bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive feelings during pregnancy, early feeding practices, and infant health
Authors: McManus Melissa A , Khalessi Ali A , Lin Joyce , Ashraf Jahanzeb , Reich Stephanie M 
Published: December 2016

AbstractBackgroundEarly parenting practices, such as infant feeding, can affect children's physical health. Additionally, negative prenatal maternal affect can influence feeding choices, such as breast‐feeding, and can have a detrimental effect on children's health. Little is known, however, about the contribution of positive maternal affect during pregnancy on feeding practices and children's health.MethodsThis study explored whether positive prenatal feelings influenced children's health during the first 18 months, and whether early feeding practices mediated the relationship between these two variables. Low‐income, ethnically diverse, primiparous women (n = 114) reported their feelings of pregnancy uplifts and hassles during their third trimester. These women were interviewed again at 2, 4, 6, 9, 12, and 18 months post‐partum about their feeding practices. A retrospective audit of their infants’ medical charts was completed from birth to 18 months.ResultsUsing structural equation modeling, having more uplifts than hassles during pregnancy was associated with longer breast‐feeding duration and greater adherence to recommended schedules for introducing fruits and vegetables, solids, and baby cereal. These feeding practices were linked to better child health outcomes, including reduced risk of upper respiratory tract infections, conjunctivitis, otitis media, and thrush.ConclusionsPositive maternal feelings during pregnancy were associated with better feeding practices, and these better feeding practices were associated with fewer common childhood illnesses. Helping expectant women focus on the positive aspects of their pregnancy may lead to postnatal care methods that are fiscally advantageous, preventive of detrimental postnatal choices, and medically beneficial for children.
Clinical feasibility of brain‐computer interface based on steady‐state visual evoked potential in patients with locked‐in syndrome: Case studies
Authors: Hwang Han‐Jeong , Han Chang‐Hee , Lim Jeong‐Hwan , Kim Yong‐Wook , Choi Soo‐In , An Kwang‐Ok , Lee Jun‐Hak , Cha Ho‐Seung , Hyun Kim Seung , Im Chang‐Hwan 
Published: December 2016

AbstractAlthough the feasibility of brain‐computer interface (BCI) systems based on steady‐state visual evoked potential (SSVEP) has been extensively investigated, only a few studies have evaluated its clinical feasibility in patients with locked‐in syndrome (LIS), who are the main targets of BCI technology. The main objective of this case report was to share our experiences of SSVEP‐based BCI experiments involving five patients with LIS, thereby providing researchers with useful information that can potentially help them to design BCI experiments for patients with LIS. In our experiments, a four‐class online SSVEP‐based BCI system was implemented and applied to four of five patients repeatedly on multiple days to investigate its test‐retest reliability. In the last experiments with two of the four patients, the practical usability of our BCI system was tested using a questionnaire survey. All five patients showed clear and distinct SSVEP responses at all four fundamental stimulation frequencies (6, 6.66, 7.5, 10 Hz), and responses at harmonic frequencies were also observed in three patients. Mean classification accuracy was 76.99% (chance level = 25%). The test‐retest reliability experiments demonstrated stable performance of our BCI system over different days even when the initial experimental settings (e.g., electrode configuration, fixation time, visual angle) used in the first experiment were used without significant modifications. Our results suggest that SSVEP‐based BCI paradigms might be successfully used to implement clinically feasible BCI systems for severely paralyzed patients.
Short‐term trained lexical categories affect preattentive shape perception: Evidence from vMMN
Authors: Yu Mengxia , Mo Ce , Zeng Tianyu , Zhao Sasa , Mo Lei 
Published: December 2016

AbstractPerceptual processing of colors and shapes in the right visual field is modulated by the lexical category information of the stimuli, a phenomenon known as the lateralized Whorfian effect. For color stimuli, lateralized Whorfian effect is characterized by preattentive occurrence and dependency on acquired lexical information, but it remains unknown whether these key features are generalizable to other domains of perceptual processing. Here, we investigated whether lateralized Whorfian effect in the shape perception domain also depends on acquired lexical category and occurs preattentively using ERPs. Participants were trained to associate novel, irregular polygons with lexical category labels via short‐term intensive training. Using the visual oddball paradigm, we found stronger visual mismatch negativity (vMMN) component elicited by the deviant stimuli whose lexical category differed from the standard stimuli when the deviant was presented in the right visual field, indicating higher perceptual conspicuity for between‐category stimuli. These findings provide direct evidence of similar preattentive lexical category‐contingent modulation on shape perception akin to color perception, suggesting that the lateralized Whorfian effect is not epiphenomenal but rather might reflect the interaction between higher‐level lexical processing and the lower‐level perceptual processing more broadly.
Statistical considerations for reporting and planning heart rate variability case‐control studies
Authors: Quintana Daniel S. 
Published: December 2016

