bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between FTO genotype and total energy and macronutrient intake in adults: a systematic review and meta‐analysis
Authors: Livingstone K. M. , Celis‐Morales C. , Lara J. , Ashor A. W. , Lovegrove J. A. , Martinez J. A. , Saris W. H. , Gibney M. , Manios Y. , Traczyk I. , Drevon C. A. , Daniel H. , Gibney E. R. , Brennan L. , Bouwman J. , Grimaldi K. A. , Mathers J. C. ,   Food4Me
Published: May 2015

SummaryRisk variants of fat mass and obesity‐associated (FTO) gene have been associated with increased obesity. However, the evidence for associations between FTO genotype and macronutrient intake has not been reviewed systematically. Our aim was to evaluate the potential associations between FTO genotype and intakes of total energy, fat, carbohydrate and protein. We undertook a systematic literature search in OVID MEDLINE, Scopus, EMBASE and Cochrane of associations between macronutrient intake and FTO genotype in adults. Beta coefficients and confidence intervals (CIs) were used for per allele comparisons. Random‐effect models assessed the pooled effect sizes. We identified 56 eligible studies reporting on 213,173 adults. For each copy of the FTO risk allele, individuals reported 6.46 kcal day−1 (95% CI: 10.76, 2.16) lower total energy intake (P = 0.003). Total fat (P = 0.028) and protein (P = 0.006), but not carbohydrate intakes, were higher in those carrying the FTO risk allele. After adjustment for body weight, total energy intakes remained significantly lower in individuals with the FTO risk genotype (P = 0.028). The FTO risk allele is associated with a lower reported total energy intake and with altered patterns of macronutrient intake. Although significant, these differences are small and further research is needed to determine whether the associations are independent of dietary misreporting.
Total parenteral nutrition treatment efficacy in adolescent eating disorders
Authors: Tamura Akira , Minami Koichi , Tsuda Yuuko , Yoshikawa Norishige 
Published: May 2015

AbstractBackgroundManagement of adolescent patients with severe eating disorders who refuse treatment for weight loss is complicated. Nutritional rehabilitation is most important during the growth period; thus, strong support in the form of total parenteral nutrition (TPN) as soon as possible is necessary in severe cases. No studies involving detailed, long‐term follow up have evaluated biochemical markers and gonadotropin in patients undergoing TPN treatment.MethodsTwenty‐five adolescent female patients admitted to hospital received TPN immediately, and biochemical marker and gonadotropin levels were measured and analyzed. If subsequent weight gain was observed, TPN treatment was gradually reduced and stopped.ResultsNo patients dropped out of the study. A significant increase in weight was observed during hospitalization (average, 8.0 kg). Under this treatment, serum total bilirubin was significantly decreased at 3 months, total cholesterol was significantly decreased at 2 months, and alkaline phosphatase (ALP) was significantly increased at 3 and 6 months. Follicle‐stimulating hormone response significantly preceded both luteinizing hormone response and appetite recovery. After this treatment, nine of the 25 patients were readmitted for recurrence of appetite loss. Two patients required additional TPN treatment, but seven immediately recovered their appetite after hospitalization without TPN treatment. Bodyweight gain per day was significantly lower and ALP on admission was significantly higher in patients with than without recurrence.ConclusionsMost patients had a remarkable recovery of appetite without refusal behaviors and without evidence of malnutrition after admission. Nutrition maintenance with TPN support is particularly important during the growth period.
Emotion suppression moderates the quadratic association between RSA and executive function
Authors: Spangler Derek P. , Bell Martha Ann , Deater‐Deckard Kirby 
Published: May 2015

