bluuebunny/crossref_metadata_2025 huggingface dataset:
What Is the Role of Paired Rapid Plasma Reagin Testing (Simultaneous Testing of Acute and Convalescent Samples) in the Diagnosis of Repeat Syphilis and the Follow-up of Syphilis?
Authors: Kenyon Chris R. , Osbak Kara Krista , Van Esbroek Marjan , Lynen Lutgarde , Crucitti Tania
Published: July 2017

Background

Repeat syphilis is playing an increasing role in syphilis transmission in several populations. The assessment of repeat syphilis and response to treatment depends on accurately measuring intraindividual changes in non–treponemal tests. For a 0- to 6-month delta rapid plasma reagin (RPR) to be determined by routine individual RPR testing, samples are tested 6 months apart with differences in reagent batches, environmental conditions, and observers all leading to measurement errors. We hypothesized that conducting paired RPR testing (simultaneous testing of acute and convalescent samples) would enable a more accurate determination of delta RPR compared with individual testing.

Methods

A total of 120 study participants with a new diagnosis of syphilis were followed up at 0, 3, 6, 9, 12, 18, and 24 months, with RPR testing performed via individual testing at each study visit and at any suspected repeat syphilis. Rapid plasma reagin paired testing was performed on samples from 0 and 6 months and at any suspected repeat syphilis.

Results

The quantitative agreement ±1 dilution among paired and individual testing was 97.2%. There was no difference in the proportion with serofast status at 6 months: 21 (19.4%) and 19 (17.6%) according to paired and individual testing, respectively (P = 0.726). There was no statistically significant difference between 0- and 6-month delta RPR as determined by paired and individual testing in predicting seroresponse at 12 months (86.1% and 91.6% agreement with 12-month serofast/nonserofast classification, respectively; P = 0.262).

Conclusions

In our setting, individual testing performed equally well compared with paired testing. Follow-up of syphilis will remain onerous for the patient and the health care provider until new tests that can more accurately assess the response to therapy and repeat syphilis/treatment failure are developed.
Epidemiology and Outcomes of Cardiac Arrest in Pediatric Cardiac ICUs*
Authors: Alten Jeffrey A. , Klugman Darren , Raymond Tia T. , Cooper David S. , Donohue Janet E. , Zhang Wenying , Pasquali Sara K. , Gaies Michael G.
Published: July 2017

Objectives:

In-hospital cardiac arrest occurs in 2.6–6% of children with cardiac disease and is associated with significant morbidity and mortality. Much remains unknown about cardiac arrest in pediatric cardiac ICUs; therefore, we aimed to describe cardiac arrest epidemiology in a contemporary multicenter cardiac ICU cohort.

Design:

Retrospective analysis within the Pediatric Cardiac Critical Care Consortium clinical registry.

Setting:

Cardiac ICUs within 23 North American hospitals.

Patients:

All cardiac medical and surgical patients admitted from August 2014 to July 2016.

Interventions:

None.

Measurements and Main Results:

There were 15,908 cardiac ICU encounters (6,498 medical, 9,410 surgical). 3.1% had cardiac arrest; rate was 4.8 cardiac arrest per 1,000 cardiac ICU days. Medical encounters had 50% higher rate of cardiac arrest compared with surgical encounters. Observed (unadjusted) cardiac ICU cardiac arrest prevalence varied from 1% to 5.5% among the 23 centers; cardiac arrest per 1,000 cardiac ICU days varied from 1.1 to 10.4. Over half cardiac arrest occur within 48 hours of admission. On multivariable analysis, prematurity, neonatal age, any Society of Thoracic Surgeons preoperative risk factor, and Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery mortality category 4, 5 had strongest association with surgical encounter cardiac arrest. In medical encounters, independent cardiac arrest risk factors were acute heart failure, prematurity, lactic acidosis greater than 3 mmol/dL, and invasive ventilation 1 hour after admission. Median cardiopulmonary resuscitation duration was 10 minutes, return of spontaneous circulation occurred in 64.5%, extracorporeal cardiopulmonary resuscitation in 27.2%. Unadjusted survival was 53.2% in encounters with cardiac arrest versus 98.2% without. Medical encounters had lower survival after cardiac arrest (37.7%) versus surgical encounters (62.5%); Norwood patients had less than half the survival after cardiac arrest (35.6%) compared with all others. Unadjusted survival after cardiac arrest varied greatly among 23 centers.

Conclusions:

We provide contemporary epidemiologic and outcome data for cardiac arrest occurring in the cardiac ICU from a multicenter clinical registry. As detailed above, we highlight high-risk patient cohorts and periods of time that may serve as targets for research and quality improvement initiatives aimed at cardiac arrest prevention.
Dilation Time in Endoscopic Papillary Balloon Dilation for Common Bile Duct Stones
Authors: Shen Yong-Hua , Yang Liu-Qing , Yao Yu-Ling , Wang Lei , Zhang Yi-Yang , Cao Jun , He Qi-Bin , Zou Xiao-Ping , Li Yun-Hong
Published: July 2017

Background:

To assess the short-term outcomes after endoscopic sphincterotomy (EST) plus endoscopic papillary balloon dilation (EPBD) versus EPBD alone and appropriate balloon dilation time in EPBD alone.

