bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic estimation of BMI
Authors: Shan Meng-Jie , Zou Yang-Fan , Guo Peng , Weng Jia-Xu , Wang Qing-Qing , Dai Ya-Lun , Liu Hui-Bin , Zhang Yuan-Meng , Jiang Guan-Yin , Xie Qi , Meng Ling-Bing
Published: May 2019

The prevalence of overweight–obesity has increased sharply among undergraduates worldwide. In 2016, approximately 52% of adults were overweight–obese. This cross-sectional study aimed to investigate the prevalence of overweight–obesity and explore in depth the connection between eating habits and overweight–obesity among Chinese undergraduates.

The study population included 536 undergraduates recruited in Shijiazhuang, China, in 2017. They were administered questionnaires for assessing demographic and daily lifestyle characteristics, including sex, region, eating speed, number of meals per day, and sweetmeat habit. Anthropometric status was assessed by calculating the body mass index (BMI). The determinants of overweight–obesity were investigated by the Pearson χ2 test, Spearman rho test, multivariable linear regression, univariate/multivariate logistic regression, and receiver operating characteristic curve analysis.

The prevalence of undergraduate overweight–obesity was 13.6%. Sex [male vs female, odds ratio (OR): 1.903; 95% confidence interval (95% CI): 1.147–3.156], region (urban vs rural, OR: 1.953; 95% CI: 1.178–3.240), number of meals per day (3 vs 2, OR: 0.290; 95% CI: 0.137–0.612), and sweetmeat habit (every day vs never, OR: 4.167; 95% CI: 1.090–15.933) were significantly associated with overweight–obesity. Eating very fast was positively associated with overweight–obesity and showed the highest OR (vs very slow/slow, OR: 5.486; 95% CI: 1.622–18.553). However, the results of multivariate logistic regression analysis indicated that only higher eating speed is a significant independent risk factor for overweight/obesity (OR: 17.392; 95% CI, 1.614–187.363; P = .019).

Scoremeng = 1.402 × scoresex + 1.269 × scoreregion + 19.004 × scoreeatin 
speed + 2.546 × scorenumber of meals per day + 1.626 × scoresweetmeat habit and BMI = 0.253 × Scoremeng + 18.592. These 2 formulas can help estimate the weight status of undergraduates and predict whether they will be overweight or obese.
Psychotropic Medications Are Associated With Increased Liver Disease Severity in Pediatric Nonalcoholic Fatty Liver Disease
Authors: Mouzaki Marialena , Yodoshi Toshifumi , Arce‐Clachar Ana C. , Bramlage Kristin , Fei Lin , Ley Sanita L. , Xanthakos Stavra A.
Published: May 2019

Objectives:

The aim of the study was to determine whether pediatric patients with nonalcoholic fatty liver disease (NAFLD) exposed to psychotropic medications have more severe liver disease compared to their counterparts who are not on these medications. We hypothesize that use of psychotropic agents is associated with liver disease severity.

Methods:

Children and adolescents with biopsy‐confirmed NAFLD were included in this study. Histology data, detailed clinical information, and results of serum biochemistries performed within 3 months of the liver biopsy were collected retrospectively. Univariate and multivariate modeling was used to determine differences between the groups and to control for confounders.

Results:

A total of 228 patients were included, 17 (8%) of whom where on psychotropic medications at the time of the liver biopsy. Patients on psychotropic medications were more likely to also be on metformin (53% vs 18%, P < 0.01) and antihypertensive medications (29% vs 8%, P < 0.01) compared to children with NAFLD who were not on psychotropic agents. There were no differences in regards to biochemical evidence of liver injury, insulin resistance, and dyslipidemia between the groups. On histology, however, the use of psychotropic medications was associated with increased steatosis severity (score 2.4 vs 1.9, P = 0.04) and increased likelihood of having an NAFLD Activity Score ≥5 (seen in 59% vs 35% or patients; P = 0.05, respectively).

Conclusions:

In this large cohort of children with biopsy‐confirmed NAFLD, the use of psychotropic medications was associated with increased liver disease severity. Exposure to psychotropic agents should be considered when risk stratifying children with NAFLD.
Effectiveness of Platelet-Rich Plasma in the Management of Knee Osteoarthritis in a Rural Clinic
Authors: Mogoi Vincent , Elder Betty , Hayes Karen , Huhman Dawna
Published: May 2019

BACKGROUND:

Osteoarthritis (OA) is a degenerative disease causing decreased mobility. Use of autologous platelet-rich plasma (PRP) provides a reparative alternative in the management of OA.

METHODS/PURPOSE:

This study assessed effectiveness of nurse practitioner-injected PRP to manage knee OA in a rural setting.

RESULTS:

Twenty patients were followed for 1 month after PRP treatment. Knee function and pain levels were assessed using a knee function score (Knee Injury and Osteoarthritis Outcome Score Physical Function Short Form [KOOS-PS]).

