bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic relationships within Diplotaxini Kirby (Coleoptera: Melolonthidae: Melolonthinae) with emphasis on LiogenysGuérin‐Méneville
Authors: CHERMAN MARIANA A. , MORÓN MIGUEL A. , ALMEIDA LÚCIA M. 
Published: June 2016

AbstractDiplotaxini Kirby is one of the 29 tribes of Melolonthinae with Nearctic, Neotropical, Paleartic, Afrotropical and Oriental distribution. According to the current classification, Diplotaxini is composed of 706 species described in 21 genera. Neotropical Diplotaxini comprise 94 species, of which 78 are members of Liogenys Guérin Méneville, the largest Neotropical genus. Until now, no phylogenetic studies on Diplotaxini have tested whether the tribe is natural or artificial. This study tested the relationships among Diplotaxini genera, created hypotheses for better defining them, and assessed the monophyly of Liogenys. Cladistic analyses using 167 adult morphological characters were performed. The 83 included taxa represent three subfamilies of Melolonthidae, four tribes of Melolonthinae, and most genera of Diplotaxini, with emphasis on Liogenys. The data were analysed using parsimony under equal and implied weights. In both analyses, the traditional concept of Diplotaxini is shown to be a polyphyletic assemblage. Empecta Erichson and Clypeasta Fairmaire are closely related to Melolontha melolontha (Linnaeus) and Pseudoliogenys Moser close to Myloxenoides Martínez (Tanyproctini). Pachrodema Blanchard is identified as the sister group of Liogenys. The monophyly of both Pacuvia Curtis and Homalochilus Blanchard is confirmed and the paraphyly of Diplotaxis Kirby is suggested. The analyses strongly supported the polyphyly of Liogenys. To render this genus monophyletic, we transferred L. ferrugata Mannerheim (related to M. melolontha) to Phyllophaga Harris, and L. micropyga Burmeister to Diplotaxis, forming Diplotaxis micropyga (Burmeister, 1855) comb.n.; and included Homoliogenys tarsalis (Moser) and Hilarianus anguliceps Blanchard in Liogenys. As H. anguliceps is syn. junior of Liogenys punctaticollis, Hilarianus is synonymized with Liogenys. Hilarianus ovalis and Hilarianus rufinus are here assigned to Manonychus, and Hilarianus uniformis and Hilarianus suboblongus to Blepharotoma, forming: Blepharotoma uniformis comb.n., Blepharotoma suboblongus comb.n., Manonychus ovalis comb.n. and Manonychus rufinus comb.n.
An efficient method for measuring copy number variation applied to improvement of nematode resistance in soybean
Authors: Lee Tong Geon , Diers Brian W. , Hudson Matthew E. 
Published: June 2016

SummaryCopy number variation (CNV) is implicated in important traits in multiple crop plants, but can be challenging to genotype using conventional methods. The Rhg1 locus of soybean, which confers resistance to soybean cyst nematode (SCN), is a CNV of multiple 31.2‐kb genomic units each containing four genes. Reliable, high‐throughput methods to quantify Rhg1 and other CNVs for selective breeding were developed. The CNV genotyping assay described here uses a homeologous gene copy within the paleopolyploid soybean genome to provide the internal control for a single‐tube TaqMan copy number assay. Using this assay, CNV in breeding populations can be tracked with high precision. We also show that extensive CNV exists within Fayette, a released, inbred SCN‐resistant soybean cultivar with a high copy number at Rhg1 derived from a single donor parent. Copy number at Rhg1 is therefore unstable within a released variety over a relatively small number of generations. Using this assay to select for individuals with altered copy number, plants were obtained with both increased copy number and increased SCN resistance relative to control plants. Thus, CNV genotyping technologies can be used as a new type of marker‐assisted selection to select for desirable traits in breeding populations, and to control for undesirable variation within cultivars.
Viral nucleic acids in human plasma pools
Authors: Zhang Wen , Li Linlin , Deng Xutao , Blümel Johannes , Nübling C. Micha , Hunfeld Andreas , Baylis Sally A. , Delwart Eric 
Published: June 2016

