bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Background

The 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).

Methods

Species 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.

Results

A 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.

Conclusions

EC-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

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

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

Objective

No 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.

Methods

This 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.

Results

During 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).

Conclusion

Chest 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

Colonial 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

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 < 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 < 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

The 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., >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

Here 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

Diffusion 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

A 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

The 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.
Puberty timing and adiposity change across childhood and adolescence: disentangling cause and consequence
Authors: O’Keeffe Linda M , Frysz Monika , Bell Joshua A. , Howe Laura D. , Fraser Abigail
Published: March 2019

Objective

To better understand if earlier puberty is more likely a result of adiposity gain in childhood than a cause of adiposity gain in adulthood.

Design

Prospective birth cohort study.

Setting

Population based study of children born in 1991/1992 in Bristol UK (Avon Longitudinal Study of Parents and Children (ALSPAC)).

Participants

4,186 participants (2,176 female and 1,990 male) of predominantly White ethnicity with 18,232 repeated measures throughout follow-up.

Exposures & outcomes

Repeated measures of height from 5y to 20y to identify puberty timing (age at peak height velocity) and repeated measures of dual-energy X-ray absorptiometry-derived fat mass from age 9y to 18y, modelled separately in females and males using models based on chronological age and time before and after puberty onset.

Results

Mean age at peak height velocity was 11.7y (standard deviation (SD)=0.8y) for females and 13.6y (SD=0.9y) for males. In adjusted models of fat mass by chronological age, a one-year later age at peak height velocity was associated with 20.4% (95% Confidence Interval (CI): 18.5% to 22.3%) and 22.8% (95% (CI): 20.7% to 24.8%) lower fat mass in females and males respectively at 9y. These differences were smaller at age 18y: 7.8% (95% (CI):5.9% to 9.6%) and 11.9% (95% (CI): 9.1%, to 14.7%) lower fat mass in females and males respectively per year later age at peak height velocity. Trajectories of fat mass by time before and after puberty onset provided strong evidence for an association of pre-pubertal fat mass with puberty timing, and little evidence of an association of puberty timing with post-pubertal changes in fat mass in females. In males, findings were less clear before puberty though there was some evidence for an association of earlier puberty timing with great post-pubertal gain in fat mass.

Conclusions

Earlier puberty is more likely a result of adiposity gain in childhood than a cause of adiposity gain in adulthood in females. In males early to puberty, differences in fat mass after puberty are driven partially by tracking of adiposity from early childhood but also greater gains in post-pubertal adiposity. Reducing levels of childhood adiposity may help prevent both earlier puberty, later life adiposity and their associated adverse social, mental and physical health sequelae.
Gender differences in attitudes toward death among Chinese university students:A survey in hunan and Heilongjiang province
Authors: Wang Yuwei , Tang Siyuan , Hu Xin , Qin Chunxiang , Ma Lin , Li Yang , Khoshnood Kaveh , Sun Mei
Published: March 2019

Background

A positive attitude toward death has significant implications for college students, and can help students establish a healthy concept of life. But most colleges and universities in Mainland China have not yet carried out systematic death education courses.

Objective

This study aims to explore the attitudes of college age students to determine how they approach the idea of death using questions that explore five separate dimensions of attitude and belief.

Methods

We invited students from seven colleges in Mainland China using invitations sent to each year’s WeChat group. Students participated by scanning a QR code, and were then directed to a website that contained a self-administered questionnaire. We received 1,206 completed interviews.

Results

We found evidence of a substantial gender difference in attitudes toward death. These differences remain after adjustment for differences between male and female in other correlates of death attitudes, and are not a function of gender differences in the dimensionality of the five scales used to characterize attitudes.