Materials and Methods:

A total of 413 patients with common bile duct stones (CBDSs) were included in the EST plus EPBD group and 84 were in the EPBD alone group. We retrospectively evaluated the safety and efficacy between EST plus EPBD and EPBD alone group. The patients in EPBD alone group were assigned to dilation time ≥5 minutes group (n=35) and time <5 minutes group (n=49). Further, we preliminarily discussed the influence of balloon dilation time on the procedure-related complications.

Results:

Compared with EST plus EPBD, the patients in EPBD alone group were younger [56.6 (range: 18 to 95) vs. 65.1 (24 to 92) y; P=0.006], had smaller diameter of the largest stone [10.4 (range: 3 to 20) vs. 12.3 (5 to 30) mm; P<0.001] and were lesser frequently performed with jaundice [22 (26.2%) vs. 189 (45.8%); P=0.001]. The mean duration of postoperative hospital stay in EPBD alone group was significantly shorter than EST plus EPBD group [6.3 (range: 1 to 18) vs. 9.2 (1 to 44) d; P<0.001]. The patients in EPBD alone group had higher risk of post endoscopic retrograde cholangiopancreatography pancreatitis than EST plus EPBD group [11 (13.1%) vs. 22 (5.3%); P=0.009]. Patients in the dilation time <5 minutes group had higher risk to suffer from postoperative pancreatitis than the EST plus EPBD group [9 (18.4%) vs. 22 (5.3%); P=0.002], while patients in the dilation time ≥5 minutes group had less procedure-related hemorrhage than the EST plus EPBD group [0 vs. 36 (8.7%); P=0.047].

Conclusion:

Long balloon dilation time in EPBD alone is safe and effective in treating CBDSs.
Incorporation of Interprofessional Education in Nutrition and Dietetics Education Programs
Authors: Eliot Kathrin A. , Wilson Mardell , Breitbach Anthony P. , Chushak-Polevska Maria
Published: July 2017

Many health professions incorporate interprofessional education (IPE) to prepare graduates for collaborative practice, although little is known about IPE implementation in nutrition and dietetics (ND) education. The purpose of this study was to evaluate IPE integration in ND programs and identify institutional factors impacting IPE availability and participation. One hundred sixty-seven directors of accredited ND programs responded to an electronic survey using the Interprofessional Education Assessment and Planning Instrument for Academic Institutions. Results showed that ND programs are incorporating IPE on a minimal basis and many institutional factors affect IPE participation, including academic unit and program accreditation type.
Registered Dietitians' Knowledge of Bariatric Nutrition Recommendations and Practice Implications
Authors: Galicki Sarah Elyse , Coccia Catherine
Published: July 2017

The role of registered dietitians (RDs) on bariatric treatment teams is not delineated. This project examines the knowledge of RDs about bariatric nutrition recommendations and the influence on dietetic practice. A 45-item Bariatric Nutrition Knowledge Questionnaire (BNKQ) was distributed through e-mail listservs associated with the Academy of Nutrition and Dietetics. The BNKQ was designed to assess practitioners' knowledge of bariatric treatment recommendations. RDs (n = 249) reported a low level of overall bariatric knowledge (mean = 63.1% ± 10.35%) for predicting practice recommendations (t = 8.60, P < .00). These findings support a need for continuing education.
Registered Dietitians' Preferred Celiac Disease Resources and Twitter, Facebook, Smartphone App, or Internet Use for Celiac Disease Patient Education
Authors: Geiger Joan , Rhee Yeong
Published: July 2017

The registered dietitian (RD) plays an integral role in helping patients manage their celiac disease (CD). The RDs were surveyed on their use of CD resources and technology (Twitter, Facebook, smartphone apps, or Internet) for their own continuing education and for use in patient education. Academic publications were the most used CD resources for self-education by the RDs. They reported using Twitter and Facebook the least and handouts the most to educate patients with CD, and technology is not a common resource for education of CD patients. The collaborative work between RDs and software developers may increase CD education efficacy by using technology.
Interprofessional Educational Experience Among Dietitians After a Pediatric Dentistry Clinical Rotation
Authors: Fernandez Jill B. , Ahearn Kelly , Atar Michael , More Frederick G. , Sasson Lisa , Rosenberg Linda , Godfrey Emilie , Sehl Rima , Daronch Marcia
Published: July 2017

Interprofessional education is interactive learning focused on collaboration and prepares professionals to improve patient care in a collaborative team environment. This article explores how registered dietitians' views and clinical practices regarding pediatric oral health and nutrition have been influenced by interprofessional education with pediatric dentists. Surveys were e-mailed to 150 dietitians who graduated from New York University and may have participated in a pediatric dental rotation between 2005 and 2010. Out of the 109 who were eligible, 36 (33%) responded. The respondents experienced positive collaboration (72%) as well as an increase in awareness (61%) and knowledge (58%) of the relationship between oral health and dietary habits. Dietitians and dentists have the potential to address overall health and the current obesity epidemic.
Reverse immunodynamics: a new method for identifying targets of protective immunity
Authors: Spensley Katrina J , Wikramaratna Paul S , Penman Bridget S , Walker Andrew , Smith Adrian L , Pybus Oliver G , Jean Létitia , Gupta Sunetra , Lourenço José
Published: July 2017