BACKGROUNDThe identification of viruses in human blood is required for epidemiologic surveillance and to detect potentially emerging threats to blood transfusion safety.STUDY DESIGN AND METHODSViral nucleic acids in plasma fractionation pools assembled from blood donors in the United States and Europe were analyzed by viral metagenomics.RESULTSAnelloviruses were detected in each of the 10 plasma pools. Human pegivirus A (HPgV; GB virus type C) sequences were identified in eight of the 10 pools, more than 90% of which belong to Genotype 2. The recently described human HPgV2 in Flaviviridae was not detected. A small number of sequence reads of human papillomavirus were also detected in three pools. In one pool, two different gemycircularvirus genomes were identified and fully sequenced. The capsid protein of one gemycircularvirus shared 83% to 84% identity to those of genomes from human serum and sewage. The presence of the gemycircularvirus genomes in the plasma pool was independently confirmed and the viral concentration estimated by digital PCR at more than 106 copies/mL assuming their origin from single donors.CONCLUSIONFurther research is required to elucidate whether gemycircularviruses can infect humans or are indicative of contamination occurring during phlebotomy, plasma pool processing, or ongoing donor fungal infections.
A randomized, double‐blinded crossover trial testing the benefit of two hydrolysed poultry‐based commercial diets for dogs with spontaneous pruritic chicken allergy
Authors: Bizikova Petra , Olivry Thierry 
Published: June 2016

BackgroundHydrolysed protein diets are used to diagnose and treat dogs with cutaneous adverse food reactions (CAFR). Little is known about what proportion of dogs hypersensitive to the native protein would react to its hydrolysed form.ObjectivesTo determine the clinical allergenicity of hydrolysed poultry feather (RCU) and chicken liver diets (HZD) in dogs with chicken induced CAFR.MethodsIn this randomized, double‐blinded, crossover trial, ten dogs with chicken induced CAFR were selected after a positive oral challenge to chicken meat and a negative one to corn. Test diets were fed for 14 days separated by a 14 day wash‐out period. Owners rated pruritus daily with a Visual Analog Scale (PVAS). The challenge was ended if a flare in pruritus occurred (i.e. PVAS ≥5/10).ResultsThe median PVAS scores before feeding RCU and HZD were 0.9 and 1.7, respectively (Wilcoxon signed rank test, P = 0.46). Pruritus scores increased significantly after feeding HZD (Friedman's test, P < 0.001) but not after feeding RCU (P = 0.895). None of the dogs fed RCU, but four dogs fed HZD (40%), were withdrawn after a flare in pruritus developed (Fisher's test, P = 0.04). The maximal PVAS score was significantly higher after HZD (median: 4.7) compared to RCU (2.5) (Wilcoxon signed rank test, P = 0.01). One dog in each group was withdrawn due to diarrhoea.ConclusionsThe hydrolysed poultry feather diet did not induce pruritus flares in dogs allergic to chicken in contrast to the hydrolysed chicken liver diet that led to pruritus flares in 40% of these dogs.
Hyponatraemia alters the biophysical properties of neuronal cells independently of osmolarity: a study on Ni2+‐sensitive current involvement
Authors: Squecco Roberta , Luciani Paola , Idrizaj Eglantina , Deledda Cristiana , Benvenuti Susanna , Giuliani Corinna , Fibbi Benedetta , Peri Alessandro , Francini Fabio 
Published: June 2016

New Findings

What is the central question of this study?
Hyponatraemia, an electrolyte disorder encountered in hospitalized patients, can cause neurological symptoms usually attributed to a reduction in plasma osmolarity. Here, we investigated whether low [Na+] per se can cause neuronal changes independent of osmolarity, focusing on involvement of the Na+–Ca2+ exchanger.

What is the main finding and its importance?
We show that hyponatraemia per se causes alterations of neuronal properties. The novel finding of Na+–Ca2+ exchanger involvement helps us to elucidate the volume regulation following hyponatraemia. This might have relevance in a translational perspective because Na+–Ca2+ exchanger could be a target for novel therapies.

Hyponatraemia is the most frequent electrolyte disorder encountered in hospitalized patients, and it can cause a wide variety of neurological symptoms. Most of the negative effects of this condition on neuronal cells are attributed to cell swelling because of the reduction of plasma osmolarity, although in hyponatraemia different membrane proteins are supposed to be involved in the conservation of neuronal volume. We have recently reported detrimental effects of hyponatraemia on two different neuronal cell lines, SK‐N‐AS and SH‐SY5Y, independent of osmotic alterations. In this study we investigated, in the same cell lines, whether hyponatraemic conditions per se can cause electrophysiological alterations and whether these effects vary over time. Accordingly, we carried out experiments in low‐sodium medium in either hyposmotic [Osm(−)] or isosmotic [Osm(+)] conditions, for a short (24 h) or long time (7 days). Using a patch pipette in voltage‐clamp conditions, we recorded possible modifications of cell capacitance (Cm) and membrane conductance (Gm). Our results indicate that in both Osm(−) and Osm(+) medium, Cm and Gm show a similar increase, but such effects are dependent on the time in culture in different ways. Notably, regarding the possible mechanisms involved in the maintenance of Cm, Gm and Gm/Cm in Osm(+) conditions, we observed a greater contribution of the Na+–Ca2+ exchanger compared with Osm(−) and control conditions. Overall, these novel electrophysiological results help us to understand the mechanisms of volume regulation after ionic perturbation. Our results might also have relevance in a translational perspective because the Na+–Ca2+ exchanger can be considered a target for planning novel therapies.
Three‐dimensional quadratic modeling and quantitative evaluation of the diaphragm on a volumetric CT scan in patients with chronic obstructive pulmonary disease
Authors: Chang Yongjun , Bae Jangpyo , Kim Namkug , Park Joo‐Young , Lee Sang Min , Seo Joon Beom 
Published: June 2016

