bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variations in the Occurrence of Resistance Phenotypes and Carbapenemase Genes Among Enterobacteriaceae Isolates in 20 Years of the SENTRY Antimicrobial Surveillance Program
Authors: Castanheira Mariana , Deshpande Lalitagauri M , Mendes Rodrigo E , Canton Rafael , Sader Helio S , Jones Ronald N 
Published: March 2019

Abstract

Background
A total of 178 825 Enterobacteriaceae isolates collected in 199 hospitals from 42 countries worldwide over 20 years (1997 to 2016) of the SENTRY Program were susceptibility tested by reference broth microdilution methods.

Methods
Trends in percentages over time were analyzed by the χ2 test. Results were reported as the percentage difference between the first (1997–2000) and the last (2013–2016) time period.

Results
Enterobacteriaceae exhibiting resistance to cephalosporins (extended-spectrum β-lactamase [ESBL] phenotype) and carbapenem resistance (CRE) significantly increased (P &lt; 0.05; χ2 test) from 10.3% to 24.0% and 0.6% to 2.9%, respectively. Similar trends were noted for all regions and infection sources. Klebsiella pneumoniae mainly drove the CRE increase. Multidrug-resistance (MDR) rates significantly increased from 7.3% to 15.3% overall, with important trends in all regions and infection sources. Significant increases were noted for MDR K. pneumoniae and Escherichia coli, polymyxin-resistant K. pneumoniae (2.0% to 5.5% overall), and aminoglycoside-resistant E. coli (7.0% to 18.0%) and K. pneumoniae (18.1% to 26.9%) over time in North America and Latin America. Carbapenemase-encoding genes were screened after 2007, and the occurrence of these genes was compared for 2007–2009 and 2014–2016. Among 1298 CRE isolates from the 2 study periods, blaKPC was detected among 186 (49.7%) and 501 (54.2%) isolates in 2007–2009 and 2014–2016, respectively. Metallo-β-lactamase genes were detected among 4.3% of the isolates from 2007 to 2009 and 12.7% of the isolates from 2014 to 2016, mainly due to the dissemination of isolates carrying blaNDM. Genes encoding IMP and VIM enzymes were observed in 1.9% and 2.4% (7 and 9 isolates) of the isolates from 2007 to 2009 and 0.4% and 1.9% of the isolates from 2014 to 2016. OXA-48 and variants increased from 4.3% in 2007–2009 to 12.6% in 2014–2016 (mainly in Europe).

Conclusions
A change in the epidemiology of carbapenemases and important increases in ESBL, CRE, MDR, and other resistant phenotypes among virtually all geographic regions and infection sources were noted in the 20 years of surveillance, highlighting the impact of antimicrobial resistance and the importance of its continuous monitoring.
Twenty Years of the SENTRY Antifungal Surveillance Program: Results for Candida Species From 1997–2016
Authors: Pfaller Michael A , Diekema Daniel J , Turnidge John D , Castanheira Mariana , Jones Ronald N 
Published: March 2019