Despite a dramatic increase in our ability to catalogue variation among pathogen genomes, we have made far fewer advances in using this information to identify targets of protective immunity. We propose a novel methodology that combines predictions from epidemiological models with phylogenetic and structural analyses to identify such targets. Epidemiological models predict that strong immune selection can cause antigenic variants to exist in non-overlapping combinations. A corollary of this theory is that targets of immunity may be identified by searching for non-overlapping associations among antigenic variants. We applied this concept to the AMA-1 protein of the malaria parasitePlasmodium falciparumand found strong signatures of immune selection among certain regions of low variability which could render them ideal vaccine candidates.
Shifts in temperature influence howBatrachochytrium dendrobatidisinfects amphibian larvae
Authors: Bradley Paul W. , Brawner Michael D. , Raffel Thomas R. , Rohr Jason R. , Olson Deanna H. , Blaustein Andrew R.
Published: July 2017

Many climate change models predict increases in mean temperature, and increases in frequency and magnitude of temperature fluctuations. These potential shifts may impact ectotherms in several ways, including how they are affected by disease. Shifts in temperature may especially affect amphibians, a group with populations that have been challenged by several pathogens. Because amphibian hosts invest more in immunity at warmer than cooler temperatures and parasites may acclimate to temperature shifts faster than hosts (creating lags in optimal host immunity), researchers have hypothesized that a temperature shift from cold-to-warm might result in increased amphibian sensitivity to pathogens, whereas a shift from warm-to-cold might result in decreased sensitivity. Support for components of this climate-variability based hypothesis have been provided by prior studies of the fungusBatrachochytrium dendrobatidis(Bd) that causes the disease chytridiomycosis in amphibians. We experimentally tested whether temperature shifts before Bd exposure alter susceptibility to Bd in the larval stage of two amphibian species – western toads (Anaxyrus boreas) and northern red legged frogs (Rana aurora). Both host species harbored elevated Bd infection intensities under constant cold (15° C) temperature in comparison to constant warm (20° C) temperature. Additionally, both species experienced an increase in Bd infection abundance when shifted to 20° C from 15° C, compared to a constant 20° C but they experienced a decrease in Bd when shifted to 15° C from 20° C, compared to a constant 15° C. These results are in contrast to prior studies of adult amphibians that found increased susceptibility to Bd infection after a temperature shift in either direction, highlighting the potential for species and stage differences in the temperature-dependence of chytridiomycosis.
Allele-specific multi-sample copy number segmentation
Authors: Ross Edith M. , Haase Kerstin , Van Loo Peter , Markowetz Florian
Published: July 2017

Motivation

Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other.

Results

Here we presentasmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT.

Availability

asmultipcfis available as part of the ASCAT R package (version 2.5) fromgithub.com/Crick-CancerGenomics/ascat
Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome
Authors: Steenwyk Jacob L. , Denis James St. , Dresch Jacqueline M. , Larochelle Denis A. , Drewell Robert A.
Published: July 2017

DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the slime mold Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methyl-cytosine in the genome is unclear. Here we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage, replicate sequencing of bisulfite converted gDNA extracted from post-starvation cells. We find an overall very low level of DNA methylation, occurring at only 462 out of the ~7.5 million (0.006%) cytosines in the genome. Despite this sparse profile, significant methylation can be detected at 51 of these sites in replicate experiments, suggesting they are robust targets for DNA methylation. These 5-methyl-cytosines are associated with a broad range of protein-coding genes, tRNA-encoding genes and retrotransposable elements. Our data provides evidence of a minimal, but functional, methylome in Dictyostelium, thereby making Dictyostelium a candidate model organism to further investigate the evolutionary function of DNA methylation.
Inherited chromosomally integrated human herpesvirus 6 genomes are ancient, intact and potentially able to reactivate from telomeres
Authors: Zhang Enjie , Bell Adam J , Wilkie Gavin S , Suárez Nicolás M , Batini Chiara , Veal Colin D , Armendáriz-Castillo Isaac , Neumann Rita , Cotton Victoria E , Huang Yan , Porteous David J , Jarrett Ruth F , Davison Andrew J , Royle Nicola J
Published: July 2017

Human herpesviruses 6A and 6B (HHV6-A and HHV-6B; speciesHuman herpesvirus 6AandHuman herpesvirus 6B) have the capacity to integrate into telomeres, the essential capping structures of chromosomes that play roles in cancer and ageing. About 1% of people worldwide are carriers of chromosomally integrated HHV-6 (ciHHV-6), which is inherited as a genetic trait. Understanding the consequences of integration for the evolution of the viral genome, for the telomere and for the risk of disease associated with carrier status is hampered by a lack of knowledge about ciHHV-6 genomes. Here, we report an analysis of 28 ciHHV-6 genomes and show that they are significantly divergent from the few modern non-integrated HHV-6 strains for which complete sequences are currently available. In addition ciHHV-6B genomes in Europeans are more closely related to each other than to ciHHV-6B genomes from China and Pakistan, suggesting regional variation of the trait. Remarkably, at least one group of European ciHHV-6B carriers has inherited the same ciHHV-6B genome, integrated in the same telomere allele, from a common ancestor estimated to have existed 24,500 ±10,600 years ago. Despite the antiquity of some, and possibly most, germline HHV-6 integrations, the majority of ciHHV-6B (95%) and ciHHV-6A (72%) genomes contain a full set of intact viral genes and therefore appear to have the capacity for viral gene expression and full reactivation.