AbstractThe calculation of heart rate variability (HRV) is a popular tool used to investigate differences in cardiac autonomic control between population samples. When interpreting effect sizes to quantify the magnitude of group differences, researchers typically use Cohen's guidelines of small (0.2), medium (0.5), and large (0.8) effects. However, these guidelines were originally proposed as a fallback for when the effect size distribution (ESD) was unknown. Despite the availability of effect sizes from hundreds of HRV studies, researchers still largely rely on Cohen's guidelines to interpret effect sizes and to perform power analyses to calculate required sample sizes for future research. This article describes an ESD analysis of 297 HRV effect sizes from between‐group/case‐control studies, revealing that the 25th, 50th, and 75th effect size percentiles correspond with effect sizes of 0.26, 0.51, and 0.88, respectively. The analyses suggest that Cohen's guidelines may underestimate the magnitude of small and large effect sizes and that HRV studies are generally underpowered. Therefore, to better reflect the observed ESD, effect sizes of 0.25, 0.5, and 0.9 should be interpreted as small, medium, and large effects (after rounding to the closest 0.05). Based on power calculations using the ESD, suggested sample sizes are also provided for planning suitably powered studies that are more likely to replicate. Researchers are encouraged to use the ESD data set or their own collected data sets in tandem with the provided analysis script to perform custom ESD and power analyses relevant to their specific research area.
Mathematical detection of aortic valve opening (B point) in impedance cardiography: A comparison of three popular algorithms
Authors: Árbol Javier Rodríguez , Perakakis Pandelis , Garrido Alba , Mata José Luis , Fernández‐Santaella M. Carmen , Vila Jaime 
Published: December 2016

AbstractThe preejection period (PEP) is an index of left ventricle contractility widely used in psychophysiological research. Its computation requires detecting the moment when the aortic valve opens, which coincides with the B point in the first derivative of impedance cardiogram (ICG). Although this operation has been traditionally made via visual inspection, several algorithms based on derivative calculations have been developed to enable an automatic performance of the task. However, despite their popularity, data about their empirical validation are not always available. The present study analyzes the performance in the estimation of the aortic valve opening of three popular algorithms, by comparing their performance with the visual detection of the B point made by two independent scorers. Algorithm 1 is based on the first derivative of the ICG, Algorithm 2 on the second derivative, and Algorithm 3 on the third derivative. Algorithm 3 showed the highest accuracy rate (78.77%), followed by Algorithm 1 (24.57%) and Algorithm 2 (13.82%). In the automatic computation of PEP, Algorithm 2 resulted in significantly more missed cycles (48.57%) than Algorithm 1 (6.3%) and Algorithm 3 (3.5%). Algorithm 2 also estimated a significantly lower average PEP (70 ms), compared with the values obtained by Algorithm 1 (119 ms) and Algorithm 3 (113 ms). Our findings indicate that the algorithm based on the third derivative of the ICG performs significantly better. Nevertheless, a visual inspection of the signal proves indispensable, and this article provides a novel visual guide to facilitate the manual detection of the B point.
Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO
2
/CH
4
Production Ratios
Authors: Juottonen Heli , Eiler Alexander , Biasi Christina , Tuittila Eeva-Stiina , Yrjälä Kim , Fritze Hannu 
Published: December 2016

ABSTRACT

Northern peatlands in general have high methane (CH
4
) emissions, but individual peatlands show considerable variation as CH
4
sources. Particularly in nutrient-poor peatlands, CH
4
production can be low and exceeded by carbon dioxide (CO
2
) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO
2
to CH
4
produced. After [
13
C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH
4
and CO
2
. The oligotrophic fen had lower CH
4
production but produced 3 to 59 times more CO
2
than CH
4
. RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH
4
production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of
Firmicutes
and by
Proteobacteria
. The oligotrophic peat with excess CO
2
production revealed a wider variety of cellobiose-C consumers, including
Firmicutes
and
Proteobacteria
, but also more unconventional degraders, such as
Telmatobacter
-related
Acidobacteria
and subphylum 3 of
Verrucomicrobia
. Prominent and potentially fermentative
Planctomycetes
and
Chloroflexi
did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH
4
production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO
2
production in peatlands.

