bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding Clostridium difficile Colonization
Authors: Crobach Monique J. T. , Vernon Jonathan J. , Loo Vivian G. , Kong Ling Yuan , Péchiné Séverine , Wilcox Mark H. , Kuijper Ed J.
Published: March 2018

Clostridium difficile
is the main causative agent of antibiotic-associated and health care-associated infective diarrhea. Recently, there has been growing interest in alternative sources of
C. difficile
other than patients with
Clostridium difficile
infection (CDI) and the hospital environment. Notably, the role of
C. difficile
-colonized patients as a possible source of transmission has received attention. In this review, we present a comprehensive overview of the current understanding of
C. difficile
colonization. Findings from gut microbiota studies yield more insights into determinants that are important for acquiring or resisting colonization and progression to CDI. In discussions on the prevalence of
C. difficile
colonization among populations and its associated risk factors, colonized patients at hospital admission merit more attention, as findings from the literature have pointed to their role in both health care-associated transmission of
C. difficile
and a higher risk of progression to CDI once admitted.
C. difficile
colonization among patients at admission may have clinical implications, although further research is needed to identify if interventions are beneficial for preventing transmission or overcoming progression to CDI.
NsrA, a Predicted β-Barrel Outer Membrane Protein Involved in Plant Signal Perception and the Control of Secondary Infection in Sinorhizobium meliloti
Authors: Garnerone Anne-Marie , Sorroche Fernando , Zou Lan , Mathieu-Demazière Céline , Tian Chang Fu , Masson-Boivin Catherine , Batut Jacques
Published: March 2018

An ongoing signal exchange fine-tunes the symbiotic interactions between rhizobia and legumes, ensuring the establishment and maintenance of mutualism. In a recently identified regulatory loop, endosymbiotic
Sinorhizobium meliloti
exerts negative feedback on root infection in response to unknown plant cues. Upon signal perception, three bacterial adenylate cyclases (ACs) of the inner membrane, namely, CyaD1, CyaD2, and CyaK, synthesize the second messenger cAMP, which, together with the cAMP-dependent Clr transcriptional activator, activates the expression of genes involved in root infection control. The pathway that links signal perception at the surface of the cell to cytoplasmic cAMP production by ACs was thus far unknown. Here we first show that CyaK is the cognate AC for the plant signal, called signal 1, that was observed previously in mature nodule and shoot extracts. We also show that inactivation of the gene immediately upstream of
cyaK
,
nsrA
(
smb20775
), which encodes a β-barrel protein of the outer membrane, abolished signal 1 perception
ex planta
, whereas
nsrA
overexpression increased signal 1 responsiveness. Inactivation of the
nsrA
gene abolished all Clr-dependent gene expression in nodules and led to a marked hyperinfection phenotype on plants, similar to that of a
cyaD1 cyaD2 cyaK
triple mutant. We suggest that the NsrA protein acts as the (co)receptor for two signal molecules, signal 1 and a hypothetical signal 1′, in mature and young nodules that cooperate in controlling secondary infection in
S. meliloti-Medicago
symbiosis. The predicted topology and domain composition of the NsrA protein hint at a mechanism of transmembrane signaling.

IMPORTANCE
Symbiotic interactions, especially mutualistic ones, rely on a continuous signal exchange between the symbionts. Here we report advances regarding a recently discovered signal transduction pathway that fine-tunes the symbiotic interaction between
S. meliloti
and its
Medicago
host plant. We have identified an outer membrane protein of
S. meliloti
, called NsrA, that transduces
Medicago
plant signals to adenylate cyclases in the inner membrane, thereby triggering a cAMP signaling cascade that controls infection. Besides their relevance for the rhizobium-legume symbiosis, these findings shed light on the mechanisms of signal perception and transduction by adenylate cyclases and transmembrane signaling in bacteria.
Performance of a Highly Sensitive Mycobacterium tuberculosis Complex Real-Time PCR Assay for Diagnosis of Pulmonary Tuberculosis in a Low-Prevalence Setting: a Prospective Intervention Study
Authors: Vinuesa Víctor , Borrás Rafael , Briones María Luisa , Clari María Ángeles , Cresencio Vicenta , Giménez Estela , Muñoz Carmen , Oltra Rosa , Servera Emilio , Scheelje Talia , Tornero Carlos , Navarro David
Published: March 2018

The potential impact of routine real-time PCR testing of respiratory specimens from patients with presumptive tuberculosis in terms of diagnostic accuracy and time to tuberculosis treatment inception in low-prevalence settings remains largely unexplored. We conducted a prospective intervention cohort study. Respiratory specimens from 1,020 patients were examined by acid-fast bacillus smear microscopy, tested by a real-time
Mycobacterium tuberculosis
complex PCR assay (Abbott RealTi
me
MTB PCR), and cultured in mycobacterial media. Seventeen patients tested positive by PCR (5 were acid-fast bacillus smear positive and 12 acid-fast bacillus smear negative), and
Mycobacterium tuberculosis
was recovered from cultures for 12 of them. Patients testing positive by PCR and negative by culture (
n
= 5) were treated and deemed to have responded to antituberculosis therapy. There were no PCR-negative/culture-positive cases, and none of the patients testing positive for nontuberculous mycobacteria (
n
= 20) yielded a positive PCR result. The data indicated that routine testing of respiratory specimens from patients with presumptive tuberculosis by the RealTi
me
MTB PCR assay improves the tuberculosis diagnostic yield and may reduce the time to antituberculosis treatment initiation. On the basis of our data, we propose a novel mycobacterial laboratory algorithm for tuberculosis diagnosis.
Infectious Bursal Disease Virus Hijacks Endosomal Membranes as the Scaffolding Structure for Viral Replication
Authors: Gimenez María Cecilia , Zanetti Flavia Adriana , Terebiznik Mauricio R. , Colombo María Isabel , Delgui Laura Ruth
Published: March 2018

