bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospects for vaccination against pathogenic African trypanosomes
Authors: Black S. J. , Mansfield J. M. 
Published: September 2016

SummaryAfrican trypanosomes cause human and animal African trypanosomiases, which are chronic, debilitating and often fatal diseases of people and livestock in sub‐Saharan Africa. The extracellular protozoan parasites are exemplars of antigenic variation. They direct host‐protective B‐cell and T‐cell immune responses towards hypervariable components of their variable surface glycoprotein coat and evade immune elimination by generating new surface coat antigenic variants at a rate that supersedes immune destruction. This results in recurring waves of parasitemia, tissue invasion and escalating immunopathology in trypanosomiasis‐susceptible hosts. Here, we discuss the possibility that host control of African trypanosomes might be improved by immunization with conserved VSG peptides and invariant surface glycoproteins. Infection‐induced T‐cell recall responses to these typically poorly expressed or nonimmunogenic parasite components induce tissue phagocytes to produce microbicidal materials that kill trypanosomes. Preliminary data that support this immune‐enhancing vaccine strategy are discussed, as are host and parasite interactions that might downregulate the protective responses. These include infection‐induced immunosuppression and increasing virulence of infecting parasites over time.
Variation in floral morphology and plant reproductive success in four Ipomoea species (Convolvulaceae) with contrasting breeding systems
Authors: Delgado‐Dávila R. , Martén‐Rodríguez S. , Huerta‐Ramos G. 
Published: September 2016

Abstract

This study tested the hypothesis that self‐compatibility would be associated with floral traits that facilitate autonomous self‐pollination to ensure reproduction under low pollinator visitation. In a comparison of two pairs of Ipomoea species with contrasting breeding systems, we predicted that self‐compatible (SC) species would have smaller, less variable flowers, reduced herkogamy, lower pollinator visitation and higher reproductive success than their self‐incompatible (SI) congeners.

We studied sympatric species pairs, I. hederacea (SC)– I. mitchellae (SI) and I. purpurea (SC)–I. indica (SI), in Mexico, over two years. We quantified variation in floral traits and nectar production, documented pollinator visitation, and determined natural fruit and seed set. Hand‐pollination and bagging experiments were conducted to determine potential for autonomous self‐pollination and apomixis.

Self‐compatible Ipomoea species had smaller flowers and lower nectar production than SI species; however, floral variation and integration did not vary according to breeding system. Bees were primary pollinators of all species, but visitation rates were seven times lower in SC than SI species. SC species had a high capacity for autonomous self‐pollination due to reduced herkogamy at the highest anther levels. Self‐compatible species had two to six times higher fruit set than SI species.

Results generally support the hypothesis that self‐compatibility and autonomous self‐pollination ensure reproduction under low pollinator visitation. However, high variation in morphological traits of SC Ipomoea species suggests they maintain variation through outcrossing. Furthermore, reduced herkogamy was associated with high potential for autonomous self‐pollination, providing a reproductive advantage that possibly underlies transitions to self‐compatibility in Ipomoea.
Reply to the Discussion by Rose of Phelps et al. (2014) ‘Oceanographic and eustatic control of carbonate platform evolution and sequence stratigraphy on the Cretaceous (Valanginian–Campanian) passive margin, northern Gulf of Mexico’, Sedimentology, 61, 461–496
Authors: Phelps Ryan M. , Kerans Charles , Loucks Robert G. 
Published: September 2016