AbstractBackgroundThe emergence of antifungal resistance threatens effective treatment of invasive fungal infection (IFI). Invasive candidiasis is the most common health care–associated IFI. We evaluated the activity of fluconazole (FLU) against 20 788 invasive isolates of Candida (37 species) collected from 135 medical centers in 39 countries (1997–2016). The activity of anidulafungin, caspofungin, and micafungin (MCF) was evaluated against 15 308 isolates worldwide (2006–2016).MethodsSpecies identification was accomplished using phenotypic (1997–2001), genotypic, and proteomic methods (2006–2016). All isolates were tested using reference methods and clinical breakpoints published in the Clinical and Laboratory Standards Institute documents.ResultsA decrease in the isolation of Candida albicans and an increase in the isolation of Candida glabrata and Candida parapsilosis were observed over time. Candida glabrata was the most common non–C. albicans species detected in all geographic regions except for Latin America, where C. parapsilosis and Candida tropicalis were more common. Six Candida auris isolates were detected: 1 each in 2009, 2013, 2014, and 2015 and 2 in 2016; all were from nosocomial bloodstream infections and were FLU-resistant (R). The highest rates of FLU-R isolates were seen in C. glabrata from North America (NA; 10.6%) and in C. tropicalis from the Asia-Pacific region (9.2%). A steady increase in isolation of C. glabrata and resistance to FLU was detected over 20 years in the United States. Echinocandin-R (EC-R) ranged from 3.5% for C. glabrata to 0.1% for C. albicans and C. parapsilosis. Resistance to MCF was highest among C. glabrata (2.8%) and C. tropicalis (1.3%) from NA. Mutations on FKS hot spot (HS) regions were detected among 70 EC-R isolates (51/70 were C. glabrata). Most isolates harboring FKS HS mutations were resistant to 2 or more ECs.ConclusionsEC-R and FLU-R remain uncommon among contemporary Candida isolates; however, a slow and steady emergence of resistance to both antifungal classes was observed in C. glabrata and C. tropicalis isolates.
Estimation of the Incidence of Guillain-Barré Syndrome During Pregnancy in the United States
Authors: Myers Tanya R , McCarthy Natalie L , Panagiotakopoulos Lakshmi , Omer Saad B 
Published: March 2019

Abstract
Guillain-Barré syndrome (GBS) is an adverse event of interest after vaccination, yet few data are available for background rates during pregnancy. We confirmed 2 cases of incident GBS and estimated an incidence of 2.8 confirmed GBS cases per million person-years (95% confidence interval, 0.5–9.3), indicating rare occurrence. Our findings will help inform safety assessments of Zika vaccines in pregnant populations.
Newborn with bilateral congenital cataracts: Never forget congenital rubella syndrome
Authors: Chacon Fonseca Inara , Wong Jacqueline , Mireskandari Kamiar , Chitayat David 
Published: March 2019

Abstract
A term, growth-restricted newborn presented with a sepsis-like picture, persistent pulmonary hypertension and bilateral cataracts. Initial review of prenatal and family history, as well as microbiological investigations were noncontributory. Following lenticular extraction, viral examination of the lenses confirmed the presence of rubella. Congenital rubella syndrome (CRS) presents with a constellation of signs and symptoms that overlap with many other conditions. The presence of bilateral cataracts in a newborn is a rare finding and this case is used to review the broad etiology of congenital cataracts. We propose a structured diagnostic approach for clinicians, remembering that CRS is a rare but possible etiology. The early diagnosis of CRS in this case, allowed us to initiate appropriate management and preventive measurements.
Management and recurrence of spontaneous pneumothorax in children
Authors: Gariépy Martin , Beaunoyer Mona , Miron Marie-Claude , Gravel Jocelyn 
Published: March 2019

AbstractObjectiveNo guideline clearly prescribes an approach to management of spontaneous pneumothorax in children. The objectives of this study were to evaluate practice variation in the management of spontaneous pneumothorax in children and its probability of recurrence.MethodsThis study was a retrospective chart review followed by a phone follow-up that included all children who had visited a tertiary care paediatric hospital for a first episode of spontaneous pneumothorax between 2008 and 2017. The primary outcomes were the management of pneumothorax (observation, oxygen, needle aspiration, intercostal chest tube, surgery) and the probability of recurrence. All charts were evaluated by a rater using a standardized report form and 10% of the charts were evaluated in duplicate. All children/families were contacted by phone to assess recurrence. The primary analyses were the proportions of each treatment modalities and recurrence, respectively.ResultsDuring the study period, 76 children were deemed eligible for the study. Among them, 59 had a primary spontaneous pneumothorax while 17 were secondary. The most common first therapeutic approaches were chest tube insertion (31), oxygen alone (27), and observation (14). A total of 54 patients were available for follow-up among whom a recurrence was observed in 28 (37% of the total cohort or 52% of available children).ConclusionChest tube insertion was the first line of treatment in about 40% of children with a first spontaneous pneumothorax. In this population, the recurrence probability is established between 37 and 52% and the majority occurs in the following months.
The Development Effects of the Extractive Colonial Economy: The Dutch Cultivation System in Java
Authors: Dell Melissa , Olken Benjamin A 
Published: March 2019