Birnaviruses are unconventional members of the group of double-stranded RNA (dsRNA) viruses that are characterized by the lack of a transcriptionally active inner core. Instead, the birnaviral particles organize their genome in ribonucleoprotein complexes (RNPs) composed by dsRNA segments, the dsRNA-binding VP3 protein, and the virally encoded RNA-dependent RNA polymerase (RdRp). This and other structural features suggest that birnaviruses may follow a completely different replication program from that followed by members of the
Reoviridae
family, supporting the hypothesis that birnaviruses are the evolutionary link between single-stranded positive RNA (+ssRNA) and dsRNA viruses. Here we demonstrate that infectious bursal disease virus (IBDV), a prototypical member of the
Birnaviridae
family, hijacks endosomal membranes of infected cells through the interaction of a viral protein, VP3, with the phospholipids on the cytosolic leaflet of these compartments for replication. Employing a mutagenesis approach, we demonstrated that VP3 domain PATCH 2 (P2) mediates the association of VP3 with the endosomal membranes. To determine the role of VP3 P2 in the context of the virus replication cycle, we used avian cells stably overexpressing VP3 P2 for IBDV infection. Importantly, the intra- and extracellular virus yields, as well as the intracellular levels of VP2 viral capsid protein, were significantly diminished in cells stably overexpressing VP3 P2. Together, our results indicate that the association of VP3 with endosomes has a relevant role in the IBDV replication cycle. This report provides direct experimental evidence for membranous compartments such as endosomes being required by a dsRNA virus for its replication. The results also support the previously proposed role of birnaviruses as an evolutionary link between +ssRNA and dsRNA viruses.

IMPORTANCE
Infectious bursal disease (IBD; also called Gumboro disease) is an acute, highly contagious immunosuppressive disease that affects young chickens and spreads worldwide. The etiological agent of IBD is infectious bursal disease virus (IBDV). This virus destroys the central immune organ (bursa of Fabricius), resulting in immunosuppression and reduced responses of chickens to vaccines, which increase their susceptibility to other pathogens. IBDV is a member of
Birnaviridae
family, which comprises unconventional members of dsRNA viruses, whose replication strategy has been scarcely studied. In this report we show that IBDV hijacks the endosomes of the infected cells for establishing viral replication complexes via the association of the ribonucleoprotein complex component VP3 with the phospholipids in the cytosolic leaflet of endosomal membranes. We show that this interaction is mediated by the VP3 PATCH 2 domain and demonstrate its relevant role in the context of viral infection.
Vaccinia Virus Phospholipase Protein F13 Promotes Rapid Entry of Extracellular Virions into Cells
Authors: Bryk Peter , Brewer Matthew G. , Ward Brian M.
Published: March 2018

The vaccinia virus protein F13, encoded by the F13L gene, is conserved across the subfamily
Chordopoxvirinae
and is critical among orthopoxviruses to produce the wrapped form of virus that is required for cell-to-cell spread. F13 is the major envelope protein on the membrane of extracellular forms of virus; however, it is not known if F13 is required in steps postwrapping. In this report, we utilize two temperature-sensitive vaccinia virus mutants from the Condit collection of temperature-sensitive viruses whose small plaque phenotypes have been mapped to the F13L gene. Despite the drastic reduction in plaque size, the temperature-sensitive viruses were found to produce levels of extracellular virions similar to those of the parental strain, Western Reserve (WR), at the permissive and nonpermissive temperatures, suggesting that they are not defective in extracellular virion formation. Analyses of extracellular virions produced by one temperature-sensitive mutant found that those produced at the nonpermissive temperature had undetectable levels of F13 and bound cells with efficiency similar to that of WR but displayed delayed cell entry kinetics. Additionally, low-pH treatment of cells bound by extracellular virions produced at the nonpermissive temperature by the temperature-sensitive reporter virus was unable to overcome a block in infection by bafilomycin A1, suggesting that these virions display increased resistance to dissolution of the extracellular virion envelope. Taken together, our results suggest that F13 plays a role both in the formation of extracellular virions and in the promotion of their rapid entry into cells by enhancing the sensitivity of the membrane to acid-induced dissolution.