IMPORTANCE

Inheritance of HHV-6A or HHV-6B integrated into a telomere occurs at a low frequency in most populations studied to date but its characteristics are poorly understood. However, stratification of ciHHV-6 carriers in modern populations due to common ancestry is an important consideration for genome-wide association studies that aim to identify disease risks for these people. Here we present full sequence analysis of 28 ciHHV-6 genomes and show that ciHHV-6B in many carriers with European ancestry most likely originated from ancient integration events in a small number of ancestors. We propose that ancient ancestral origins for ciHHV-6A and ciHHV-6B are also likely in other populations. Moreover, despite their antiquity, all of the ciHHV-6 genomes appear to retain the capacity to express viral genes and most are predicted to be capable of full viral reactivation. These discoveries represent potentially important considerations in immune-compromised patients, in particular in organ transplantation and in stem cell therapy.
Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution
Authors: Raghwani Jayna , Thompson Robin , Koelle Katia
Published: July 2017

Most studies on seasonal influenza A/H3N2 virus adaptation have focused on the main antigenic gene, haemagglutinin. However, there is increasing evidence that the genome-wide genetic background of novel antigenic variants can influence these variants’ emergence probabilities and impact their patterns of dominance in the population. This suggests that non-antigenic genes may be important in shaping the viral evolutionary dynamics. To better understand the role of selection on non-antigenic genes in the adaptive evolution of seasonal influenza viruses, we here develop a simple population genetic model that considers a virus with one antigenic and one non-antigenic gene segment. By simulating this model under different regimes of selection and reassortment, we find that the empirical patterns of lineage turnover for the antigenic and non-antigenic gene segments are best captured when there is both limited viral coinfection and selection operating on both gene segments. In contrast, under a scenario of only neutral evolution in the non-antigenic gene segment, we see persistence of multiple lineages for long periods of time in that segment, which is not compatible with the observed molecular evolutionary patterns. Further, we find that reassortment, occurring in coinfected individuals, can increase the speed of viral adaptive evolution by primarily reducing selective interference and genetic linkage effects mediated by the non-antigenic gene segment. Together, these findings suggest that, for influenza, with 6 internal or non-antigenic gene segments, the evolutionary dynamics of novel antigenic variants are likely to be influenced by the genome-wide genetic background as a result of linked selection among both beneficial and deleterious mutations.
Multi-modal meta-analysis of 1494 hepatocellular carcinoma samples reveals vast impacts of consensus driver genes on phenotypes
Authors: Chaudhary Kumardeep , Poirion Olivier B , Lu Liangqun , Huang Sijia , Ching Travers , Garmire Lana X
Published: July 2017

Although driver genes in hepatocellular carcinoma (HCC) have been investigated in various previous genetic studies, prevalence of key driver genes among heterogeneous populations is unknown. Moreover, the phenotypic associations of these driver genes are poorly understood. This report aims to reveal the phenotypic impacts of a group of consensus driver genes in HCC. We used MutSigCV and OncodriveFM modules implemented in the IntOGen pipeline to identify consensus driver genes across six HCC cohorts comprising 1,494 samples in total. To access their global impacts, we used TCGA mutations and copy number variations to predict the transcriptomics data, under generalized linear models. We further investigated the associations of the consensus driver genes to patient survival, age, gender, race and risk factors. We identify 10 consensus driver genes across six HCC cohorts in total. Integrative analysis of driver mutations, copy number variations and transcriptomic data reveals that these consensus driver mutations and their copy number variations are associated with majority (62.5%) of the mRNA transcriptome, but only a small fraction (8.9%) of miRNAs. Genes associated withTP53, CTNNB1, andARID1Amutations contribute to the tripod of most densely connected pathway clusters. These driver genes are significantly associated with patients’ overall survival. Some driver genes are significantly linked to HCC gender (CTNNB1, ALB, TP53andAXIN1), race (TP53andCDKN2A), and age (RB1) disparities. This study prioritizes a group of consensus drivers in HCC, which collectively show vast impacts on the phenotypes. These driver genes may warrant as valuable therapeutic targets of HCC.
The Emergence of Egalitarianism in a Model of Early Human Societies
Authors: Calmettes Guillaume , Weiss James N.
Published: July 2017

How did egalitarianism emerge in early human societies? In contrast to dominance hierarchies in non-human primates, human simple forager bands are typically egalitarian, with male hunters often serving as the collective alpha. Here we present a thermodynamics-inspired simple population model, based on stochastic optimization of dominance relationships, in which a dominance hierarchy of individuals with exclusively self-centered characteristics (the desire to dominate, resentment at being dominated) transitions spontaneously to egalitarianism as their capacity for language develops. Language, specifically gossip, allows resentment against being dominated to promote the formation of antidominance coalitions which destabilize the alpha position for individuals, leading to a phase transition in which a coalition of the full population suddenly becomes dominant. Thus, egalitarianism emerges suddenly as the optimal power sharing arrangement in a population of selfish individuals without any inherently altruistic qualities. We speculate that egalitarianism driven by punishment for exhibiting alpha-like behavior may then set the stage for genuinely altruistic traits to propagate as predicted by game theory models. Based on model simulations, we also predict that egalitarianism is a pre-condition for adaptation of tools as weapons. Potential implications for origins of human moral belief systems are discussed.
Fibroblasts cell lines misclassified as cancer cell lines
Authors: de Weck Antoine , Bitter Hans , Kauffmann Audrey
Published: July 2017

