Complete genome sequences of three Prunus-infecting nepoviruses: apricot latent ringspot virus, myrobalan latent ringspot virus, and a novel virus from smooth stone peach (Prunus mira Koehne).

The complete genome sequences of two poorly studied Prunus-infecting nepoviruses, apricot latent ringspot virus (ALRSV) and myrobalan latent ringspot virus (MLRSV) were determined, confirming that they are members of subgroup C. Serological, biological, and molecular data, in particular a low level (58.8%) of amino acid sequence identity in the coat protein, suggest that ALRSV and MLRSV should be considered taxonomically distinct. In addition, data mining of public RNASeq data from wild and ornamental Prunus identified two contigs representing the nearly complete genome of a new subgroup A nepovirus from a smooth stone peach (Prunus mira) dataset (SRR8369794) from the Himalayas, for which the name "Prunus mira virus A" is proposed.

Identification of two novel putative satellite RNAs with hammerhead structures in the virome of French and Spanish carrot samples.

Carrot virome analysis using high-throughput sequencing revealed the presence of two RNA molecules with properties of satellite RNAs that are homologous to the satellite RNA of cereal yellow dwarf virus-RPV (CYDV-RPV). Satellite 1 is 298 nt long, while satellite 2 is 368 nt long. Their positive and negative genome strands contain hammerhead ribozymes similar to those found in other self-cleaving satellite RNAs. While both satellites were detected in Spanish carrot populations, only satellite 2 was found in French carrot populations. The most likely helper virus for these two satellites is carrot red leaf virus (CtRLV), which, like CYDV-RPV, is a polerovirus.

Influence of dielectric layer thickness on charge injection, accumulation and transport phenomena in thin silicon oxynitride layers: a nanoscale study.

Charge injection and retention in thin dielectric layers remain critical issues due to the great number of failure mechanisms they inflict. Achieving a better understanding and control of charge injection, trapping and transport phenomena in thin dielectric films is of high priority aiming at increasing lifetime and improving reliability of dielectric parts in electronic and electrical devices. Thermal silica is an excellent dielectric but for many of the current technological developments more flexible processes are required for synthesizing high quality dielectric materials such as amorphous silicon oxynitride layers using plasma methods. In this article, the studied dielectric layers are plasma deposited SiO x N y . Independently on the layer thickness, they are structurally identical: optically transparent, having the same refractive index, equal to the one of thermal silica. Influence of the dielectric film thickness on charging phenomena in such layers is investigated at nanoscale using Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy. The main effect of the dielectric film thickness variation concerns the charge flow in the layer during the charge injection step. According to the SiO x N y layer thickness two distinct trends of the measured surface potential and current are found, thus defining ultrathin (up to 15 nm thickness) and thin (15-150 nm thickness) layers. Nevertheless, analyses of KPFM surface potential measurements associated with results from finite element modeling of the structures show that the dielectric layer thickness has weak influence on the amount of injected charge and on the decay dynamics, meaning that pretty homogeneous layers can be processed. The charge penetration depth in such dielectric layers is evaluated to 10 nm regardless the dielectric thickness.

Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1.

Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annotation revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name "Grapevine polerovirus 1" is proposed.

Complete genome sequence of cherry virus T, a novel cherry-infecting tepovirus.

Double-stranded RNA and total RNA purified from sour cherry leaves (Prunus cerasus, cv. Amarelka Chvalkovicka) was analyzed by high-throughput sequencing. BLAST annotation identified contigs with homology to several already known cherry-infecting viruses (prune dwarf virus, prunus necrotic ringspot virus, prunus virus F, little cherry virus 1) as well as contigs with sequences more distantly related to those of members of the family Betaflexiviridae and in particular to prunus virus T of the genus Tepovirus. The full genome sequence of a putative virus (6,847 nucleotides [nt]; GenBank no. MT090966) was assembled and completed at the genome ends. The genome has a typical tepovirus organization, containing three overlapping open reading frames (ORFs), encoding a replication-associated protein, a movement protein and a capsid protein, respectively. Both its genome organization and its phylogenetic relationships show that the virus belongs to the genus Tepovirus, but considering the species demarcation criteria for the family Betaflexiviridae, it appears to represent a novel virus species, and we propose the name "cherry virus T" (ChVT) for this virus.