IMPORTANCE
Vaccinia virus (VACV) is an orthopoxvirus and produces two infectious forms, mature virions (MV) and extracellular virions (EV). EV are derived from MV and contain an additional membrane that must first be removed prior to cell entry. F13 is critical for the formation of EV, but a postenvelopment role has not been described. Here, two temperature-sensitive VACV mutants whose deficiencies were previously mapped to the F13L locus are characterized. Both viruses produced EV at the nonpermissive temperature at levels similar to those of a virus that has F13L, yet they had a small plaque phenotype and rate of spread similar to that of an F13L deletion virus. F13 was undetectable on the EV membrane at the nonpermissive temperature, and these EV exhibited delayed cell entry kinetics compared to EV containing F13. This study is the first to conclusively demonstrate a novel role for F13 in cell entry of the EV form of the virus.
Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring
Authors: McCormack Ursula M. , Curião Tânia , Wilkinson Toby , Metzler-Zebeli Barbara U. , Reyer Henry , Ryan Tomas , Calderon-Diaz Julia A. , Crispie Fiona , Cotter Paul D. , Creevey Christopher J. , Gardiner Gillian E. , Lawlor Peadar G.
Published: March 2018

Here, for the first time, we investigate FMT as a novel strategy to modulate the porcine intestinal microbiota in an attempt to improve FE in pigs. However, reprogramming the maternal and/or offspring microbiome by using fecal transplants derived from highly feed-efficient pigs did not recapitulate the highly efficient phenotype in the offspring and, in fact, had detrimental effects on lifetime growth. Although these findings may not be wholly attributable to microbiota transplantation, as antibiotic and purgative were also part of the regime in sows, similar effects were also seen in offspring, in which these interventions were not used. Nonetheless, additional work is needed to unravel the effects of each component of the FMT regime and to provide additional mechanistic insights. This may lead to the development of an FMT procedure with practical applications for the improvement of FE in pigs, which could in turn improve the profitability of pig production.
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples
Authors: Minich Jeremiah J. , Zhu Qiyun , Janssen Stefan , Hendrickson Ryan , Amir Amnon , Vetter Russ , Hyde John , Doty Megan M. , Stillwell Kristina , Benardini James , Kim Jae H. , Allen Eric E. , Venkateswaran Kasthuri , Knight Rob
Published: March 2018

Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility.
Elevated platelet counts in a cohort of children with moderate-severe osteogenesis imperfecta suggest that inflammation is present
Authors: Salter Lois , Offiah Amaka C , Bishop Nicholas
Published: March 2018

Background

Elevated platelet counts are observed in cancer, autoimmunity and inflammation with concurrent illness. Proinflammatory cytokines are elevated in murine osteogenesis imperfecta (OI) models. We hypothesised that platelet counts might be elevated in children with moderate-severe OI.

Methods

We reviewed the hospital records of 71 children with moderate-severe OI, treated in the Sheffield Children’s Hospital’s Severe, Complex and Atypical Osteogenesis Imperfecta Highly Specialised Service. Data relating platelet count (below/above average, above upper limit) to prior and concurrent events were summarised as event proportions per child. Additionally, we created platelet SD scores to assess age and time-related trends, and relationship with OI type.

Results

1206 platelet counts were recorded. Platelet SD scores were right-shifted by 0.89 SD overall. 49 of 71 (69%) patients had at least one platelet count above the normal range and 246 (20.4%) of all counts were above the upper limit of normal. Of these, 101 (41%) were high despite no confounding factors being present. For the 47 children with data at age less than 2 years, 89 (30.0%) platelet counts were above the upper limit of normal and 39 (44%) had no associated confounding factor. Elevated platelet counts were recorded most often for children with new or existing vertebral fractures.

Conclusions

Raised platelet counts were observed in association with new and healing vertebral fractures, but also (41%–44%) in the absence of identified proinflammatory factors or events. We speculate that these findings are evidence for a proinflammatory component to OI that could be a target for therapeutic intervention.
Feasibility of using touch screen technology for early cognitive assessment in children
Authors: Twomey Deirdre M , Wrigley Conal , Ahearne Caroline , Murphy Raegan , De Haan Michelle , Marlow Neil , Murray Deirdre M
Published: March 2018

Objective

To explore the feasibility of using a touch screen assessment tool to measure cognitive capacity in toddlers.

Design

112 typically developing children with a median age of 31 months (IQR: 26–34) interacted with a touch screen cognitive assessment tool. We examined the sensitivity of the tool to age-related changes in cognition by comparing the number of items completed, speed of task completion and accuracy in two age groups; 24–29 months versus 30–36 months.

Results

Children aged 30–36 months completed more tasks (median: 18, IQR: 18–18) than those aged 24–29 months (median: 17, IQR: 15–18). Older children also completed two of the three working memory tasks and an object permanence task faster than their younger peers. Children became faster at completing the working memory items with each exposure and registered similar completion times on the hidden object retrieval items, despite task demands being twofold on the second exposure. A novel item required children to integrate what they had learnt on preceding items. The older group was more likely to complete this item and to do so faster than the younger group.

Conclusions

Children as young as 24 months can complete items requiring cognitive engagement on a touch screen device, with no verbal instruction and minimal child–administrator interaction. This paves the way for using touch screen technology for language and administrator independent developmental assessment in toddlers.
Ovarian teratoma associated with anti-NMDA (N-methyl D-aspartate) receptor encephalitis
Authors: LEEL Nellihela , Thakkar Hemanshoo, S , Drake David , Bouhadiba Nordeen
Published: March 2018