Conclusion

Using previous research on gender differences as a guide, we speculate that these differences originate in culturally-defined expectations that are gender-related, as well as in substantial differences in individual family experiences of death. These speculations can take the form of testable hypotheses that should explain differences within genders as well as between genders. We believe that better education about death for college students can shape healthier attitudes among both male and female.
treeClust improves protein co-regulation analysis due to robust selectivity for close linear relationships
Authors: Kustatscher Georg , Grabowski Piotr , Rappsilber Juri
Published: March 2019

Gene co-expression analysis is a widespread method to identify the potential biological function of uncharacterised genes. Recent evidence suggests that proteome profiling may provide more accurate results than transcriptome profiling. However, it is unclear which statistical measure is best suited to detect proteins that are co-regulated. We have previously shown that expression similarities calculated using treeClust, an unsupervised machine-learning algorithm, outperformed correlation-based analysis of a large proteomics dataset. The reason for this improvement is unknown. Here we systematically explore the characteristics of treeClust similarities. Leveraging synthetic data, we find that tree-based similarities are exceptionally robust against outliers and detect only close-fitting, linear protein – protein associations. We then use proteomics data to demonstrate that both of these features contribute to the improved performance of treeClust relative to Pearson, Spearman and robust correlation. Our results suggest that, for large proteomics datasets, unsupervised machine-learning algorithms such as treeClust may significantly improve the detection of biologically relevant protein – protein associations relative to correlation metrics.
Microbiological, biochemical, physicochemical surface properties and biofilm forming ability ofBrettanomyces bruxellensis
Authors: Dimopoulou Maria , Renault Margareth , Dols-Lafargue Marguerite , Albertin-Leguay Warren , Herry Jean-Marie , Bellon-Fontaine Marie-Noëlle , Masneuf-Pomarede Isabelle
Published: March 2019

Brettanomyces bruxellensisis a serious source of concern for winemakers. The production of volatile phenols by the yeast species confers to wine unpleasant sensory characteristics which are unacceptable by the consumers and inevitably provoke economic loss for the wine industry. This ubiquitous yeast is able to adapt to all winemaking steps and to withstand various environmental conditions. Moreover, the ability ofB. bruxellensisto adhere and colonize inert materials can be the cause of the yeast persistence in the cellars and thus recurrent wine spoilage. We therefore investigated the surface properties, biofilm formation capacity and the factors which may affect the attachment of the yeast cells to surfaces with eight strains representative of the genetic diversity of the species. Our results show that the biofilm formation ability is strain-dependent and suggest a possible link between the physicochemical properties of the studied strains and their corresponding genetic group.
Optimization of 3D bioprinting of human neuroblastoma cells using sodium alginate hydrogel
Authors: Lewicki Jakub , Bergman Joost , Kerins Caoimhe , Hermanson Ola
Published: March 2019

There are many parameters in extrusion-based three-dimensional (3D) bioprinting of different materials that require fine-tuning to obtain the optimal print resolution and cell viability. To standardize this process, methods such as parameter optimization index (POI) have been introduced. The POI aims at pinpointing the optimal printing speed and pressure to achieve the highest accuracy keeping theoretical shear stress low. Here we applied the POI to optimize the process of 3D bioprinting human neuroblastoma cell-laden 2% sodium alginate (SA) hydrogel using freeform reversible embedding of suspended hydrogels (FRESH). Our results demonstrate a notable difference between optimal parameters for printing 2% SA with and without cells in the hydrogel. We also detected a significant influence of long-term cell culture on the printed constructs. This observation suggests that the POI has to be evaluated in the perspective of the final application. When taking these conditions into consideration, we could define a set of parameters that resulted in good quality prints maintaining high neuroblastoma cell viability (83% viable cells) during 7 days of cell culture using 2% SA and FRESH bioprinting. These results can be further used to manufacture neuroblastoma in vitro 3D culture systems to be used for cancer research.
Avoiding potential biases in ses.PD estimations with the Picante software package
Authors: Molina-Venegas Rafael
Published: March 2019

Faith’s phylogenetic diversity (PD) is one of the most widespread used indices of phylogenetic structure in the eco-phylogenetic literature. The metric became notably popular with the publication of the function pd as part of the Picante R package, which is nowadays a reference software for phylogenetic analyses.

Because PD is not statistically independent of species richness, the routine procedure is to standardize the observed PD values for unequal richness across samples. The function ses.pd, which is also implemented in the Picante R package, is the reference function to conduct such standardization.

Unfortunately, I have detected an anomaly in the function that may result in biased estimations of standardized PD values, particularly in communities with low species richness (i.e. less than four species) and unbalanced phylogenies.

