bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a reliable, automated method of individual alpha frequency (IAF) quantification
Authors: Corcoran Andrew W. , Alday Phillip M. , Schlesewsky Matthias , Bornkessel‐Schlesewsky Ina 
Published: January 2018

AbstractIndividual alpha frequency (IAF) is a promising electrophysiological marker of interindividual differences in cognitive function. IAF has been linked with trait‐like differences in information processing and general intelligence, and provides an empirical basis for the definition of individualized frequency bands. Despite its widespread application, however, there is little consensus on the optimal method for estimating IAF, and many common approaches are prone to bias and inconsistency. Here, we describe an automated strategy for deriving two of the most prevalent IAF estimators in the literature: peak alpha frequency (PAF) and center of gravity (CoG). These indices are calculated from resting‐state power spectra that have been smoothed using a Savitzky‐Golay filter (SGF). We evaluate the performance characteristics of this analysis procedure in both empirical and simulated EEG data sets. Applying the SGF technique to resting‐state data from n = 63 healthy adults furnished 61 PAF and 62 CoG estimates. The statistical properties of these estimates were consistent with previous reports. Simulation analyses revealed that the SGF routine was able to reliably extract target alpha components, even under relatively noisy spectral conditions. The routine consistently outperformed a simpler method of automated peak detection that did not involve spectral smoothing. The SGF technique is fast, open source, and available in two popular programming languages (MATLAB, Python), and thus can easily be integrated within the most popular M/EEG toolsets (EEGLAB, FieldTrip, MNE‐Python). As such, it affords a convenient tool for improving the reliability and replicability of future IAF‐related research.
Monitoring changes in back fat thickness and its effect on the restoration of ovarian activity and fertility in Bos indicus cows
Authors: Díaz BR , Galina CS , Rubio I , Corro M , Pablos JL , Orihuela A 
Published: January 2018

ContentsWith the objective of testing the hypothesis if animals with a stable layer of body fat (FAT) during the peripartum have a better chance of becoming pregnant after calving, fifty‐nine multiparous Brahman cows in their last trimester of pregnancy were used. Animals averaged four parturitions and were stocked at a rate of 1.25 animal units per hectare and divided into two groups depending on the time postpartum (dpp) that the intravaginal releasing device CIDR was inserted; Group 1 (<30 dpp; n = 30) received the implant at 25.2 ± 4.21 and withdrawn 9 days later. Group 2 (≥30 dpp; n = 29) received the CIDR at 38.41 ± 5.8. Animals were AI at detected oestrus until 170 dpp and calculated as pregnant at first service or requiring more than one service (1s and >1s), not pregnant but cycling (not pregnant) and those not cycling at all (anestrus). The FAT measurements were taken twice each month from the last trimester of gestation until 96 dpp. The onset of ovarian activity was monitored through blood levels of progesterone (P4) at days 14 and 9 prior to CIDR insertion and days 10, 13, 30 and 33 after CIDR withdrawal. Animals pregnant did not have any major changes in their fat thickness. In contrast, cows pregnant in the group ≥30 dpp had changes in their FAT homoeostasis, and pregnant animals in the 1s and >1s groups did not show differences in dorsal back fat in the last trimester of pregnancy and early postpartum. In contrast, animals not pregnant and in anestrus FAT values decreased considerably after parturition. Overall, fertility was 49%, but 18% of all the animals remained anestrus losing FAT. Thus, animals with adequate metabolic conditions will have a better chance of pregnancy regardless of the time postpartum when the reproductive programme starts.
Introduction: Firm Level Analysis With Administrative Data
Authors: Arndt Channing , Davies Rob , Gavin Elizabeth , Mcmillan Landon 
Published: January 2018

AbstractThis special issue focuses on a collaborative effort between the National Treasury and the South African Revenue Service (SARS) to employ administrative record data from SARS for economic policy analysis. It contains six research articles plus a synthesis article designed to draw out potential policy implications and to place this research into a broader context. Exploitation of tax administrative record data has become global best practice. We conclude that this effort demonstrates strong prospects for developing a better understanding of the South African economy with positive implications for economic policy formulation.
New Data, New Approaches and New Evidence: A Policy Synthesis
Authors: Arndt Channing 
Published: January 2018