CONCLUSIONS:

Overall, the 20 patients who participated in this study experienced significant improvement in knee function scores, decreased pain, and decreased use of pain medications.
Bioconversion of glycosides isoflavones to aglycone isoflavones by Lactobacillus rhamnosus BHN-LAB 76 under anaerobic conditions
Authors: Kim Byung-Hyuk , Jang Jong-Ok , Lee Jun-Hyeong , Park Ye-Eun , Kim Jung-Gyu , Yoon Yeo-Cho , Jeong Su Jin , Kwon Gi-Seok , Lee Jung-Bok
Published: May 2019

Isoflavones exhibit an estrogenic activity and have been reported extensively for their potential role in preventing chronic diseases, such as cancer, osteoporosis, and postmenopausal syndrome. Pueraria is a medicinally important leguminous plant producing several glycoside isoflavones, such as daidzin, daidzein, genistin, and puerarin. However, daidzin and genistin mainly exist as nonabsorbable and biologically inactive glycosides. The bioavailability of glucosides is increased by hydrolysis of the sugar moiety using β-glucosidase. Furthermore, intestinal microorganisms can enhance the biological activity of these isoflavones through biotransformation. Lactic acid bacteria (LAB) are typical probiotic microorganisms used in fermented foods, as feed additives, and in pharmaceuticals. Therefore, we isolated Lactobacillus rhamnosus BHN-LAB 76 from Korean traditional fermented food and assessed its isoflavone-transforming activity in the production of daidzein using HPLC. The Pueraria lobata extract was fermented with L. rhamnosus BHN-LAB 76 for 72 h at 37℃ under anaerobic conditions. L. rhamnosus BHN-LAB 76 could convert about 25% of daidzin to daidzein. These results confirmed the potential of L. rhamnosus BHN-LAB 76 as a probiotic culture, which can be utilized in the manufacture of fermented and functional foods.
Increased production of GABA in non-alcoholic Makgeolli by optimization of lactic acid fermentation using Lactobacillus plantarum
Authors: Choe Ji-Yeon , Lim Jong-Soon , Lee Sam-Pin
Published: May 2019

Lactic acid fermentation of non-alcoholic Makgeolli a traditional Korean rice wine was optimized for increased production of γ-aminobutyric acid (GABA). The Makgeolli was concentrated by vacuum evaporation at 85℃ for 30 min to yield non-alcoholic Makgeolli and sterilize the indigenous microorganisms. As a result, yeast and lactic acid bacteria were not observed in the non-alcoholic Makgeolli. The non-alcoholic Makgeolli had an unpleasant odor in the absence of glucose in lactic acid fermentation. Therefore, the non-alcoholic Makgeolli was mixed with 3% mono sodium-L-glutamate (MSG) and 1% glucose followed by fermentation with Lactobacillus plantarum EJ2014 at 30℃ for 7 days in stationary culture. During this period, the pH increased from 5.1 to 5.5 and acidity decreased from 0.41% to 0.2%. The viable cell count increased to 3.0×108 CFU/mL by the end of the 7 day period. The production was determined using TLC; results showed that Most of the MSG was bio-converted on within 5 days. of lactic acid fermentation. HPLC analysis confirmed GABA production 1.59%. In conclusion, non-alcoholic Makgeolli with 1% glucose and 3% MSG could produce functional rice ingredients including GABA and probiotics as well as wholesome rice products through lactic acid fermentation.
Antioxidant properties and oxidative stability of oregano seed ethanol extract
Authors: Han Chang Hee , Kim Min-Ah , Kim Mi-Ja
Published: May 2019

This study aimed to evaluate the antioxidant ability and inhibitory effects of oregano seed ethanol extract (OSEE). In vitro antioxidant assays including DPPH radical scavenging and ABTS cation radical scavenging were conducted, and, ORAC, total phenolic content, and FRAP value were determined. In addition, headspace oxygen, conjugated dienoic acid (CDA) value, and ρ-anisidine value (ρ-AV) for exploring oxidative stability were examined in an oil system with 100 ppm OSEE. The radical scavenging activities of 125 μg/mL OSEE using DPPH and ABTS were 84.6% and 32.2%, respectively. ORAC was significantly higher at a concentration of 100 μg/mL of OSEE as compared with the control without OSEE (p<0.05). The antioxidant ability of the sample was concentration dependent manner. Additionally, the total phenolic content and FRAP value of OSEE were 264.64 μg/mL tannic acid equivalent/g extract and 339.78 μg/mL ascorbic acid equivalent/g extract, respectively. CDA and ρ-AV were significantly reduced to 56.3% and 76.5%, respectively, in 7 h of oil oxidation in OSEE, as compared with the control oil. OSEE exhibited excellent in vitro antioxidant ability and oxidative stability in the oil matrix. Furthermore, the major volatile compounds of OSEE were limonene, linalool, o-cymene, thymol, α-pinene, and γ-terpinene. Therefore, it is evident that oregano seed can be used as a functional ingredient in the natural antioxidant market.
Physicochemical characteristics and antioxidant capacities of peach fruits in the development stages
Authors: Kim Chang-Seob , Lee Suk-Hee , Chung Shin-Kyo
Published: May 2019