I conduct a simple simulation exercise to illustrate the issue and propose two alternative and easy to implement solutions to go around the problem.
An approximate derivate-based controller for regulating gene expression
Authors: Modi Saurabh , Dey Supravat , Singh Abhyudai
Published: March 2019

Inside individual cells, protein population counts are subject to molecular noise due to low copy numbers and the inherent probabilistic nature of biochemical processes. Such random fluctuations in the level of a protein critically impact functioning of intracellular biological networks, and not surprisingly, cells encode diverse regulatory mechanisms to buffer noise. We investigate the effectiveness of proportional and derivative-based feedback controllers to suppress protein count fluctuations originating from two noise sources: bursty expression of the protein, and external disturbance in protein synthesis. Designs of biochemical reactions that function as proportional and derivative controllers are discussed, and the corresponding closed-loop system is analyzed for stochastic controller realizations. Our results show that proportional controllers are effective in buffering protein copy number fluctuations from both noise sources, but this noise suppression comes at the cost of reduced static sensitivity of the output to the input signal. Next, we discuss the design of a coupled feedforward-feedback biochemical circuit that approximately functions as a derivate controller. Analysis using both analytical methods and Monte Carlo simulations reveals that this derivative controller effectively buffers output fluctuations from bursty stochastic expression, while maintaining the static input-output sensitivity of the open-loop system. As expected, the derivative controller performs poorly in terms of rejecting external disturbances. In summary, this study provides a systematic stochastic analysis of biochemical controllers, and paves the way for their synthetic design and implementation to minimize deleterious fluctuations in gene product levels.
Timing and Duration ofGbx2Expression Delineates Thalamocortical and Dopaminergic Medial Forebrain Bundle Circuitry
Authors: Normand Elizabeth , Browning Catherine , Zervas Mark
Published: March 2019

Gene expression is a dynamic process, which is highly coordinated during development to ensure the proper allocation and identity of neuronal cell types within the brain. Equally important during neurodevelopment is how cohorts of neurons establish axonal projections that innervate terminal target sites. We sought to bridge the temporal dynamics of gene expression, within a specific genetic lineage, to the establishment of neuronal circuits derived from cohorts of the lineage-specific progenitors. A central goal was to be able to accomplish genetic inducible circuit mapping non-invasively and with commonly available CreER/loxPtechnology. Specifically, we genetically marked thalamic neuron progenitors that expressed the transcription factorGbx2at an early embryonic stage and tracked the formation of lineage-derived thalamocortical axons during embryogenesis. We then assessed the neural circuitry at an early postnatal stage. We show that the temporal specificity of lineage marking provides a high degree of clarity for following neural circuit development. We also determined that the onset and duration of gene expression can delineate subsets of neural circuits derived from a common lineage. For example, we uncovered a novel contribution ofGbx2-expressing progenitors to midbrain dopamine neurons and dopaminergic axons of the medial forebrain bundle. We anticipate that this system can be instructive in elucidating changes in neural circuit development in both normal development and in mutant mice in which neural circuit formation is altered.
Improved Stability of Polyglycerol Polyricinoleate‐Substituted Nanostructured Lipid Carrier Cholecalciferol Emulsions with Different Carrier Oils
Authors: Seo Tae‐Rang , Lee Inil , Chun Yong‐Gi , Park Dong‐June , Lee Sang‐Hoon , Kim Bum‐Keun
Published: March 2019

Cholecalciferol, also known as vitamin D3, is a recognized therapeutic agent for treatment of bone diseases and cancer. However, instability and poor bioavailability have been major challenges for delivering Vitamin D3. The objective of this study was to formulate improved nanostructured lipid carrier (NLC) vitamin D3 emulsions. We tested the effect of different carrier oils and the use of a solid lipid nanoparticle emulsifier, polyglycerol polyricinoleate (PGPR) on the stability of the vitamin D3 emulsions. In contrast to the control that used glyceryl monostearate (GMS) the PGPR substitution resulted in relatively small particle sizes (0.30 to 0.43 μm), with high absolute value of zeta potentials (39.5 to 67.8 mV) and high encapsulation efficiency (85.2% to 90.4%). The stability of the NLC emulsions against environmental stresses was evaluated under varying conditions of ionic strength, pH, freeze–thaw cycles, and storage at different temperatures. Although NLC emulsions were stable at high ionic strengths, they were found to be unstable at low pH (<3), which led to aggregation and coalescence of emulsion droplets. In case of freeze–thaw stress, although relatively stable compared to control NLC, the PGPR substituted groups exhibited a slight increase in particle size and a decrease in zeta potential when the cycle was repeated five times. Additionally, we found that PGPR‐substituted emulsions showed higher liquid dispersion stability than controls at 25 and 65 °C. Thus, we have formulated a modified NLC vitamin D3 emulsion that can be widely used in the food industry.