AbstractThere is uncertainty about whether respiratory sinus arrhythmia (RSA), a cardiac marker of adaptive emotion regulation, is involved in relatively low or high executive function performance. In the present study, we investigated (a) whether RSA during rest and tasks predict both relatively low and high executive function within a larger quadratic association among the two variables, and (b) the extent to which this quadratic trend was moderated by individual differences in emotion regulation. To achieve these aims, a sample of ethnically and socioeconomically diverse women self‐reported reappraisal and emotion suppression. They next experienced a 2‐min resting period during which electrocardiogram (ECG) was continually assessed. In the next phase, the women completed an array of executive function and nonexecutive cognitive tasks while ECG was measured throughout. As anticipated, resting RSA showed a quadratic association with executive function that was strongest for high suppression. These results suggest that relatively high resting RSA may predict poor executive function ability when emotion regulation consumes executive control resources needed for ongoing cognitive performance.
O‐Methyltransferases involved in biphenyl and dibenzofuran biosynthesis
Authors: Khalil Mohammed N.A. , Brandt Wolfgang , Beuerle Till , Reckwell Dennis , Groeneveld Josephine , Hänsch Robert , Gaid Mariam M. , Liu Benye , Beerhues Ludger 
Published: May 2015

SummaryBiphenyls and dibenzofurans are the phytoalexins of the Malinae involving apple and pear. Biosynthesis of the defence compounds includes two O‐methylation reactions. cDNAs encoding the O‐methyltransferase (OMT) enzymes were isolated from rowan (Sorbus aucuparia) cell cultures after treatment with an elicitor preparation from the scab‐causing fungus, Venturia inaequalis. The preferred substrate for SaOMT1 was 3,5‐dihydroxybiphenyl, supplied by the first pathway‐specific enzyme, biphenyl synthase (BIS). 3,5‐Dihydroxybiphenyl underwent a single methylation reaction in the presence of S‐adenosyl‐l‐methionine (SAM). The second enzyme, SaOMT2, exhibited its highest affinity for noraucuparin, however the turnover rate was greater with 5‐hydroxyferulic acid. Both substrates were only methylated at the meta‐positioned hydroxyl group. The substrate specificities of the OMTs and the regiospecificities of their reactions were rationalized by homology modeling and substrate docking. Interaction of the substrates with SAM also took place at a position other than the sulfur group. Expression of SaOMT1, SaOMT2 and SaBIS3 was transiently induced in rowan cell cultures by the addition of the fungal elicitor. While the immediate SaOMT1 products were not detectable in elicitor‐treated cell cultures, noraucuparin and noreriobofuran accumulated transiently, followed by increasing levels of the SaOMT2 products aucuparin and eriobofuran. SaOMT1, SaOMT2 and SaBIS3 were N‐ and C‐terminally fused with the super cyan fluorescent protein and a modified yellow fluorescent protein, respectively. All the fluorescent reporter fusions were localized to the cytoplasm of Nicotiana benthamiana leaf epidermis cells. A revised biosynthetic pathway of biphenyls and dibenzofurans in the Malinae is presented.
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
Authors: Warren René L. , Keeling Christopher I. , Yuen Macaire Man Saint , Raymond Anthony , Taylor Greg A. , Vandervalk Benjamin P. , Mohamadi Hamid , Paulino Daniel , Chiu Readman , Jackman Shaun D. , Robertson Gordon , Yang Chen , Boyle Brian , Hoffmann Margarete , Weigel Detlef , Nelson David R. , Ritland Carol , Isabel Nathalie , Jaquish Barry , Yanchuk Alvin , Bousquet Jean , Jones Steven J. M. , MacKay John , Birol Inanc , Bohlmann Joerg 
Published: May 2015

SummaryWhite spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree‐breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER‐P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
Function-led design of new porous materials
Authors: Slater Anna G. , Cooper Andrew I. 
Published: May 2015

It's all about the holes
From kitchen sieves and strainers to coffee filters, porous materials have a wide range of uses. On an industrial scale, they are used as sorbents, filters, membranes, and catalysts. Slater and Cooper review how each application will limit the materials that can be used, and also the size and connectivity of the pores required. They go on to compare and contrast a growing range of porous materials that are finding increasing use in academic and industrial applications.