Sentinel lymph node biopsy without axillary lymphadenectomy after neoadjuvant chemotherapy is accurate and safe for selected patients: the GANEA 2 study.

PURPOSE: GANEA2 study was designed to assess accuracy and safety of sentinel lymph node (SLN) after neo-adjuvant chemotherapy (NAC) in breast cancer patients. METHODS: Early breast cancer patients treated with NAC were included. Before NAC, patients with cytologically proven node involvement were allocated into the pN1 group, other patient were allocated into the cN0 group. After NAC, pN1 group patients underwent SLN and axillary lymph node dissection (ALND); cN0 group patients underwent SLN and ALND only in case of mapping failure or SLN involvement. The main endpoint was SLN false negative rate (FNR). Secondary endpoints were predictive factors for remaining positive ALND and survival of patients treated with SLN alone. RESULTS: From 2010 to 2014, 957 patients were included. Among the 419 patients from the cN0 group treated with SLN alone, one axillary relapse occurred during the follow-up. Among pN1 group patients, with successful mapping, 103 had a negative SLN. The FNR was 11.9% (95% CI 7.3-17.9%). Multivariate analysis showed that residual breast tumor size after NAC ≥ 5 mm and lympho-vascular invasion remained independent predictors for involved ALND. For patients with initially involved node, with negative SLN after NAC, no lympho-vascular invasion and a remaining breast tumor size 5 mm, the risk of a positive ALND is 3.7% regardless the number of SLN removed. CONCLUSION: In patients with no initial node involvement, negative SLN after NAC allows to safely avoid an ALND. Residual breast tumor and lympho-vascular invasion after NAC allow identifying patients with initially involved node with a low risk of ALND involvement.

Impact of a gestational exposure to diesel exhaust on offspring gonadal development: experimental study in the rabbit.

The aim of the present work was to address experimentally the possible impact of exposure to air pollution during gestation on the differentiation and function of the gonads of the offspring using a rabbit model. Rabbits were exposed daily to diluted diesel exhaust gas or filtered air from the 3rd until the 27th day of gestation, during which time germ cells migrate in genital ridges and divide, and fetal sex is determined. Offspring gonads were collected shortly before birth (28th day of gestation) or after puberty (7.5 months after birth). The structure of the gonads was analyzed by histological and immunohistological methods. Serum concentrations of testosterone and anti-Müllerian hormone were determined using ELISA. The morphology and the endocrine function of the gonads collected just at the arrest of the exposure were similar in polluted and control animals in both sexes. No differences were observed as well in gonads collected after puberty. Sperm was collected at the head of the epididymis in adults. Sperm motility and DNA fragmentation were measured. Among all parameters analyzed, only the sperm DNA fragmentation rate was increased three-fold in exposed males. Mechanisms responsible for these modifications and their physiological consequences are to be further clarified.

Biological and Genetic Characterization of New and Known Necroviruses Causing an Emerging Systemic Necrosis Disease of Corn Salad (Valerianella locusta) in France.

An emerging systemic necrosis disease of corn salad was first observed in the Nantes region of France in the late 2000s. Classical virology and high-throughput sequencing approaches demonstrated that the disease is associated with four different necroviruses: tobacco necrosis virus A (TNVA), tobacco necrosis virus D (TNVD), olive mild mosaic virus (OMMV), and a novel recombinant Alphanecrovirus for which the name corn salad necrosis virus (CSNV) is proposed. Satellite tobacco necrosis virus was also frequently observed. Koch's postulates were completed for all four agents, each one alone being able to cause systemic necrosis of varying severity in corn salad. OMMV was the most frequently observed virus and causes the most severe symptoms. TNVA was the second, both in terms of prevalence and symptom severity while TNVD and CSNV were only rarely observed and caused the less severe symptoms. The emergence of this systemic disease may have been favored by the short and repeated cropping cycles used for corn salad, possibly allowing the selection of necrovirus isolates with an improved ability to systemically invade this specialty crop.