In order to promote the utilization of peach fruits, we investigated the physicochemical characteristics of three different varieties of peach, namely, Wild Peach, Hikawa Hakuho, and Baekhyang, in various development stages (stone-hardening, fruit enlargement, and ripening). The peach fruits increased in length, width, and weight in the development stage. Baekhyang had the highest size among all the varieties in the development stage. The ratio of the length and width was the highest in the stone hardening stage and decreased thereafter. The hardness of the peach fruits decreased, except Wild Peach (p<0.05). The sugar content in all the varieties increased during the development stage, but the acidity decreased. The ratio of sugar and acidity increased with the progress of the development stage. The total phenolic content (TPC) was the highest in Baekhyang in the stone-hardening stage. All the varieties had the highest TPC in the stone-hardening stage, among all the development stages. No significant difference in the DPPH radical scavenging activity was observed in the fruit enlargement and ripening stage across the different varieties. The length, width, and weight of peach fruits increased, but the hardness decreased in the fruit development stage. The ratio of sugar and acidity increased, but the antioxidant capacity decreased.
Effect of ethanol leaching conditions on the properties of liqueur prepared from Citrus junos fruit peels
Authors: Chung Hun-Sik , Park Han-Sol , Kim Han-Soo , Lee Young-Guen , Seong Jong-Hwan
Published: May 2019

This study was conducted to prepare liqueur using Citrus junos fruit peels. Effects of ethanol concentration (EC) and mixing ratio (MR) of leaching solvents with fruit peels on the quality characteristics of the liqueur were investigated. Sliced peels separated from C. junos with an MR of 25% were placed in glass jars and mixed with leaching solvents with ECs of 10%, 20%, 30%, 40%, or 50%. Additionally, sliced peels with MRs of 5%, 15%, 25%, 35%, or 45% were placed in glass jars, mixed with a leaching solvent with an EC of 30%, and then leached for 30 days at 20℃. As the EC increased, the soluble solid and vitamin C contents of the liqueur decreased slightly, while the phenolic compound content increased. The soluble solid content, titratable acidity, phenolic compound content, vitamin C content, antioxidant activity, and color properties (-a* value, b* value) increased linearly with increasing MR. From these results, it was confirmed that C. junos fruit peels could be used to produce liqueur. It was concluded that an MR of 45% or more was suitable for liqueur production.
Antioxidant and anti-inflammatory activity on sea tangle (Laminaria japonica) adding vinegar
Authors: Ahn You Seong
Published: May 2019

The objective of this study was to evaluate the antioxidant and anti-inflammatory activity of vinegar with added sea tangle (Laminaria japonica) (VAST). To determine the antioxidant activity, DPPH and ABTS radical scavenging activity, reducing power, and total polyphenolic and flavonoid contents were evaluated. The anti-inflammatory activity was determined using lipopolysaccharide (LPS) induced macrophage (RAW 264.7). Finally, the antioxidant and anti-inflammatory activities of VAST were compared with those of vinegar without added sea tangle (VNAST). The antioxidant activity, total polyphenol content, and total flavonoid content were all higher in VAST than in VNAST. Moreover, neither VAST nor VNAST displayed toxicity toward RAW 246.7 cells at up to 200-fold dilution. In LPS-induced RAW 264.7 cells, VAST treatment significantly decreased the production of nitric oxide and inflammatory cytokine (TNF-α) compared with VNAST treatment. Overall, VAST showed exhibited superior antioxidant and anti-inflammatory activities compared with VNAST. These results clearly indicate that VAST has the potential for use as an anti-oxidant and anti-inflammatory agent in functional foods.
Comparison of biological activity between Stellaria aquatica seed extracts
Authors: Cho Hyun-Dong , Kang Won-Sik , Kim Du-Hyun , Ku Ja-Jung , Seo Kwon-Il
Published: May 2019

Stellaria aquatica, belong to the family Caryophyllaceae (commonly known as the carnation family), is a perennial plant found in subtropical and temperate regions. In addition, the seeds of S. aquatica are known to be polyphenol-rich; however, the biological activities of S. aquatica seeds have not yet been evaluated. To enhance the use of S. aquatica seeds as functional food and natural medicine, the total polyphenolic content, and anti-oxidant, anti-cancer, and immune-modulatory activities of S. aquatica seed extracts were investigated. The radical scavenging and reducing power activities of 1,000 μg/mL S. aquatica seed extracts were similar to those of BHT and α-tocopherol. In addition, total polyphenol and flavonoid contents of S. aquatica seed extracts were the highest in 70% EtOH extract (27.30 mg GAE/g and 23.22 mg QE/g, individually). In the case of HepG2, A549, MCF-7, and B16 cells, IC50 value of the 70% EtOH extract was lesser than that of other extracts, whereas the lowest IC50 activity of EtOH extracts was noted in HT-29 and PC-3 cells. Furthermore, EtOH, MeOH and 70% EtOH extract-induced cancer cell death was related to apoptosis. In RAW 264.7 macrophages, 70% EtOH extract significantly improved immune-modulatory activity by increasing nitric oxide (NO) production without inducing significant cytotoxicity. Taken together, our results provide important insights into the bioactive potential of S. aquatica seed extracts as functional food ingredient and natural medicine.
Investigating the effect of Crataegus pinnatifida, a functional food, on cognition and memory deficit
Authors: Lee Jihye , Park Sang Hyeok , Lee Chanhee , Kim Hye-Jeong , Jung Chul Jong , Beik Gyung Yun , Shin Jin Gi , Jung Ji Wook
Published: May 2019