IMPORTANCE
Peatlands are major sources of the greenhouse gas methane (CH
4
), yet in many peatlands, CO
2
production from unresolved anaerobic processes exceeds CH
4
production. Anaerobic degradation produces the precursors of CH
4
production but also represents competing processes. We show that anaerobic degradation leading to high or low CH
4
production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH
4
production, while novel and unconventional degraders could be identified in a site where CO
2
production greatly exceeds CH
4
production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH
4
production and reveal bacteria potentially producing the excess CO
2
in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH
4
emission from peatlands.
Development of an Improved System for the Generation of Knockout Mutants of Amycolatopsis sp. Strain ATCC 39116
Authors: Meyer Florian , Pupkes Hilke , Steinbüchel Alexander 
Published: December 2016

ABSTRACT

The Gram-positive actinomycete
Amycolatopsis
sp. strain ATCC 39116 is used for the industrial production of natural vanillin. Previously, the only gene deletion performed in this strain targeted the gene
vdh
, coding for a vanillin dehydrogenase. The generation of this mutant suffered from a high number of illegitimate recombinations and a low rate of homologous recombination. To alleviate this, we constructed an optimized deletion system based on a modified suicide vector. Thereby, we were able to increase the rate of homologous integration from less than 1% of the analyzed clones to 20% or 50%, depending on the targeted gene. We were furthermore able to reduce the screening effort needed to identify homogenotes through the use of the
rpsL
gene from
Saccharopolyspora erythraea
, which confers streptomycin sensitivity on clones still carrying the suicide vector. The new suicide vector is p6SUI5ERPSL, and its applicability was demonstrated by the deletion of three
Amycolatopsis
gene clusters. The deletion of the first of the gene clusters, coding for an aldehyde oxidase (
yagRST
), led to no altered phenotype compared to the parent strain; deletion of the second, coding for a vanillic acid decarboxylase (
vdcBCD
), led to a phenotype that was strongly impaired in its growth with vanillic acid as the sole carbon source and also unable to form guaiacol; and deletion of the third, coding for a vanillate demethylase (
vanAB
), led to only a negligible impact in comparison. Therefore, we showed that decarboxylation of vanillic acid is the main degradation pathway in
Amycolatopsis
sp. ATCC 39116 while the demethylation plays only a minor role and does not compensate the deletion of
vdcBCD
.

IMPORTANCE
Amycolatopsis
sp. ATCC 39116 is an important microorganism used for the production of natural vanillin from ferulic acid. In contrast to this importance, it has previously been shown that this strain is hard to manipulate on a genetic level. We therefore generated an optimized system to facilitate the deletion of genes in this strain. This allowed us to greatly reduce the time and work requirements for generating deletions. This could allow the improvement of vanillin production in the future and also the elucidation of metabolic pathways. To test our deletion system, we deleted three gene clusters in
Amycolatopsis
sp. ATCC 39116. One showed no involvement in the metabolism of vanillin, while the second proved to be the main pathway of vanillic acid degradation and completely stopped the formation of the off-flavor guaiacol. The third appeared to have only a negligible impact on the degradation of vanillic acid.
A Novel Rhamnose-Rich Hetero-exopolysaccharide Isolated from Lactobacillus paracasei DG Activates THP-1 Human Monocytic Cells
Authors: Balzaretti Silvia , Taverniti Valentina , Guglielmetti Simone , Fiore Walter , Minuzzo Mario , Ngo Hansel N. , Ngere Judith B. , Sadiq Sohaib , Humphreys Paul N. , Laws Andrew P. 
Published: December 2016

ABSTRACT

Lactobacillus paracasei
DG is a bacterial strain with recognized probiotic properties and is used in commercial probiotic products. However, the mechanisms underlying its probiotic properties are mainly unknown. In this study, we tested the hypothesis that the ability of strain DG to interact with the host is at least partly associated with its ability to synthesize a surface-associated exopolysaccharide (EPS). Comparative genomics revealed the presence of putative EPS gene clusters in the DG genome; accordingly, EPS was isolated from the surface of the bacterium. A sample of the pure EPS from strain DG (DG-EPS), upon nuclear magnetic resonance (NMR) and chemical analyses, was shown to be a novel branched hetero-EPS with a repeat unit composed of
l
-rhamnose,
d
-galactose, and
N
-acetyl-
d
-galactosamine in a ratio of 4:1:1. Subsequently, we demonstrated that DG-EPS displays immunostimulating properties by enhancing the gene expression of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6), and particularly that of the chemokines IL-8 and CCL20, in the human monocytic cell line THP-1. In contrast, the expression of the cyclooxygenase enzyme COX-2 was not affected. In conclusion, DG-EPS is a bacterial macromolecule with the ability to boost the immune system either as a secreted molecule released from the bacterium or as a capsular envelope on the bacterial cell wall. This study provides additional information about the mechanisms supporting the cross talk between
L. paracasei
DG and the host.