Purpose:In patients with chronic obstructive pulmonary disease (COPD), diaphragm function may deteriorate due to reduced muscle fiber length. Quantitative analysis of the morphology of the diaphragm is therefore important. In the authors current study, they propose a diaphragm segmentation method for COPD patients that uses volumetric chest computed tomography (CT) data, and they provide a quantitative analysis of the diaphragmatic dimensions.Methods:Volumetric CT data were obtained from 30 COPD patients and 10 normal control patients using a 16‐row multidetector CT scanner (Siemens Sensation 16) with 0.75‐mm collimation. Diaphragm segmentation using 3D ray projections on the lower surface of the lungs was performed to identify the draft diaphragmatic lung surface, which was modeled using quadratic 3D surface fitting and robust regression in order to minimize the effects of segmentation error and parameterize diaphragm morphology. This result was visually evaluated by an expert thoracic radiologist. To take into consideration the shape features of the diaphragm, several quantification parameters—including the shape index on the apex (SIA) (which was computed using gradient set to 0), principal curvatures on the apex on the fitted diaphragm surface (CA), the height between the apex and the base plane (H), the diaphragm lengths along the x‐, y‐, and z‐axes (XL, YL, ZL), quadratic‐fitted diaphragm lengths on the z‐axis (FZL), average curvature (C), and surface area (SA)—were measured using in‐house software and compared with the pulmonary function test (PFT) results.Results:The overall accuracy of the combined segmentation method was 97.22% ± 4.44% while the visual accuracy of the models for the segmented diaphragms was 95.28% ± 2.52% (mean ± SD). The quantitative parameters, including SIA, CA, H, XL, YL, ZL, FZL, C, and SA were 0.85 ± 0.05 (mm−1), 0.01 ± 0.00 (mm−1), 17.93 ± 10.78 (mm), 129.80 ± 11.66 (mm), 163.19 ± 13.45 (mm), 71.27 ± 17.52 (mm), 61.59 ± 16.98 (mm), 0.01 ± 0.00 (mm−1), and 34 380.75 ± 6680.06 (mm2), respectively. Several parameters were correlated with the PFT parameters.Conclusions:The authors propose an automatic method for quantitatively evaluating the morphological parameters of the diaphragm on volumetric chest CT in COPD patients. By measuring not only the conventional length and surface area but also the shape features of the diaphragm using quadratic 3D surface modeling, the proposed method is especially useful for quantifying diaphragm characteristics. Their method may be useful for assessing morphological diaphragmatic changes in COPD patients.
Evaluation of a Multiplex Real-Time PCR Assay for Detecting Major Bacterial Enteric Pathogens in Fecal Specimens: Intestinal Inflammation and Bacterial Load Are Correlated in Campylobacter Infections
Authors: Wohlwend Nadia , Tiermann Sacha , Risch Lorenz , Risch Martin , Bodmer Thomas 
Published: June 2016

ABSTRACT

A total of 1,056 native or Cary-Blair-preserved stool specimens were simultaneously tested by conventional stool culturing and by enteric bacterial panel (EBP) multiplex real-time PCR for
Campylobacter jejuni
,
Campylobacter coli
,
Salmonella
spp., and shigellosis disease-causing agents (
Shigella
spp. and enteroinvasive
Escherichia coli
[EIEC]). Overall, 143 (13.5%) specimens tested positive by PCR for the targets named above; 3 coinfections and 109 (10.4%)
Campylobacter
spp., 17 (1.6%)
Salmonella
spp., and 20 (1.9%)
Shigella
spp./EIEC infections were detected. The respective positive stool culture rates were 75 (7.1%), 14 (1.3%), and 7 (0.7%). The median threshold cycle (

C
T

) values of culture-positive specimens were significantly lower than those of culture-negative ones (

