bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of
epsD
Authors: Frantzen Cyril A. , Kleppen Hans Petter , Holo Helge 
Published: December 2017

ABSTRACT

Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of
Lactococcus lactis
and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of
Lactococcus lactis
strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21
L. lactis
subsp
. lactis
and 28
L. lactis
subsp.
cremoris
lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using
purR
, a core gene, and
epsD
, present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture
Lactococcus lactis
and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk.

IMPORTANCE
In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of more robust starter cultures and assist in maintaining the efficiency and stability of the production process by ensuring the presence of key bacteria that are important to the characteristics of the product.
Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway
Authors: Shettigar Madhura , Balotra Sahil , Cahill David , Warden Andrew C. , Lacey Michael J. , Kohler Hans-Peter E. , Rentsch Daniel , Oakeshott John G. , Pandey Gunjan 
Published: December 2017

ABSTRACT

Pinoresinol is a dimer of two β-β′-linked coniferyl alcohol molecules. It is both a plant defense molecule synthesized through the shikimic acid pathway and a representative of several β-β-linked dimers produced during the microbial degradation of lignin in dead plant material. Until now, little has been known about the bacterial catabolism of such dimers. Here we report the isolation of the efficient (+)-pinoresinol-mineralizing
Pseudomonas
sp. strain SG-MS2 and its catabolic pathway. Degradation of pinoresinol in this strain is inducible and proceeds via a novel oxidative route, which is in contrast to the previously reported reductive transformation by other bacteria. Based on enzyme assays and bacterial growth, cell suspension, and resting cell studies, we provide conclusive evidence that pinoresinol degradation in strain SG-MS2 is initiated by benzylic hydroxylation, generating a hemiketal via a quinone methide intermediate, which is then hydrated at the benzylic carbon by water. The hemiketal, which stays in equilibrium with the corresponding keto alcohol, undergoes an aryl-alkyl cleavage to generate a lactone and 2-methoxyhydroquinone. While the fate of 2-methoxyhydroquinone is not investigated further, it is assumed to be assimilated by ring cleavage. The lactone is further metabolized via two routes, namely, lactone ring cleavage and benzylic hydroxylation via a quinone methide intermediate, as described above. The resulting hemiketal again exists in equilibrium with a keto alcohol. Our evidence suggests that both routes of lactone metabolism lead to vanillin and vanillic acid, which we show can then be mineralized by strain SG-MS2.

IMPORTANCE
The oxidative catabolism of (+)-pinoresinol degradation elucidated here is fundamentally different from the reductive cometabolism reported for two previously characterized bacteria. Our findings open up new opportunities to use lignin for the biosynthesis of vanillin, a key flavoring agent in foods, beverages, and pharmaceuticals, as well as various new lactones. Our work also has implications for the study of new pinoresinol metabolites in human health. The enterodiol and enterolactone produced through reductive transformation of pinoresinol by gut microbes have already been associated with decreased risks of cancer and cardiovascular diseases. The metabolites from oxidative metabolism we find here also deserve attention in this respect.
Draft Genome Sequence of Haloparvum sedimenti Strain DYS4, the Type Species of the Genus
Haloparvum
, Isolated from a Salt Mine
Authors: Chen Shaoxing , Wang Chuanming , Li He , Shen Yunmei 
Published: December 2017

ABSTRACT

Here is the genome sequence of
Haloparvum sedimenti
DYS4, the type species of the genus
Haloparvum
, isolated from a salt mine. The DNA G+C content of this genome was 68.27 mol%. The scaffold
N
50
was 96,635 bp. The completely sequenced and annotated genome is 3,243,052 bp and contains 3,313 genes.
Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons
Authors: Brown Lisa M. , Gunasekera Thusitha S. , Ruiz Oscar N. 
Published: December 2017

ABSTRACT

Pseudomonas stutzeri
strain 19 is a Gram-negative bacterium capable of degrading aromatic hydrocarbons. The draft genome of
P. stutzeri
19 is estimated to be 5.1 Mb, containing 4,652 protein-coding genes and a G+C content of 63.3%. Multiple genes responsible for the degradation of aromatics are present in this strain.
HPV vaccination rate in French adolescent girls: an example of vaccine distrust
Authors: Lefèvre Hervé , Schrimpf Cécile , Moro Marie Rose , Lachal Jonathan 
Published: December 2017

