bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
Authors: Landry Zachary , Swan Brandon K. , Herndl Gerhard J. , Stepanauskas Ramunas , Giovannoni Stephen J. 
Published: April 2017

ABSTRACT
Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist.

IMPORTANCE
Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.
Outcome of a screening programme for the prevention of neonatal invasive early-onset group B Streptococcus infection in a UK maternity unit: an observational study
Authors: Gopal Rao G , Nartey G , McAree T , O'Reilly A , Hiles S , Lee T , Wallace S , Batura R , Khanna P , Abbas H , Tilsed C , Nicholl R , Lamagni T , Bassett P 
Published: April 2017

BackgroundAgainst a background of failure to prevent neonatal invasive early-onset group BStreptococcusinfections (GBS) in our maternity unit using risk-based approach for intrapartum antibiotic prophylaxis, we introduced an antenatal GBS carriage screening programme to identify additional women to target for prophylaxis.ObjectivesTo describe the implementation and outcome of an antepartum screening programme for prevention of invasive early-onset GBS infection in a UK maternity unit.DesignObservational study of outcome of screening programme (intervention) with comparison to historical controls (preintervention).SettingHospital and community-based maternity services provided by Northwick Park and Central Middlesex Hospitals in North West London.ParticipantsWomen who gave birth between March 2014 and December 2015 at Northwick Park Hospital.MethodsWomen were screened for GBS at 35–37 weeks and carriers offered intrapartum antibiotic prophylaxis. Screening programme was first introduced in hospital (March 2014) and then in community (August 2014). Compliance was audited by review of randomly selected case records. Invasive early-onset GBS infections were defined through GBS being cultured from neonatal blood, cerebrospinal fluid or sterile fluids within 0–6 days of birth.Main outcomeIncidence of early-onset GBS infections.Results6309 (69%) of the 9098 eligible women were tested. Screening rate improved progressively from 42% in 2014 to 75% in 2015. Audit showed that 98% of women accepted the offer of screening. Recto-vaginal GBS carriage rate was 29.4% (1822/6193). All strains were susceptible to penicillin but 11.3% (206/1822) were resistant to clindamycin. Early onset GBS rate fell from 0.99/1000 live births (25/25276) in the prescreening period to 0.33/1000 in the screening period (Rate Ratio=0.33; p=0.08). In the subset of mothers actually screened, the rate was 0.16/1000 live births (1/6309), (Rate Ratio=0.16; p<0.05).ConclusionsOur findings confirm that an antenatal screening programme for prevention of early-onset GBS infection can be implemented in a UK maternity setting and is associated with a fall in infection rates.
Comparison of optomotor and optokinetic reflexes in mice
Authors: Kretschmer Friedrich , Tariq Momina , Chatila Walid , Wu Beverly , Badea Tudor Constantin 
Published: April 2017

During animal locomotion or position adjustments, the visual system uses image stabilization reflexes to compensate for global shifts in the visual scene. These reflexes elicit compensatory head movements (optomotor response, OMR) in unrestrained animals or compensatory eye movements (optokinetic response, OKR) in head-fixed or unrestrained animals exposed to globally rotating striped patterns. In mice, OMR are relatively easy to observe and find broad use in the rapid evaluation of visual function. OKR determinations are more involved experimentally but yield more stereotypical, easily quantifiable results. The relative contributions of head and eye movements to image stabilization in mice have not been investigated. We are using newly developed software and apparatus to accurately quantitate mouse head movements during OMR, quantitate eye movements during OKR, and determine eye movements in freely behaving mice. We provide the first direct comparison of OMR and OKR gains (head or eye velocity/stimulus velocity) and find that the two reflexes have comparable dependencies on stimulus luminance, contrast, spatial frequency, and velocity. OMR and OKR are similarly affected in genetically modified mice with defects in retinal ganglion cells (RGC) compared with wild-type, suggesting they are driven by the same sensory input (RGC type). OKR eye movements have much higher gains than the OMR head movements, but neither can fully compensate global visual shifts. However, combined eye and head movements can be detected in unrestrained mice performing OMR, suggesting they can cooperate to achieve image stabilization, as previously described for other species. NEW & NOTEWORTHY We provide the first quantitation of head gain during optomotor response in mice and show that optomotor and optokinetic responses have similar psychometric curves. Head gains are far smaller than eye gains. Unrestrained mice combine head and eye movements to respond to visual stimuli, and both monocular and binocular fields are used during optokinetic responses. Mouse OMR and OKR movements are heterogeneous under optimal and suboptimal stimulation and are affected in mice lacking ON direction-selective retinal ganglion cells.
Prediction suppression and surprise enhancement in monkey inferotemporal cortex
Authors: Ramachandran Suchitra , Meyer Travis , Olson Carl R. 
Published: April 2017