Science
, this issue
10.1126/science.aaa8075
Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Healthy Canine Oral Cavities
Authors: Manfredi Pablo , Renzi Francesco , Cornelis Guy R. 
Published: May 2015

ABSTRACT

Here, we present the draft genome sequences of three strains of
Capnocytophaga canimorsus
, each isolated from a different dog's mouth. Genome analysis provided evidence that these organisms may belong to a different nonpathogenic subtype of
C. canimorsus
.
Rapid, Sensitive, and Specific Escherichia coli H Antigen Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight-Based Peptide Mass Fingerprinting
Authors: Chui Huixia , Chan Michael , Hernandez Drexler , Chong Patrick , McCorrister Stuart , Robinson Alyssia , Walker Matthew , Peterson Lorea A. M. , Ratnam Sam , Haldane David J. M. , Bekal Sadjia , Wylie John , Chui Linda , Westmacott Garrett , Xu Bianli , Drebot Mike , Nadon Celine , Knox J. David , Wang Gehua , Cheng Keding 
Published: May 2015

ABSTRACTMatrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has gained popularity in recent years for rapid bacterial identification, mostly at the genus or species level. In this study, a rapid method to identify theEscherichia coliflagellar antigen (H antigen) at the subspecies level was developed using a MALDI-TOF MS platform with high specificity and sensitivity. Flagella were trapped on a filter membrane, and on-filter trypsin digestion was performed. The tryptic digests of each flagellin then were collected and analyzed by MALDI-TOF MS through peptide mass fingerprinting. Sixty-one reference strains containing all 53 H types and 85 clinical strains were tested and compared to serotyping designations. Whole-genome sequencing was used to resolve conflicting results between the two methods. It was found that DHB (2,5-dihydroxybenzoic acid) worked better than CHCA (α-cyano-4-hydroxycinnamic acid) as the matrix for MALDI-TOF MS, with higher confidence during protein identification. After method optimization, reference strains representing all 53E. coliH types were identified correctly by MALDI-TOF MS. A customE. coliflagellar/H antigen database was crucial for clearly identifying theE. coliH antigens. Of 85 clinical isolates tested by MALDI-TOF MS-H, 75 identified MS-H types (88.2%) matched results obtained from traditional serotyping. Among 10 isolates where the results of MALDI-TOF MS-H and serotyping did not agree, 60% of H types characterized by whole-genome sequencing agreed with those identified by MALDI-TOF MS-H, compared to only 20% by serotyping. This MALDI-TOF MS-H platform can be used for rapid and cost-effectiveE. coliH antigen identification, especially duringE. colioutbreaks.
Analysis of Vancomycin Susceptibility Testing Results for Presumptive Categorization of Telavancin
Authors: Mendes Rodrigo E. , Farrell David J. , Flamm Robert K. , Sader Helio S. , Jones Ronald N. 
Published: May 2015

ABSTRACT

Scattergrams between vancomycin and telavancin demonstrated susceptibility agreement rates of 99.96, 99.65, and 100.00% for
Staphylococcus aureus
,
Enterococcus faecalis
, and streptococci, respectively. A single very major error was obtained against
E. faecalis
, while vancomycin-intermediate
S. aureus
(VISA) and vancomycin-resistant and teicoplanin-susceptible (VanB phenotype)
E. faecalis
were responsible for major and minor errors. These results support the use of vancomycin to infer telavancin susceptibility among indicated pathogens, except VISA, which should be tested for telavancin susceptibility.
Fatal Case of Polymicrobial Meningitis Caused by Cryptococcus liquefaciens and Mycobacterium tuberculosis Complex in a Human Immunodeficiency Virus-Infected Patient
Authors: Conde-Pereira César , Rodas-Rodríguez Lia , Díaz-Paz Manuel , Palacios-Rivera Hilda , Firacative Carolina , Meyer Wieland , Alcázar-Castillo Myriam 
Published: May 2015

ABSTRACT

We describe a fatal case of polymicrobial meningitis in a human immunodeficiency virus-infected patient from Guatemala caused by
Cryptococcus liquefaciens
and
Mycobacterium tuberculosis
complex. Central nervous system infections caused concurrently by these species are extremely rare. This is also the first report of disseminated disease caused by
C. liquefaciens
.
Performance Characteristics of Xpert Flu/RSV XC Assay
Authors: Popowitch Elena B. , Miller Melissa B. 
Published: May 2015