Anti-N-methyl D-aspartate receptor (NMDAR) encephalitis is a paraneoplastic, immune-mediated encephalopathy with a known association with ovarian teratomas. We present the first case in the UK of a 7-year-old patient presenting with this condition. Having been previously fit and healthy, the patient presented with an acute onset of cognitive disturbances. The initial suspicion was that of an infective encephalopathy; however, the lumbar puncture results were negative. Electroencephalography reported diffuse background slowing, supporting a diagnosis of encephalopathy. Extensive autoimmune screening was done and found to be positive for anti-NMDAR antibodies. A whole body MRI found a right adnexal lesion consistent with ovarian teratoma. At laparoscopy, the right ovary was excised and histology confirmed a mature cystic teratoma with neural tissue. There were no postoperative complications with the patient’s neurology recovering progressively at follow-up.
Subannular reconstruction in secondary mitral regurgitation: a meta-analysis
Authors: Harmel Eva Karolina , Reichenspurner Hermann , Girdauskas Evaldas
Published: March 2018

Objective

Mitral valve repair using an undersized complete annuloplasty ring in secondary mitral regurgitation with restricted leaflet motion during systole (Carpentier’s surgical classification of mitral valve pathology: type IIIb) only inadequately addresses the underlying left ventricular disease. This may lead to an ongoing ventricular remodelling and progressive papillary muscle displacement with increasing leaflet tethering. Several subannular techniques have been proposed to counteract the reoccurrence of mitral regurgitation after mitral valve repair. We aimed to evaluate the potential additive effect of such subannular techniques on the late reoccurrence rate of secondary mitral regurgitation.

Methods

Systematic literature review and meta-analysis were performed on PubMed, Embase and Google Scholar for studies published up to March 2016 and reporting late reoccurrence of mitral regurgitation after mitral valve repair using standard annuloplasty (control group) versus annuloplasty with subannular correction (study group) cohorts. Primary endpoint was late reoccurrence of mitral regurgitation ≥2 after surgical mitral valve repair, as defined by follow-up echocardiography.

Results

The cumulative number of 1093 patients in 12 included studies served as our study population. A total of 743 patients underwent combined mitral valve repair including annuloplasty and subannular manoeuvre (ie, study group), while the remaining 350 patients underwent an isolated ring annuloplasty (ie, control group). Secondary mitral regurgitation was caused by ischaemic heart disease in 733/743 patients in the study group and 334/350 patients in the control group. Mean echocardiographic follow-up was 42.7±13.9 months. Pooled outcome analysis demonstrated that the combination of subannular repair with ring annuloplasty was associated with a significantly lower reoccurrence rate of mitral regurgitation ≥2 as compared with annuloplasty alone (OR 0.27, 95% CI 0.19 to 0.38, P=0.0001).

Conclusion

The combination of subannular reconstruction and mitral valve annuloplasty is associated with a lower late reoccurrence of mitral regurgitation after surgical mitral valve repair, as compared with annuloplasty alone.
Effectiveness of new antiplatelets in the prevention of recurrent myocardial infarction
Authors: Grimaldi-Bensouda Lamiae , Danchin Nicolas , Dallongeville Jean , Falissard Bruno , Furber Alain , Cottin Yves , Bonello Laurent , Morel Olivier , Leclercq Florence , Puymirat Etienne , Ghanem Fahmi , Delarche Nicolas , Benichou Jacques , Abenhaim Lucien
Published: March 2018

Objective

To compare ticagrelor and prasugrel with clopidogrel for recurrent fatal and non-fatal myocardial infarction (reMI) in real-life conditions.

Methods

Case-referent study using the Pharmacoepidemiological General Research eXtension (PGRx)-acute coronary syndrome (ACS) registry. Cases were patients with reMI from a cohort with index ACS or external to the cohort (same sites). Referents from the cohort, without recurrent event, were matched on index ACS type and date, age and sex with reMI cases. Multivariate conditional logistic regression assessed the OR (95% CI) for reMI associated with ticagrelor and prasugrel vs clopidogrel, adjusted for aspirin use and cardiovascular risk factors.

Results

1047 cases and 2234 matched referents were included. Compared with clopidogrel, ticagrelor and prasugrel were associated with respective ORs of 0.65 (95% CI 0.52 to 0.81) and 0.71 (95% CI 0.53 to 0.96) for reMI occurrence. ORs for ticagrelor and prasugrel vs clopidogrel were: 0.50 (95% CI 0.38 to 0.67) and 0.66 (95% CI 0.45 to 0.95), 0.39 (95% CI 0.24 to 0.62) and 0.44 (95% CI 0.26 to 0.75), 0.63 (95% CI 0.43 to 0.92) and 1.20 (95% CI 0.69 to 2.07), 1.11 (95% CI 0.72 to 1.72) and 0.82 (95% CI 0.44 to 1.54) when index ACS was a first MI, a first ST-elevated MI (STEMI), a first non-STEMI and a recurrent ACS, respectively, and 0.63 (95% CI 0.45 to 0.87) and 0.77 (95% CI 0.41 to 1.45) for patients aged ≥70  years.