Crataegus pinnatifida (hawthorn) is highly popular as a pleasant-tasting functional food and herb that can also be used for treating cardiovascular diseases. The improvements in learning and memory brought about by C. pinnatifida have been investigated, and the mechanism of action in scopolamine-induced amnesia model in mice was elucidated. C. pinnatifida extract was orally administered to the mice, and scopolamine, a muscarinic acetylcholine receptor antagonist, was injected 30 min before the Y-maze, passive avoidance, and Morris water maze test. It was observed that C. pinnatifida extract improved the percentage of spontaneous alternation, increased the step-through latency, and shortened the escape latency, respectively. C. pinnatifida extract contained 380.70 kcal energy, which had contributions from carbohydrate (92.5%), sugars (92.4%), crude protein (1.1%) and crude fat (0.7%). Polyphenol and flavonoid contents assessed using Folin-Denis’ reagent and aluminium nitrate revealed 9.8±0.3 mg tannic acid equivalent/g of polyphenol and 18.9±0.4 mg quercetin equivalent/g of flavonoid, respectively. Furthermore, C. pinnatifida extract inhibited acetylcholinesterase in the whole brain. Taken together, this study demonstrated that C. pinnatifida ameliorated memory and cognitive function, indicating that it might be useful as a functional food and could also be an efficient candidate as an anti-amnesia agents.
Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation
Authors: Raab Jesse R , Tulasi Deepthi Y , Wager Kortney E , Morowitz Jeremy M , Magness Scott T , Gracz Adam D
Published: May 2019

Intestinal stem cell (ISC) plasticity is thought to be regulated by broadly-permissive chromatin shared between ISCs and their progeny. Here, we utilize a Sox9EGFP reporter to examine chromatin across ISC differentiation. We find that open chromatin regions (OCRs) can be defined as broadly-permissive or dynamic in a locus-specific manner, with dynamic OCRs found primarily in loci consistent with distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) motifs in context of Sox9EGFP populations, we classify broadly-permissive and dynamic chromatin relative to TF usage. These analyses identify known and potential regulators of ISC differentiation via their association with dynamic changes in chromatin. We observe ISC expansion in Id3-null mice, consistent with computational predictions. Finally, we examine the relationship between gene expression and 5-hydroxymethylcytosine (5hmC) in Sox9EGFP populations, which reveals 5hmC enrichment in absorptive lineage specific genes. Our data demonstrate that intestinal chromatin dynamics can be quantitatively defined in a locus-specific manner, identify novel potential regulators of ISC differentiation, and provide a chromatin roadmap for further dissecting the role of cis regulation of cell fate in the intestine.
Recreational fisheries as a driver of salmonid population conservation
Authors: Worthington Thomas A. , Worthington Ian , Vaughan Ian P. , Ormerod Steve J , Durance Isabelle
Published: May 2019

The need to monitor and protect biodiversity has never been greater, yet resources are often constrained economically. The ecosystem service paradigm could promote nature conservation while sustaining economic activity and other societal benefits, but most efforts to assess biodiversity-ecosystem service (B-ES) links have focused on diversity measures, with little attention on how species abundance relates to the magnitude of ES provision.

Here, we utilised four national scale, multi-decadal, Atlantic salmon (Salmo salar) datasets to investigate links between juvenile density, the abundance of returning adults, and two measures of recreational angling provision: rod catches and angling effort.

Recreational rod catches only tracked juvenile density and returning adult numbers in catchments where juvenile and adult numbers were decreasing, implying important early-warning of ES decline. In contrast, angling effort declined consistently through time.

Synthesis and applications. These data illustrate i) the difficulty in measuring ES in ways that explicitly relate human resource use to nature conservation, and ii) the need for better quantification of populations at all life stages that determine ES provision, particularly in species where long-distance movements bring exposure to multiple global pressures. We suggest additional opportunities (e.g., monitoring of smolts, eDNA and citizen science initiatives) to facilitate conservation efforts and increase capacity to monitor ecosystem service sustainability.
PICKLE recruits RETINOBLASTOMA RELATED 1 to Control Lateral Root Formation inArabidopsis
Authors: Ötvös Krisztina , Miskolczi Pál , Marhavý Peter , Cruz-Ramírez Alfredo , Benková Eva , Robert Stéphanie , Bakó László
Published: May 2019

Lateral root (LR) formation is an example of plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PICKLE interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress theLATERAL ORGAN BOUNDARIES-DOMAIN 16(LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL-RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL-RBR1 is counteracted by auxin indicating that in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.
A carbohydrate-binding protein, FLOURY ENDOSPERM 6 influences the initiation of A- and B-type starch granules in wheat
Authors: Chia Tansy , Chirico Marcella , King Rob , Ramirez-Gonzalez Ricardo , Saccomanno Benedetta , Seung David , Simmonds James , Trick Martin , Uauy Cristobal , Verhoeven Tamara , Trafford Kay
Published: May 2019

