E. coli carrying a closely related transposon, Tn4400, exhibits energy-dependent efflux of tetracycline as well as tetracycline-inactivating activity (B. H. Park and S. B. Levy, Antimicrob. Agents Chemother. 32:1797-1800, 1988). This result raised the question of whether efflux or inactivation or a combination of the two was necessary for resistance conferred by both transposons. We showed that cells carrying Tn4351 did not exhibit the clear-cut efflux activity seen with cells carrying Tn4400 but rather exhibited a tetracycline accumulation profile which could be explained solely on the basis of inactivation of tetracycline in the cytoplasm and rapid diffusion of altered tetracycline out of the cell. Additionally, we were able to clone the efflux and tetracycline-modifying genes of Tn4400 separately. The region carrying the efflux gene spanned one of the two regions in which Tn4400 differs from Tn4351. A clone containing the corresponding region of Tn4351 did not exhibit efflux. Thus, it appears that Tn4351 does not have the efflux gene and that efflux makes no contribution to the resistance conferred by Tn4351. The MIC for cells carrying the subclone from Tn4400 that contained only the gene for tetracycline inactivation was the same that for cells carrying both the inactivation and efflux genes. Cells carrying only the gene for tetracycline efflux were tetracycline sensitive. This was true even when the efflux gene was on a high-copy-number plasmid which increased the level of efflux to that associated with the Tcr gene on pBR328. These results indicate that efflux activity does not contribute significantly to the tetracycline resistance conferred by Tn4400.
mprA, an Escherichia coli gene that reduces growth-phase-dependent synthesis of microcins B17 and C7 and blocks osmoinduction of proU when cloned on a high-copy-number plasmid
Authors: del Castillo I , Gómez J M , Moreno F
Published: January 2017

Microcins B17 and C7 are plasmid-determined, peptide antibiotics produced by Escherichia coli when cells enter the stationary phase of growth. Microcinogenic strains are immune to the action of the microcin they synthesize. A well-characterized deficient-immunity phenotype is exhibited by microcin B17-producing cells in the absence of the immunity gene mcbG (M.C. Garrido, M. Herrero, R. Kolter, and F. Moreno, EMBO J. 7:1853-1862, 1988). A 14.6-kilobase-pair EcoRI chromosomal fragment was isolated by its ability to suppress this phenotype when cloned into a multicopy vector. This fragment was mapped to 57.5 min on the E. coli genetic map. The position of the gene responsible for suppression, designated mprA, was determined by insertional mutagenesis and deletion analysis. mprA was shown to be transcribed clockwise on the E. coli chromosome, and its product was identified as a 19-kilodalton polypeptide. Suppression was shown to be achieved by decreasing microcin B17 production. Increased mprA gene dosage also caused a decrease in microcin C7 production and blocked the osmoinduction of the proU locus in high-osmolarity media. Our results suggest that the mprA gene product could play a regulatory role on expression of several E. coli genes, this control being exerted at the transcriptional level.
Neurospora endo-exonuclease is immunochemically related to the recC gene product of Escherichia coli
Authors: Fraser M J , Koa H , Chow T Y
Published: January 2017

Immunochemical cross-reaction between the endo-exonuclease of Neurospora crassa, an enzyme previously implicated in recombination and recombinational DNA repair, and the recC-encoded polypeptide of Escherichia coli has been detected by immunoblotting extracts of strains of E. coli having a deletion that includes the recBCD genes but carrying multicopy plasmids bearing all three of the recBCD genes or only one or two of these genes. It was predicted that homology would also be found at the amino acid sequence level between the recC polypeptide and both nuclear and mitochondrial endo-exonucleases of Saccharomyces cerevisiae, which cross-react with antibodies raised to the N. crassa endo-exonuclease. Since the gene for the S. cerevisiae mitochondrial enzyme, NUC1, has been cloned and sequenced and the predicted amino acid sequence is known, this sequence was aligned with the predicted amino acid sequence of the recC polypeptide. Extensive homology was found by aligning 306 of the 329 amino acids of the yeast mitochondrial nuclease sequence with the carboxy-terminal one-quarter of the amino acid sequence of the recC polypeptide.
Use of both translation initiation sites of the middle wall protein gene in Bacillus brevis 47
Authors: Adachi T , Yamagata H , Tsukagoshi N , Udaka S
Published: January 2017