Practical Application

Vitamin D3, an essential micronutrient, is often added as supplements in food products and beverages for added health benefits. However, the stability of vitamin D3 emulsions that are used in the preparation of such products has been a major concern. We have developed a modified emulsion that has improved stability against environmental stresses. We believe, in future, this formulation can be efficiently used in the food industry.
The Triacylglycerol Profile of Oil Bodies and Oil Extracted from Argania spinosa Using the UPLC Along with the Electrospray Ionization Quadrupole‐Time‐of‐Flight Mass Spectrometry (LC‐Q‐TOF‐MS)
Authors: Zaaboul Farah , Cao Chen , Raza Husnain , Jun Zhao Zheng , Xu Yong Jiang , Liu Yuan Fa
Published: March 2019

The triacylglycerol (TAG) matrix of argan oil (AO) bodies (AOB) along with the TAGs of AO extracted from the same kernels using an organic solvent, were identified and quantified using the ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry. Generally, both samples showed a similar TAGs profile but AO found to have three extra TAGs in low amount. In total 23 and 26 different TAGs were identified in AOBs and AO, respectively. The most abundant TAGs were OOL, POO, OOO, and POL in both samples. Furthermore, oleic acid, linoleic acid, and palmitic acid were the major fatty acids in both AOBs and AO. To the best of our knowledge, this is the first research that studied the TAGs matrix of an oil body revealing no major difference between the TAGs profile protected by the AOBs membrane and the oil extracted from the whole seed.

Practical Application

Seed and kernels oil bodies emulsion tend to be the new source of emulsified oil in food and cosmetic industries. However, before replacing a product with another, we have to make sure that the new alternative can offer better or at least similar benefits. Our results showed that the triacylglycerols (TAGs) matrix and the argan oil (AO) share the same TAGs profile with a relatively close percentage. Therefore, AO bodies can be the perfect pre‐emulsified oil for some food products like sauces and creams.
sars: an R package for fitting, evaluating and comparing species–area relationship models
Authors: Matthews Thomas J. , Triantis Kostas A. , Whittaker Robert J. , Guilhaumon François
Published: March 2019

The species–area relationship (SAR) constitutes one of the most general ecological patterns globally. A number of different SAR models have been proposed. Recent work has shown that no single model universally provides the best fit to empirical SAR datasets: multiple models may be of practical and theoretical interest. However, there are no software packages available that a) allow users to fit the full range of published SAR models, or b) provide functions to undertake a range of additional SAR‐related analyses. To address these needs, we have developed the R package ‘sars’ that provides a wide variety of SAR‐related functionality. The package provides functions to: a) fit 20 SAR models using non‐linear and linear regression, b) calculate multi‐model averaged curves using various information criteria, and c) generate confidence intervals using bootstrapping. Plotting functions allow users to depict and scrutinize the fits of individual models and multi‐model averaged curves. The package also provides additional SAR functionality, including functions to fit, plot and evaluate the random placement model using a species–sites abundance matrix, and to fit the general dynamic model of oceanic island biogeography. The ‘sars’ R package will aid future SAR research by providing a comprehensive set of simple to use tools that enable in‐depth exploration of SARs and SAR‐related patterns. The package has been designed to allow other researchers to add new functions and models in the future and thus the package represents a resource for future SAR work that can be built on and expanded by workers in the field.
Hippocampal atrophy disrupts the language network but not hemispheric language lateralization
Authors: Lopes Tátila Martins , de Campos Brunno Machado , Zanão Tamires Araújo , Balthazar Marcio L. F. , Yasuda Clarissa Lin , Cendes Fernando
Published: March 2019

Objective

It is still unclear how temporal lobe epilepsy (TLE) with and without hippocampal atrophy (HA) affects cortical language distribution. We aimed to investigate the role of the hippocampus on language lateralization, activation pattern, and functional connectivity (FC) in patients with TLE.