AbstractColonial powers typically organized economic activity in the colonies to maximize their economic returns. While the literature has emphasized long-run negative economic impacts via institutional quality, the changes in economic organization implemented to spur production historically could also directly influence economic organization in the long-run, exerting countervailing effects. We examine these in the context of the Dutch Cultivation System, the integrated industrial and agricultural system for producing sugar that formed the core of the Dutch colonial enterprise in 19th century Java. We show that areas close to where the Dutch established sugar factories in the mid-19th century are today more industrialized, have better infrastructure, are more educated, and are richer than nearby counterfactual locations that would have been similarly suitable for colonial sugar factories. We also show, using a spatial regression discontinuity design on the catchment areas around each factory, that villages forced to grow sugar cane have more village-owned land and also have more schools and substantially higher education levels, both historically and today. The results suggest that the economic structures implemented by colonizers to facilitate production can continue to promote economic activity in the long run, and we discuss the contexts where such effects are most likely to be important.
Impact of corn silage moisture at harvest on performance of growing steers with supplemental rumen undegradable protein, finishing steer performance, and nutrient digestibility by lambs1
Authors: Hilscher F Henry , Burken Dirk B , Bittner Curt J , Gramkow Jana L , Bondurant Robert G , Jolly-Breithaupt Melissa L , Watson Andrea K , MacDonald Jim C , Klopfenstein Terry J , Erickson Galen E 
Published: March 2019

Abstract
Three experiments evaluated delaying corn silage harvest, silage concentration, and source of supplemental protein on performance and nutrient digestibility in growing and finishing diets. Experiment 1 used 180 crossbred yearling steers (body weight [BW] = 428; SD = 39 kg) to evaluate corn silage dry matter (DM) (37% or 43%) and replacing corn with silage (15% or 45% of diet DM) in finishing diets containing 40% modified distillers grains with solubles. Experiment 2 used 60 crossbred steers (BW = 271; SD = 32 kg) to evaluate corn silage harvest DM (37% or 43%) and response to rumen undegradable protein (RUP) supplementation (0.5%, 1.4%, 2.4%, 3.3%, or 4.2% of diet DM) in silage growing diets. Experiment 3 used 9 crossbred lambs (BW = 30.1; SD = 4.1 kg) to evaluate nutrient digestibility of 37% or 43% DM corn silage in silage growing diets fed ad libitum or restricted to 1.5% of BW. In experiment 1, as corn silage concentration increased from 15% to 45%, average daily gain (ADG) and gain-to-feed ratio (G:F) decreased (P ≤ 0.04). Carcass-adjusted final BW and hot carcass weight (HCW) were lower (P ≤ 0.04) for steers fed 45% corn silage compared to 15% when fed for equal days. As DM of corn silage was increased from 37% to 43%, no differences (P ≥ 0.30) in dry matter intake (DMI), ADG, G:F, or HCW were observed. In experiment 2, as DM of corn silage increased from 37% to 43%, ADG and G:F decreased (P ≤ 0.04). Increasing supplemental RUP in the diet increased (P ≤ 0.05) ending BW, DMI, ADG, and G:F linearly as supplemental RUP increased from 0.5% to 4.2%. In experiment 3, there were no differences (P ≥ 0.56) in DM digestibility and organic matter digestibility between silage harvest DM and intake level. Neutral detergent fiber (NDF) intake was reduced (P &lt; 0.01) for lambs fed the delayed harvest corn silage compared to earlier corn silage harvest. As silage harvest was delayed from 37% to 43% DM, NDF digestibility decreased (P &lt; 0.01) from 64.39% to 53.41%. Although increasing corn silage concentration in place of corn in finishing diets reduced ADG and G:F, delayed silage harvest did not affect performance of finishing cattle. Delayed silage harvest in growing cattle resulted in lower ADG and G:F, possibly due to increased starch or maturity leading to decreased NDF digestibility. The addition of RUP to silage-based, growing diets improves performance by supplying more metabolizable protein and suggests RUP of corn silage is limiting.
Applying the California net energy system to growing goats1
Authors: Teixeira Izabelle A M A , Almeida Amélia K , Fernandes Márcia H M R , Resende Kleber T 
Published: March 2019