Large collections of immortalized cancer cell lines have been widely used as model systems for cancer research and drug discovery. Some of these models however display more fibroblast-like than cancer-like characteristics based on their genetic and genomic characterization. The correct annotation of these cell lines remains a challenge. Here, we report the outcome of our analysis on a large cancer cell line collection, where we found a subset of cell lines misclassified.
Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses
Authors: Harrington Lia X. , Way Gregory P. , Doherty Jennifer A. , Greene Casey S.
Published: July 2017

Differential expression experiments or other analyses often end in a list of genes. Pathway enrichment analysis is one method to discern important biological signals and patterns from noisy expression data. However, pathway enrichment analysis may perform suboptimally in situations where there are multiple implicated pathways – such as in the case of genes that define subtypes of complex diseases. Our simulation study shows that in this setting, standard overrepresentation analysis identifies many false positive pathways along with the true positives. These false positives hamper investigators’ attempts to glean biological insights from enrichment analysis. We develop and evaluate an approach that combines community detection over functional networks with pathway enrichment to reduce false positives. Our simulation study demonstrates that a large reduction in false positives can be obtained with a small decrease in power. Though we hypothesized that multiple communities might underlie previously described subtypes of high-grade serous ovarian cancer and applied this approach, our results do not support this hypothesis. In summary, applying community detection before enrichment analysis may ease interpretation for complex gene sets that represent multiple distinct pathways.
Environmental anchoring of grid-like representations minimizes spatial uncertainty during navigation
Authors: Navarro Schröder Tobias , Towse Benjamin W. , Nau Matthias , Burgess Neil , Barry Caswell , Doeller Christian F.
Published: July 2017

Minimizing spatial uncertainty is essential for navigation, but the neural mechanisms remain elusive. Here we combine predictions of a simulated grid cell system with behavioural and fMRI measures in humans during virtual navigation. First, we showed that polarising cues produce anisotropy in motion parallax. Secondly, we simulated entorhinal grid cells in an environment with anisotropic information and found that self-location is decoded best when grid-patterns are aligned with the axis of greatest information. Thirdly, when exposing human participants to polarised virtual reality environments, we found that navigation performance is anisotropic, in line with the use of parallax. Eye movements showed that participants preferentially viewed polarising cues, which correlated with navigation performance. Finally, using fMRI we found that the orientation of grid-cell-like representations in entorhinal cortex anchored to the environmental axis of greatest parallax information, orthogonal to the polarisation axis. In sum, we demonstrate a crucial role of the entorhinal grid system in reducing uncertainty in representations of self-location and find evidence for adaptive spatial computations underlying entorhinal representations in service of optimal navigation.
Chiral bis(mandelato)borate salts for resolution via metathesis crystallization
Authors: Wong Lawrence W.-Y. , Kan Jack W.-H. , Sung Herman H.-Y. , Williams Ian D.
Published: July 2017

Spiroborate anions have potential for crystallization or resolution and chiral bis(mandelato)borate anions can be used for the efficient resolution of a diverse range of racemic cations via diastereomeric salt formation. The syntheses, X-ray crystal structures and solubilities of three chiral bis(mandelato)borate salts, namely poly[[aqua-μ3-bis[(R)-mandelato]borato-lithium(I)] monohydrate], [Li(C16H12BO6)(H2O)]
n
or Li[B(R-Man)2]·H2O, (1), ammonium bis[(R)-mandelato]borate, NH4
+·C16H12BO6
− or NH4[B(R-Man)2], (2), and tetra-n-butylammonium bis[(R)-mandelato]borate, C16H36N+·C16H12BO6
− or NBu4[B(R-Man)2], (3), are reported. They all have a B
S
configuration and show a reasonably well-conserved anion geometry. The main conformational variation is the orientation of the two phenyl groups, supporting the idea that [B(Man)2]− is a semi-rigid anion. The salts are differentially soluble in a range of solvents, meaning they could be useful as reagents for resolution via a metathesis crystallization approach.
Steric repulsion and supramolecular assemblies via a two-dimensional plate by C—H...O hydrogen bonds in two closely related 2-(benzofuran-2-yl)-2-oxoethyl benzoates
Authors: Then Li Yee , Chidan Kumar C. S. , Kwong Huey Chong , Win Yip-Foo , Mah Siau Hui , Quah Ching Kheng , Naveen S. , Warad Ismail
Published: July 2017