Methods

We investigated 93 patients with TLE—divided into right HA (RHA), left HA (LHA), and negative magnetic resonance imaging (MRI) (non‐HA)—and 101 controls using a semantic‐language functional MRI (fMRI) task and the Boston Naming Test (BNT).

Results

Groups did not differ in the frequency of atypical language lateralization (LL), which correlated differently with handedness in each brain region and group. Blood‐oxygen‐level dependend (BOLD) activation patterns and region of interest (ROI)‐to‐ROI FC differed between LHA and controls, as well as between LHA and non‐HA patients. In the task activation pattern analysis, there was a decrease in the activation of patients with LHA relative to controls, exactly in the left hippocampus. However, non‐HA patients had increased FC relative to controls in the left superior temporal gyrus region. Seed‐to‐voxel FC demonstrated greater differences between patients and controls and smaller differences among patient groups. The non‐HA group was similar to controls, except for increased BOLD activation and increase FC in the superior temporal gyri. RHA and LHA differed from controls in BNT. BNT correlated with fMRI activation in RHA and non‐HA groups.

Significance

LHA affected naming performance, fMRI semantic task activation pattern, and FC more than RHA and non‐HA. Contrary to our expectations, LHA did not increase the frequency of atypical LL. Regardless of the side, HA impacts negatively on the language network but not on hemispheric language lateralization.
The role of intraspecific competition in the dispersal of an invasive fish
Authors: Grabowska Joanna , Zięba Grzegorz , Przybylski Mirosław , Smith Carl
Published: March 2019

Ponto‐Caspian gobies are among the most successful fish invaders in inland waters of Europe and in the Great Lakes of North America. Their invasions appear to comprise a combination of passive and active dispersal mechanisms, both natural and human‐mediated. Despite the significance of Ponto‐Caspian gobies as invasive species, there is little information about the mechanisms underpinning their dispersal. They are relatively small benthic fish, with high site affinity. Thus, actively dispersing individuals must express a behavioural motivation to engage in persistent directional movement.

Several recent studies have suggested that inter‐individual behavioural differences in boldness, activity level and tendency to explore might underpin dispersal. In addition, because males are highly territorial, intraspecific competition may lead to density‐dependent dispersal of subordinate individuals. To date, studies on this subject have focused mainly on comparisons between individuals from the core of established populations with those at the margins and, thus, address the outcome of dispersal rather than the mechanism itself.

We conducted a series of experiments on the racer goby Babka gymnotrachelus to address the question of what behavioural and physiological traits predict the tendency of an individual to perform dispersal behaviour, specifically considering the role of conspecifics in influencing the tendency to disperse. We used an artificial channel to measure dispersal tendency in this species in combination with behavioural trials.

Our results showed that fish with a greater tendency to disperse in an experimental channel grew more slowly and were bolder; that is displayed a greater propensity to emerge from a cryptic background onto a white background and performed worse in prey capture trials. As predicted, intraspecific competition played a primary role in the dispersal of the racer goby. Dominant males showed a tendency to monopolise limited shelters with an outcome that subordinates were forced to disperse upstream. The specific growth rate of individuals appeared to be a good indicator of social position. Subordinate males expressed the lowest rates of growth, probably as a result of long‐term deprivation of food in the presence of dominant conspecifics. They were also quicker to explore novel environments, possibly to search for food. Contrary to expectations, subordinate individuals performed relatively poorly in feeding trials when tested individually.