AbstractDiscussion points raised by Rose () concentrate on late Albian stratigraphic relationships between formations of the East Texas Basin and the San Marcos Arch of the Comanche Platform in the northern Gulf of Mexico. Criticisms of Phelps et al. (2014) regarding stratigraphic nomenclature, palaeogeography and regional lithostratigraphic correlations generally focus on interpretive aspects of the study or do not account for the full scope of published information. Revisions to the top Aptian–Albian Supersequence boundary by Rose are incompatible with the relative location of a subaerial unconformity, as well as deepening lithofacies trends and retrogradational stratigraphic patterns below the interpreted boundary. Rose's placement of the top Aptian–Albian Supersequence boundary precisely at the Albian–Cenomanian stage boundary also implies ca 1·4 Ma of diachroneity in second order sea‐level patterns between the northern Gulf of Mexico and other documented global sedimentary basins.
The elusive role of soil quality in nutrient cycling: a review
Authors: Schröder J. J. , Schulte R. P. O. , Creamer R. E. , Delgado A. , van Leeuwen J. , Lehtinen T. , Rutgers M. , Spiegel H. , Staes J. , Tóth G. , Wall D. P. 
Published: September 2016

AbstractCycling of nutrients, including nitrogen and phosphorus, is one of the ecosystem services we expect agricultural soils to deliver. Nutrient cycling incorporates the reuse of agricultural, industrial and municipal organic residues that, misleadingly, are often referred to as ‘wastes’. The present review disentangles the processes underlying the cycling of nutrients to better understand which soil properties determine the performance of that function. Four processes are identified (i) the capacity to receive nutrients, (ii) the capacity to make and keep nutrients available to crops, (iii) the capacity to support the uptake of nutrients by crops and (iv) the capacity to support their successful removal in harvested crop. Soil properties matter but it is imperative that, as constituents of ‘soil quality’, they should be evaluated in the context of management options and climate and not as ends in their own right. The effect of a soil property may vary depending on the prevailing climatic and hydrologic conditions and on other soil properties. We recognize that individual soil properties may be enhancing one of the processes underlying the cycling of nutrients but simultaneously weakening others. Competing demands on soil properties are even more obvious when considering other soil functions such as primary production, purification and flow regulation of water, climate modification and habitat provision, as shown by examples. Consequently, evaluations of soil properties and management actions need to be site‐specific, taking account of local aspects of their suitability and potential challenges.
Serological blind spots for variants of human IgG3 and IgG4 by a commonly used anti‐immunoglobulin reagent
Authors: Howie Heather L. , Delaney Meghan , Wang Xiaohong , Er Lay See , Vidarsson Gestur , Stegmann Tamara C. , Kapp Linda , Lebedev Jenna N. , Wu Yanyun , AuBuchon James P. , Zimring James C. 
Published: September 2016

BACKGROUNDHuman immunoglobulin G (IgG) includes four different subtypes (IgG1, IgG2, IgG3, and IgG4), and it is also now appreciated that there are genetic variations within IgG subtypes (called isoallotypes). Twenty‐nine different isoallotypes have been described, with 7, 4, 15, and 3 isoallotypes described for IgG1, IgG2, IgG3, and IgG4, respectively. The reactivity of anti‐IgG with different isoallotypes has not been characterized.STUDY DESIGN AND METHODSA novel monoclonal anti‐K antibody (PugetSound Monoclonal Antibody 1 [PUMA1]) was isolated and sequenced, and a panel of PUMA1 variants was expressed, consisting of the 29 known IgG isoallotypes. The resulting panel of antibodies was preincubated with K‐positive red blood cells (RBCs) and then subjected to testing with currently approved anti‐IgG by flow cytometry, solid phase systems, gel cards, and tube testing.RESULTSA US Food and Drug Administration (FDA)‐approved monoclonal anti‐IgG (gamma‐clone) failed to recognize 2 of 15 IgG3 isoallotypes (IgG3‐03 and IgG3‐13) and 3 of 3 IgG4 isoallotypes (IgG4‐01, IgG4‐02, and IgG4‐03). In contrast, an FDA‐approved rabbit polyclonal anti‐IgG recognized each of the known human IgG isoallotypes.CONCLUSIONThese findings demonstrate “blind spots” in isoalloantibody detection by a monoclonal anti‐IgG. If a patient has anti‐RBC antibodies predominantly of an IgG3 subtype (the IgG3‐03 and/or IgG3‐13 variety), then it is possible that a clinically significant alloantibody would be missed. IgG‐03 and IgG‐13 have an estimated frequency of 1% to 3% in Caucasian populations and 20% to 30% in certain African populations. Nonreactivity with IgG4 is a known characteristic of this monoclonal anti‐IgG, but IgG4 isoallotypes have not been previously reported.
New perspectives on amyotrophic lateral sclerosis: the role of glial cells at the neuromuscular junction
Authors: Arbour Danielle , Vande Velde Christine , Robitaille Richard 
Published: September 2016