AbstractThe Republic of South Africa faces the imperative of escaping economic stagnation. This article seeks to synthesise results from a series of research efforts, including but not limited to the articles presented in this special issue, and consider policy options for escaping economic stagnation. The focus is on South Africa and South African policies yielding relatively quick dividends in terms of growth and taking the rest of the world as given. Four broad implications are presented. These could form part of a concerted effort to escape from South Africa's long running economic malaise.
Towards a theory of functional magnetic resonance spectroscopy (fMRS): A meta‐analysis and discussion of usingMRSto measure changes in neurotransmitters in real time
Authors: Mullins Paul G. 
Published: January 2018

Proton magnetic resonance spectroscopy is a powerful tool to investigate neurochemistry and physiology in vivo. Recently researchers have started to useMRSto measure neurotransmitter changes related to neural activity, so called functionalMRS(fMRS). Particular interest has been placed on measuring glutamate changes associated with neural function, but differences are reported in the size of changes seen. This review discussesfMRS, and includes meta‐analyses of the relative size of glutamate changes seen infMRS, and the impact experimental design and stimulus paradigm may have. On average glutamate was found to increase by 6.97% (±1.739%) in response to neural activation. However, factors of experimental design may have a large impact on the size of these changes. For example an increase of 4.749% (±1.45%) is seen in block studies compared to an increase of 13.429% (±3.59) in studies using event related paradigms. The stimulus being investigated also seems to play a role with prolonged visual stimuli showing a small mean increase in glutamate of 2.318% (±1.227%) while at the other extreme, pain stimuli show a mean stimulation effect of 14.458% (±3.736%). These differences are discussed with regards to possible physiologic interpretations, as well experimental design implications.
Pension system reform in China: Who gets what pensions?
Authors: Zhu Huoyun , Walker Alan 
Published: January 2018

AbstractThis article is the first examination of pension reform in China and its effects on different social groups over the past three decades. China's pension system has undergone radical transition from the state‐employer model to a state‐society one based on the combination of an underlying aim of supporting the economic reforms and learning from international experience. Although the pension system has expanded over the past three decades and the majority of people are now covered by social pensions, this remarkable policy change has created new inequalities. First, an important aspect of social stratification has been reshaped into five distinct pension scheme classes. Second, the new pension model has strengthened the link between benefits and contributions, which privileges the better off. In this newly stratified pension system, those with high human capital and family capital, and who are in the more developed regions are the clear winners. To tackle these inequalities, future pension reform in China should focus on promoting equalization and de‐stratification.
Seroprevalence of leptospiral antibodies among market workers and food handlers in the central state of Malaysia
Authors: Samsudin S. , Sakinah S. N. S. , Malina O. , Norliza B. A. , Noh M. A. , Fairuz A. , Jamaluddin T. Z. M. T. , Hamat R. A. , Zahiruddin W. M. , Mohd Nazri S. , Sukeri S. , Aziah B. D. , Zawaha I. , Zainudin A. W. , Munirah N. A. , Desa M. N. , Neela V. , Masri S. N. 
Published: January 2018

AbstractObjectiveThe high prevalence of leptospirosis in humans is of great public health concern, particularly in tropical and subtropical regions. This study aimed to determine the seroprevalence of leptospiral antibodies and distribution of serovars, and to assess the usefulness of enzyme‐linked immunosorbent assay (ELISA) as a screening method for leptospiral antibodies in a high‐risk healthy community.MethodsCross‐sectional study of 231 market workers and food handlers in wet markets and food premises from two localities in central Malaysia. Respondents’ background information was obtained using a questionnaire. Serum samples were tested for leptospiral antibodies using ELISA and microscopic agglutination test (MAT).ResultsSeroprevalence of leptospirosis among healthy workers was 46.3%. Detection of seropositivity was higher by MAT (46%) than ELISA (15%). We observed high seropositivity among local workers (49%), food handlers (49.5%), females (60.8%) and those aged 34 years and older (46.3%). Local strain LEP175 was the predominant serovar, followed by WHO strain Patoc.ConclusionOverall seroprevalence among healthy food handlers and market workers was high in this study. The workplace places susceptible individuals at risk of leptospirosis.
A Computational Investigation of Sources of Variability in Sentence Comprehension Difficulty in Aphasia
Authors: Mätzig Paul , Vasishth Shravan , Engelmann Felix , Caplan David , Burchert Frank 
Published: January 2018