Previously, we identified a quantitative trait locus on the group 4 chromosomes of Aegilops and bread wheat that controls B-type starch-granule content. Here, we identify a candidate gene by fine-mapping in Aegilops and confirm its function using wheat TILLING mutants. This gene is orthologous to the FLOURY ENDOSPERM 6 (FLO6) gene of rice and barley and the PTST2 gene of Arabidopsis. In Triticeae endosperm, reduction in the gene dose of functional FLO6 alleles results in reduction, or loss, of B-granules. This is due to repression of granule initiation in late-grain development, but has no deleterious impact on the synthesis of A-granules. The complete absence of functional FLO6, however, results in reduced numbers of normal A-type and B-type granules and the production of highly-abnormal granules that vary in size and shape. This polymorphous starch seen in a wheat flo6 triple mutant is similar to that observed in the barley mutant Franubet. Analysis of Franubet (fractured Nubet) starch suggests that the mutant A-granules are not fractured but compound, due to stimulation of granule initiation in plastids during early-grain development. Thus, in different situations in Triticeae, FLO6 either stimulates or represses granule initiation.
GRANAR, a new computational tool to better understand the functional importance of root anatomy
Authors: Heymans Adrien , Couvreur Valentin , LaRue Therese , Paez-Garcia Ana , Lobet Guillaume
Published: May 2019

Root hydraulic conductivity is an important determinant of plant water uptake capacity. In particular, the root radial conductivity is often thought to be a limiting factor along the water pathways between the soil and the leaf. The root radial conductivity is itself defined by cell scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex, and time-consuming, experimental procedures.

We present a new computation tool, the Generator of Root ANAtomy in R (GRANAR) that can be used to rapidly generate digital versions of root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties.

We used GRANAR to re-analyse large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally, over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA. This enabled us to quantify the effect of individual anatomical features on the root radial conductivity. In particular, our simulations highlight the large importance of the width of the stele and the cortex.

GRANAR is an open-source project available here: http://granar.github.io

One-Sentence summary

Generator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks.
An oscillator ensemble model of sequence learning
Authors: Maye Alexander , Wang Peng , Daume Jonathan , Hu Xiaolin , Engel Andreas K.
Published: May 2019

Learning and memorizing sequences of events is an important function of the human brain and the basis for forming expectations and making predictions. Learning is facilitated by repeating a sequence several times, causing rhythmic appearance of the individual sequence elements. This observation invites to consider the resulting multitude of rhythms as a spectral ‘fingerprint’ which characterizes the respective sequence. Here we explore the implications of this perspective by developing a neurobiologically plausible computational model which captures this ‘fingerprint’ by attuning an ensemble of neural oscillators. In our model, this attuning process is based on a number of oscillatory phenomena that have been observed in electrophysiological recordings of brain activity like synchronization, phase locking and reset as well as cross-frequency coupling. We compare the learning properties of the model with behavioral results from a study in human participants and observe good agreement of the errors for different levels of complexity of the sequence to be memorized. Finally, we suggest an extension of the model for processing sequences that extend over several sensory modalities.
In V4, pair-wise synchrony and correlations depend on the structure of the population code
Authors: Koren Veronika , Andrei Ariana R. , Hu Ming , Dragoi Valentin , Obermayer Klaus
Published: May 2019

In visual areas of primates, neurons activate in parallel while the animal is engaged in a behavioral task. In this study, we examine the structure of the population code while the animal performs delayed match to sample task on complex natural images. The macaque monkeys visualized two consecutive stimuli that were either the same or different, while recorded with laminar arrays across the cortical depth in cortical areas V1 and V4. We decoded correct choice behavior from neural populations of simultaneously recorded units. Utilizing decoding weights, we divide neurons in most informative and less informative, and show that most informative neurons in V4, but not in V1, are more strongly synchronized, coupled and correlated than less informative neurons. As neurons are divided in two coding pools according to their coding preference, in V4, but not in V1, spiking synchrony, coupling and correlations within the coding pool are stronger than across coding pools.

Highlights

In a match-to-sample visual task, responses of neural populations in V1 and in V4 predict the stimulus class better than chance.

In V4, informative neurons are more strongly coupled, correlated and synchronized than less informative neurons.

In V4, neurons are more strongly coupled, correlated and synchronized within coding pools compared to across coding pools.

Correlations within coding pools harm the performance of the classifier in both V1 and V4.
Insulin-like growth factor 1 is related to the expression of plumage traits in a passerine species
Authors: Mahr Katharina , Vincze Orsolya , Tóth Zsófia , Hoi Herbert , Lendvai Ádám Z.
Published: May 2019