AbstractAmyotrophic lateral sclerosis (ALS) is a disease leading to the death of motor neurons (MNs). It is also recognized as a non‐cell autonomous disease where glial cells in the CNS are involved in its pathogenesis and progression. However, although denervation of neuromuscular junctions (NMJs) represents an early and major event in ALS, the importance of glial cells at this synapse receives little attention. An interesting possibility is that altered relationships between glial cells and MNs in the spinal cord in ALS may also take place at the NMJ. Perisynaptic Schwann cells (PSCs), which are glial cells at the NMJ, show great morphological and functional adaptability to ensure NMJ stability, maintenance and repair. More specifically, PSCs change their properties according to the state of innervation. Hence, abnormal changes or lack of changes can have detrimental effects on NMJs in ALS. This review will provide an overview of known and hypothesized interactions between MN nerve terminals and PSCs at NMJs during development, aging and ALS‐induced denervation. These neuron–PSC interactions may be crucial to the understanding of how degenerative changes begin and progress at NMJs in ALS, and represent a novel therapeutic target.
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Central control of interlimb coordination and speed‐dependent gait expression in quadrupeds
Authors: Danner Simon M. , Wilshin Simon D. , Shevtsova Natalia A. , Rybak Ilya A. 
Published: September 2016

Key points
Quadrupeds express different gaits depending on speed of locomotion.
Central pattern generators (one per limb) within the spinal cord generate locomotor oscillations and control limb movements. Neural interactions between these generators define interlimb coordination and gait.
We present a computational model of spinal circuits representing four rhythm generators with left–right excitatory and inhibitory commissural and fore–hind inhibitory interactions within the cord.
Increasing brainstem drive to all rhythm generators and excitatory commissural interneurons induces an increasing frequency of locomotor oscillations accompanied by speed‐dependent gait changes from walk to trot and to gallop and bound.
The model closely reproduces and suggests explanations for multiple experimental data, including speed‐dependent gait transitions in intact mice and changes in gait expression in mutants lacking certain types of commissural interneurons. The model suggests the possible circuit organization in the spinal cord and proposes predictions that can be tested experimentally.
AbstractAs speed of locomotion is increasing, most quadrupeds, including mice, demonstrate sequential gait transitions from walk to trot and to gallop and bound. The neural mechanisms underlying these transitions are poorly understood. We propose that the speed‐dependent expression of different gaits results from speed‐dependent changes in the interactions between spinal circuits controlling different limbs and interlimb coordination. As a result, the expression of each gait depends on (1) left–right interactions within the spinal cord mediated by different commissural interneurons (CINs), (2) fore–hind interactions on each side of the spinal cord and (3) brainstem drives to rhythm‐generating circuits and CIN pathways. We developed a computational model of spinal circuits consisting of four rhythm generators (RGs) with bilateral left–right interactions mediated by V0 CINs (V0D and V0V sub‐types) providing left–right alternation, and conditional V3 CINs promoting left–right synchronization. Fore and hind RGs mutually inhibited each other. We demonstrate that linearly increasing excitatory drives to the RGs and V3 CINs can produce a progressive increase in the locomotor speed accompanied by sequential changes of gaits from walk to trot and to gallop and bound. The model closely reproduces and suggests explanations for the speed‐dependent gait expression observed in vivo in intact mice and in mutants lacking V0V or all V0 CINs. Specifically, trot is not expressed after removal of V0V CINs, and only bound is expressed after removal of all V0 CINs. The model provides important insights into the organization of spinal circuits and neural control of locomotion.
First Directly Sequenced Genome of Hepatitis E Virus from the Serum of a Patient from the United Kingdom
Authors: Caddy Sarah L. , Goodfellow Ian , Jalal Hamid 
Published: September 2016