AbstractWe present a computational evaluation of three hypotheses about sources of deficit in sentence comprehension in aphasia: slowed processing, intermittent deficiency, and resource reduction. The ACT‐R based Lewis and Vasishth (2005) model is used to implement these three proposals. Slowed processing is implemented as slowed execution time of parse steps; intermittent deficiency as increased random noise in activation of elements in memory; and resource reduction as reduced spreading activation. As data, we considered subject vs. object relative sentences, presented in a self‐paced listening modality to 56 individuals with aphasia (IWA) and 46 matched controls. The participants heard the sentences and carried out a picture verification task to decide on an interpretation of the sentence. These response accuracies are used to identify the best parameters (for each participant) that correspond to the three hypotheses mentioned above. We show that controls have more tightly clustered (less variable) parameter values than IWA; specifically, compared to controls, among IWA there are more individuals with slow parsing times, high noise, and low spreading activation. We find that (a) individual IWA show differential amounts of deficit along the three dimensions of slowed processing, intermittent deficiency, and resource reduction, (b) overall, there is evidence for all three sources of deficit playing a role, and (c) IWA have a more variable range of parameter values than controls. An important implication is that it may be meaningless to talk about sources of deficit with respect to an abstract verage IWA; the focus should be on the individual's differential degrees of deficit along different dimensions, and on understanding the causes of variability in deficit between participants.
Defective XRN3‐mediated transcription termination in Arabidopsis affects the expression of protein‐coding genes
Authors: Krzyszton Michal , Zakrzewska‐Placzek Monika , Kwasnik Aleksandra , Dojer Norbert , Karlowski Wojciech , Kufel Joanna 
Published: January 2018

SummaryArabidopsis thaliana contains two nuclear XRN2/3 5′–3′ exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand‐specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read‐through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3‐mediated changes in the expression of a subset of genes are caused by upstream read‐through transcription and these effects are enhanced by RNA–mRNA chimeras generated in xrn3 plants. In turn, read‐through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.
Characteristics of particle removals in a compressible media filter system
Authors: Kim Yeseul , Nam Seong‐Nam , Jeong Seolhwa , Oh Jeill 
Published: January 2018

AbstractThe ability to adjust the properties of the filter medium by altering the degree of the medium compression is important because the different porosities in media affect the ideal filter performance according to the properties of influent wastewater. This study therefore focused on the particle size distribution (PSD) of compressible media filter (CMF) effluents depending on the compression ratio (0–30%) and the filter bed depth (Layers 1–5) in order to evaluate the CMF performance. The results showed that the removal efficiency for particles larger than 10 µm was more than 90% while that for particles smaller than 10 µm was less than 85% of removal efficiency. From the power law fit, substantial decreases in the number of large‐sized particles were observed in the PSD. Particle removal efficiencies increased along with the average compression ratio increase. Furthermore, the results demonstrated that each layer in the bed had a different role in the filter performance, and it was found that a filter bed of about 0.45–0.60 m would be needed for the production of the desired effluent quality in this study. The detachment phenomenon was observed in particles larger than 5 µm, especially in 5–15 µm particles.
Investigation of the effect of coagulation bath composition on PVDF/CA membrane by evaluating critical flux and antifouling properties in lab‐scale submerged MBR
Authors: Razzaghi Mohammad Hossein , Tavakolmoghadam Maryam , Rekabdar Fatemeh , Oveisi Fatemeh 
Published: January 2018