Ovarian suppression failure during GnRH agonist treatment: A report of three breast cancer patients.

In premenopausal women treated for breast cancer, endocrine therapy combining an aromatase inhibitor (AI) and a gonadotropin-releasing hormone (GnRH) agonist (GA) for ovarian suppression may be indicated in high-risk or in metastatic cancer. AIs are effective in premenopausal women only when ovarian estrogen production is suppressed, a state achievable through the use of GAs. However, a complete suppression sometimes proves elusive. We report here three cases of ovarian suppression failure in premenopausal breast cancer patients who received adjuvant AI+GA. Frequency of GA administration, BMI, and young age could affect gonadotropin suppression and may be implied in these failures. Clinical monitoring of these patients is advisable, and hormone assays and pelvic ultrasound should be performed in case of symptoms of estrogen activity.

[Use of hydroxychloroquine and prednisone in the presence of serum autoimmunity in female infertility]. / Utilisation de l'hydroxychloroquine et de la prednisone en présence d'une auto-immunité sérique dans l'infertilité féminine.

OBJECTIVE: Presence of non-specific autoimmunity (antinuclear antibodies without antigenic specificities and/or antiphospholipid antibodies without criteria of antiphospholipid syndrome) seems to be associated with unexplained female infertility. The objective is to study the characteristics of patients who undergone treatment for non-specific antibodies in Medically Assisted Procreation (MAP). METHODS: Ten patients were prospectively followed at MAP center of Grenoble University Hospital. Patient characteristics were collected and evaluated. All patients had a consultation in internal medicine unit as well as an autoimmune assessment (antinuclear antibodies, APL especially) in search of defined autoimmune disease (exclusion criterion). The treatments undertaken were at clinician' discretion. RESULTS: One patient received quadritherapy (heparin, platelet antiaggregant, prednisone and hydroxychloroquine), 5 received triple therapy, 3 had dual therapy, and one patient had prednisone only. The 10 patients had a pregnancy under treatment, 8 of which were completed without complications. The control of autoimmunity under treatment appears to show a decrease in serum antibody levels. Tolerance was good (delayed hypersensitivity to hydrochloroquine resulted in discontinuation of therapy in only one patient). CONCLUSION: The presence of non-specific serum autoimmunity in a context of infertility appears to be pathogenic and immunomodulatory treatments are clinically and/or biologically effective. A prospective and interventional study with a larger number of patients is needed to assess the efficacy of such treatments in patients with unexplained infertility.

Adsorption properties of BSA and DsRed proteins deposited on thin SiO2 layers: optically non-absorbing versus absorbing proteins.

Protein adsorption on solid surfaces is of interest for many industrial and biomedical applications, where it represents the conditioning step for micro-organism adhesion and biofilm formation. To understand the driving forces of such an interaction we focus in this paper on the investigation of the adsorption of bovine serum albumin (BSA) (optically non-absorbing, model protein) and DsRed (optically absorbing, naturally fluorescent protein) on silica surfaces. Specifically, we propose synthesis of thin protein layers by means of dip coating of the dielectric surface in protein solutions with different concentrations (0.01-5.0 g l-1). We employed spectroscopic ellipsometry as the most suitable and non-destructive technique for evaluation of the protein layers' thickness and optical properties (refractive index and extinction coefficient) after dehydration, using two different optical models, Cauchy for BSA and Lorentz for DsRed. We demonstrate that the thickness, the optical properties and the wettability of the thin protein layers can be finely controlled by proper tuning of the protein concentration in the solution. These results are correlated with the thin layer morphology, investigated by AFM, FTIR and PL analyses. It is shown that the proteins do not undergo denaturation after dehydration on the silica surface. The proteins arrange themselves in a lace-like network for BSA and in a rod-like structure for DsRed to form mono- and multi-layers, due to different mechanisms driving the organization stage.

Tolerance of latissimus dorsi in immediate breast reconstruction without implant to radiotherapy.