The middle wall protein gene of Bacillus brevis 47 has two potential translation initiation sites located tandemly in the same reading frame. We demonstrate here that both sites are utilized to start translation in B. brevis 47. Translation from the first site (located upstream) gives rise to a precursor of the middle wall protein with an extension peptide of 31 amino acids preceding the signal peptide. The precursor was cleaved at the same position as that of the precursor translated from the second site. The TTG codon seems to play an appreciable role in the initiation of translation in B. brevis 47.
Inactivation, sequence, and lacZ fusion analysis of a regulatory locus required for repression of nitrogen fixation genes in Rhodobacter capsulatus
Authors: Kranz R G , Pace V M , Caldicott I M
Published: January 2017

Transcription of the genes that code for proteins involved in nitrogen fixation in free-living diazotrophs is typically repressed by high internal oxygen concentrations or exogenous fixed nitrogen. The DNA sequence of a regulatory locus required for repression of Rhodobacter capsulatus nitrogen fixation genes was determined. It was shown that this locus, defined by Tn5 insertions and by ethyl methanesulfonate-derived mutations, is homologous to the glnB gene of other organisms. The R. capsulatus glnB gene was upstream of glnA, the gene for glutamine synthetase, in a glnBA operon. beta-Galactosidase expression from an R. capsulatus glnBA-lacZ translational fusion was increased twofold in cells induced by nitrogen limitation relative to that in cells under nitrogen-sufficient conditions. R. capsulatus nifR1, a gene that was previously shown to be homologous to ntrC and that is required for transcription of nitrogen fixation genes, was responsible for approximately 50% of the transcriptional activation of this glnBA fusion in cells induced under nitrogen-limiting conditions. R. capsulatus GLNB, NIFR1, and NIFR2 (a protein homologous to NTRB) were proposed to transduce the nitrogen status in the cell into repression or activation of other R. capsulatus nif genes. Repression of nif genes in response to oxygen was still present in R. capsulatus glnB mutants and must have occurred at a different level of control in the regulatory circuit.
Interaction of monoclonal antibodies with the enzymatic domains of penicillin-binding protein 1b of Escherichia coli
Authors: den Blaauwen T , Aarsman M , Nanninga N
Published: January 2017

Monoclonal antibodies (MAbs) against four different antigenic determinants of penicillin-binding protein (PBP) 1b were used to study the transglycosylase and transpeptidase activities of PBP 1b. Enzyme kinetics in the presence of and without the MAbs were determined, and the synthesized murein was analyzed. Two MAbs against the transglycosylase domain of PBP 1b appeared to inhibit this reaction. One MAb inhibited only the transpeptidase reaction, and one inhibited both enzymatic activities of PBP 1b. The latter two MAbs bound to the transpeptidase domain of PBP 1b. The following major conclusions were deduced from the results. (i) Transpeptidation is the rate-limiting step of the reaction cascade, and it is dependent on the product of transglycosylation. (ii) PBP 1b has only one type of transpeptidase activity, i.e., a penta-tetra transpeptidase activity. (iii) PBP 1b is probably a globular protein which has two intimately associated enzymatic domains.
Cell volume increase in Escherichia coli after shifts to richer media
Authors: Kubitschek H E
Published: January 2017

Synchronous cultures of Escherichia coli 15-THU and WP2s, which were selected by velocity sedimentation from exponential-phase cultures growing in an acetate-minimal salts medium, were shifted to richer media at various times during the cell cycle by the addition of glucose or nutrient broth. Cell numbers and mean cell volumes were measured electronically. The duration of the division cycle of the shifted generation was not altered significantly by the addition of either nutrient. Growth rates, measured as rates of cell volume increase, were constant throughout the cycle in unshifted acetate control cultures. When glucose was added, growth rates also remained unchanged during the remainder of the cell cycle and then increased abruptly at or after cell division. When nutrient broth was added, growth rates remained unchanged from periods of 0.2 to 0.4 generations and then increased abruptly to their final values. In all cases, the cell volume increase was linear both before and after the growth rate transition. The strongest support for a linear cell volume increase during the cell cycle of E. coli in slowly growing acetate cultures, however, was obtained in unshifted cultures, in complete agreement with earlier observations of cell volumes at much more rapid growth rates. Although cell growth and division are under the control of the synthesizing machinery in the cell responsible for RNA and protein synthesis, the results indicate that growth is also regulated by membrane-associated transport systems.
Enhanced Antibody Detection and Diagnosis of Coccidioidomycosis with the MiraVista IgG and IgM Detection Enzyme Immunoassay
Authors: Malo Joshua , Holbrook Eric , Zangeneh Tirdad , Strawter Chris , Oren Eyal , Robey Ian , Erickson Heidi , Chahal Racquel , Durkin Michelle , Thompson Cindy , Hoover Susan E. , Ampel Neil M. , Wheat L. Joseph , Knox Kenneth S.
Published: January 2017

