bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of competition between Vicia faba and Camelina sativa as a model weed in breeding for organic conditions
Authors: Ghaouti L , Schierholt A , Link W 
Published: January 2016

SummaryWeeds can have a detrimental effect on faba bean (Vicia faba) crops in organic farming. Breeding for competitive cultivars is one option for weed control in organic conditions. The aim of this study was to analyse the impact of heterozygosity and heterogeneity levels and plant height on the competitive ability of faba bean genotypes. A set of 24 genotypes, classified as genotype groups (eight inbred lines, eight polycross progenies, two inbred line bulks, two hybrid bulks and four controls), was tested under two treatments: with and without a model weed. Each group of genotypes was equally composed of tall and short genotypes. The competitive ability of the faba bean genotypes was tested with Camelina sativa (false flax) as the model weed in two German locations over the course of 2 years. Yield loss due to weed competition, as recorded per faba bean genotype, was mainly dependent on the heterozygosity level of the genotypes; hybrid bulks were the most competitive genotype group with an average loss of yield of only 6%, whereas the inbred lines were the least competitive genotype group and recorded an average yield loss of 35%. Within the genotype group, no correlations were found between either the yield performance of the genotypes or their plant height and their competitive responses. The competitive ability of faba bean against weeds was mainly determined by their level of heterozygosity; thus, highly heterozygous cultivars should be promoted for breeding.
Rate of utilization of a given fraction of W′ (the curvature constant of the power–duration relationship) does not affect fatigue during severe‐intensity exercise
Authors: de Souza Kristopher Mendes , Dekerle Jeanne , Salvador Paulo Cesar do Nascimento , de Lucas Ricardo Dantas , Guglielmo Luiz Guilherme Antonacci , Greco Camila Coelho , Denadai Benedito Sérgio 
Published: January 2016

New Findings

What is the central question of this study?
Does the rate of utilization of W′ (the curvature constant of the power–duration relationship) affect fatigue during severe‐intensity exercise?

What is the main finding and its importance?
The magnitude of fatigue after two severe‐intensity exercises designed to deplete the same fraction of W′ (70%) at two different rates of utilization (fast versus slow) was similar after both exercises. Moreover, the magnitude of fatigue was related to critical power (CP), supporting the contention that CP is a key determinant in fatigue development during high‐intensity exercise. Thus, the CP model is a suitable approach to investigate fatigue mechanisms during high‐intensity exercise.

The depletion of W′ (the curvature constant of the power–duration relationship) seems to contribute to fatigue during severe‐intensity exercise. Therefore, the aim of this study was to determine the effect of a fast versus a slow rate of utilization of W′ on the occurrence of fatigue within the severe‐intensity domain. Fifteen healthy male subjects performed tests to determine the critical power, W′ and peak torque in the control condition (TCON) and immediately after two fatiguing work rates (THREE and TEN) set to deplete 70% W′ in either 3 (TTHREE) or 10 min (TTEN). The TTHREE and TTEN were significantly reduced (F = 19.68, P = 0.01) in comparison to TCON. However, the magnitude of reduction in peak torque (TTHREE = −19.8 ± 10.1% versus TTEN = −16.8 ± 13.3%) was the same in the two fatiguing exercises (t = −0.76, P = 0.46). There was a significant inverse relationship between the critical power and the reduction in peak torque during both THREE (r = −0.49, P = 0.03) and TEN (r = −0.62, P = 0.02). In contrast, the W′ was not significantly correlated with the reduction in peak torque during both THREE (r = −0.14, P = 0.33) and TEN (r = −0.30, P = 0.10). Thus, fatigue following severe‐intensity exercises performed at different rates of utilization of W′ was similar when the same work was done above the critical power (i.e. same amount of W′ used).
Commentary: Impact of CLSI Breakpoint Changes on Microbiology Laboratories and Antimicrobial Stewardship Programs
Authors: Heil Emily L. , Johnson J. Kristie 
Published: January 2016

ABSTRACT

In 2010, the Clinical and Laboratory Standards Institute (CLSI) lowered the MIC breakpoints for many beta-lactam antibiotics to enhance detection of known resistance among
Enterobacteriaceae
. The decision to implement these new breakpoints, including the changes announced in both 2010 and 2014, can have a significant impact on both microbiology laboratories and antimicrobial stewardship programs. In this commentary, we discuss the changes and how implementation of these updated CLSI breakpoints requires partnership between antimicrobial stewardship programs and the microbiology laboratory, including data on the impact that the changes had on antibiotic usage at our own institution.
Comparison of Nonculture Blood-Based Tests for Diagnosing Invasive Aspergillosis in an Animal Model
Authors: White P. Lewis , Wiederhold Nathan P. , Loeffler Juergen , Najvar Laura K. , Melchers Willem , Herrera Monica , Bretagne Stephane , Wickes Brian , Kirkpatrick William R. , Barnes Rosemary A. , Donnelly J. Peter , Patterson Thomas F. 
Published: January 2016