Avian plumage colors and ornaments are ideal models to study the endocrine mechanisms linking sexually selected traits and individual parameters of quality and condition. The insulin-like growth factor 1 (IGF-1), an evolutionarily highly conserved peptide hormone, represents a link between body condition and the individual capacity to grow elaborated ornamental features, due to its regulatory role in cell proliferation and differentiation and its high sensitivity to the nutritional state of individuals. We investigated whether IGF-1 levels during molting affect the expression of multiple ornaments in a sexually dichromatic passerine species, the bearded reedling (Panurus biarmicus). We collected blood samples of males and females shortly before the molting completed and measured the size and colors of ornamental traits. Our results indicate that in males, structural plumage colors, the size of the melanin based ornament (beard) and tail length are independent traits. IGF-1 levels predict the length of the tail and the expression of male structural plumage components (UV-coloration), but not the melanin based ornament. In females plumage color and tail length were independent traits, which were not related to IGF-1 levels. Overall, our results indicate for the first time that IGF-1 could play a role in the development of secondary sexual characters in a passerine species.
Cross-species cortical alignment identifies different types of neuroanatomical reorganization in the temporal lobe of higher primates
Authors: Eichert Nicole , Robinson Emma C. , Bryant Katherine L. , Jbabdi Saad , Jenkinson Mark , Li Longchuan , Krug Kristine , Watkins Kate E. , Mars Rogier B.
Published: May 2019

Evolutionary modifications of the temporo-parietal cortex are considered to be a critical adaptation of the human brain. Cortical adaptations, however, can affect different aspects of brain architecture, including areal expansion or changes in connectivity profiles. We propose to distinguishing different types of brain reorganization using a computational neuroanatomy approach. We investigate the extent to which between-species alignment based on cortical myelin can predict changes in connectivity patterns across macaque, chimpanzee and human. We show that expansion and relocation of brain areas are sufficient to predict terminations of several white matter tracts in temporo-parietal cortex, including the middle and superior longitudinal fasciculus, but not of the arcuate fasciculus. This demonstrates that the arcuate fasciculus underwent additional evolutionary modifications affecting the connectivity pattern of the temporal lobe. The presented approach can flexibly be extended to include other features of cortical organization and other species, allowing direct tests of comparative hypotheses of brain organization.
SciBet: a portable and fast single cell type identifier
Authors: Li Chenwei , Liu Baolin , Kang Boxi , Liu Zedao , Liu Yedan , Chen Changya , Ren Xianwen , Zhang Zemin
Published: May 2019

Fast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a Bayesian classifier that accurately predicts cell identity for newly sequenced cells or cell clusters. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. This user-friendly and cross-platform tool can be widely useful for single cell type identification.
Spatiotemporal patterns of urbanization in three Swiss urban agglomerations: insights from landscape metrics, growth modes and fractal analysis
Authors: Bosch Martí , Chenal Jérôme
Published: May 2019

Urbanization is currently a global phenomenon that has become the most important form of landscape change and is increasingly affecting biodiversity and ecosystem functions. In order to evaluate the impacts of urbanization and inform urban planning, it is important to understand the spatiotemporal patterns of land use change associated to urbanization. This paper exploits three different frameworks, namely landscape metrics, urban growth modes and fractal analysis to characterize the spatiotemporal patterns of urbanization of the Swiss urban agglomerations of Zurich, Bern and Lausanne. The land use inventory provided by the Swiss Federal Statistical Office was used to assemble four temporal snapshots from 1980 to 2016 at the extent of the urban agglomerations. The time series of landscape metrics generally supports the diffusion and coalescence model of urban growth, with Zurich exhibiting most characteristics of coalescence while Bern and Lausanne seem to be at the transition between diffusion and coalescence. Nevertheless, the analysis of the urban growth modes suggest that leapfrog development occurs at all periods, which contributes to an increasing fragmentation of natural patches and maintains the fractal configuration of the landscape. The discussion reviews potential explanations for the observed landscape changes, and concludes with some planning implications.
A single bacterial genus maintains root development in a complex microbiome
Authors: Finkel Omri M. , Salas-González Isai , Castrillo Gabriel , Conway Jonathan M. , Law Theresa F. , Teixeira Paulo José Pereira Lima , Wilson Ellie D. , Fitzpatrick Connor R. , Jones Corbin D. , Dangl Jeffery L.
Published: May 2019

Plants grow within a complex web of species interacting with each other and with the plant. Many of these interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development. To understand how microbe-microbe interactions influence root development in Arabidopsis, we established a model system for plant-microbe-microbe-environment interactions. We inoculated seedlings with a 185-member bacterial synthetic community (SynCom), manipulated the abiotic environment, and measured bacterial colonization of the plant. This enabled classification of the SynCom into four modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying microbe-microbe interactions that determine root phenotypes. These interactions primarily involve a single bacterial genus, Variovorax, which completely reverts severe root growth inhibition (RGI) induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulate plant hormone levels to balance this ecologically realistic root community’s effects on root development. We identify a novel auxin degradation operon in the Variovorax genome that is necessary and sufficient for RGI reversion. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the root’s developmental program. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising new ecological strategy towards the development of more resilient and productive crops.
The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans
Authors: Roberts Buceta Paloma M. , Romanelli-Cedrez Laura , Babcock Shannon J. , Xun Helen , VonPaige Miranda L. , Higley Thomas W. , Schlatter Tyler D. , Davis Dakota C. , Drexelius Julia A. , Culver John C. , Carrera Inés , Shepherd Jennifer N. , Salinas Gustavo
Published: May 2019