ObjectivesTo explore the clinical issues of human papillomavirus (HPV) vaccination to develop explanatory hypotheses for the low level of vaccination among adolescent girls in France where the full course coverage is low (<15%).DesignWe used semistructured interviews. Our qualitative and phenomenological procedure applied interpretative phenomenological analysis.Participants16 physicians regularly faced with the prescription of HPV vaccine, represented several medical specialties (paediatrics, general practice, internal medicine, gynaecology), with hospitalist or private practices.Main outcome measuresThe results connect three superordinate themes grouping three concentric levels: within society, during the consultation and in the individual doctor’s feelings.ResultsThe modalities and contents of the information about HPV vaccination raise questions about the limitations of the information doctors receive. The ineluctable association between sexuality and HPV vaccination explains their reluctance to raise topics considered to be private. The reasons for HPV vaccination illustrate the difficulty of arguing in favour of it. In view of the frequent parental reluctance, which weakens the parent–physician alliance, physicians must take responsibility for defending the benefits of vaccination. They nonetheless remain citizens whose opinions may implicitly echo the general reluctance, promoted by disinformation. In delaying or avoiding the subject of vaccination, they involuntarily become an instrument of anti-vaccination discourse.ConclusionsIt is imperative to improve the distribution of credible information about vaccination, unbiased and scientifically supported by a strong institutional position and to rethink the place of the clinician in the system of adolescent health and disease prevention in France.
Dose-dependent relationship between acidosis at birth and likelihood of death or cerebral palsy
Authors: Kelly Rod , Ramaiah SM , Sheridan Helen , Cruickshank Hilary , Rudnicka Magda , Kissack Chris , Becher Julie-Clare , Stenson Ben J 
Published: December 2017

BackgroundThe acid-base status of infants around birth can provide information about their past, current and future condition. Although umbilical cord blood pH <7.0 or base deficit ≥12 mmol/L is associated with increased risk of adverse outcome, there is uncertainty about the prognostic value of degree of acidosis as previous studies have used different variables, thresholds, outcomes and populations.MethodsRetrospective review of routinely collected clinical data in all live-born inborn infants of 35 weeks gestation or more delivered between January 2005 and December 2013 at the Simpson Centre for Reproductive Health, Edinburgh, UK. Infants were included if their lowest recorded pH was <7 and/or highest base deficit ≥12 mmol/L on either umbilical cord blood and/or neonatal blood gas within 1 hour of birth. Neurodevelopmental outcome of the infants with encephalopathy was collected from the targeted follow-up database.Results56 574 infants were eligible. 506 infants (0.9%) met inclusion criteria. Poor condition at birth and all adverse outcomes increased with worsening acidosis. Combined outcome of death or cerebral palsy was 3%, 10% and 40% at lowest pH of 6.9–6.99, 6.8–6.89 and <6.8, respectively, and 8%, 14% and 59% at a base deficit of 12–15.9, 16–19.9 and 20 mmol/L or more, respectively.ConclusionsThere is a dose-dependent relationship between the degree of acidosis within an hour of delivery, and the likelihood of adverse neonatal and later neurodevelopmental outcome in infants born at 35 weeks gestation or more.
Ambulatory versus inpatient management of severe nausea and vomiting of pregnancy: a randomised control trial with patient preference arm
Authors: Mitchell-Jones Nicola , Farren Jessica Alice , Tobias Aurelio , Bourne Tom , Bottomley Cecilia 
Published: December 2017

ObjectiveTo determine whether ambulatory (outpatient (OP)) treatment of severe nausea and vomiting of pregnancy (NVP) is as effective as inpatient (IP) care.DesignNon-blinded randomised control trial (RCT) with patient preference arm.SettingTwo multicentre teaching hospitals in London.ParticipantsWomen less than 20 weeks’ pregnant with severe NVP and associated ketonuria (>1+).MethodsWomen who agreed to the RCT were randomised via web-based application to either ambulatory or IP treatment. Women who declined randomisation underwent the treatment of their choice in the patient preference trial (PPT) arm. Treatment protocols, data collection and follow-up were the same for all participants.Main outcome measuresPrimary outcome was reduction in Pregnancy Unique Quantification of Emesis (PUQE) score 48 hours after starting treatment. Secondary outcome measures were duration of treatment, improvement in symptom scores and ketonuria at 48 hours, reattendances within 7 days of discharge and comparison of symptoms at 7 days postdischarge.Results152/174 eligible women agreed to participate with 77/152 (51%) recruited to the RCT and 75/152 (49%) to the PPT.Patients were initially compared in four groups (randomised IP, randomised OP, non-randomised IP and non-randomised OP). Comprehensive cohort analysis of participants in the randomised group (RCT) and non-randomised group (PPT) did not demonstrate any differences in patient demographics or baseline clinical characteristics. Pooled analysis of IP versus OP groups showed no difference in reduction in PUQE score at 48 hours (p=0.86). There was no difference in change in eating score (p=0.69), drinking score (p=0.77), well-being rating (p=0.64) or reduction in ketonuria (p=0.47) at 48 hours, with no difference in duration of index treatment episode (p=0.83) or reattendances within 7 days (p=0.52).ConclusionsAmbulatory management is an effective direct alternative to IP management of severe NVP. The trial also demonstrated that many women requiring treatment for severe NVP have strong preferences regarding treatment setting, which may need to be considered by care providers, especially given the psychological impact of severe NVP.Trial registration numberhttp://www.isrctn.com/ISRCTN24659467(March 2014).
Epigenetic Regulation of the Promotor Region of Vascular Endothelial Growth Factor-A and Nerve Growth Factor in Opioid-Maintained Patients
Authors: Groh Adrian , Jahn Kirsten , Burkert Alexandra , Neyazi Alexandra , Schares Laura , Janke Eva , Rehme Marie , Schuster Rilana , Hillemacher Thomas , Bleich Stefan , Frieling Helge , Heberlein Annemarie 
Published: December 2017