ABSTRACT

The European
Aspergillus
PCR Initiative (EAPCRI) has provided recommendations for the PCR testing of whole blood (WB) and serum/plasma. It is important to test these recommended protocols on nonsimulated “
in vivo
” specimens before full clinical evaluation. The testing of an animal model of invasive aspergillosis (IA) overcomes the low incidence of disease and provides experimental design and control that is not possible in the clinical setting. Inadequate performance of the recommended protocols at this stage would require reassessment of methods before clinical trials are performed and utility assessed. The manuscript describes the performance of EAPCRI protocols in an animal model of invasive aspergillosis. Blood samples taken from a guinea pig model of IA were used for WB and serum PCR. Galactomannan and β-
d
-glucan detection were evaluated, with particular focus on the timing of positivity and on the interpretation of combination testing. The overall sensitivities for WB PCR, serum PCR, galactomannan, and β-
d
-glucan were 73%, 65%, 68%, and 46%, respectively. The corresponding specificities were 92%, 79%, 80%, and 100%, respectively. PCR provided the earliest indicator of IA, and increasing galactomannan and β-
d
-glucan values were indicators of disease progression. The combination of WB PCR with galactomannan and β-
d
-glucan proved optimal (area under the curve [AUC], 0.95), and IA was confidently diagnosed or excluded. The EAPRCI-recommended PCR protocols provide performance comparable to commercial antigen tests, and clinical trials are warranted. By combining multiple tests, IA can be excluded or confirmed, highlighting the need for a combined diagnostic strategy. However, this approach must be balanced against the practicality and cost of using multiple tests.
Permissive Sense and Antisense Transcription from the 5′ and 3′ Long Terminal Repeats of Human T-Cell Leukemia Virus Type 1
Authors: Laverdure Sylvain , Polakowski Nicholas , Hoang Kimson , Lemasson Isabelle 
Published: January 2016

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus, and, as such, its genome becomes chromosomally integrated following infection. The resulting provirus contains identical 5′ and 3′ peripheral long terminal repeats (LTRs) containing bidirectional promoters. Antisense transcription from the 3′ LTR regulates expression of a single gene,
hbz
, while sense transcription from the 5′ LTR controls expression of all other viral genes, including
tax
. Both the HBZ and Tax proteins are implicated in the development of adult T-cell leukemia (ATL), a T-cell malignancy caused by HTLV-1 infection. However, these proteins appear to harbor opposing molecular functions, indicating that they may act independently and at different time points prior to leukemogenesis. Here, we used bidirectional reporter constructs to test whether transcriptional interference serves as a mechanism that inhibits simultaneous expression of Tax and HBZ. We found that sense transcription did not interfere with antisense transcription from the 3′ LTR and vice versa, even with strong transcription emanating from the opposing direction. Therefore, bidirectional transcription across the provirus might not restrict
hbz
or
tax
expression. Single-cell analyses revealed that antisense transcription predominates in the absence of Tax, which transactivates viral sense transcription. Interestingly, a population of Tax-expressing cells exhibited antisense but not activated sense transcription. Consistent with the ability of Tax to induce cell cycle arrest, this population was arrested in G
0
/G
1
phase. These results imply that cell cycle arrest inhibits Tax-mediated activation of sense transcription without affecting antisense transcription, which may be important for long-term viral latency.

IMPORTANCE
The chromosomally integrated form of the retrovirus human T-cell leukemia virus type 1 (HTLV-1) contains identical DNA sequences, known as long terminal repeats (LTRs), at its 5′ and 3′ ends. The LTRs modulate transcription in both forward (sense) and reverse (antisense) directions. We found that sense transcription from the 5′ LTR does not interfere with antisense transcription from the 3′ LTR, allowing viral genes encoded on opposite DNA strands to be simultaneously transcribed. Two such genes are
tax
and
hbz
, and while they are thought to function at different times during the course of infection to promote leukemogenesis of infected T cells, our results indicate that they can be simultaneously transcribed. We also found that the ability of Tax to induce cell cycle arrest inhibits its fundamental function of activating viral sense transcription but does not affect antisense transcription. This regulatory mechanism may be important for long-term HTLV-1 infection.
Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1
Authors: Baer Alan , Lundberg Lindsay , Swales Danielle , Waybright Nicole , Pinkham Chelsea , Dinman Jonathan D. , Jacobs Jonathan L. , Kehn-Hall Kylene 
Published: January 2016