Conclusions

This real-world study showed a significant reduction of reMI with new antiplatelets compared with clopidogrel, ticagrelor being associated with a greater decrease of risk notably for first, either STEMI or non-STEMI. The larger magnitude of effect may be attributed to potential residual confounding or higher effectiveness compared with efficacy reported in trials (EMA Post Authorisation Study Registry Number EUPAS5905).
Short preheating at 41°C leads to a red blood cells count comparable to that in RET channel of Sysmex analysers in samples showing cold agglutination
Authors: La Gioia Antonio , Fumi Maurizio , Fiorini Fabiana , Pezzati Paola , Balboni Fiamma , Bombara Maria , Marini Alessandra , Pancione Ylenia , Solarino Leonardo , Marchese Elisa , Sale Silvia , Rocco Vincenzo , Fiorini Marcello
Published: March 2018

Aims

The presence of cold agglutinin in blood samples can cause a spontaneous agglutination of red blood cells (RBCs) when low temperature occurs. This phenomenon causes a spurious lowering of RBC count on the automated haematological analysers that are detected by incongruous values (≥370 g/L) of the mean cellular haemoglobi concentration (MCHC). A preheating at 37°C can remove the RBC agglutination generally resulting in a reliable count. It has been reported that the same result can be reached by using the optical reticulocyte (RET) channel of Sysmex analysers where the RBC count is not influenced by the presence of cold agglutinin. This study aims to evaluate these data in a larger population, with regard to environmental conditions on Sysmex analysers. We have also evaluated the influence of different thermal pretreatments on the RBC count.

Methods

This study was performed on 96 remnants of peripheral blood samples (48 with MCHC in normal range and 48 with MCHC>370 g/L) which have been analysed in different preanalytical conditions on the Sysmex analysers.

Results

A preheating of samples at 41°C for 1 min leads to a reversibility of the cold agglutination comparable to the one observed in the RET channel and yields better results compared with 37°C for 2 hours.

Conclusions

None of described procedures assure the complete cold agglutination reversibility in every case. Consequently, since the haematological analysers not yet provide reliable parameters to confirm the complete resolution of agglutination, further verification of RBC count accuracy needs to be performed.
Breast cancer histologic grading using digital microscopy: concordance and outcome association
Authors: Rakha Emad A , Aleskandarani Mohamed , Toss Michael S , Green Andrew R , Ball Graham , Ellis Ian O , Dalton Leslie W
Published: March 2018

Aims

Virtual microscopy utilising digital whole slide imaging (WSI) is increasingly used in breast pathology. Histologic grade is one of the strongest prognostic factors in breast cancer (BC). This study aims at investigating the agreement between BC grading using traditional light microscopy (LM) and digital WSI with consideration of reproducibility and impact on outcome prediction.

Methods

A large (n=1675) well-characterised cohort of BC originally graded by LM was re-graded using WSI. Two separate virtual-based grading sessions (V1 and V2) were performed with a 3-month washout period. Outcome was assessed using BC-specific and distant metastasis-free survival.

Results

The concordance between LM grading and WSI was strong (LM/WSI Cramer’s V: V1=0.576, and V2=0.579). The agreement regarding grade components was as follows: tubule formation=0.538, pleomorphism=0.422 and mitosis=0.514. Greatest discordance was observed between adjacent grades, whereas high/low grade discordance was uncommon (1.5%). The intraobserver agreement for the two WSI sessions was substantial for grade (V1/V2 Cramer’s V=0.676; kappa=0.648) and grade components (Cramer’s V T=0.628, p=0.573 and M=0.580). Grading using both platforms showed strong association with outcome (all p values <0.001). Although mitotic scores assessed using both platforms were strongly associated with outcome, WSI tends to underestimate mitotic counts.

Conclusions

Virtual microscopy is a reliable and reproducible method for assessing BC histologic grade. Regardless of the observer or assessment platform, histologic grade is a significant predictor of outcome. Continuing advances in imaging technology could potentially provide improved performance of WSI BC grading and in particular mitotic count assessment.
The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics
Authors: Fumagalli Caterina , Vacirca Davide , Rappa Alessandra , Passaro Antonio , Guarize Juliana , Rafaniello Raviele Paola , de Marinis Filippo , Spaggiari Lorenzo , Casadio Chiara , Viale Giuseppe , Barberis Massimo , Guerini-Rocco Elena
Published: March 2018

Background

Molecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously.

Aims

To evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC.

Methods

A single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes.

Results

441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed inKRAS,TP53,EGFR,STK11andMETgenes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairingKRASor EGFR in association withTP53alterations.

Conclusions

The study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.
Interface response-based soil classification framework
Authors: Hebeler G.L. , Martinez A. , Frost J.D.
Published: March 2018

Current soil classification systems based on cone penetration testing (CPT) utilize a combination of the tip resistance (qt), pore pressure (u2), and friction sleeve (fs) measurements as inputs. While the qt measurements are typically normalized by the overburden stress, the fs measurements are often normalized by the net tip resistance, leading to the use of parameters that are dependent on each other. This paper presents the development of a soil classification framework that utilizes a normalized multi-friction parameter (MFP) and the CPT normalized tip resistance. The MFP parameter is obtained from measurements with textured friction sleeves from soundings with multi-sleeve attachments. The use of textured friction sleeves allows for fundamental differences in soil–structure interface behavior and particle sizes to be captured due to the significant degree of shearing induced within the soil. This classification framework was developed with results from over 30 soundings at six different sites. The analysis of samples taken from the field indicates that the proposed framework provides a classification that better agrees with the grain-size distribution for residuum, calcareous and intermediate soils, as compared to existing CPT-based systems. The potential development of a simplified probe with just one additional friction sleeve sensor can provide appropriate classification results and would facilitate adoption for use in practice.
Castor bean cake detoxified with calcium hydroxide in diets for pigs at growing and finishing phases
Authors: Gomes da Silva Taisa Rocha , Pascoal Leonardo Augusto Fonseca , Costa Fernando Guilherme Perazzo , Watanabe Pedro Henrique , Dantas Martins Terezinha Domiciano
Published: March 2018