ABSTRACT

The Xpert Flu/RSV XC assay was compared to laboratory-developed tests (LDTs) (
n
= 207) and the Xpert Flu assay (
n
= 147) using archived nasopharyngeal swabs. The percentages of positive agreements with LDTs were 97.8% for influenza A, 97.2% for influenza B, and 89.3% for RSV. The sensitivity of influenza detection was improved with the Xpert Flu/RSV XC assay compared to the Xpert Flu assay.
Head-to-Head Comparison of the RNA-Based Aptima Human Papillomavirus (HPV) Assay and the DNA-Based Hybrid Capture 2 HPV Test in a Routine Screening Population of Women Aged 30 to 60 Years in Germany
Authors: Iftner Thomas , Becker Sven , Neis Klaus-Joachim , Castanon Alejandra , Iftner Angelika , Holz Barbara , Staebler Annette , Henes Melanie , Rall Katharina , Haedicke Juliane , von Weyhern Claus Hann , Clad Andreas , Brucker Sara , Sasieni Peter 
Published: May 2015

ABSTRACT

Testing for E6/E7 mRNA in cells infected with high-risk (HR) human papillomavirus (HPV) might improve the specificity of HPV testing for the identification of cervical precancerous lesions. Here we compared the RNA-based Aptima HPV (AHPV) assay (Hologic) and the DNA-based Hybrid Capture 2 (HC2) HPV test (Qiagen) to liquid-based cytology (LBC) for women undergoing routine cervical screening. A total of 10,040 women, 30 to 60 years of age, were invited to participate in the study, 9,451 of whom were included in the analysis. Specimens were tested centrally by LBC, the AHPV test, and the HC2 test, and women who tested positive on any test were referred for colposcopy. Genotyping was performed on all HR-HPV-positive samples. Test characteristics were calculated based on histological review. As a result, we identified 90 women with cervical intraepithelial neoplasia grade 2+ (CIN2+), including 43 women with CIN3+. Sensitivity differences between the AHPV test and the HC2 test in detecting CIN2+ (
P
= 0.180) or CIN3+ (
P
= 0.0625) lesions were statistically nonsignificant. Of three CIN3 cases that were missed with the AHPV test, two cases presented lesion-free cones and one had a non-HR HPV67 infection. The specificity (<CIN2) and positive predictive value (CIN2+) of the AHPV test were significantly higher (both
P
< 0.001) than those of the HC2 test. The overall agreement between the tests was substantial (κ = 0.77). Finally, we present results for several possible triage strategies, based on the primary screening test being either the AHPV test or the HC2 test. In summary, the AHPV assay is both specific and sensitive for the detection of high-grade precancerous lesions and may be used in primary cervical cancer screening for women ≥30 years of age.
Comparative Analysis of the Glycosylation Profiles of Membrane-Anchored HIV-1 Envelope Glycoprotein Trimers and Soluble gp140
Authors: Go Eden P. , Herschhorn Alon , Gu Christopher , Castillo-Menendez Luis , Zhang Shijian , Mao Youdong , Chen Haiyan , Ding Haitao , Wakefield John K. , Hua David , Liao Hua-Xin , Kappes John C. , Sodroski Joseph , Desaire Heather 
Published: May 2015

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer, which consists of the gp120 and gp41 subunits, is the focus of multiple strategies for vaccine development. Extensive Env glycosylation provides HIV-1 with protection from the immune system, yet the glycans are also essential components of binding epitopes for numerous broadly neutralizing antibodies. Recent studies have shown that when Env is isolated from virions, its glycosylation profile differs significantly from that of soluble forms of Env (gp120 or gp140) predominantly used in vaccine discovery research. Here we show that exogenous membrane-anchored Envs, which can be produced in large quantities in mammalian cells, also display a virion-like glycan profile, where the glycoprotein is extensively decorated with high-mannose glycans. Additionally, because we characterized the glycosylation with a high-fidelity profiling method, glycopeptide analysis, an unprecedented level of molecular detail regarding membrane Env glycosylation and its heterogeneity is presented. Each glycosylation site was characterized individually, with about 500 glycoforms characterized per Env protein. While many of the sites contain exclusively high-mannose glycans, others retain complex glycans, resulting in a glycan profile that cannot currently be mimicked on soluble gp120 or gp140 preparations. These site-level studies are important for understanding antibody-glycan interactions on native Env trimers. Additionally, we report a newly observed
O
-linked glycosylation site, T606, and we show that the full
O
-linked glycosylation profile of membrane-associated Env is similar to that of soluble gp140. These findings provide new insight into Env glycosylation and clarify key molecular-level differences between membrane-anchored Env and soluble gp140.