Exposing monkeys, over the course of days and weeks, to pairs of images presented in fixed sequence, so that each leading image becomes a predictor for the corresponding trailing image, affects neuronal visual responsiveness in area TE. At the end of the training period, neurons respond relatively weakly to a trailing image when it appears in a trained sequence and, thus, confirms prediction, whereas they respond relatively strongly to the same image when it appears in an untrained sequence and, thus, violates prediction. This effect could arise from prediction suppression (reduced firing in response to the occurrence of a probable event) or surprise enhancement (elevated firing in response to the omission of a probable event). To identify its cause, we compared firing under the prediction-confirming and prediction-violating conditions to firing under a prediction-neutral condition. The results provide strong evidence for prediction suppression and limited evidence for surprise enhancement. NEW & NOTEWORTHY In predictive coding models of the visual system, neurons carry signed prediction error signals. We show here that monkey inferotemporal neurons exhibit prediction-modulated firing, as posited by these models, but that the signal is unsigned. The response to a prediction-confirming image is suppressed, and the response to a prediction-violating image may be enhanced. These results are better explained by a model in which the visual system emphasizes unpredicted events than by a predictive coding model.
Intra- and Interobserver Reproducibility Assessment of PD-L1 Biomarker in Non–Small Cell Lung Cancer
Authors: Cooper Wendy A. , Russell Prudence A. , Cherian Maya , Duhig Edwina E. , Godbolt David , Jessup Peter J. , Khoo Christine , Leslie Connull , Mahar Annabelle , Moffat David F. , Sivasubramaniam Vanathi , Faure Celine , Reznichenko Alena , Grattan Amanda , Fox Stephen B. 
Published: April 2017

Abstract
Purpose: Reliable and reproducible methods for identifying PD-L1 expression on tumor cells are necessary to identify responders to anti–PD-1 therapy. We tested the reproducibility of the assessment of PD-L1 expression in non–small cell lung cancer (NSCLC) tissue samples by pathologists.
Experimental Design: NSCLC samples were stained with PD-L1 22C3 pharmDx kit using the Dako Autostainer Link 48 Platform. Two sample sets of 60 samples each were designed to assess inter- and intraobserver reproducibility considering two cut points for positivity: 1% or 50% of PD-L1 stained tumor cells. A randomization process was used to obtain equal distribution of PD-L1 positive and negative samples within each sample set. Ten pathologists were randomly assigned to two subgroups. Subgroup 1 analyzed all samples on two consecutive days. Subgroup 2 performed the same assessments, except they received a 1-hour training session prior to the second assessment.
Results: For intraobserver reproducibility, the overall percent agreement (OPA) was 89.7% [95% confidence interval (CI), 85.7–92.6] for the 1% cut point and 91.3% (95% CI, 87.6–94.0) for the 50% cut point. For interobserver reproducibility, OPA was 84.2% (95% CI, 82.8–85.5) for the 1% cut point and 81.9% (95% CI, 80.4–83.3) for the 50% cut point, and Cohen's κ coefficients were 0.68 (95% CI, 0.65–0.71) and 0.58 (95% CI, 0.55–0.62), respectively. The training was found to have no or very little impact on intra- or interobserver reproducibility.
Conclusions: Pathologists reported good reproducibility at both 1% and 50% cut points. More adapted training could potentially increase reliability, in particular for samples with PD-L1 proportion, scores around 50%. Clin Cancer Res; 23(16); 4569–77. ©2017 AACR.
Minerais do grupo da crichtonita em veios de quartzo da Serra do Espinhaço (Minas Gerais e Bahia)
Authors: Chaves Mario Luiz de Sá Carneiro , Menezes Filho Luiz Alberto Dias 
Published: April 2017