AbstractUltrafiltration membranes were prepared from blends of poly(vinylidene fluoride) (PVDF)/cellulose acetate (CA) via phase inversion method. The effect of different coagulation bath compositions on the morphology and performance of the blend membrane prepared from casting solution of PVDF/CA with ratio of 80/20 was investigated using sewage wastewater. NaCl and ethanol were used as additives of coagulation bath. Fouling analysis was conducted with Bovine Serum Albumin solution and critical flux evaluation was performed using a lab‐scale membrane bioreactor. In terms of morphological structure, the macrovoids decreased and changed to finger‐like structure. The irreversible fouling reduced and the flux recovery ratio (FRR) of the modified membranes increased remarkably while the reversible fouling caused by deposition of foulants on the surface of the membranes increased. The maximum values of FRR and critical flux of irreversibility were reached by the membrane which was prepared in the coagulation bath containing the highest concentration of NaCl.
Population Pharmacokinetic Model-Based Evaluation of Standard Dosing Regimens for Cefuroxime Used in Coronary Artery Bypass Graft Surgery with Cardiopulmonary Bypass
Authors: Alqahtani Saeed A. , Alsultan Abdullah S. , Alqattan Hussain M. , Eldemerdash Ahmed , Albacker Turki B. 
Published: January 2018

ABSTRACT

The purpose of this study was to investigate the population pharmacokinetics (PK) of cefuroxime in patients undergoing coronary artery bypass graft (CABG) surgery. In this observational pharmacokinetic study, multiple blood samples were collected over a 48-h interval of intravenous cefuroxime administration. The samples were analyzed by using a validated high-performance liquid chromatography (HPLC) method. Population pharmacokinetic models were developed using Monolix (version 4.4) software. Pharmacokinetic-pharmacodynamic (PD) simulations were performed to explore the ability of different dosage regimens to achieve the pharmacodynamic targets. A total of 468 blood samples from 78 patients were analyzed. The PK for cefuroxime were best described by a two-compartment model with between-subject variability on clearance, the volume of distribution of the central compartment, and the volume of distribution of the peripheral compartment. The clearance of cefuroxime was related to creatinine clearance (CL
CR
). Dosing simulations showed that standard dosing regimens of 1.5 g could achieve the PK-PD target of the percentage of the time that the free concentration is maintained above the MIC during a dosing interval (
fT
MIC
) of 65% for an MIC of 8 mg/liter in patients with a CL
CR
of 30, 60, or 90 ml/min, whereas this dosing regimen failed to achieve the PK-PD target in patients with a CL
CR
of ≥125 ml/min. In conclusion, administration of standard doses of 1.5 g three times daily provided adequate antibiotic prophylaxis in patients undergoing CABG surgery. Lower doses failed to achieve the PK-PD target. Patients with high CL
CR
values required either higher doses or shorter intervals of cefuroxime dosing. On the other hand, lower doses (1 g three times daily) produced adequate target attainment for patients with low CL
CR
values (≤30 ml/min).
An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles
Authors: Speed Michael Clayton , Burkhart Brett W. , Picking Jonathan W. , Santangelo Thomas J. 
Published: January 2018

ABSTRACT

Robust genetic systems for the hyperthermophilic
Thermococcales
have facilitated the overexpression of native genes, enabled the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and aided the introduction of sequences encoding new proteins in these fast-growing fermentative heterotrophs. However, tightly controlled and easily manipulated systems facilitating regulated gene expression are limited for these hosts. Here, we describe an alternative method for regulatory control reliant on a
cis
-encoded functional riboswitch in the model archaeon
Thermococcus kodakarensis
. Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria and similarly functions to regulate a component-conserved fluoride export pathway. Deleting components of the fluoride export pathway generates
T. kodakarensis
strains with increased fluoride sensitivity. The mechanism underlying regulated expression suggested that the riboswitch-encoding sequences could be utilized as a tunable expression cassette. When appended to a reporter gene, the riboswitch-mediated control system provides fluoride-dependent tunable regulatory potential, offering an alternative system for regulating gene expression. Riboswitch-regulated expression is thus ubiquitous in extant life and can be exploited to generate regulated expression systems for hyperthermophiles.