IMPORTANCE
A vaccine that protects against human immunodeficiency virus type 1 (HIV-1) infection should elicit antibodies that bind to the surface envelope glycoproteins on the membrane of the virus. The envelope glycoproteins have an extensive coat of carbohydrates (glycans), some of which are recognized by virus-neutralizing antibodies and some of which protect the virus from neutralizing antibodies. We found that the HIV-1 membrane envelope glycoproteins have a unique pattern of carbohydrates, with many high-mannose glycans and also, in some places, complex glycans. This pattern was very different from the carbohydrate profile seen for a more easily produced soluble version of the envelope glycoprotein. Our results provide a detailed characterization of the glycans on the natural membrane envelope glycoproteins of HIV-1, a carbohydrate profile that would be desirable to mimic with a vaccine.
Discovery of Dengue Virus NS4B Inhibitors
Authors: Wang Qing-Yin , Dong Hongping , Zou Bin , Karuna Ratna , Wan Kah Fei , Zou Jing , Susila Agatha , Yip Andy , Shan Chao , Yeo Kim Long , Xu Haoying , Ding Mei , Chan Wai Ling , Gu Feng , Seah Peck Gee , Liu Wei , Lakshminarayana Suresh B. , Kang CongBao , Lescar Julien , Blasco Francesca , Smith Paul W. , Shi Pei-Yong 
Published: May 2015

ABSTRACT

The four serotypes of dengue virus (DENV-1 to -4) represent the most prevalent mosquito-borne viral pathogens in humans. No clinically approved vaccine or antiviral is currently available for DENV. Here we report a spiropyrazolopyridone compound that potently inhibits DENV both
in vitro
and
in vivo
. The inhibitor was identified through screening of a 1.8-million-compound library by using a DENV-2 replicon assay. The compound selectively inhibits DENV-2 and -3 (50% effective concentration [EC
50
], 10 to 80 nM) but not DENV-1 and -4 (EC
50
, >20 μM). Resistance analysis showed that a mutation at amino acid 63 of DENV-2 NS4B (a nonenzymatic transmembrane protein and a component of the viral replication complex) could confer resistance to compound inhibition. Genetic studies demonstrate that variations at amino acid 63 of viral NS4B are responsible for the selective inhibition of DENV-2 and -3. Medicinal chemistry improved the physicochemical properties of the initial “hit” (compound 1), leading to compound 14a, which has good
in vivo
pharmacokinetics. Treatment of DENV-2-infected AG129 mice with compound 14a suppressed viremia, even when the treatment started after viral infection. The results have proven the concept that inhibitors of NS4B could potentially be developed for clinical treatment of DENV infection. Compound 14a represents a potential preclinical candidate for treatment of DENV-2- and -3-infected patients.

IMPORTANCE
Dengue virus (DENV) threatens up to 2.5 billion people and is now spreading in many regions in the world where it was not previously endemic. While there are several promising vaccine candidates in clinical trials, approved vaccines or antivirals are not yet available. Here we describe the identification and characterization of a spiropyrazolopyridone as a novel inhibitor of DENV by targeting the viral NS4B protein. The compound potently inhibits two of the four serotypes of DENV (DENV-2 and -3) both
in vitro
and
in vivo
. Our results validate, for the first time, that NS4B inhibitors could potentially be developed for antiviral therapy for treatment of DENV infection in humans.
Population Bottlenecks and Pathogen Extinction: “Make This Everyone's Mission to Mars, Including Yours”
Authors: Policicchio Benjamin B. , Pandrea Ivona , Apetrei Cristian 
Published: May 2015

ABSTRACT

Kapusinszky et al. (J Virol 89:8152–8161, 2015,
http://dx.doi.org/10.1128/JVI.00671-15
) report that host population bottlenecks may result in pathogen extinction, which provides a compelling argument for an alternative approach to vaccination for the control of virus spread. By comparing the prevalence levels of three viral pathogens in two populations of African green monkeys (AGMs) (
Chlorocebus sabaeus
) from Africa and two Caribbean Islands, they convincingly show that a major host bottleneck resulted in the eradication of select pathogens from a given host.