AbstractThe aim of this review is to describe the main findings of studies carried out during the last decades applying the California net energy system (CNES) in goats. This review also highlights the strengths and pitfalls while using CNES in studies with goats, as well as provides future perspectives on energy requirements of goats. The nonlinear relationship between heat production and metabolizable energy intake was used to estimate net energy requirements for maintenance (NEm). Our studies showed that NEm of intact and castrated male Saanen goats were approximately 15% greater than female Saanen goats. Similarly, NEm of meat goats (i.e., &gt;50% Boer) was 8.5% greater than NEm of dairy and indigenous goats. The first partial derivative of allometric equations using empty body weight (EBW) as independent variable and body energy as dependent variable was used to estimate net energy requirements for gain (NEg). In this matter, female Saanen goats had greater NEg than males; also, castrated males had greater NEg than intact males. This means that females have more body fat than males when evaluated at a given EBW or that degree of maturity affects NEg. Our preliminary results showed that indigenous goats had NEg 14% and 27.5% greater than meat and dairy goats, respectively. Sex and genotype also affect the efficiency of energy use for growth. The present study suggests that losses in urine and methane in goats are lower than previously reported for bovine and sheep, resulting in greater metabolizable energy:digestible energy ratio (i.e., 0.87 to 0.90). It was demonstrated that the CNES successfully works for goats and that the use of comparative slaughter technique enhances the understanding of energy partition in this species, allowing the development of models applied specifically to goat. However, these models require their evaluation in real-world conditions, permitting continuous adjustments.
Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy
Authors: Swaney Justin , Kamentsky Lee , Evans Nicholas B , Xie Katherine , Park Young-Gyun , Drummond Gabrielle , Yun Dae Hee , Chung Kwanghun 
Published: March 2019

AbstractHere we describe an image processing pipeline for quantitative analysis of terabyte-scale volumetric images of SHIELD-processed mouse brains imaged with light-sheet microscopy. The pipeline utilizes open-source packages for destriping, stitching, and atlas alignment that are optimized for parallel processing. The destriping step removes stripe artifacts, corrects uneven illumination, and offers over 100x speed improvements compared to previously reported algorithms. The stitching module builds upon Terastitcher to create a single volumetric image quickly from individual image stacks with parallel processing enabled by default. The atlas alignment module provides an interactive web-based interface that automatically calculates an initial alignment to a reference image which can be manually refined. The atlas alignment module also provides summary statistics of fluorescence for each brain region as well as region segmentations for visualization. The expected runtime of our pipeline on a whole mouse brain hemisphere is 1-2 d depending on the available computational resources and the dataset size.
High angular resolution diffusion MRI reveals conserved and deviant programs in the paths that guide human cortical circuitry
Authors: Charvet Christine J. , Das Avilash , Song Jae W. , Tindal-Burgess Deselyn J. , Kabaria Priya , Dai Guangping , Kane Tara , Takahashi Emi 
Published: March 2019