A key metabolic adaptation for some species that face hypoxia as part of their life-cycle involves an alternative electron transport chain in which rhodoquinone (RQ) is required for fumarate reduction and ATP production. RQ biosynthesis in bacteria and protists requires ubiquinone (Q) as a precursor. In contrast, Q is not a precursor for RQ biosynthesis in animals such as parasitic helminths, and this pathway has remained elusive. We used Caenorhabditis elegans as a model animal to elucidate several key steps in RQ biosynthesis. Through RNA interference and a series of mutants, we found that arylamine metabolites from the kynurenine pathway are essential precursors for RQ biosynthesis de novo. Deletion of kynu-1, which encodes a kynureninase that converts L-kynurenine (KYN) into anthranilic acid (AA), and 3-hydroxykynurenine (HKYN) into 3-hydroxyanthranilic acid (3HAA), completely abolishes RQ biosynthesis, but does not affect Q levels. Deletion of kmo-1, which encodes a kynurenine 3-monooxygenase that converts KYN to HKYN, drastically reduces RQ, but not Q levels. Knockdown of the Q biosynthetic genes, coq-5 and coq-6, affects both Q and RQ levels demonstrating that common enzymes are used in both biosynthetic pathways. Our study reveals that two pathways for RQ biosynthesis have independently evolved. In contrast to bacteria, where amination is the last step in RQ biosynthesis, worms begin with the arylamine precursor, AA or 3HAA. Since RQ is absent in mammalian hosts of helminths, inhibition of RQ biosynthesis may have broad implications for targeting parasitic infections which cause important neglected tropical diseases.
Molecular basis for feedback inhibition of Notch signaling by the Notch regulated ankyrin repeat protein NRARP
Authors: Jarrett Sanchez M. , Seegar Tom C. M. , Andrews Mark , Adelmant Guillaume , Marto Jarrod A. , Aster Jon C. , Blacklow Stephen C.
Published: May 2019

The Notch regulated ankyrin repeat protein (NRARP) is a negative feedback regulator of Notch signaling in higher organisms. The molecular basis for NRARP function, however, has remained elusive. Mass spectrometry-based proteomic studies show that human NRARP associates with the core Notch transcriptional activation complex (NTC), containing the RBPJ transcription factor, the Notch intracellular domain (NICD), and a Mastermind-like co-activator. Binding of NRARP is direct, requires both RBPJ and NICD, and is independent of Mastermind-like proteins or DNA. The X-ray structure of an NRARP/RBPJ/NOTCH1/DNA complex, determined to 3.75 Å resolution, reveals a non-canonical mode of binding in which NRARP extends the NOTCH1 ankyrin-repeat stack by three additional repeats. Mutations of NRARP residues at the binding interface disrupt entry into complexes and suppress feedback inhibition in signaling assays. These studies establish the structural basis for NTC engagement by NRARP and provide insight into its mechanism of feedback inhibition of Notch signaling.
Motility of Enzyme-Powered Vesicles
Authors: Ghosh Subhadip , Mohajerani Farzad , Son Seoyoung , Velegol Darrell , Butler Peter J. , Sen Ayusman
Published: May 2019

Autonomous nanovehicles powered by energy derived from chemical catalysis have potential applications as active delivery agents. For in vivo applications, it is necessary that the engine and its fuel, as well as the chassis itself, be biocompatible. Enzyme molecules have been shown to generate mechanical force through substrate turnover and are attractive candidates as engines; phospholipid vesicles are biocompatible and can serve as cargo containers. Herein, we describe the autonomous movement of vesicles with membrane-bound enzymes in the presence of the substrate. We find that the motility of the vesicles increases with increasing enzymatic turnover rate. The enhanced diffusion of these enzyme-powered systems was further substantiated in real time by tracking the motion of the vesicles using optical microscopy. The membrane-bound protocells that move by transducing chemical energy into mechanical motion serve as models for motile living cells and are key to the elucidation of the fundamental mechanisms governing active membrane dynamics and cellular movement.

“For Table of Contents Only”
Disease Resistance Genetics and Genomics in Octoploid Strawberry
Authors: Barbey Christopher , Lee Seonghee , Verma Sujeet , Bird Kevin A. , Yocca Alan E. , Edger Patrick P. , Knapp Steven J. , Whitaker Vance M. , Folta Kevin M.
Published: May 2019

Octoploid strawberry (Fragaria × ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, eQTL analysis and RenSeq analysis in cultivars. Octoploid fruit transcript expression quantitative trait loci (eQTL) were identified for 77 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. × ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance towards exploiting variation for strawberry cultivar improvement.
Iron-deficiency and estrogen are associated with ischemic stroke by up-regulating transferrin to induce hypercoagulability
Authors: Tang Xiaopeng , Fang Mingqian , Cheng Ruomei , Zhang Zhiye , Wang Yuming , Shen Chuanbin , Han Yajun , Lu Qiumin , Du Yingrong , Liu Yingying , Sun Zhaohui , Zhu Liping , Mwangi James , Xue Min , Long Chengbo , Lai Ren
Published: May 2019