Coccidioidomycosis is a common cause of community-acquired pneumonia in areas of the southwestern United States in which the disease is endemic. Clinical presentations range from self-limited disease to severe disseminated disease. Therefore, early and accurate diagnosis is essential to ensure appropriate treatment and monitoring. Currently available diagnostic tests have variable accuracy, particularly in certain patient populations, and new tests may offer improved accuracy for the diagnosis of coccidioidomycosis. Serum samples from 103 cases of coccidioidomycosis and 373 controls were tested for IgG and IgM antibodies using the MVista anti-
Coccidioides
antibody enzyme immunoassay. Serum specimens from 170 controls from areas in which the disease is endemic and 44 cases were tested by immunodiffusion at MiraVista Diagnostics. The sensitivity of the MVista antibody assay was 88.3%, and the specificity was 90%. The sensitivity was maintained in the presence of immunocompromising conditions or immunosuppressive therapies. The sensitivity of immunodiffusion was 60.2%, and the specificity was 98.8%. The sensitivity of complement fixation (62 cases) was 66.1%, but the specificity could not be determined. The MVista anti-
Coccidioides
antibody enzyme immunoassay offers improved sensitivity, compared with immunodiffusion and complement fixation, is not impaired in immunocompromised patients, and permits highly reproducible semiquantification.
Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment
Authors: Li Tengguo , Unger Elizabeth R. , Batra Dhwani , Sheth Mili , Steinau Martin , Jasinski Jean , Jones Jennifer , Rajeevan Mangalathu S.
Published: January 2017

We designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.
Calibration of BK Virus Nucleic Acid Amplification Testing to the 1st WHO International Standard for BK Virus
Authors: Tan Susanna K. , Milligan Stephen , Sahoo Malaya K. , Taylor Nathaniel , Pinsky Benjamin A.
Published: January 2017

Significant interassay variability in the quantification of BK virus (BKV) DNA precludes establishing broadly applicable thresholds for the management of BKV infection in transplantation. The 1st WHO International Standard for BKV (primary standard) was introduced in 2016 as a common calibrator for improving the harmonization of BKV nucleic acid amplification testing (NAAT) and enabling comparisons of biological measurements worldwide. Here, we evaluated the Altona RealStar BKV assay (Altona) and calibrated the results to the international unit (IU) using the Exact Diagnostics BKV verification panel, a secondary standard traceable to the primary standard. The primary and secondary standards on Altona had nearly identical linear regression equations (primary standard, Y = 1.05X − 0.28,
R
2
= 0.99; secondary standard, Y = 1.04X − 0.26,
R
2
= 0.99) and conversion factors (primary standard, 1.11 IU/copy; secondary standard, 1.09 IU/copy). A comparison of Altona with a laboratory-developed BKV NAAT assay in IU/ml versus copies/ml using Passing-Bablok regression revealed similar regression lines, no proportional bias, and improvement in the systematic bias (95% confidence interval of intercepts: copies/ml, −0.52 to −1.01; IU/ml, 0.07 to −0.36). Additionally, Bland-Altman analyses revealed a clinically significant reduction of bias when results were reported in IU/ml (IU/ml, −0.10 log
10
; copies/ml, −0.70 log
10
). These results indicate that the use of a common calibrator improved the agreement between the two assays. As clinical laboratories worldwide use calibrators traceable to the primary standard to harmonize BKV NAAT results, we anticipate improved interassay comparisons with a potential for establishing broadly applicable quantitative BKV DNA load cutoffs for clinical practice.
GRP78 Is an Important Host Factor for Japanese Encephalitis Virus Entry and Replication in Mammalian Cells
Authors: Nain Minu , Mukherjee Sriparna , Karmakar Sonali Porey , Paton Adrienne W. , Paton James C. , Abdin M. Z. , Basu Anirban , Kalia Manjula , Vrati Sudhanshu
Published: January 2017

Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is the leading cause of viral encephalitis in Southeast Asia with potential to become a global pathogen. Here, we identify glucose-regulated protein 78 (GRP78) as an important host protein for virus entry and replication. Using the plasma membrane fractions from mouse neuronal (Neuro2a) cells, mass spectroscopy analysis identified GRP78 as a protein interacting with recombinant JEV envelope protein domain III. GRP78 was found to be expressed on the plasma membranes of Neuro2a cells, mouse primary neurons, and human epithelial Huh-7 cells. Antibodies against GRP78 significantly inhibited JEV entry in all three cell types, suggesting an important role of the protein in virus entry. Depletion of GRP78 by small interfering RNA (siRNA) significantly blocked JEV entry into Neuro2a cells, further supporting its role in virus uptake. Immunofluorescence studies showed extensive colocalization of GRP78 with JEV envelope protein in virus-infected cells. This interaction was also confirmed by immunoprecipitation studies. Additionally, GRP78 was shown to have an important role in JEV replication, as treatment of cells post-virus entry with subtilase cytotoxin that specifically cleaved GRP78 led to a substantial reduction in viral RNA replication and protein synthesis, resulting in significantly reduced extracellular virus titers. Our results indicate that GRP78, an endoplasmic reticulum chaperon of the HSP70 family, is a novel host factor involved at multiple steps of the JEV life cycle and could be a potential therapeutic target.

IMPORTANCE
Recent years have seen a rapid spread of mosquito-borne diseases caused by flaviviruses. The flavivirus family includes West Nile, dengue, Japanese encephalitis, and Zika viruses, which are major threats to public health with potential to become global pathogens. JEV is the major cause of viral encephalitis in several parts of Southeast Asia, affecting a predominantly pediatric population with a high mortality rate. This study is focused on identification of crucial host factors that could be targeted to cripple virus infection and ultimately lead to development of effective antivirals. We have identified a cellular protein, GRP78, that plays a dual role in virus entry and virus replication, two crucial steps of the virus life cycle, and thus is a novel host factor that could be a potential therapeutic target.
Ethnic differences in coeliac disease autoimmunity in childhood: the Generation R Study
Authors: Jansen Michelle A E , Beth Sytske A , van den Heuvel Diana , Kiefte-de Jong Jessica C , Raat Hein , Jaddoe Vincent W V , van Zelm Menno C , Moll Henriette A
Published: January 2017

Objective

The aim was to identify whether ethnic differences in coeliac disease autoimmunity (CDA) in children at 6 years of age exist, and when present, to evaluate how these differences may be explained by sociodemographic and environmental factors.

Design

This study was embedded within a multi-ethnic population-based prospective cohort study.

Setting and patients

4442 six-year-old children born between 2002 and 2006 were included. Information on ethnicity, environmental and lifestyle characteristics was assessed by questionnaires. Ethnicity was categorised into Western (Dutch, European, Indonesian, American, Oceanian) and non-Western (Turkish, Moroccan, Cape Verdean, Antillean, Surinamese). Serum transglutaminase type 2 antibody (TG2A) levels were measured with fluorescence enzyme immunoassay. Serum IgG levels against cytomegalovirus (CMV) were measured by ELISA.

Main outcome measures

TG2A positivity was defined as TG2A ≥7 U/mL, strong TG2A positivity as TG2A ≥10 upper limit normal (70 U/mL).

Results

Of 4442 children, 60 (1.4%) children were TG2A positive, of whom 31 were strong positive. 66% of children were Western, 33% non-Western. Western ethnicity, high socioeconomic position and daycare attendance were positively associated with strong TG2A positivity (odds ratio (OR) 6.85 (1.62 to 28.8) p<0.01, OR 3.70 (1.40 to 9.82) p<0.01, OR 3.90 (1.38 to 11.0) p=0.01 resp.), whereas CMV seropositivity was inversely related to strong TG2A positivity (OR 0.32 (0.12 to 0.84) p=0.02). Together, these factors explained up to 47% (−67 to −17; p=0.02) of the ethnic differences in TG2A positivity between Western and non-Western children.

Conclusions

Ethnic differences in children with CDA are present in childhood. Socioeconomic position, daycare attendance and CMV seropositivity partly explained these differences, which may serve as targets for prevention strategies for CDA.
Cancer incidence and mortality risks in a large US Barrett's oesophagus cohort
Authors: Cook Michael B , Coburn Sally B , Lam Jameson R , Taylor Philip R , Schneider Jennifer L , Corley Douglas A
Published: January 2017

Objective

Barrett's oesophagus (BE) increases the risk of oesophageal adenocarcinoma by 10–55 times that of the general population, but no community-based cancer-specific incidence and cause-specific mortality risk estimates exist for large cohorts in the USA.

Design

Within Kaiser Permanente Northern California (KPNC), we identified patients with BE diagnosed during 1995–2012. KPNC cancer registry and mortality files were used to estimate standardised incidence ratios (SIR), standardised mortality ratios (SMR) and excess absolute risks.