2-(Benzofuran-2-yl)-2-oxoethyl 2-chlorobenzoate, C17H11ClO4 (I), and 2-(benzofuran-2-yl)-2-oxoethyl 2-methoxybenzoate, C18H14O5 (II), were synthesized under mild conditions. Their chemical and molecular structures were analyzed by spectroscopic and single-crystal X-ray diffraction studies, respectively. These compounds possess different ortho-substituted functional groups on their phenyl rings, thus experiencing extra steric repulsion force within their molecules as the substituent changes from 2-chloro (I) to 2-methoxy (II). The crystal packing of compound (I) depends on weak intermolecular hydrogen bonds and π–π interactions. Molecules are related by inversion into centrosymmetric dimers via C—H...O hydrogen bonds, and further strengthened by π–π interactions between furan rings. Conversely, molecules in compound (II) are linked into alternating dimeric chains propagating along the [101] direction, which develop into a two-dimensional plate through extensive intermolecular hydrogen bonds. These plates are further stabilized by π–π and C—H...π interactions.
Crystal structure of bis[N-(2-hydroxyethyl)-N-methyldithiocarbamato-κ2
S,S′](pyridine)zinc(II) pyridine monosolvate and its N-ethyl analogue
Authors: Poplaukhin Pavel , Tiekink Edward R. T.
Published: July 2017

The common structural feature of the title compounds, [Zn(C4H8NOS2)2(C5H5N)]·C5H5N (I) and [Zn(C5H10NOS2)2(C5H5N)]·C5H5N (II), which differ by having dithiocarbamate N-bound methyl (I) and ethyl (II) groups, is the coordination of each ZnII atom by two non-symmetrically chelating dithiocarbamate ligands and by a pyridine ligand; in each case, the non-coordinating pyridine molecule is connected to the Zn-containing molecule via a (hydroxy)O—H...N(pyridine) hydrogen bond. The resulting NS4 coordination geometry is closer to a square-pyramid than a trigonal bipyramid in the case of (I), but almost intermediate between the two extremes in (II). The molecular packing features (hydroxy)O—H...O(hydroxy) hydrogen bonds, leading to supramolecular chains with a zigzag arrangement along [10-1] (I) or a helical arrangement along [010] (II). In (I), π–π [inter-centroid distances = 3.4738 (10) and 3.4848 (10) Å] between coordinating and non-coordinating pyridine molecules lead to stacks comprising alternating rings along the a axis. In (II), weaker π–π contacts occur between centrosymmetrically related pairs of coordinating pyridine molecules [inter-centroid separation = 3.9815 (14) Å]. Further interactions, including C—H...π(chelate) interactions in (I), lead to a three-dimensional architecture in each case.
(4Z)-4-(2-Oxopropylidene)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-2-one
Authors: Sebhaoui Jihad , El Bakri Youness , Essassi El Mokhtar , Mague Joel T.
Published: July 2017

In the title compound, C12H12N2O2, the seven-membered ring adopts a boat conformation. The orientation of the acetyl substituent on this ring is partly determined by an intramolecular N—H...O hydrogen bond. In the crystal, wrinkled sheets stacked along the a-axis direction are formed by pairwise N—H...O and C—H...O hydrogen bonds. The sheets are connected through additional N—H...O and C—H...O hydrogen bonds stacking the molecules along the a-axis direction. The structure was refined as a three-component twin.
Bis{2-[({[3-(dimethylazaniumyl)propyl]imino}methyl)phenyl]sulfanido}nickel(II) tetraphenylborate
Authors: Meloccaro Alexandra , Zimmerman Joshua R. , Eichhorn David M.
Published: July 2017

In the title compound, [Ni(C12H18N2S)2](C24H20B)2, the NiII atom is coordinated by two ligands via the thiolate S and the imine N atoms. The amine N atoms are protonated and interact with the phenyl rings of the BPh4 anions.
Growth strategies and threshold responses to water deficit modulate effects of warming on tree seedlings from forest to alpine
Authors: Lazarus Brynne E. , Castanha Cristina , Germino Matthew J. , Kueppers Lara M. , Moyes Andrew B.
Published: July 2017

Predictions of upslope range shifts for tree species with warming are based on assumptions of moisture stress at lower elevation limits and low‐temperature stress at high‐elevation limits. However, recent studies have shown that warming can reduce tree seedling establishment across the entire gradient from subalpine forest to alpine via moisture limitation. Warming effects also vary with species, potentially resulting in community shifts in high‐elevation forests.

We examined the growth and physiology underlying effects of warming on seedling demographic patterns. We evaluated dry mass (DM), root length, allocation above‐ and below‐ground, and relative growth rate (RGR) of whole seedlings, and their ability to avoid or endure water stress via water‐use efficiency and resisting turgor loss, for Pinus flexilis, Picea engelmannii and Pinus contorta seeded below, at and above tree line in experimentally warmed, watered and control plots in the Rocky Mountains, USA. We expected that growth and allocation responses to warming would relate to moisture status and that variation in drought tolerance traits would explain species differences in survival rates.

Across treatments and elevations, seedlings of all species had weak turgor‐loss resistance, and growth was marginal with negative RGR in the first growth phase (−0.01 to −0.04 g g−1 day−1). Growth was correlated with soil moisture, particularly in the relatively small‐seeded P. contorta and P. engelmannii. Pinus flexilis, known to have the highest survivorship, attained the greatest DM and longest root but was also the slowest growing and most water‐use efficient. This was likely due to its greater reliance on seed reserves. Seedlings developed 15% less total DM, 25% less root DM and 11% shorter roots in heated compared with unheated plots. Higher temperatures slightly increased DM, root length and RGR where soils were wettest, but more strongly decreased these variables under drier conditions.