In the accompanying manuscript, transferrin has been demonstrated to maintain coagulation balance by interacting with clotting factors, suggesting that elevated transferrin causes thromboembolic diseases and factors up-regulating transferrin is associated with thrombosis. Here we show that transferrin and transferrin-thrombin/FXIIa complexes are elevated in plasma and cerebrospinal fluid of ischemic stroke (IS) patients with iron-deficiency anemia (IDA) history, IDA patients and venous thromboembolism patients using combined oral contraceptives (CC) as well as ID mice, suggesting an association of transferrin up-regulation with ID and CC. ID and estrogen up-regulated transferrin through hypoxia and estrogen response elements located at transferrin gene enhancer and promoter region, respectively. ID, exogenous transferrin/estrogen administration or transferrin over-expression promoted hypercoagulability and aggravated IS, while anti-transferrin antibody, transferrin knockdown or designed peptide inhibitors interfering transferrin-thrombin/FXIIa interaction exerted anti-IS effects invivo. Collectively, the results reveal that factors (i.e., ID and CC) up-regulating transferrin are risk factors of thromboembolic diseases.
Regulation of KRAS4A/B splicing in cancer stem cells by the RBM39 splicing complex
Authors: Chen Wei-Ching , To Minh D. , Westcott Peter M.K. , Delrosario Reyno , Kim Il-Jin , Philips Mark , Tran Quan , Bayani Nora , Balmain Allan
Published: May 2019

The KRAS oncogene is expressed as major KRAS4B and minor KRAS4A splice isoforms, the distinct functions of which in cancer are unknown. We demonstrate here that KRAS4A is enriched in cancer stem-like cells, and is activated by hypoxia, whereas KRAS4B is more widely expressed and responds to ER stress. Mice completely lacking either isoform are viable but resistant to lung cancer development, as are Kras4A/B double heterozygous mice expressing both isoforms, but in which splice regulation has been uncoupled. Splicing of KRAS4A, but not KRAS4B, in human tumor cells can be inhibited by treatment with the splice inhibitor indisulam, or by CRISPR/Cas inhibition of the RBM39 splicing complex. Our data suggest that control of KRAS4A/B splicing is a targetable vulnerability in KRAS mutant tumors.
BOLD and EEG Signal Variability at Rest Differently Relate to Aging in the Human Brain
Authors: Kumral D. , Şansal F. , Cesnaite E. , Mahjoory K. , Al E. , Gaebler M. , Nikulin V. V. , Villringer A.
Published: May 2019

Variability of neural activity is regarded as a crucial feature of healthy brain function, and several neuroimaging approaches have been employed to assess it noninvasively. Studies on the variability of both evoked brain response and spontaneous brain signals have shown remarkable changes with aging but it is unclear if the different measures of brain signal variability – identified with either hemodynamic or electrophysiological methods – reflect the same underlying physiology. In this study, we aimed to explore age differences of spontaneous brain signal variability with two different imaging modalities (EEG, fMRI) in healthy younger (25±3 years, N=135) and older (67±4 years, N=54) adults. Consistent with the previous studies, we found lower blood oxygenation level dependent (BOLD) variability in the older subjects as well as less signal variability in the amplitude of low-frequency oscillations (1–12 Hz), measured in source space. These age-related reductions were mostly observed in the areas that overlap with the default mode network. Moreover, age-related increases of variability in the amplitude of beta-band frequency EEG oscillations (15–25 Hz) were seen predominantly in temporal brain regions. There were significant sex differences in EEG signal variability in various brain regions while no significant sex differences were observed in BOLD signal variability. Bivariate and multivariate correlation analyses revealed no significant associations between EEG- and fMRI-based variability measures. In summary, we show that both BOLD and EEG signal variability reflect aging-related processes but are likely to be dominated by different physiological origins, which relate differentially to age and sex.
miR-26a regulates extracellular vesicle secretion from prostate cancer cells via targeting SHC4, PFDN4 and CHORDC1
Authors: Urabe Fumihiko , Kosaka Nobuyoshi , Sawa Yurika , Yamamoto Tomofumi , Yamamoto Yusuke , Ito Kagenori , Kimura Takahiro , Egawa Shin , Ochiya Takahiro
Published: May 2019

Extracellular vesicles (EVs) are known to be involved in intercellular communication during cancer progression; thus, elucidating the detailed mechanism will contribute to the development of a novel strategy for EV-targeted cancer treatment. However, the biogenesis of EVs in cancer cells is not completely understood. MicroRNAs (miRNAs) regulate a variety of physiological and pathological phenomena; thus, miRNAs could regulate EV secretion. Here, we performed high-throughput miRNA-based screening to identify the regulators of EV secretion using an ExoScreen assay. By using this miRNA-based screening, we identified miR-26a, which was reported as a tumor suppressive miRNA, as a miRNA involved in EV secretion from prostate cancer (PCa) cells. In addition, we found that the SHC4, PFDN4, and CHORDC1 genes regulate EV secretion in PCa cells. Suppression of these genes by siRNAs significantly inhibited the secretion of EVs in PCa cells. Furthermore, the progression of PCa cells was inhibited in an in vivo study. On the other hand, injection of EVs isolated from PCa cells partially rescued this suppressive effect on tumor growth. Taken together, our findings suggest that miR-26a regulates EV secretion via targeting SHC4, PFDN4, and CHORDC1 in PCa cells, resulting in the suppression of PCa progression.