Our findings suggest that intraspecific competition in racer goby males is an important mechanism for active dispersal. It can also influence inter‐individual variation in traits such as boldness and tendency to explore novel environments. Similar responses to competitive interactions may have encouraged the invasive expansion of other Ponto‐Caspian gobies following establishment in new environments, as well as other fish species that exhibit territorial behaviour.
Urbanisation alters fatty acids in stream food webs
Authors: Whorley Sarah B. , Smucker Nathan J. , Kuhn Anne , Wehr John D.
Published: March 2019

Fatty acids are essential to macroinvertebrate growth and reproduction and can indicate food web structure and nutritional quality of basal resources. However, broad‐scale examinations of how catchment land cover and associated stressors affect the proportions of fatty acids (FAs) in stream food webs are few.

Here, we: (1) examine relationships among proportions of FAs among benthic periphyton and macroinvertebrate collector/gatherers, shredders, and predators; and (2) test if relationships between periphytic and macroinvertebrate FAs were altered due to the intensity of urban development in catchments.

Proportions of the ≥20‐C eicosapentaenoic acid (EPA 20:5ω3), arachidonic acid (ARA 20:4ω6), and docosahexaenoic acid (22:6ω3) indicated collector/gatherers had a diet richer in periphyton than in shredders, which had significantly lower proportions of these FAs. Collector/gatherers were in turn likely to be high‐quality sources of ω3 and ≥ 20‐C FAs for predators, which also had significantly greater EPA and ARA proportions than those in shredders. Linoleic (18:2ω6) and α‐linolenic acid (18:3ω3) comprised the greatest proportions of FAs in shredders, which suggested a diet dominated by leaf litter and associated hyphomycetes.

As catchment urbanisation increased, proportions of total ω3 FAs and EPA in periphyton were significantly greater. This pattern also was seen through macroinvertebrate consumers and predators, given that proportions of these FAs in macroinvertebrates also were significantly correlated with factors associated with catchment urbanisation. The significant increase in total ω3 FAs and EPA proportions within shredders indicated that periphyton growth, and their FAs, increased on leaf litter, probably due to greater nutrient concentrations associated with catchment urbanisation. Proportions of total ω6 FAs in biota were not significantly correlated with factors associated with urban development, which could indicate that they were of sufficient abundance for consumers regardless of urban intensity or possible changes in their sources.

Our study provides an informative first step that identified notable differences in proportions of FAs among macroinvertebrates in urban streams and an increase in proportions of total ω3 FAs and EPA in periphyton, consumers, and predators as catchment urbanisation increases. Identifying how FA relationships within food webs change in response to catchment alterations and stressors could inform land use and management decisions by linking environmental changes to measures important to ecosystem outcomes.
Habitat amount, not patch size and isolation, drives species richness of macro‐moth communities in countryside landscapes
Authors: Merckx Thomas , Dantas de Miranda Murilo , Pereira Henrique M.
Published: March 2019

Aim

Our aim was to test whether species richness patterns are best explained by the effect of the total amount of habitat within the landscape, or instead by a combination of patch size and patch isolation effects. To this end, we jointly contrast the habitat amount hypothesis and countryside biogeography with patch size and isolation concepts from island biogeography.

Location

Three multi‐habitat landscapes in Peneda‐Gerês National Park, NW Portugal.

Taxon

Macro‐moths (Lepidoptera).

Methods

Light‐trapping using a semi‐nested design at 84 fixed sites which were each repeatedly sampled six times.

Results

Autocovariate models show that sampling sites with a higher number of forest and meadow macro‐moth species (alpha diversity) were surrounded by a higher amount of forest and meadow habitat, respectively within a 160 and 320 m radius (scale of effect). These top‐ranked models, containing only habitat amount as a significant variable, had lower Akaike's information criteria (AIC) than models (only) containing patch size and/or isolation. Complementary to this, the countryside species–area relationship (SAR) model outperforms the classic SAR model, so that the effective area of habitat explains landscape species richness (gamma diversity) across spatial scales (beta diversity) better than the classic SAR. Specifically, we show that forest macro‐moths have a higher spatial turnover than meadow macro‐moths and that, on average, there are more species in forest than in meadow habitat.

Main conclusions

The habitat amount hypothesis predicts alpha species richness in multi‐habitat landscapes better than do patch size and isolation while the countryside SAR predicts beta and gamma diversity better than the classic SAR. We suggest that evidence is mounting to revise the application of the classical approaches of island biogeography and metapopulation theory to conservation biogeography.