C
T

values, 24.3 versus 28.7;
P
< 0.001), indicating that the relative bacterial load per fecal specimen was significantly associated with the culture results. In
Campylobacter
infections, the respective median fecal calprotectin concentrations in PCR-negative/culture-negative (
n =
40), PCR-positive/culture-negative (
n =
14), and PCR-positive/culture-positive (
n =
15) specimens were 134 mg/kg (interquartile range [IQR], 30 to 1,374 mg/kg), 1,913 mg/kg (IQR, 165 to 3,813 mg/kg), and 5,327 mg/kg (IQR, 1,836 to 18,213 mg/kg). Significant differences were observed among the three groups (
P
< 0.001), and a significant linear trend was identified (
P
< 0.001). Furthermore, the fecal calprotectin concentrations and

C
T

values were found to be correlated (
r
= −0.658). Our results demonstrate that molecular screening of
Campylobacter
spp.,
Salmonella
spp., and
Shigella
spp./EIEC using the BD Max EBP assay will result in timely diagnosis and improved sensitivity. The determination of inflammatory markers, such as calprotectin, in fecal specimens may aid in the interpretation of PCR results, particularly for enteric pathogens associated with mucosal damage and colonic inflammation.
Rapid Detection of Polymyxin-Resistant Enterobacteriaceae from Blood Cultures
Authors: Jayol Aurélie , Dubois Véronique , Poirel Laurent , Nordmann Patrice 
Published: June 2016

ABSTRACT

Enterobacterial strains resistant to polymyxins are being increasingly reported worldwide. The conventional methods for detection of colistin-resistant isolates such as broth microdilution remain time-consuming (24 to 48 h), and methods such as disc diffusion and Etest are not reliable. Recently, the rapid polymyxin NP test was developed for rapid identification of polymyxin-resistant
Enterobacteriaceae
. This test is based on the detection of glucose metabolism related to bacterial growth in the presence of a defined concentration of colistin (or polymyxin B). The formation of acid metabolites is evidenced by a color change of a pH indicator (red phenol) in less than 2 h. In this study, the polymyxin NP test was evaluated for detection of colistin-resistant
Enterobacteriaceae
directly from blood cultures. The test was performed with 73 blood culture sets (either spiked or clinical blood cultures) with various enterobacterial species. The test exhibited excellent discrimination between polymyxin-resistant and polymyxin-susceptible enterobacterial isolates, and results are obtained from blood cultures within 4 h. It is easy to perform and requires neither subculture nor a centrifugation step. This test is rapid, specific, and sensitive and allows early identification of polymyxin-resistant
Enterobacteriaceae
directly from blood cultures.
Evaluation of the Hologic Panther Transcription-Mediated Amplification Assay for Detection of Mycoplasma genitalium
Authors: Tabrizi S. N. , Costa A. M. , Su J. , Lowe P. , Bradshaw C. S. , Fairley C. K. , Garland S. M. 
Published: June 2016

ABSTRACT

The detection of
Mycoplasma genitalium
was evaluated on 1,080 urine samples by the use of a Panther instrument. Overall sensitivity, specificity, positive predictive values, and negative predictive values were 100%, 99.4%, 93.6%, and 100%, respectively. Detection of
M. genitalium
by the use of the Panther transcription-mediated amplification assay offers a simple, accurate, and sensitive platform for diagnostic laboratories.
Capsid-CPSF6 Interaction Is Dispensable for HIV-1 Replication in Primary Cells but Is Selected during Virus Passage
In Vivo
Authors: Saito Akatsuki , Henning Matthew S. , Serrao Erik , Dubose Brittany N. , Teng Samantha , Huang Jing , Li Xiangming , Saito Namiko , Roy Saumendra Prasad , Siddiqui Mohammad Adnan , Ahn Jinwoo , Tsuji Moriya , Hatziioannou Theodora , Engelman Alan N. , Yamashita Masahiro 
Published: June 2016

ABSTRACT

Cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a host factor that interacts with the HIV-1 capsid (CA) protein, is implicated in diverse functions during the early part of the HIV-1 life cycle, including uncoating, nuclear entry, and integration targeting. Preservation of CA binding to CPSF6
in vivo
suggests that this interaction is fine-tuned for efficient HIV-1 replication in physiologically relevant settings. Nevertheless, this possibility has not been formally examined. To assess the requirement for optimal CPSF6-CA binding during infection of primary cells and
in vivo
, we utilized a novel CA mutation, A77V, that significantly reduced CA binding to CPSF6. The A77V mutation rendered HIV-1 largely independent from TNPO3, NUP358, and NUP153 for infection and altered the integration site preference of HIV-1 without any discernible effects during the late steps of the virus life cycle. Surprisingly, the A77V mutant virus maintained the ability to replicate in monocyte-derived macrophages, primary CD4
+
T cells, and humanized mice at a level comparable to that for the wild-type (WT) virus. Nonetheless, revertant viruses that restored the WT CA sequence and hence CA binding to CPSF6 emerged in three out of four A77V-infected animals. These results suggest that the optimal interaction of CA with CPSF6, though not absolutely essential for HIV-1 replication in physiologically relevant settings, confers a significant fitness advantage to the virus and thus is strictly conserved among naturally circulating HIV-1 strains.