O trabalho descreve quatro minerais do grupo da crichtonita encontrados em veios hidrotermais de quartzo, que cortam diversas formações geológicas da Serra do Espinhaço (Supergrupo Espinhaço). Esses minerais – senaíta, crichtonita, almeidaíta e gramaccioliíta-(Y) – foram coletados em duas regiões: Presidente Kubitschek, ao sul de Diamantina (MG), e Novo Horizonte, na Chapada Diamantina Ocidental (BA). A idade de tais veios é relacionada ao final do Ciclo Brasiliano, em ca. 490 Ma. A senaíta é um mineral descoberto no Brasil e classicamente identificado nos aluviões diamantíferos da região de Diamantina; sua primeira ocorrência primária é aqui descrita. A crichtonita, apesar de conhecida desde longa data, teve seu primeiro depósito no país reportado nessa mesma região. A almeidaíta é o 61º e um dos mais recentes dos “minerais brasileiros”, sendo encontrada na região de Novo Horizonte. A gramaccioliíta-(Y), uma espécie descoberta na última década (Itália), tem sua primeira ocorrência brasileira descrita também nessa região. Os depósitos e as composições químicas desses minerais são caracterizados, bem como as problemáticas envolvidas até suas definições finais.
Associations Between Left Ventricular Dysfunction and Brain Structure and Function: Findings From the SABRE (Southall and Brent Revisited) Study
Authors: Park Chloe M. , Williams Emily D. , Chaturvedi Nish , Tillin Therese , Stewart Robert J. , Richards Marcus , Shibata Dean , Mayet Jamil , Hughes Alun D. 
Published: April 2017

Background

Subclinical left ventricular (
LV
) dysfunction has been inconsistently associated with early cognitive impairment, and mechanistic pathways have been poorly considered. We investigated the cross‐sectional relationship between
LV
dysfunction and structural/functional measures of the brain and explored the role of potential mechanisms.

Method and Results

A total of 1338 individuals (69±6 years) from the Southall and Brent Revisited study underwent echocardiography for systolic (tissue Doppler imaging peak systolic wave) and diastolic (left atrial diameter) assessment. Cognitive function was assessed and total and hippocampal brain volumes were measured by magnetic resonance imaging. Global
LV
function was assessed by circulating N‐terminal pro–brain natriuretic peptide. The role of potential mechanistic pathways of arterial stiffness, atherosclerosis, microvascular disease, and inflammation were explored. After adjusting for age, sex, and ethnicity, lower systolic function was associated with lower total brain (beta±standard error, 14.9±3.2 cm
3
;
P
<0.0001) and hippocampal volumes (0.05±0.02 cm
3
,
P
=0.01). Reduced diastolic function was associated with poorer working memory (−0.21±0.07,
P
=0.004) and fluency scores (−0.18±0.08,
P
=0.02). Reduced global
LV
function was associated with smaller hippocampal volume (−0.10±0.03 cm
3
,
P
=0.004) and adverse visual memory (−0.076±0.03,
P
=0.02) and processing speed (0.063±0.02,
P
=0.006) scores. Separate adjustment for concomitant cardiovascular risk factors attenuated associations with hippocampal volume and fluency only. Further adjustment for the alternative pathways of microvascular disease or arterial stiffness attenuated the relationship between global
LV
function and visual memory.