ABSTRACT

Venezuelan equine encephalitis virus (VEEV) is a previously weaponized arthropod-borne virus responsible for causing acute and fatal encephalitis in animal and human hosts. The increased circulation and spread in the Americas of VEEV and other encephalitic arboviruses, such as eastern equine encephalitis virus and West Nile virus, underscore the need for research aimed at characterizing the pathogenesis of viral encephalomyelitis for the development of novel medical countermeasures. The host-pathogen dynamics of VEEV Trinidad donkey-infected human astrocytoma U87MG cells were determined by carrying out RNA sequencing (RNA-Seq) of poly(A) and mRNAs. To identify the critical alterations that take place in the host transcriptome following VEEV infection, samples were collected at 4, 8, and 16 h postinfection and RNA-Seq data were acquired using an Ion Torrent PGM platform. Differential expression of interferon response, stress response factors, and components of the unfolded protein response (UPR) was observed. The protein kinase RNA-like endoplasmic reticulum kinase (PERK) arm of the UPR was activated, as the expression of both activating transcription factor 4 (ATF4) and CHOP (DDIT3), critical regulators of the pathway, was altered after infection. Expression of the transcription factor early growth response 1 (EGR1) was induced in a PERK-dependent manner. EGR1
−/−
mouse embryonic fibroblasts (MEFs) demonstrated lower susceptibility to VEEV-induced cell death than isogenic wild-type MEFs, indicating that EGR1 modulates proapoptotic pathways following VEEV infection. The influence of EGR1 is of great importance, as neuronal damage can lead to long-term sequelae in individuals who have survived VEEV infection.

IMPORTANCE
Alphaviruses represent a group of clinically relevant viruses transmitted by mosquitoes to humans. In severe cases, viral spread targets neuronal tissue, resulting in significant and life-threatening inflammation dependent on a combination of virus-host interactions. Currently there are no therapeutics for infections cause by encephalitic alphaviruses due to an incomplete understanding of their molecular pathogenesis. Venezuelan equine encephalitis virus (VEEV) is an alphavirus that is prevalent in the Americas and that is capable of infecting horses and humans. Here we utilized next-generation RNA sequencing to identify differential alterations in VEEV-infected astrocytes. Our results indicated that the abundance of transcripts associated with the interferon and the unfolded protein response pathways was altered following infection and demonstrated that early growth response 1 (EGR1) contributed to VEEV-induced cell death.
DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation
Authors: Thulasi Raman Sathya N. , Liu Guanqun , Pyo Hyun Mi , Cui Ya Cheng , Xu Fang , Ayalew Lisanework E. , Tikoo Suresh K. , Zhou Yan 
Published: January 2016

ABSTRACT
DDX3 belongs to the DEAD box RNA helicase family and is a multifunctional protein affecting the life cycle of a variety of viruses. However, its role in influenza virus infection is unknown. In this study, we explored the potential role of DDX3 in influenza virus life cycle and discovered that DDX3 is an antiviral protein. Since many host proteins affect virus life cycle by interacting with certain components of the viral machinery, we first verified whether DDX3 has any viral interaction partners. Immunoprecipitation studies revealed NS1 and NP as direct interaction partners of DDX3. Stress granules (SGs) are known to be antiviral and do form in influenza virus-infected cells expressing defective NS1 protein. Additionally, a recent study showed that DDX3 is an important SG-nucleating factor. We thus explored whether DDX3 plays a role in influenza virus infection through regulation of SGs. Our results showed that SGs were formed in infected cells upon infection with a mutant influenza virus lacking functional NS1 (del NS1) protein, and DDX3 colocalized with NP in SGs. We further determined that the DDX3 helicase domain did not interact with NS1 and NP; however, it was essential for DDX3 localization in virus-induced SGs. Knockdown of DDX3 resulted in impaired SG formation and led to increased virus titers. Taken together, our results identified DDX3 as an antiviral protein with a role in virus-induced SG formation.