IMPORTANCE
The consumption of food products and supplements called probiotics (i.e., containing live microbial cells) to potentially prevent or treat specific diseases is constantly gaining popularity. The lack of knowledge on the precise mechanisms supporting their potential health-promoting properties, however, greatly limits a more appropriate use of each single probiotic strain. In this context, we studied a well-known probiotic,
Lactobacillus paracasei
DG, in order to identify the constitutive molecules that can explain the documented health-promoting properties of this bacterium. We found a novel polysaccharide molecule, named DG-EPS, that is secreted by and covers the bacterium. We demonstrated that this molecule, which has a chemical structure never identified before, has immunostimulatory properties and therefore may contribute to the ability of the probiotic
L. paracasei
DG to interact with the immune system.
New Arsenate Reductase Gene (
arrA
) PCR Primers for Diversity Assessment and Quantification in Environmental Samples
Authors: Mirza Babur S. , Sorensen Darwin L. , Dupont R. Ryan , McLean Joan E. 
Published: December 2016

ABSTRACT

The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (
arrA
), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the
arrA
gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated
in silico
and empirically tested for amplification of
arrA
genes in clones and for amplification and high-throughput sequencing of
arrA
genes from soil and groundwater samples.
In silico
, this primer pair matched (≥90% DNA identity) 86% of
arrA
gene sequences from GenBank. Empirical evaluation showed successful amplification of
arrA
gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of
arrA
genes. The
arrA
gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between
arrA
gene abundance, quantified through qPCR, and reduced arsenic (As
III
) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters.

IMPORTANCE
Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of As
V
to As
III
. In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant
arrA
gene diversity in the CVB soil and groundwater samples, and
arrA
gene abundance was significantly correlated with the reduced arsenic (As
III
) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments.
Mutagenesis of NosM Leader Peptide Reveals Important Elements in Nosiheptide Biosynthesis
Authors: Jin Liang , Wu Xuri , Xue Yanjiu , Jin Yue , Wang Shuzhen , Chen Yijun 
Published: December 2016

ABSTRACT

Nosiheptide, a typical member of the ribosomally synthesized and posttranslationally modified peptides (RiPPs), exhibits potent activity against multidrug-resistant Gram-positive bacterial pathogens. The precursor peptide of nosiheptide (NosM) is comprised of a leader peptide with 37 amino acids and a core peptide containing 13 amino acids. To pinpoint elements in the leader peptide that are essential for nosiheptide biosynthesis, a collection of mutants with unique sequence features, including N- and C-terminal motifs, peptide length, and specific sites in the leader peptide, was generated by mutagenesis
in vivo
. The effects of various mutants on nosiheptide biosynthesis were evaluated. In addition to the necessity of a conserved motif LEIS box, native length and the N-terminal 12 amino acid residues were indispensable, and single-site substitutions of these 12 amino acid residues resulted in changes ranging from a greater-than-5-fold decrease to a 2-fold increase of nosiheptide production, depending on the sites and substituted residues. Moreover, although the C-terminal motif is not conservative, significant effects of this portion on nosiheptide production were also evident. Taken together, the present results further highlight the importance of the leader peptide in nosiheptide biosynthesis, and provide new insights into the diversity and specificity of leader peptides in the biosynthesis of various RiPPs.

IMPORTANCE
As a representative thiopeptide, nosiheptide exhibits excellent antibacterial activity. Although the biosynthetic gene cluster and several modification steps have been revealed, the presence and roles of the leader peptide within the precursor peptide of the nosiheptide gene cluster remain elusive. Thus, identification of specific elements in the leader peptide can significantly facilitate the genetic manipulation of the gene cluster for increasing nosiheptide production or generating diverse analogues. Given the complexity of the biosynthetic process, the instability of the leader peptide, and the unavailability of intermediates, cocrystallization of intermediates, leader peptide, and modification enzymes is currently not feasible. Therefore, a mutagenesis approach was used to construct a series of leader peptide mutants to uncover a number of crucial and characteristic elements affecting nosiheptide biosynthesis, which moves a considerable distance toward a thorough understanding of the biosynthetic machinery for thiopeptides.