Synthesis. The surprising heat inhibition of tree seedling establishment at the cold edge of forests appears to have a physiological basis: newly germinated seedlings have poor moisture stress tolerance, which appears related to marginal initial growth and heavy reliance on seed reserves. Variation in these attributes among tree species at tree line helps explain their different climate responses.
Fatal attraction of non‐vector impairs fitness of manipulating plant virus
Authors: Ángeles‐López Yesenia Ithaí , Rivera‐Bustamante Rafael , Heil Martin
Published: July 2017

Host manipulation refers to the expression of a host phenotype that is partly under the genetic control of a parasite. This phenomenon can enhance parasite transmission rates and is responsible for biological marvels such as “Zombie‐ants” and the “fatal attraction” of Toxoplasma‐infected rodents to their feline predators. Such host manipulation has evolved in all major phylogenetic lineages of parasites and is assumed to enhance the fitness of the parasite.

However, the capacity to manipulate is not ubiquitous; that is, many clades of parasites comprise manipulating and non‐manipulating species. This pattern leads to the prediction of costs that select against the evolution of manipulation, but this has been difficult to show empirically.

In the present study, we used a tripartitate system consisting of chili (Capsicum annuum) plants infected with Pepper golden mosaic virus and colonized by non‐vector whiteflies (Trialeurodes vaporariorum), to study the effects on viral load when a non‐vector herbivore feeds on the infected plants.

We observed that virus‐infected plants emitted odours that attracted adult whiteflies, contained three times more amino acids in the phloem than mock‐inoculated controls and supported higher whitefly reproduction as compared to controls. However, viral load decreased almost 100‐fold in whitefly‐carrying plants, which was associated with a depletion of phloem amino acids.

Synthesis. We show that a plant virus can suffer from a reduced within‐host reproduction rate when virus‐induced alterations of the plant cause a “fatal attraction” of a non‐vector insect that exploits the altered plant phenotype at its own benefits. The resulting fitness costs might represent a force that can select against the evolution of host manipulation by parasites.
Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments
Authors: Doyle Conor J. , O'Toole Paul W. , Cotter Paul D.
Published: July 2017

Metagenomic‐based analyses have the potential to revolutionize our understanding of the microbiology of food production and processing environments. By adopting such approaches, it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimize quality and safety. This mini‐review will discuss the merits of adopting metagenostic‐based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented.
Regulatory roles of introns in fungicide sensitivity of Fusarium graminearum
Authors: Li Yanjun , Luo Shunwen , Jia Xiaojing , Zhu Yuanye , Chen Dongming , Duan Yabing , Hou Yiping , Zhou Mingguo
Published: July 2017

Although the roles of introns have been much debated in eukaryotic organisms, none of them have been functionally characterized in Fusarium graminearum. In this study, we characterized the roles of introns in regulation of fungicide‐sensitivity of F. graminearum. β2tub, cyp51A and myosin‐5 are important target genes of benzimidazoles, triazoles and cyanoacrylates respectively. To explore the sensitivity regulation functions of introns in target genes, several detailed deletion studies were completed on the intronic regions of β2tub, cyp51A and myosin‐5. Phenotypic analyses showed that deletion of the fourth intron from β2tub gene (designated β2Δi4), the sole intron from cyp51A gene (cyp51A‐Δi) and the second intron from myosin‐5 gene (myo5‐Δi2) exhibited an increased sensitivity to corresponding fungicides. In contrast, deletion of the first or second intron from β2tub gene exhibited a decreased sensitivity to carbendazim. qRT‐PCR showed that the mRNA transcript levels of target genes were significantly downregulated in β2Δi4, cyp51A‐Δi and myo5‐Δi2 respectively. Meanwhile, Western blot assays revealed that the protein expression levels of β2tub was also dramatically reduced in β2Δi4, but accumulated in β2Δi1 and β2Δi2. Overall, our results indicate that introns in target genes significantly regulate the fungicide‐sensitivity by influencing expression of the corresponding resident genes in F. graminearum.
Eyeball Position in Facial Approximation: Accuracy of Methods for Predicting Globe Positioning in Lateral View
Authors: Zednikova Mala Pavla , Veleminska Jana
Published: July 2017

This study measured the accuracy of traditional and validated newly proposed methods for globe positioning in lateral view. Eighty lateral head cephalograms of adult subjects from Central Europe were taken, and the actual and predicted dimensions were compared. The anteroposterior eyeball position was estimated as the most accurate method based on the proportion of the orbital height (SEE = 1.9 mm) and was followed by the “tangent to the iris method” showing SEE = 2.4 mm. The traditional “tangent to the cornea method” underestimated the eyeball projection by SEE = 5.8 mm. Concerning the superoinferior eyeball position, the results showed a deviation from a central to a more superior position by 0.3 mm, on average, and the traditional method of central positioning of the globe could not be rejected as inaccurate (SEE = 0.3 mm). Based on regression analyzes or proportionality of the orbital height, the SEE = 2.1 mm.
The Frontal Sinus Cavity Exhibits Sexual Dimorphism in 3D Cone‐beam CT Images and can be Used for Sex Determination
Authors: Choi Isabela G. G. , Duailibi‐Neto Eduardo F. , Beaini Thiago L. , da Silva Renan L. B. , Chilvarquer Israel
Published: July 2017