IMPORTANCE
DDX3 is a multifunctional RNA helicase and has been reported to be involved in regulating various virus life cycles. However, its function during influenza A virus infection remains unknown. In this study, we demonstrated that DDX3 is capable of interacting with influenza virus NS1 and NP proteins; DDX3 and NP colocalize in the del NS1 virus-induced SGs. Furthermore, knockdown of DDX3 impaired SG formation and led to a decreased virus titer. Thus, we provided evidence that DDX3 is an antiviral protein during influenza virus infection and its antiviral activity is through regulation of SG formation. Our findings provide knowledge about the function of DDX3 in the influenza virus life cycle and information for future work on manipulating the SG pathway and its components to fight influenza virus infection.
Amino Acid Substitutions That Affect Receptor Binding and Stability of the Hemagglutinin of Influenza A/H7N9 Virus
Authors: Schrauwen Eefje J. A. , Richard Mathilde , Burke David F. , Rimmelzwaan Guus F. , Herfst Sander , Fouchier Ron A. M. 
Published: January 2016

ABSTRACT
Receptor-binding preference and stability of hemagglutinin have been implicated as crucial determinants of airborne transmission of influenza viruses. Here, amino acid substitutions previously identified to affect these traits were tested in the context of an A/H7N9 virus. Some combinations of substitutions, most notably G219S and K58I, resulted in relatively high affinity for α2,6-linked sialic acid receptor and acid and temperature stability. Thus, the hemagglutinin of the A/H7N9 virus may adopt traits associated with airborne transmission.
Dissecting the Molecular Mechanisms of the Tropism of Varicella-Zoster Virus for Human T Cells
Authors: Sen Nandini , Arvin Ann M. 
Published: January 2016

ABSTRACT
Studies of varicella-zoster virus (VZV) tropism for T cells support their role in viral transport to the skin during primary infection. Multiparametric single-cell mass cytometry demonstrates that, instead of preferentially infecting skin-homing T cells, VZV alters cell signaling and remodels surface proteins to enhance T cell skin trafficking. Viral proteins dispensable in skin, such as that encoded by open reading frame 66, are necessary in T cells. Interference with VZV T cell tropism may offer novel strategies for drug and vaccine design.
Anthropometric markers and their association with incident type 2 diabetes mellitus: which marker is best for prediction? Pooled analysis of four German population-based cohort studies and comparison with a nationwide cohort study
Authors: Hartwig Saskia , Kluttig Alexander , Tiller Daniel , Fricke Julia , Müller Grit , Schipf Sabine , Völzke Henry , Schunk Michaela , Meisinger Christa , Schienkiewitz Anja , Heidemann Christin , Moebus Susanne , Pechlivanis Sonali , Werdan Karl , Kuss Oliver , Tamayo Teresa , Haerting Johannes , Greiser Karin Halina 
Published: January 2016

ObjectiveTo compare the association between different anthropometric measurements and incident type 2 diabetes mellitus (T2DM) and to assess their predictive ability in different regions of Germany.MethodsData of 10 258 participants from 4 prospective population-based cohorts were pooled to assess the association of body weight, body mass index (BMI), waist circumference (WC), waist-to-hip-ratio (WHR) and waist-to-height-ratio (WHtR) with incident T2DM by calculating HRs of the crude, adjusted and standardised markers, as well as providing receiver operator characteristic (ROC) curves. Differences between HRs and ROCs for the different anthropometric markers were calculated to compare their predictive ability. In addition, data of 3105 participants from the nationwide survey were analysed separately using the same methods to provide a nationally representative comparison.ResultsStrong associations were found for each anthropometric marker and incidence of T2DM. Among the standardised anthropometric measures, we found the strongest effect on incident T2DM for WC and WHtR in the pooled sample (HR for 1 SD difference in WC 1.97, 95% CI 1.75 to 2.22, HR for WHtR 1.93, 95% CI 1.71 to 2.17 in women) and in female DEGS participants (HR for WC 2.24, 95% CI 1.91 to 2.63, HR for WHtR 2.10, 95% CI 1.81 to 2.44), whereas the strongest association in men was found for WHR among DEGS participants (HR 2.29, 95% CI 1.89 to 2.78). ROC analysis showed WHtR to be the strongest predictor for incident T2DM. Differences in HR and ROCs between the different markers confirmed WC and WHtR to be the best predictors of incident T2DM. Findings were consistent across study regions and age groups (<65 vs ≥65 years).ConclusionsWe found stronger associations between anthropometric markers that reflect abdominal obesity (ie, WC and WHtR) and incident T2DM than for BMI and weight. The use of these measurements in risk prediction should be encouraged.
Facing the enigma of the vascular network in hepatocellular carcinomas in cirrhotic and non-cirrhotic livers
Authors: Vasuri Francesco , Fittipaldi Silvia , Giunchi Francesca , Monica Melissa , Ravaioli Matteo , Degiovanni Alessio , Bonora Sonia , Golfieri Rita , Bolondi Luigi , Grigioni Walter F , Pasquinelli Gianandrea , D'Errico-Grigioni Antonia 
Published: January 2016