ABSTRACT
Hepatitis E virus (HEV) genotype 3 is endemic in the United Kingdom but the complete sequence of HEV, generated directly from a clinical sample, is lacking. We report a near full-length genome sequence of genotype 3 HEV from the serum of a patient with acute hepatitis.
Complete Genome Sequence of Lactobacillus oris J-1, a Potential Probiotic Isolated from the Human Oral Microbiome
Authors: Jia Fang 
Published: September 2016

ABSTRACT

Lactobacilli can exert health-promoting effects in the human oral microbiome through many mechanisms, including pathogen inhibition, maintenance of microbial balance, immunomodulation, and enhancement of the epithelial barrier function. Here, we present the complete genome sequence of a potential probiotic,
Lactobacillus oris
J-1, that was isolated from the oral cavity of a health child.
Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough
Authors: Eby Joshua C. , Turner Lauren , Nguyen Bryan , Kang June , Neville Carly , Temple Louise 
Published: September 2016

ABSTRACT

The number of cases of pertussis has increased in the United States despite vaccination. We present the genome of an isolate of
Bordetella pertussis
from a vaccinated patient from Virginia. The genome was sequenced by long-read methodology and compared to that of a clinical isolate used for laboratory studies, D420.
Draft Genome Sequence of
Leptolyngbya
sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes
Authors: Kim Ji Hyung , Kang Do-Hyung 
Published: September 2016

ABSTRACT

Here, we report the draft genome of cyanobacterium
Leptolyngbya
sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes.
Draft Genome Sequences of Four Novel Thermal- and Alkaline-Tolerant Egyptian
Rhizobium
Strains Nodulating Berseem Clover
Authors: Shamseldin Abdelaal , Nelson Matthew S. , Staley Christopher , Guhlin Joseph , Sadowsky Michael J. 
Published: September 2016

ABSTRACT

Four
Rhizobium
strains were isolated from berseem clover in Egypt. The symbiotically effective, salt-tolerant, strain Rhiz950 was identified as new species,
Rhizobium aegypticaum
sv.
trifolii
(USDA 7124
T
). The other three thermal- and pH-tolerant strains were identified as
Rhizobium bangladeshense
sv.
trifolii
, the type strain is USDA 7125
T
.
Permanent Draft Genome Sequence of
Frankia
sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of
Casuarina equisetifolia
Authors: D'Angelo Timothy , Oshone Rediet , Abebe-Akele Feseha , Simpson Stephen , Morris Krystalynne , Thomas W. Kelley , Tisa Louis S. 
Published: September 2016

ABSTRACT

Frankia
sp. strain BR is a member of
Frankia
lineage Ic and is able to reinfect plants of the
Casuarinaceae
family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
Cambrian geology of the Baraboo Hills
Authors: Dott Robert H. , Byers Charles W. 
Published: September 2016