IMPORTANCE
CPSF6 interacts with the HIV-1 capsid (CA) protein and has been implicated in nuclear entry and integration targeting. Preservation of CPSF6-CA binding across various HIV-1 strains suggested that the optimal interaction between CA and CPSF6 is critical during HIV-1 replication
in vivo
. Here, we identified a novel HIV-1 capsid mutant that reduces binding to CPSF6, is largely independent from the known cofactors for nuclear entry, and alters integration site preference. Despite these changes, virus carrying this mutation replicated in humanized mice at levels indistinguishable from those of the wild-type virus. However, in the majority of the animals, the mutant virus reverted back to the wild-type sequence, hence restoring the wild-type level of CA-CPSF6 interactions. These results suggest that optimal binding of CA to CPSF6 is not absolutely essential for HIV-1 replication
in vivo
but provides a fitness advantage that leads to the widespread usage of CPSF6 by HIV-1
in vivo
.
Repair of a Mutation Disrupting the Guinea Pig Cytomegalovirus Pentameric Complex Acquired during Fibroblast Passage Restores Pathogenesis in Immune-Suppressed Guinea Pigs and in the Context of Congenital Infection
Authors: McVoy Michael A. , Wang Jian Ben , Dittmer Dirk P. , Bierle Craig J. , Swanson Elizabeth C. , Fernández-Alarcón Claudia , Hernandez-Alvarado Nelmary , Zabeli Jason C. , Schleiss Mark R. 
Published: June 2016

ABSTRACT

Guinea pig cytomegalovirus (GPCMV) provides a valuable model for congenital cytomegalovirus transmission. Salivary gland (SG)-passaged stocks of GPCMV are pathogenic, while tissue culture (TC) passage in fibroblasts results in attenuation. Nonpathogenic TC-derived virus N13R10 (cloned as a bacterial artificial chromosome [BAC]) has a 4-bp deletion that disrupts
GP129
, which encodes a subunit of the GPCMV pentameric complex (PC) believed to govern viral entry into select cell types, and
GP130
, an overlapping open reading frame (ORF) of unknown function. To determine if this deletion contributes to attenuation of N13R10, markerless gene transfer in
Escherichia coli
was used to construct virus r129, a variant of N13R10 in which the 4-bp deletion is repaired. Virions from r129 were found to contain GP129 as well as two other PC subunit proteins, GP131 and GP133, whereas these three PC subunits were absent from N13R10 virions. Replication of r129 in fibroblasts appeared unaltered compared to that of N13R10. However, following experimental challenge of immunocompromised guinea pigs, r129 induced significant weight loss, longer duration of viremia, and dramatically higher (up to 1.5 × 10
6
-fold) viral loads in blood and end organs compared to N13R10. In pregnant guinea pigs, challenge with doses of r129 virus of ≥5 × 10
6
PFU resulted in levels of maternal viremia, congenital transmission, pup viral loads, intrauterine growth restriction, and pup mortality comparable to that induced by pathogenic SG virus, although higher doses of r129 were required. These results suggest that the
GP129-GP130
mutation is a significant contributor to attenuation of N13R10, likely by abrogating expression of a functional PC.

IMPORTANCE
Tissue culture adaptation of cytomegaloviruses rapidly selects for mutations, deletions, and rearrangements in the genome, particularly for viruses passaged in fibroblast cells. Some of these mutations are focused in the region of the genome encoding components of the pentameric complex (PC), in particular homologs of human cytomegalovirus (HCMV) proteins UL128, UL130, and UL131A. These mutations can attenuate the course of infection when the virus is reintroduced into animals for vaccine and pathogenesis studies. This study demonstrates that a deletion that arose during the process of tissue culture passage can be repaired, with subsequent restoration of pathogenicity, using BAC-based mutagenesis. Restoration of pathogenicity by repair of a frameshift mutation in GPCMV gene
GP129
using this approach provides a valuable genetic platform for future studies using the guinea pig model of congenital CMV infection.