Few studies have assessed the use of the frontal sinus cavities for sex differentiation. In this study, a new methodology was used to assess the reliability of CBCT images of the frontal sinus cavity for determining sex based on the sexual dimorphism found in this anatomical structure. The survey sample consisted of 130 scans that were reconstructed three‐dimensionally. 3D images of the cavity volume in the frontal, lateral, and basal views were exported in TIFF. The following variables were measured in a second program: area, perimeter, bounding rectangle, ellipse fit, circularity, aspect ratio, roundness, solidity, and Feret's diameter. The methodology demonstrated the existence of sexual dimorphism with an accuracy of 80.0% in the logistic regression model. The basal view had the greatest explanatory power in the final model. This methodology may be used as an alternative way of determining a reliable biological profile during the analysis of skeletal remains.
Plant infection by two different viruses induce contrasting changes of vectors fitness and behavior
Authors: Chesnais Quentin , Couty Aude , Uzest Maryline , Brault Véronique , Ameline Arnaud
Published: July 2017

Insect‐vectored plant viruses can induce changes in plant phenotypes, thus influencing plant–vector interactions in a way that may promote their dispersal according to their mode of transmission (i.e., circulative vs. noncirculative). This indirect vector manipulation requires host–virus–vector coevolution and would thus be effective solely in very specific plant–virus–vector species associations. Some studies suggest this manipulation may depend on multiple factors relative to various intrinsic characteristics of vectors such as transmission efficiency. In anintegrative study, we tested the effects of infection of the Brassicaceae Camelina sativa with the noncirculative Cauliflower mosaic virus (CaMV) or the circulative Turnip yellows virus (TuYV) on the host‐plant colonization of two aphid species differing in their virus transmission efficiency: the polyphagous Myzus persicae, efficient vector of both viruses, and the Brassicaceae specialist Brevicoryne brassicae, poor vector of TuYV and efficient vector of CaMV. Results confirmed the important role of virus mode of transmission as plant‐mediated effects of CaMV on the two aphid species induced negative alterations of feeding behavior (i.e., decreased phloem sap ingestion) and performance that were both conducive for virus fitness by promoting dispersion after a rapid acquisition. In addition, virus transmission efficiency may also play a role in vector manipulation by viruses as only the responses of the efficient vector to plant‐mediated effects of TuYV, that is, enhanced feeding behavior and performances, were favorable to their acquisition and further dispersal. Altogether, this work demonstrated that vector transmission efficiency also has to be considered when studying the mechanisms underlying vector manipulation by viruses. Our results also reinforce the idea that vector manipulation requires coevolution between plant, virus and vector.
Identification and functional characterization of an odorant receptor in pea aphid, Acyrthosiphon pisum
Authors: Zhang Rui‐Bin , Liu Yang , Yan Shan‐Chun , Wang Gui‐Rong
Published: July 2017

The sensitive olfactory system is necessary for survival of insects. Odorant receptors (ORs) are located on the dendrites of olfactory receptor neurons and play a critical role in odor detection. Insect ORs are functionally analyzed via heterologous expression in a Xenopus oocyte system using a two‐electrode voltage‐clamp (TEVC) electrophysiological recording. Here, we have identified a novel OR in the pea aphid, Acyrthosiphon pisum, then we cloned and named it ApisOR4. We analyzed the ApisOR4 tissue expression patterns and found expression only in antennae tissues. Further functional analysis using TEVC revealed that ApisOR4 is broadly tuned to eight volatiles, which elicit electrophysiological response in pea aphid antennae. This study provides an initial functional analysis of aphid ORs and identifies candidate volatiles to be used in developing new strategies for aphid control.
Attempt to Harvest a Sufficient Number of Mononuclear Cells in an Appropriate Blood Product Volume By Modification of the Default Apheresis Setting
Authors: Tanaka Yumi , Ohishi Kohshi , Sawai Toshiki , Iwasaki Hitoshi , Kageyama Shinichi , Masuya Masahiro , Matsumoto Takeshi , Tanigawa Takashi , Wada Hideo , Shiku Hiroshi , Ito Masaaki , Katayama Naoyuki
Published: July 2017

To harvest for T cell therapy, a 1.6‐fold higher number of CD3+ T cells was collected with MNC mode (N = 10) compared with Auto PBSC mode (N = 5) in COBE Spectra cell separator, but the blood product volume was increased by 3.5‐fold. For therapeutic angiogenesis therapy, apheresis was initially performed using Auto PBSC mode (N = 4) to fine tune the blood product volume to omit cell concentration, but the collected number of mononuclear cells was lower than expected. However, an increase of the harvest cycle number from 3.8 ± 0.5 to 7.4 ± 2.0 cycles (N = 19) resulted in a 2.1‐fold higher number of collected mononuclear cells (8.7 ± 4.1 × 109 vs. 4.1 ± 1.0 × 109 cells, P < 0.05). The increase in blood product volume by this modification appeared to be lower than that expected with MNC mode. These data show that optimal harvesting can be achieved by modification of default collection settings.