Conclusions

In a community‐based sample of older people, measures of
LV
function were associated with structural/functional measures of the brain. These associations were not wholly explained by concomitant risk factors or potential mechanistic pathways.
The Dependence of the Predictability of Mesoscale Convective Systems on the Horizontal Scale and Amplitude of Initial Errors in Idealized Simulations
Authors: Weyn Jonathan A. , Durran Dale R. 
Published: April 2017

Abstract
Recent work has suggested that modest initial relative errors on scales of O(100) km in a numerical weather forecast may exert more control on the predictability of mesoscale convective systems at lead times beyond about 5 h than 100% relative errors at smaller scales. Using an idealized model, the predictability of deep convection organized by several different profiles of environmental vertical wind shear is investigated as a function of the horizontal scale and amplitude of initial errors in the low-level moisture field. Small- and large-scale initial errors are found to have virtually identical impacts on predictability at lead times of 4–5 h for all wind shear profiles. Both small- and large-scale errors grow primarily up in amplitude at all scales rather than through an upscale cascade between adjacent scales. Reducing the amplitude of the initial errors improves predictability lead times, but this improvement diminishes with further reductions in the error amplitude, suggesting a limit to the intrinsic predictability in these simulations of slightly more than 6 h at scales less than 20 km. Additionally, all the simulated convective systems produce a k−5/3 spectrum of kinetic energy, providing evidence of the importance of the unbalanced, divergent gravity wave component of the flow produced by thunderstorms in generating the observed atmospheric kinetic energy spectrum.
Evaluation of Precipitable Water Vapor from Four Satellite Products and Four Reanalysis Datasets against GPS Measurements on the Southern Tibetan Plateau
Authors: Wang Yan , Yang Kun , Pan Zhengyang , Qin Jun , Chen Deliang , Lin Changgui , Chen Yingying , Lazhu  , Tang Wenjun , Han Menglei , Lu Ning , Wu Hui 
Published: April 2017

AbstractThe southern Tibetan Plateau (STP) is the region in which water vapor passes from South Asia into the Tibetan Plateau (TP). The accuracy of precipitable water vapor (PWV) modeling for this region depends strongly on the quality of the available estimates of water vapor advection and the parameterization of land evaporation models. While climate simulation is frequently improved by assimilating relevant satellite and reanalysis products, this requires an understanding of the accuracy of these products. In this study, PWV data from MODIS infrared and near-infrared measurements, AIRS Level-2 and Level-3, MERRA, ERA-Interim, JRA-55, and NCEP final reanalysis (NCEP-Final) are evaluated against ground-based GPS measurements at nine stations over the STP, which covers the summer monsoon season from 2007 to 2013. The MODIS infrared product is shown to underestimate water vapor levels by more than 20% (1.84 mm), while the MODIS near-infrared product overestimates them by over 40% (3.52 mm). The AIRS PWV product appears to be most useful for constructing high-resolution and high-quality PWV datasets over the TP; particularly the AIRS Level-2 product has a relatively low bias (0.48 mm) and RMSE (1.83 mm) and correlates strongly with the GPS measurements (R = 0.90). The four reanalysis datasets exhibit similar performance in terms of their correlation coefficients (R = 0.87–0.90), bias (0.72–1.49 mm), and RMSE (2.19–2.35 mm). The key finding is that all the reanalyses have positive biases along the PWV seasonal cycle, which is linked to the well-known wet bias over the TP of current climate models.
Effect of Mechanical Ventilation on the Thermal Offset of Pyranometers during Cloud-Free Summer Conditions
Authors: Sanchez G. , Serrano A. , Cancillo M. L. 
Published: April 2017

AbstractThermal offset is a significant source of uncertainty for solar radiation measurements. This study assesses the influence of mechanical ventilation on the daytime thermal offset of pyranometers. Toward this goal, an intensive unprecedented campaign of measurements was conducted in Badajoz, Spain, during four selected summer days under cloud-free conditions, covering a large range of solar zenith angle, irradiance, and temperature. Three leading manufacturers participated in the campaign, providing secondary standard pyranometers and compatible ventilation units. The thermal offset was experimentally measured following the capping methodology. A total of 372 capping events were conducted, the largest number ever reported in the literature. Each pyranometer was tested under different operational conditions (with/without ventilation and measuring global/diffuse irradiance). Results show that mechanical ventilation generally reduces the thermal offset. The magnitude of this reduction is different for each pyranometer model and depends on whether the instrument is shadowed (for measuring diffuse irradiance) or not (for measuring global irradiance). Mechanical ventilation tends to homogenize the temperature around the pyranometer and therefore reduces the impact of environmental conditions on the thermal offset. CMP11 and SPP pyranometers show notable tendencies in the thermal offset even when mechanical ventilation is applied. The Dutton et al. model, which aimed to correct the daytime thermal offset, is evaluated. Results show this model performs well for the SPP pyranometer but underestimates the absolute value of thermal offset for the CMP11 and SR20 pyranometers.
Serologic characterization of anti-protamine/heparin and anti-PF4/heparin antibodies
Authors: Lee Grace M. , Joglekar Manali , Kuchibhatla Maragatha , Khandelwal Sanjay , Qi Rui , Rauova Lubica , Arepally Gowthami M. 
Published: April 2017