Abstract
Cambrian strata in Wisconsin compose a sheet of mostly marine sandstone, with minor dolomite, deposited during the fluctuating advance of the North American epeiric sea. Sedimentary features and fossils indicate that deposition took place in both shallower, current-dominated regimes and deeper quiet-water settings swept by episodic storm surges. The sand sheet surrounds inliers of Precambrian rocks in the Baraboo area. The Baraboo inliers are remnants of an elliptical ring of islands in a subtropical shallow sea, which were gradually buried by Cambrian and Ordovician sediments. Spectacular conglomerates composed of red quartzite clasts accumulated around the islands, which were pounded repeatedly by waves that we presume to have been generated by tropical storms. Paleomagnetic evidence places Cambrian Wisconsin in the southern tropics. Boulders up to 1.5 m in diameter are well rounded whereas larger ones (up to 8 m) are not. This suggests the possibility of estimating the magnitude of the Cambrian storm waves using knowledge from modern oceanography and from wave trough experiments by coastal engineers. Such analysis suggests waves necessary to tumble quartzite boulders 1.5 m in diameter were of the order of 7–8 m high at their point of breaking. Such magnitudes are not uncommon today during storms on many modern rocky coasts.
Mixed methods study of engagement in behaviors to prevent type 2 diabetes among employees with pre-diabetes
Authors: Kullgren Jeffrey T , Knaus Megan , Jenkins Kristi Rahrig , Heisler Michele 
Published: September 2016

BackgroundMany employers use screenings to identify and recommend modification of employees' risk factors for type 2 diabetes, yet little is known about how often employees then engage in recommended behaviors and what factors influence engagement. We examined the frequency of, facilitators of, and barriers to engagement in recommended behaviors among employees found to have pre-diabetes during a workplace screening.MethodsWe surveyed 82 University of Michigan employees who were found to have pre-diabetes during a 2014 workplace screening and compared the characteristics of employees who 3 months later were and were not engaged in recommended behaviors. We interviewed 40 of these employees to identify the facilitators of and barriers to engagement in recommended behaviors.Results3 months after screening, 54% of employees with pre-diabetes reported attempting to lose weight and getting recommended levels of physical activity, had asked their primary care provider about metformin for diabetes prevention, or had attended a Diabetes Prevention Program. These employees had higher median levels of motivation to prevent type 2 diabetes (9/10 vs 7/10, p<0.001) and lower median estimations of their risk for type 2 diabetes (40% vs 60%, p=0.02). Key facilitators of engagement were high motivation and social and external supports. Key barriers were lack of motivation and resources, and competing demands.ConclusionsMost employees found to have pre-diabetes through a workplace screening were engaged in a recommended preventive behavior 3 months after the screening. This engagement could be enhanced by optimizing motivation and risk perception as well as leveraging social networks and external supports.
Validity of peptic ulcer disease and upper gastrointestinal bleeding diagnoses in administrative databases: a systematic review protocol
Authors: Montedori Alessandro , Abraha Iosief , Chiatti Carlos , Cozzolino Francesco , Orso Massimiliano , Luchetta Maria Laura , Rimland Joseph M , Ambrosio Giuseppe 
Published: September 2016

IntroductionAdministrative healthcare databases are useful to investigate the epidemiology, health outcomes, quality indicators and healthcare utilisation concerning peptic ulcers and gastrointestinal bleeding, but the databases need to be validated in order to be a reliable source for research. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases, 9th Revision and 10th version (ICD-9 and ICD-10) codes for peptic ulcer and upper gastrointestinal bleeding diagnoses.Methods and analysisMEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched, using appropriate search strategies. We will include validation studies that used administrative data to identify peptic ulcer disease and upper gastrointestinal bleeding diagnoses or studies that evaluated the validity of peptic ulcer and upper gastrointestinal bleeding codes in administrative data. The following inclusion criteria will be used: (a) the presence of a reference standard case definition for the diseases of interest; (b) the presence of at least one test measure (eg, sensitivity, etc) and (c) the use of an administrative database as a source of data. Pairs of reviewers will independently abstract data using standardised forms and will evaluate quality using the checklist of the Standards for Reporting of Diagnostic Accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol (PRISMA-P) 2015 statement.Ethics and disseminationEthics approval is not required given that this is a protocol for a systematic review. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide for researchers validating administrative healthcare databases to determine appropriate case definitions for peptic ulcer disease and upper gastrointestinal bleeding, as well as to perform outcome research using administrative healthcare databases of these conditions.Trial registration numberCRD42015029216.