IMPORTANCE
Gene expression is controlled by a myriad of interconnected mechanisms that interpret metabolic states and environmental cues to balance cell physiology. Transcription regulation in
Archaea
is known to employ both typical repressors-operators and transcription activators to regulate transcription initiation in addition to the regulation afforded by chromatin structure. It was perhaps surprising that the presumed ancient mechanism of riboswitch-mediated regulation is found in
Bacteria
and
Eukarya
, but seemingly absent in
Archaea
. We demonstrate here that a fluoride-responsive riboswitch functions to regulate a detoxification pathway in the hyperthermophilic archaeon
Thermococcus kodakarensis
. The results obtained define a universal role for riboswitch-mediated regulation, adumbrate the presence of several riboswitch-regulated genes in
Thermococcus kodakarensis
, demonstrate the utility of RNA-based regulation at high temperatures, and provide a novel riboswitch-regulated expression system to employ in hyperthermophiles.
Cryptic Production of
trans
-3-Hydroxyproline in Echinocandin B Biosynthesis
Authors: Mattay Johanna , Houwaart Stefanie , Hüttel Wolfgang 
Published: January 2018

ABSTRACT

Echinocandins are antifungal nonribosomal hexapeptides produced by fungi. Two of the amino acids are hydroxy-
l
-prolines:
trans
-4-hydroxy-
l
-proline and, in most echinocandin structures, (
trans
-2,3)-3-hydroxy-(
trans
-2,4)-4-methyl-
l
-proline. In the case of echinocandin biosynthesis by
Glarea lozoyensis
, both amino acids are found in pneumocandin A
0
, while in pneumocandin B
0
the latter residue is replaced by
trans
-3-hydroxy-
l
-proline (3-Hyp). We have recently reported that all three amino acids are generated by the 2-oxoglutarate-dependent proline hydroxylase GloF. In echinocandin B biosynthesis by
Aspergillus
species, 3-Hyp derivatives have not been reported. Here we describe the heterologous production and kinetic characterization of HtyE, the 2-oxoglutarate-dependent proline hydroxylase from the echinocandin B biosynthetic cluster in
Aspergillus pachycristatus
. Surprisingly,
l
-proline hydroxylation with HtyE resulted in an even higher proportion (∼30%) of 3-Hyp than that with GloF. This suggests that the selectivity for methylated 3-Hyp in echinocandin B biosynthesis is due solely to a substrate-specific adenylation domain of the nonribosomal peptide synthetase. Moreover, we observed that one product of HtyE catalysis, 3-hydroxy-4-methyl-
l
-proline, is slowly further oxidized at the methyl group, giving 3-hydroxy-4-hydroxymethyl-
l
-proline, upon prolonged incubation with HtyE. This dihydroxylated amino acid has been reported as a building block of cryptocandin, an echinocandin produced by
Cryptosporiopsis
.

IMPORTANCE
Secondary metabolites from bacteria and fungi are often produced by sets of biosynthetic enzymes encoded in distinct gene clusters. Usually, each enzyme catalyzes one biosynthetic step, but multiple reactions are also possible. Pneumocandins A
0
and B
0
are produced by the fungus
Glarea lozoyensis
. They belong to the echinocandin family, a group of nonribosomal cyclic lipopeptides that exhibit a strong antifungal activity. Chemical derivatives are important drugs for the treatment of systemic fungal infections. We have recently shown that in the biosynthesis of pneumocandins A
0
and B
0
, three hydroxyproline building blocks are provided by one proline hydroxylase. Here we demonstrate that the proline hydroxylase from echinocandin B biosynthesis in
Aspergillus pachycristatus
produces the same hydroxyprolines, with an increased proportion of
trans
-3-hydroxyproline. However, echinocandin B biosynthesis does not require
trans
-3-hydroxyproline; its formation remains cryptic. While one can only speculate on the evolutionary background of this unexpected finding, proline hydroxylation in
G. lozoyensis
and
A. pachycristatus
provides an unusual insight into peptide antibiotic biosynthesis—namely, the complex interplay between the selectivity of a hydroxylase and the substrate specificity of a nonribosomal peptide synthetase.