The present study was aimed to evaluate the use of increasing levels of castor bean cake detoxified with calcium hydroxide in diets for pigs at growing and finishing phases on performance, diet digestibility, weight of digestive organs, carcass traits, and economic evaluation. A total of 40 barrows with 44.59 ± 5.16 kg initial weight were fed diets with 0%, 7%, 14%, and 21% detoxified castor bean cake. Increasing levels of detoxified castor bean cake in diets resulted in linear worsening in the average daily gain of the pigs. Dry matter, crude protein, and gross energy digestibilities were adversely affected by the levels of detoxified castor bean cake. A linear decrease in loin eye area and ham yield was detected depending on detoxified castor bean cake inclusion levels. Although the detoxified castor bean cake had no effect on the assessed economic variables, its use in diets for growing and finishing pigs is not recommended.
Saccharomyces cerevisiae var. boulardii CNCM I-1079 and Lactobacillus acidophilus BT1386 influence innate immune response and serum levels of acute-phase proteins during weaning in Holstein calves
Authors: Fomenky Bridget E. , Chiquette Johanne , Lessard Martin , Bissonnette Nathalie , Talbot Guylaine , Chouinard Yvan P. , Ibeagha-Awemu Eveline M.
Published: March 2018

The aims of this study were to investigate the effect of Saccharomyces cerevisiae var. boulardii CNCM I-1079 (SCB) or Lactobacillus acidophilus BT1386 (LA) on (1) innate immune response, (2) markers of acute-phase reaction, and (3) immune gene expression of rumen and ileum tissues of Holstein calves. Forty eight calves (∼5 d old) were randomly allocated to four treatments as follows: (1) control (CTRL) fed milk replacer followed by starter feed, (2) CTRL supplemented with SCB in milk and feed, (3) CTRL supplemented with LA in milk and feed, and (4) CTRL supplemented with antibiotics (ATB; chlortetracycline and neomycin in milk, and chlortetracycline in feed). Tumor necrosis factor α (TNF-α) decreased (P < 0.05) on day 66 (post-weaning) for the ATB-treated calves. There were no treatment effects on production of interferon γ (IFN-γ) and interleukin 6 (IL-6) proteins and on expression of TLR4, TLR6, TLR9, TLR10, CLDN3, MUC1, and MUC20 genes. Calves fed SCB or LA had a greater (P < 0.05) oxidative burst at weaning (day 53) compared with CTRL. Oxidative burst was also greater (P < 0.05) after weaning (day 59 and day 87) for SCB-fed calves. Calves fed SCB and ATB had higher (P < 0.05) phagocytosis activity during weaning (day 47) compared with CTRL. The concentration of serum amyloid A2 (SAA2) increased (P < 0.05) in SCB- and LA-fed calves (day 53), whereas the concentration of C-reactive protein (CRP) increased (P < 0.05) in SCB-fed calves during weaning as compared with CTRL. Our results suggest that SCB could improve innate immune response (oxidative burst and phagocytosis) and markers of acute-phase reaction (CRP and SAA2), especially during critical periods like weaning.
Estimation of direct and maternal genetic parameters for individual birth weight and probe weight using cross-fostering information
Authors: Alves K. , Schenkel F.S. , Brito L.F. , Robinson J.A.B.
Published: March 2018

A total of 246 357 measurements of birth (BW) and probe (PW) weights of purebred Yorkshire and Landrace pigs were used to compare the fitting of two alternate models including either common-litter effect or cross-fostering group effect to account for common environmental variation. PW, is a live ultrasonic weight measurement taken when the pigs are 100 ± 30 kg, following national standards. The common-litter effect was defined as piglets born into the same litter, and the group effect was used to account for cross-fostering, and defined as the effect common to piglets raised by the same nurse-sow, regardless of whether that piglet was born into that litter or not. It was found that the cross-fostering group explained 5% more environmental variation in BW when compared with the common-litter effect, indication that BW is a criterion in cross-fostering. Cross-fostering also explained 1% more environmental variation in PW in both the Yorkshire and Landrace. When the cross-fostering group effect was included in place of the common-litter effect, the direct and maternal genetic heritability estimates were similar, but residual variances were reduced. This study advanced the understanding of the effects of cross-fostering on PW, its association with BW and its implications in modern pig breeding programs.
Petrogenesis and tectonic implications of Late Jurassic – Early Cretaceous granitic magmatism in the Xing’an Block, Northeast China: geochronological, geochemical, and Hf isotopic evidence
Authors: He Yue , He Zhong-Hua , Ge Wen-Chun , Yang Hao , Wang Zhi-Hui , Dong Yu , Bi Jun-Hui , Zhao Di
Published: March 2018