INTRODUCTION: Immediate breast reconstruction (IBR) improves the quality of life of patients who undergo mastectomy. The latissimus dorsi flap (LDF) method provides particularly good aesthetic results, but its tolerance to subsequent radiotherapy remains unclear. We thus sought to assess tolerance and esthetic results and satisfaction, as reported by patients who underwent IBR by LDF with or without subsequent radiotherapy. MATERIALS AND METHODS: We performed a retrospective case-control study in a population of women who were diagnosed with breast cancer between January 1999 and January 2014 and who had mastectomies with IBR by LDF without prostheses. We paired 29 patients who needed postoperative radiotherapy to 58 control patients who did not. These patients responded to a questionnaire to evaluate tolerance and their satisfaction with the aesthetic results of the reconstruction. RESULTS: In total, 86.2% of all patients reported "very good" or "good" overall aesthetic satisfaction. Consistency was judged as "very good" or "good" by 82.7% of control patients and by 93.1% of case patients. No statistically significant differences were identified between the two groups with regard to reconstruction results. The number of surgical procedures needed did not differ significantly between the two groups. CONCLUSION: In our study, IBR by LDF appeared to have excellent tolerance to subsequent radiotherapy, the latter having no impact on patient aesthetic satisfaction. Our results suggest that the possibility of postoperative radiotherapy should not prevent physicians from proposing this method to women who are candidates for it.

Methodology for extraction of space charge density profiles at nanoscale from Kelvin probe force microscopy measurements.

To understand the physical phenomena occurring at metal/dielectric interfaces, determination of the charge density profile at nanoscale is crucial. To deal with this issue, charges were injected applying a DC voltage on lateral Al-electrodes embedded in a SiN x thin dielectric layer. The surface potential induced by the injected charges was probed by Kelvin probe force microscopy (KPFM). It was found that the KPFM frequency mode is a better adapted method to probe accurately the charge profile. To extract the charge density profile from the surface potential two numerical approaches based on the solution to Poisson's equation for electrostatics were investigated: the second derivative model method, already reported in the literature, and a new 2D method based on the finite element method (FEM). Results highlight that the FEM is more robust to noise or artifacts in the case of a non-flat initial surface potential. Moreover, according to theoretical study the FEM appears to be a good candidate for determining charge density in dielectric films with thicknesses in the range from 10 nm to 10 µm. By applying this method, the charge density profile was determined at nanoscale, highlighting that the charge cloud remains close to the interface.

Genomic alterations and radioresistance in breast cancer: an analysis of the ProfiLER protocol.

BACKGROUND: Breast cancer (BC) patients with comparable prognostic features have heterogeneous outcomes, party related to a possible radiotherapy resistance leading to local-regional recurrences (LRR). The objective of the present study was to identify predictive molecular biomarkers of LRR of BC. PATIENTS AND METHODS: Genetic profile of 146 BC patients' tumours included in the ProfiLER clinical trial (NC01774409) between 2013 and 2016 were analysed using next-generation-sequencing and comparative-genomic-hybridization tests. Patients and tumour characteristics were retrospectively collected and analysed for association with genomic rearrangements (mutations, amplification, deletions). Only gene alterations observed in >3% of the tumours were selected. RESULTS: A total of 193 genomic rearrangements were identified, and 16 were observed in >3% of tumours. One was statistically correlated to the risk of local relapse. A median loco-regional progression-free survival (LRPFS) of 23.6 years was reported for PIK3CA mutation carriers (n = 31, 21.2%) versus 9.9 years for PIK3CA wild-type patients (HR 0.27, 95% CI 0.12-0.65, P = 0.002 in univariate analysis). PIK3CA mutation was identified as an independent protective factor on LRR using multivariate analysis (HR 0.29, 95% CI 0.09-0.99, P = 0.047). All other mutations, amplifications or deletions were not found associated with LRPFS. CONCLUSION: PIK3CA mutation was associated with a lower risk of local relapse in this population of BCs. This is consistent with recent studies suggesting PIK3CA to be part of biological pathways impacting the radiosensitivity.

Nanoscale investigations on interchain organization in thin films of polymer-liquid crystal blend.