AimsIn this paper we aimed to analyse the typology and the phenotype of the different vascular modifications in human hepatocellular carcinomas (HCCs) with a new immunomorphological and gene expression approach. We also attempted to correlate these modifications with the histological parameters of tumour aggressiveness and the surrounding liver parenchyma.MethodsNinety-six HCCs (from 80 patients) were retrospectively enrolled, 46 occurring in non-cirrhotic livers, and 50 in livers transplanted for cirrhosis. Histopathological analysis, immunohistochemistry for CD34, Nestin and WT1 and RT-PCR for Nestin, transforming growth factor-β1 (TGFβ1) and insulin-like growth factor 1 (IGF1R) mRNA were performed in all nodules.ResultsBy correlating the CD34 and Nestin immunoreactivity in HCC vasculature with the tumorous architecture, we identified four vascular patterns (named from ‘a’ to ‘d’). Each of them was characterised by different expressions of TGFβ1 and IGF1R mRNA. Pattern a showed CD34-positive/Nestin-negative sinusoids, and was prevalent in microtrabecular lesions. Pattern b showed similar morphology and architecture as pattern a, but with Nestin-positive sinusoids and a significant ‘boost’ in IGF1R and TGFβ1 mRNAs. In patterns c and d a progressive sinusoid loss and a gain of newly formed arterioles were seen. Notably, HCCs with pattern a arose more frequently in cirrhosis (p=0.024), and showed lower incidence of microvascular invasion (p=0.002) and infiltration (p=0.005) compared with HCCs with other patterns.ConclusionsAlthough future studies are surely required, the identification of different vascular profiles in HCCs from cirrhotic and non-cirrhotic livers may help clarify the relationship between HCC progression and aggressiveness.
Reticulocyte parameters of delta beta thalassaemia trait, beta thalassaemia trait and iron deficiency anaemia
Authors: Velasco-Rodríguez Diego , Alonso-Domínguez Juan-Manuel , González-Fernández Fernando-Ataúlfo , Villarrubia Jesús , Sopeña María , Abalo Lorena , Ropero Paloma , Martínez-Nieto Jorge , de la Fuente Gonzalo Félix , Cava Fernando 
Published: January 2016

AimsTo analyse the differences in reticulocyte indices between delta beta thalassaemia trait (δβ-TT), beta thalassaemia trait (β-TT) and iron deficiency anaemia (IDA), and to correlate those differences with the physiopathological features of these three types of microcytoses.MethodsWe performed a descriptive study of 428 samples (43 δβ-TT, 179 β-TT and 206 IDA) that were run on Advia 2120 analyser (Siemens). The following reticulocyte indices were assessed: absolute reticulocyte count (ARC), percentage of reticulocytes, mean corpuscular volume of reticulocytes (MCVr), haemoglobin content of reticulocytes (CHr), mean corpuscular haemoglobin concentration of reticulocytes, red blood cell distribution width of reticulocytes (RDWr), haemoglobin distribution width of reticulocytes (HDWr) and reticulocyte subpopulations based on their fluorescence according to mRNA (low (L-R), medium (M-R) and high (H-R)), MCV ratio and MCHC ratio. Correlation between fetal haemoglobin (HbF) and RDWr in patients with thalassaemia was evaluated.ResultsRDWr was significantly higher in δβ-TT compared with β-TT (15.03% vs 13.82%, p<0.001), and so were HDWr (3.65% vs 3.27%, p<0.001), CHr (23.68 vs 22.66 pg, p<0.001) and MCVr (88.3 vs 85.5 fL, p<0.001). A good correlation was observed between HbF and RDWr (r=0.551, p<0.001). IDA subjects have more immature reticulocytes, but less ARC than β-TT, suggesting a certain degree of inefficient erythropoiesis in IDA in comparison with β-TT.ConclusionsPreviously described differences between δβ-TT, β-TT and IDA in the corpuscular indices of mature red blood cell can also be observed in reticulocytes. The degree of anisocytosis in reticulocytes from patients with thalassaemia is correlated with HbF.