This study presents new geochronological, whole-rock geochemical, and zircon Hf isotopic evidence for the age, petrogenesis, and source of Mesozoic granitic rocks of the Xing’an Block, Northeast China. This evidence reveals the Late Mesozoic tectonic evolution of the eastern section of the Central Asian Orogenic Belt. Laser-ablation inductively coupled plasma – mass spectrometryzircon U–Pb age data indicate that the syenogranite, monzogranite, and alkali feldspar granite units, as well as their associated diorite microgranular enclaves, were emplaced between 150–142 Ma, providing evidence of Late Jurassic to Early Cretaceous magmatic events within the Xing’an Block. The granites contain high concentrations of SiO2 (65.24%–75.73 wt.%) and K2O (3.94%–5.30 wt.%), low concentrations of MgO (0.10%–1.30 wt.%), and A/CNK values of 0.92–1.06. In addition, Hf isotopic analysis of zircons from the 150–142 Ma granites yields εHf(t) values of +4.54 to +12.16 and two-stage Hf model aged from 906 to 423 Ma, indicating that they formed from magmas generated by partial melting of a juvenile Neoproterozoic–Phanerozoic accreted crustal source. The basic magma source for the diorite microgranular enclaves most likely formed from partial melting of a depleted mantle that had been metasomatized by subduction-related fluids. Combining these new geochemical data with the geology of this region, Late Jurassic to Early Cretaceous magmatism in the Xing’an Block most likely occurred in an extensional environment associated with closure of the Mongol–Okhotsk Ocean.
Comparison of the first whole genome sequence of ‘Haemophilus quentini’ with two new strains of ‘Haemophilus quentini’ and other species ofHaemophilus
Authors: Hubbard Alasdair T.M. , Davies Sian E.W. , Baxter Laura , Thompson Sarah , Collery Mark M. , Hand Daniel C. , Thomas D. John I. , Fink Colin G.
Published: March 2018

Comparison of the genome of the Gram negative human pathogen Haemophilus quentini MP1 with other species of Haemophilus revealed that, although it is more closely related to Haemophilus haemolyticus than Haemophilus influenzae, the pathogen is in fact genetically distinct, a finding confirmed by phylogenetic analysis using the H. influenzae multilocus sequence typing genes. Further comparison with two other H. quentini strains recently identified in Canada revealed that these three genomes are more closely related than any other species of Haemophilus; however, there is still some sequence variation. There was no evidence of acquired antimicrobial resistance within the H. quentini MP1 genome nor any mutations within the DNA gyrase or topoisomerase IV genes known to confer resistance to fluoroquinolones, which has been previously identified in other H. quentini isolates. We hope by presenting the annotation and genetic comparison of the H. quentini MP1 genome it will aid the future molecular detection of this potentially emerging pathogen via the identification of unique genes that differentiate it from other species of Haemophilus.
Wedge-local observables for factorizing S-matrix with gap in the coupling constant
Authors: Cadamuro Daniela , Tanimoto Yoh
Published: March 2018

In the bootstrap approach to integrable quantum field theories in the [Formula: see text]-dimensional Minkowski space, one conjectures the two-particle S-matrix and tries to study local observables. We find a family of two-particle S-matrices parametrized by two positive numbers, which are separated from the free field or any other known S-matrix. We propose candidates for observables in wedge-shaped regions and prove their commutativity in the weak sense.

The sine-Gordon model is conjectured to be equivalent to the Thirring model, and its breather–breather S-matrix components (where the first breather corresponds to the scalar field of the sine-Gordon model) are closed under fusion. Yet, the residues of the poles in this breather–breather S-matrix have wrong signs and cannot be considered as a separate model. Our S-matrices differ from the breather–breather S-matrix in the sine-Gordon model by CDD factors which adjust the signs, so that this sector alone satisfies reasonable assumptions.
Demystifying the constancy of the Ermakov–Lewis invariant for a time-dependent oscillator
Authors: Padmanabhan T.
Published: March 2018

It is well known that the time-dependent harmonic oscillator (TDHO) possesses a conserved quantity, usually called Ermakov–Lewis invariant. I provide a simple physical interpretation of this invariant as well as a whole family of related invariants. This interpretation does not seem to have been noticed in the literature before. The procedure also allows one to tackle some key conceptual issues which arise in the study of quantum fields in the external, time-dependent backgrounds like in the case of particle production in an expanding universe and Schwinger effect.
Complexities’ day-to-day dynamic evolution analysis and prediction for a Didi taxi trip network based on complex network theory
Authors: Zhang Lin , Lu Jian , Zhou Jialin , Zhu Jinqing , Li Yunxuan , Wan Qian
Published: March 2018

Didi Dache is the most popular taxi order mobile app in China, which provides online taxi-hailing service. The obtained big database from this app could be used to analyze the complexities’ day-to-day dynamic evolution of Didi taxi trip network (DTTN) from the level of complex network dynamics. First, this paper proposes the data cleaning and modeling methods for expressing Nanjing’s DTTN as a complex network. Second, the three consecutive weeks’ data are cleaned to establish 21 DTTNs based on the proposed big data processing technology. Then, multiple topology measures that characterize the complexities’ day-to-day dynamic evolution of these networks are provided. Third, these measures of 21 DTTNs are calculated and subsequently explained with actual implications. They are used as a training set for modeling the BP neural network which is designed for predicting DTTN complexities evolution. Finally, the reliability of the designed BP neural network is verified by comparing with the actual data and the results obtained from ARIMA method simultaneously. Because network complexities are the basis for modeling cascading failures and conducting link prediction in complex system, this proposed research framework not only provides a novel perspective for analyzing DTTN from the level of system aggregated behavior, but can also be used to improve the DTTN management level.
Connectedness Between Soft Sets
Authors: Thakur Samajh Singh , Rajput Alpa Singh
Published: March 2018