Results

There were 8929 patients with BE providing 50 147 person-years of follow-up. Compared with the greater KPNC population, patients with BE had increased risks of any cancer (SIR=1.40, 95% CI 1.31 to 1.49), which slightly decreased after excluding oesophageal cancer. Oesophageal adenocarcinoma risk was increased 24 times, which translated into an excess absolute risk of 24 cases per 10 000 person-years. Although oesophageal adenocarcinoma risk decreased with time since BE diagnosis, oesophageal cancer mortality did not, indicating that the true risk is stable and persistent with time. Relative risks of cardia and stomach cancers were increased, but excess absolute risks were modest. Risks of colorectal, lung and prostate cancers were unaltered. All-cause mortality was slightly increased after excluding oesophageal cancer (SMR=1.24, 95% CI 1.18 to 1.31), but time-stratified analyses indicated that this was likely attributable to diagnostic bias. Cause-specific SMRs were elevated for ischaemic heart disease (SMR=1.39, 95% CI 1.18 to 1.63), respiratory system diseases (SMR=1.51, 95% CI 1.29 to 1.75) and digestive system diseases (SMR=2.20 95% CI 1.75 to 2.75).

Conclusions

Patients with BE had a persistent excess risk of oesophageal adenocarcinoma over time, although their absolute excess risks for this cancer, any cancer and overall mortality were modest.
Effects of phosphatidic acid supplementation on muscle thickness and strength in resistance-trained men
Authors: Gonzalez Adam M. , Sell Katie M. , Ghigiarelli Jamie J. , Kelly Christopher F. , Shone Edward W. , Accetta Matthew R. , Baum Jamie B. , Mangine Gerald T.
Published: January 2017

The purpose of this study was to investigate the effects of phosphatidic acid (PA) supplementation on muscle thickness and strength following an 8 week supervised resistance-training program. Fifteen resistance trained men (22.8 ± 3.5 years; 80.6 ± 8.7 kg; 178.1 ± 5.6 cm; 14.6% ± 8.8% body fat) were randomly assigned to a group that either consumed 750 mg of PA or a placebo (PL). Testing was carried out before (PRE) and after (POST) training/supplementation for muscle thickness and strength. Muscle thickness of the rectus femoris (RF), vastus lateralis (VL), biceps brachii (BB), and triceps brachii (TB) muscles were measured via ultrasonography, along with 1 repetition maximum (1RM) of squat, deadlift, and bench press. Analysis of covariance (ANCOVA), using PRE values as the covariate, did not reveal any group differences for measures of muscle thickness in the RF (PA: 3.6% ± 5.2%; PL: 3.2% ± 4.2%, p = 0.97), VL (PA: 23.4% ± 18.1%, PL: 12.5% ± 15.4%, p = 0.37), BB (PA: 3.7% ± 6.4%, PL: 9.6% ± 12.4%, p = 0.86), or TB (PA: 15.1% ± 17.9%, PL: 10.7% ± 19.3%, p = 0.79). Likewise, no group differences were observed in changes in squat (PA: 8.4% ± 4.1%, PL: 8.1% ± 4.2%, p = 0.79), deadlift (PA: 10.1% ± 10.1%, PL: 8.9% ± 9.5%, p = 0.66), or bench press (PA: 5.7% ± 5.5%, PL: 5.1% ± 3.0%, p = 0.76) exercises. Collectively, however, all participants experienced significant (p < 0.05) improvements in each measure of muscle thickness and strength. Results of this study suggest that PA supplementation, in combination with a 3 days·week−1 resistance-training program for 8 weeks, did not have a differential effect compared with PL on changes in muscle thickness or 1RM strength.
Entanglement of two-electron spin states in a double quantum dot
Authors: Bagrov V. G. , Gitman D. M. , Levin A. D. , Meireles M. S.
Published: January 2017

Recently, an implementation of a universal set of one- and two-quantum-bit gates for quantum computation using spin states of coupled single-electron quantum dots was proposed. It was demonstrated that it is possible to execute a coherent control of a quantum system based on two-electron spin states in a double quantum dot, allowing state preparation, coherent manipulation, and projective readout. This possibility is based on rapid electrical control of the spin exchange interaction. These results motivated us to develop a formal theoretical study of the corresponding model of two coupled spins placed in a magnetic field and subjected to a time-dependent mutual Heisenberg interaction. Using possible exact solutions of the corresponding quantum problem, we study entangling of different separable initial states in this model. It is demonstrated that the entanglement due to a time-dependent Heisenberg interaction is dominating in comparison with the entanglement due to the action of an external magnetic field.