Optimized nanomorphology in organic thin active layers is crucial for good performance in organic solar cells. However, the relation between morphology and electronic properties at nanoscale remains not completely understood. Here, we study the effect of film thickness and temperature annealing on the ordering of poly(3-hexylthiophene) chains when the polymer is blended with a columnar liquid crystalline molecule. Electronic absorption, atomic force microscopy measurements, and Raman spectroscopy show that morphology and chain ordering of the blend depend on the film thickness. We highlight the benefit of using a liquid crystal in organic blends, opening the way to use simple processing methods for the fabrication of organic electronic devices.

Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine.

The complete nucleotide sequence of an isolate of grapevine satellite virus (GV-Sat) was determined by next-generation sequencing (NGS) and compared with the single available complete sequence. The NGS data unexpectedly provided evidence for the existence of multimeric forms of GV-Sat, which were experimentally confirmed, allowing the redefinition of GV-Sat genomic ends.

Increased mean corpuscular haemoglobin concentration: artefact or pathological condition?

INTRODUCTION: In daily practice in haematology laboratories, spurious increased MCHC induces an analytical alarm and needs prompt corrective action to ensure delivery of the right results to the clinicians. The aim of this study was to establish a 'decision tree' using the new parameters red blood cells (RBC-O) and haemoglobin (HGB-O) from the Sysmex XN-10 RET obtained by flow cytometry to deliver appropriate results. METHODS: From 128 unknown patients with MCHC > 365 g/L, all erythrocyte parameters including reticulocyte parameters were measured and analysed in parallel with blood smears, chemistry index and osmolarity. Differences between optical parameters (RBC-O, HGB-O) and usual parameters (RBC, HGB) obtained by impedance and photometry were reported also. RESULTS: Four groups were defined from observations: -RBC agglutination (n = 22); -optical interference (n = 17); -RBC disease (n = 18); and -others (n = 71). The use of RBC-O and HGB-O permitted efficient correction of the abnormalities when RBC agglutination and/or optical interference were present in 36 of 39 patients. Reticulocyte parameters permitted to elaborate an RBC score that allowed a highly sensitive detection of RBC disease patients (17/18). CONCLUSION: Based on new parameters, we propose a 'decision tree' that delivers time savings and supports biological interpretation in case of elevated MCHC.

Treatment with Hizentra in patients with primary and secondary immunodeficiencies: a real-life, non-interventional trial.

BACKGROUND: Although Hizentra is indicated for immunoglobulin replacement therapy in patients with primary and secondary immunodeficiencies, phase III trials have focused on patients with primary immunodeficiencies. In this 9-month, real-life, prospective, non-interventional, longitudinal, multicenter study of patients with primary and secondary immunodeficiencies in France, treatment modalities (primary endpoint), efficacy, safety, tolerability, quality of life, and treatment satisfaction were evaluated using descriptive statistics. RESULTS: Starting in January 2012, 117 patients were enrolled (99 adults, 18 children). Secondary immunodeficiencies were present in 48.7 % of patients. At follow-up, injections were administered every 7 days in 92.2 % of patients. Nine patients (7.8 %) were taking Hizentra every 10-14 days. The median dose of Hizentra administered was 0.1 g/kg/injection. Fifty-six patients were administered doses <0.1 g/kg/injection and 13 patients were administered doses >0.2 g/kg/injection. Mean trough IgG titers were 9.0 ± 3.3 g/L (median 8.3 g/L). The mean yearly rate of infection was 1.2 ± 1.9. Mean scores on the Short Form-36 physical and mental component summaries were 46.3 ± 10.0 and 46.6 ± 9.3, respectively. Scores on the Treatment Satisfaction Questionnaire for Medication ranged from 69.9 ± 19.9 to 88.3 ± 21.2 depending on the domain. Treatment with Hizentra was well tolerated. No single drug-related systemic reaction occurred in more than one patient and few local reactions were reported (n = 5). CONCLUSIONS: Under real-life conditions and in a cohort that included patients with primary and secondary immunodeficiencies, treatment with Hizentra was effective and well tolerated and patients were generally satisfied with the treatment.