AbstractDiffusion MR tractography represents a novel opportunity to investigate conserved and deviant developmental programs between humans and other species such as mice. To that end, we acquired high angular resolution diffusion MR scans of mice (embryonic day [E] 10.5 to post-natal week [PW] 4) and human brains (gestational week [GW] 17 to 30) at successive stages of fetal development to investigate potential evolutionary changes in radial organization and emerging pathways between humans and mice. We compare radial glial development as well as commissural development (e.g., corpus callosum), primarily because our findings can be integrated with previous work. We also compare corpus callosal growth trajectories across primates (i.e., humans, rhesus macaques) and rodents (i.e., mice). One major finding is that the developing cortex of humans is predominated by pathways likely associated with a radial glial organization at GW 17-20, which is not as evident in age-matched mice (E 16.5, 17.5). Another finding is that, early in development, the corpus callosum follows a similar developmental timetable in primates (i.e., macaques, humans) as in mice. However, the corpus callosum grows for an extended period of time in primates compared with rodents. Taken together, these findings highlight deviant developmental programs underlying the emergence of cortical pathways in the human brain.
Applying continuous functional traits to large brown macroalgae: variation across tidal emersion and wave exposure gradients
Authors: Cappelatti Laura , Mauffrey Alizée R. L. , Griffin John N. 
Published: March 2019

ABSTRACTA functional trait-based approach seeks a general understanding of organism - environment interactions, but, among primary producers, its empirical basis rests on vascular plants. We hypothesised that with increasing intertidal elevation, traits of large brown macroalgae would reflect a resource-acquisition vs. conservation (stress tolerance) trade-off at species and community levels. Across the elevation gradient at four UK sites of varying wave exposure, we: i) screened species’ relevant morphological traits, using principal component analysis to reduce dimensionality; and ii) up-scaled species’ traits using community weighted trait means (CWMs). The first principal component (PC1) strongly related to specific thallus area and thallus dry matter content, representing an acquisition - conservation trade-off. Although species generally shifted to the conservative end of this axis as elevation increased, mid-shore Ascophyllum nodosum sat at the extreme conservative end. PC2 associated with holdfast ratio, thickness and length, with A. nodusum scoring higher than other mid-shore species. CWMs of PC1 decreased with elevation at two sites indicating a shift from ‘fast’ to ‘slow’ ecosystem functioning, but this relationship was disrupted by A. nodusum at the sheltered site, and by the up-shore extent of Laminaria digitata at the most exposed site. The anomalous traits of A. nodusum reflect its unique competitive strategy (slow, persistent growth) in the relatively stressful mid-shore. Seaweed functional traits show promise in linking species’ identities to their strategies and ecosystem contributions. However, because resource conservation traits can be related to competitive as well as stress tolerance strategies, predicting seaweed trait responses to environmental stress gradients is challenging.
A Comparison Of Robust Mendelian Randomization Methods Using Summary Data
Authors: Slob Eric A.W. , Burgess Stephen 
Published: March 2019

AbstractThe number of Mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. This is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. Since it is unlikely that all genetic variants will be valid instrumental variables, several robust methods have been proposed. We compare nine robust methods for Mendelian randomization based on summary data that can be implemented using standard statistical software. Methods were compared in three ways: by reviewing their theoretical properties, in an extensive simulation study, and in an empirical example to investigate the effect of body mass index on coronary artery disease risk. In the simulation study, the overall best methods, judged by mean squared error, were the contamination mixture method and the mode based estimation method. These methods generally had well-controlled Type 1 error rates with up to 50% invalid instruments across a range of scenarios. Outlier-robust methods such as MR-Lasso, MR-Robust, and MR-PRESSO, had the narrowest confidence intervals in the empirical example. They performed well when most variants were valid instruments with a few outliers, but less well with several invalid instruments. With isolated exceptions, all methods performed badly when over 50% of the variants were invalid instruments. Our recommendation for investigators is to perform a variety of robust methods that operate in different ways and rely on different assumptions for valid inferences to assess the reliability of Mendelian randomization analyses.