<b><i>Aims:</i></b> The nerve growth factor (NGF) and the vascular endothelial growth factor-A (VEGF-A) may be of importance for psychiatric diseases including substance use disorders. The aim of the study was to identify differences in the regulation of both neuropeptides via the DNA-methylation status of the promotor regions of NGF and VEGF-A in different forms of maintenance therapy for opioid dependence and the related stress regulation via the hypothalamic-pituitary-adrenal axis. <b><i>Methods:</i></b> We compared methylation levels of opioid-dependent patients receiving treatment with diamorphine (<i>n</i> = 28) or levomethadone (<i>n</i> = 54) and similar levels in a healthy control group (<i>n</i> = 72). <b><i>Results:</i></b> There was a significantly higher methylation of VEGF-A in opioid-maintained patients with levomethadone compared to that in the control group (estimated marginal means [EMM] [SE]): 0.036 [0.003] vs. 0.020 [0.003]; <i>p</i> &#x3c; 0.001). We performed a cluster analysis for NGF, splitting up the results in 4 clusters. We found significant changes in methylation rates of the opioid-maintained patients compared to the controls in cluster I ([EMM] [SE]: 0.064 [0.005] vs. 0.084 [0.006]; <i>p</i> = 0.03), cluster II ([EMM] [SE]: 0.133 [0.013] vs. 0.187 [0.014]; <i>p</i> &#x3c; 0.001) and cluster III ([EMM] [SE]: 0.190 [0.014] vs. 0.128 [0.016]; <i>p</i> &#x3c; 0.001). <b><i>Conclusions:</i></b> The results are of importance, as they indicate that long-term changes in stress regulation regulated by neurotrophines are a crucial part of the symptomatology of opioid dependence, thus influencing drug consumption and the different forms of opioid-maintenance therapies.
Prevalence and Clinical Characteristics of Refractory Hypertension
Authors: Armario Pedro , Calhoun David A. , Oliveras Anna , Blanch Pedro , Vinyoles Ernest , Banegas Jose R. , Gorostidi Manuel , Segura Julián , Ruilope Luis M. , Dudenbostel Tanja , de la Sierra Alejandro 
Published: December 2017

Background

We aimed to estimate the prevalence of refractory hypertension (RfH) and to determine the clinical differences between these patients and resistant hypertensives (
RH
). Secondly, we assessed the prevalence of white‐coat RfH and clinical differences between true‐ and white‐coat RfH patients.

Methods and Results

The present analysis was conducted on the Spanish Ambulatory Blood Pressure Monitoring Registry database containing 70 997 treated hypertensive patients.
RH
and RfH were defined by the presence of elevated office blood pressure (≥140 and/or 90 mm Hg) in patients treated with at least 3 (
RH
) and 5 (RfH) antihypertensive drugs. White‐coat RfH was defined by RfH with normal (<130/80 mm Hg) 24‐hour blood pressure. A total of 11.972 (16.9%) patients fulfilled the standard criteria of
RH
, and 955 (1.4%) were considered as having RfH. Compared with
RH
patients, those with RfH were younger, more frequently male, and after adjusting for age and sex, had increased prevalence of target organ damage, and previous cardiovascular disease. The prevalence of white coat RfH was lower than white‐coat
RH
(26.7% versus 37.1%,
P
<0.001). White‐coat RfH, in comparison with those with true RfH, showed a lower prevalence of both left ventricular hypertrophy (22% versus 29.7%;
P
=0.018) and microalbuminuria (28.3% versus 42.9%;
P
=0.047).