Key PointsMonoclonal and polyclonal anti-PRT/heparin antibodies are serologically distinct from anti-PF4/heparin antibodies. Binding of anti-PRT/heparin antibodies to PRT/dextran complexes correlates with PRT/GAG reactivity.
Hepatic Insulin Resistance and Altered Gluconeogenic Pathway in Premature Baboons
Authors: McGill-Vargas Lisa , Gastaldelli Amalia , Liang Hanyu , Anzueto Guerra Diana , Johnson-Pais Teresa , Seidner Steven , McCurnin Donald , Muscogiuri Giovanna , DeFronzo Ralph , Musi Nicolas , Blanco Cynthia 
Published: April 2017

Abstract
Premature infants have altered glucose regulation early in life and increased risk for diabetes in adulthood. Although prematurity leads to an increased risk of diabetes and metabolic syndrome in adult life, the role of hepatic glucose regulation and adaptation to an early extrauterine environment in preterm infants remain unknown. The purpose of this study was to investigate developmental differences in glucose metabolism, hepatic protein content, and gene expression of key insulin-signaling/gluconeogenic molecules. Fetal baboons were delivered at 67%, 75%, and term gestational age and euthanized at birth. Neonatal baboons were delivered prematurely (67% gestation), survived for two weeks, and compared with similar postnatal term animals and underwent serial hyperinsulinemic-euglycemic clamp studies. Premature baboons had decreased endogenous glucose production (EGP) compared with term animals. Consistent with these results, the gluconeogenic molecule, phosphoenolpyruvate carboxykinase messenger RNA, was decreased in preterm baboons compared with terms. Hepatic insulin signaling was altered by preterm birth as evidenced by decreased insulin receptor–β, p85 subunit of phosphoinositide 3-kinase, phosphorylated insulin receptor substrate 1, and Akt-1 under insulin-stimulated conditions. Furthermore, preterm baboons failed to have the normal increase in glycogen synthase kinase-α from fetal to postnatal life. The blunted responses in hepatic insulin signaling may contribute to the hyperglycemia of prematurity, while impaired EGP leads to hypoglycemia of prematurity.
A Thyroid Hormone–Based Strategy for Correcting the Biochemical Abnormality in X-Linked Adrenoleukodystrophy
Authors: Hartley Meredith D. , Kirkemo Lisa L. , Banerji Tapasree , Scanlan Thomas S. 
Published: April 2017

Abstract
X-linked adrenoleukodystrophy (X-ALD) is a rare, genetic disorder characterized by adrenal insufficiency and central nervous system (CNS) demyelination. All patients with X-ALD have the biochemical abnormality of elevated blood and tissue levels of very long chain fatty acids (VLCFAs), saturated fatty acids with 24 to 26 carbons. X-ALD results from loss of function mutations in the gene encoding the peroxisomal transporter ABCD1, which is responsible for uptake of VLCFAs into peroxisomes for degradation by oxidation. One proposed therapeutic strategy for genetic complementation of ABCD1 is pharmacologic upregulation of ABCD2, a gene encoding a homologous peroxisomal transporter. Here, we show that thyroid hormone or sobetirome, a clinical-stage selective thyroid hormone receptor agonist, increases cerebral Abcd2 and lowers VLCFAs in blood, peripheral organs, and brains of mice with defective Abcd1. These results support an approach to treating X-ALD that involves a thyromimetic agent that reactivates VLCFA disposal both in the periphery and the CNS.