In the present paper, the concepts of soft connectedness between soft sets, soft set-connected and soft weakly continuous mappings in soft topological spaces have been introduced and studied.
Myeloid-specificAcat1ablation attenuates inflammatory responses in macrophages, improves insulin sensitivity, and suppresses diet-induced obesity
Authors: Huang Li-Hao , Melton Elaina M. , Li Haibo , Sohn Paul , Jung DaeYoung , Tsai Ching-Yi , Ma Tian , Sano Hiroyuki , Ha HyeKyung , Friedline Randall H. , Kim Jason K. , Usherwood Edward , Chang Catherine C. Y. , Chang Ta-Yuan
Published: March 2018

Macrophages are phagocytes that play important roles in health and diseases. Acyl-CoA:cholesterol acyltransferase 1 (ACAT1) converts cellular cholesterol to cholesteryl esters and is expressed in many cell types. Unlike global Acat1 knockout (KO), myeloid-specific Acat1 KO ( Acat1−) does not cause overt abnormalities in mice. Here, we performed analyses in age- and sex-matched Acat1−M/−Mand wild-type mice on chow or Western diet and discovered that Acat1−M/−Mmice exhibit resistance to Western diet-induced obesity. On both chow and Western diets, Acat1−M/−Mmice display decreased adipocyte size and increased insulin sensitivity. When fed with Western diet, Acat1−M/−Mmice contain fewer infiltrating macrophages in white adipose tissue (WAT), with significantly diminished inflammatory phenotype. Without Acat1, the Ly6Chimonocytes express reduced levels of integrin-β1, which plays a key role in the interaction between monocytes and the inflamed endothelium. Adoptive transfer experiment showed that the appearance of leukocytes from Acat1−M/−Mmice to the inflamed WAT of wild-type mice is significantly diminished. Under Western diet, Acat1−M/−Mcauses suppression of multiple proinflammatory genes in WAT. Cell culture experiments show that in RAW 264.7 macrophages, inhibiting ACAT1 with a small-molecule ACAT1-specific inhibitor reduces inflammatory responses to lipopolysaccharide. We conclude that under Western diet, blocking ACAT1 in macrophages attenuates inflammation in WAT. Other results show that Acat1−M/−Mdoes not compromise antiviral immune response. Our work reveals that blocking ACAT1 suppresses diet-induced obesity in part by slowing down monocyte infiltration to WAT as well as by reducing the inflammatory responses of adipose tissue macrophages.
The Encapsulation of Lycopene in Nanoliposomes Enhances Its Protective Potential in Methotrexate‐Induced Kidney Injury Model
Authors: Stojiljkovic Nenad , Ilic Sonja , Jakovljevic Vladimir , Stojanovic Nikola , Stojnev Slavica , Kocic Hristina , Stojanovic Marko , Kocic Gordana
Published: March 2018

Methotrexate is an antimetabolic drug with a myriad of serious side effects including nephrotoxicity, which presumably occurs due to oxidative tissue damage. Here, we evaluated the potential protective effect of lycopene, a potent antioxidant carotenoid, given in two different pharmaceutical forms in methotrexate‐induced kidney damage in rats. Serum biochemical (urea and creatinine) and tissue oxidative damage markers and histopathological kidney changes were evaluated after systemic administration of both lycopene dissolved in corn oil and lycopene encapsulated in nanoliposomes. Similar to previous studies, single dose of methotrexate induced severe functional and morphological alterations of kidneys with cell desquamation, tubular vacuolation, and focal necrosis, which were followed by serum urea and creatinine increase and disturbances of tissue antioxidant status. Application of both forms of lycopene concomitantly with methotrexate ameliorated changes in serum urea and creatinine and oxidative damage markers and markedly reversed structural changes of kidney tissue. Moreover, animals that received lycopene in nanoliposome‐encapsulated form showed higher degree of recovery than those treated with free lycopene form. The findings of this study indicate that treatment with nanoliposome‐encapsulated lycopene comparing to lycopene in standard vehicle has an advantage as it more efficiently reduces methotrexate‐induced kidney dysfunction.
The Hypoxia-Mimetic Agent Cobalt Chloride Differently Affects Human Mesenchymal Stem Cells in Their Chondrogenic Potential
Authors: Teti Gabriella , Focaroli Stefano , Salvatore Viviana , Mazzotti Eleonora , Ingra’ Laura , Mazzotti Antonio , Falconi Mirella
Published: March 2018

Adult stem cells are a promising cell source for cartilage regeneration. They resided in a special microenvironment known as the stem-cell niche, characterized by the presence of low oxygen concentration. Cobalt chloride (CoCl2) imitates hypoxia in vitro by stabilizing hypoxia-inducible factor-alpha (HIF-1α), which is the master regulator in the cellular adaptive response to hypoxia. In this study, the influence of CoCl2 on the chondrogenic potential of human MSCs, isolated from dental pulp, umbilical cord, and adipose tissue, was investigated. Cells were treated with concentrations of CoCl2 ranging from 50 to 400 μM. Cell viability, HIF-1α protein synthesis, and the expression of the chondrogenic markers were analyzed. The results showed that the CoCl2 supplementation had no effect on cell viability, while the upregulation of chondrogenic markers such as SOX9, COL2A1, VCAN, and ACAN was dependent on the cellular source. This study shows that hypoxia, induced by CoCl2 treatment, can differently influence the behavior of MSCs, isolated from different sources, in their chondrogenic potential. These findings should be taken into consideration in the treatment of cartilage repair and regeneration based on stem cell therapies.