Conclusions

The prevalence of RfH was low and these patients had a greater cardiovascular risk profile compared with
RH
. One out of 4 patients with RfH have normal 24‐hour blood pressure and less target organ damage, thus indicating the important role of ambulatory blood pressure monitoring in guiding antihypertensive therapy in difficult‐to‐treat patients.
An Enhanced PIRATA Dataset for Tropical Atlantic Ocean–Atmosphere Research
Authors: Foltz Gregory R. , Schmid Claudia , Lumpkin Rick 
Published: December 2017

AbstractThe Prediction and Research Moored Array in the Tropical Atlantic (PIRATA) provides measurements of the upper ocean and near-surface atmosphere at 18 locations. Time series from many moorings are nearly 20 years in length. However, instrumental biases, data dropouts, and the coarse vertical resolutions of the oceanic measurements complicate their use for research. Here an enhanced PIRATA dataset (ePIRATA) is presented for the 17 PIRATA moorings with record lengths of at least seven years. Data in ePIRATA are corrected for instrumental biases, temporal gaps are filled using supplementary datasets, and the subsurface temperature and salinity time series are mapped to a uniform 5-m vertical grid. All original PIRATA data that pass quality control and that do not require bias correction are retained without modification, and detailed error estimates are provided. The terms in the mixed-layer heat and temperature budgets are calculated and included, with error bars. As an example of ePIRATA’s application, the vertical exchange of heat at the base of the mixed layer (Q−h) is calculated at each PIRATA location as the difference between the heat storage rate and the sum of the net surface heat flux and horizontal advection. Off-equatorial locations are found to have annual mean cooling rates of 20–60 W m−2, while cooling at equatorial locations reaches 85–110 W m−2 between 10° and 35°W and decreases to 40 W m−2 at 0°. At most off-equatorial locations, the strongest seasonal cooling from Q−h occurs when winds are weak. Possible explanations are discussed, including the importance of seasonal modulations of mixed-layer depth and the diurnal cycle.
Role of Air–Sea Interaction in the 30–60-Day Boreal Summer Intraseasonal Oscillation over the Western North Pacific
Authors: Wang Tianyi , Yang Xiu-Qun , Fang Jiabei , Sun Xuguang , Ren Xuejuan 
Published: December 2017

AbstractThis study investigates the role of air–sea interaction in the 30–60-day boreal summer intraseasonal oscillation (BSISO) over the western North Pacific with daily outgoing longwave radiation (OLR), CFSR, and OAFlux datasets for 1985–2009. The BSISO events are identified with the first principal component of 30–60-day bandpass filtered OLR anomalies. Composite analysis of these events reveals that during the northward migration of BSISO, the convection can interact with underlying sea surface temperature (SST). A near-quadrature phase relationship exists between the convection and SST anomalies. An active (a suppressed) convection tends to induce a cold (warm) underlying SST anomaly by reducing (increasing) downward solar radiation but a warm SST anomaly in its northern (southern) portion by reducing near-surface wind and upward latent and sensible heat fluxes, resulting in a 10-day delayed maximized warm SST anomaly ahead of the active convection. In turn, this warm SST anomaly tends to increase upward surface sensible and latent heat fluxes via amplifying sea–air temperature and humidity differences. This oceanic feedback acts to heat, moisten, and destabilize the low-level atmosphere, favoring the trigger of shallow convection, which can further develop into deep convection. The maximum warm SST anomaly lies in the southern (northern) portion of the convectively suppressed (enhanced) area, which weakens the anomalous descending motion in the southern portion of convectively suppressed area and preconditions the boundary layer to promote convection development in the northern portion of convectively enhanced area. Such a spatial and temporal phase relationship between the convection and SST anomalies suggest that air–sea interaction can play a delayed negative feedback role in the BSISO cycle and provide an alternative mechanism responsible for its northward propagation.
A review of mental health policies from Commonwealth countries
Authors: Bhugra Dinesh , Pathare Soumitra , Joshi Rajlaxmi , Kalra Gurvinder , Torales Julio , Ventriglio Antonio 
Published: December 2017

Background: The burden of disease related to mental disorders across the world is substantial. However, there remains inequality between funding for clinical and research activities between physical illness and mental illness in almost all countries. Aims: One way of reducing this inequality is to ensure that mental health policies reflect this. We were interested in looking at the policies of members of Commonwealth. Method: We decided to survey 52 member countries of the Commonwealth to explore whether mental health policies existed and whether there was equity between physical and mental health services funding. Using World Health Organization (WHO) data sets and other sources when indicated, we looked at the existence and contents of mental health policies. Results: We found that less than half of the countries had a mental health policy. Deinstitutionalization was not seen as a priority in many countries and there was no equity between physical and mental health funding. Although integration between physical and mental health care was recommended in many countries, there was a clear gap. Conclusion: It is apparent that there is still a long way to go in terms of equity between physical and mental health in terms of funding in member states of the Commonwealth. These findings confirm earlier observations of discrimination against people with mental illness. We suggest that there must be mechanisms in place to facilitate and support change wherever required.