bluuebunny/crossref_metadata_2025 huggingface dataset:
Annual parallax measurements of a semi-regular variable star SV Pegasus with VERA
Authors: Sudou Hiroshi , Omodaka Toshihiro , Murakami Kotone , Nagayama Takahiro , Nakagawa Akiharu , Urago Riku , Nagayama Takumi , Hirano Ken , Honma Mareki
Published: November 2018

Many studies have shown that there are clear sequences in the period–luminosity relationship (PLR) for Mira variables and semi-regular variables (SRVs) in the Large Magellanic Cloud (LMC). To investigate the PLR for SRVs in our galaxy, we examined the annual parallax measurement and conducted K΄-band photometric monitoring of an SRV star SV Pegasus (SV Peg). We measured the position change of the associated H2O maser spots by phase-referencing Very Long Baseline Interferometry (VLBI) observations with VERA at 22 GHz, spanning approximately 3 yr, and detected an annual parallax of π = 3.00 ± 0.06 mas, corresponding to a distance of D = 333 ± 7 pc. This result is in good agreement with the Hipparcos parallax and improves the accuracy of the distance from 35% to 2%. However, the Gaia DR2 catalog gave a parallax of π = 1.12 ± 0.28 mas for SV Peg. This indicates that the Gaia result might be blurred by the effect of the stellar size because the estimated stellar radius was ∼5 mas, which is comparable to the parallax. We obtained a K΄-band mean magnitude of $m_{K^{\prime }} = -0.48\:$mag and a period of P = 177 d from our photometric monitoring with a 1 m telescope. Using the trigonometric distance, we derived an absolute magnitude of $M_{K^{\prime }}=-8.09 \pm 0.05\:$mag. This result shows that the position of SV Peg in the PLR falls on the C’ sequence found in the PLR in the LMC, which is similar to other SRVs in our galaxy.
Core Outcome Measures for Chronic Musculoskeletal Pain Research: Recommendations from a Veterans Health Administration Work Group
Authors: Kroenke Kurt , Krebs Erin E , Turk Dennis , Von Korff Michael , Bair Matthew J , Allen Kelli D , Sandbrink Friedhelm , Cheville Andrea L , DeBar Lynn , Lorenz Karl A , Kerns Robert D
Published: November 2018

Objective

Chronic musculoskeletal pain (CMSP) disorders are among the most prevalent and disabling conditions worldwide. It would be advantageous to have common outcome measures when comparing results across different CMSP research studies.

Methods

The Veterans Health Administration appointed a work group to recommend core outcome measures for assessing pain intensity and interference as well as important secondary domains in clinical research. The work group used three streams of data to inform their recommendations: 1) literature synthesis augmented by three recently completed trials; 2) review and comparison of measures recommended by other expert groups; 3) two Delphi surveys of work group members.

Results

The single-item numerical rating scale and seven-item Brief Pain Inventory interference scale emerged as the recommended measures for assessing pain intensity and interference, respectively. The secondary domains ranked most important included physical functioning and depression, followed by sleep, anxiety, and patient-reported global impression of change (PGIC). For these domains, the work group recommended the Patient-Reported Outcome Information System four-item physical function and sleep scales, the Patient Health Questionnaire two-item depression scale, the Generalized Anxiety Disorder two-item anxiety scale, and the single-item PGIC. Finally, a single-item National Health Interview Survey item was favored for defining chronic pain.

Conclusions

Two scales comprising eight items are recommended as core outcome measures for pain intensity and interference in all studies of chronic musculoskeletal pain, and brief scales comprising 13 additional items can be added when possible to assess important secondary domains.
Delivering information about medication assisted treatment to individuals who misuse opioids through a mobile app: a pilot study
Authors: Cavazos-Rehg Patricia A , Krauss Melissa J , Costello Shaina J , Ramsey Alex T , Petkas Demetrie , Gunderson Sean , Bierut Laura J , Marsch Lisa A
Published: November 2018

Background

Digital therapeutic tools (e.g. mobile applications) can be accessible, low-cost interventions that counter misconceptions about medication assisted treatment (MAT) and/or improve deficits in MAT knowledge that are common barriers to treatment entry among individuals with opioid dependence. The purpose of this pilot study was to examine the preliminary effectiveness of a mobile application, ‘uMAT-R’, that includes health information about OUD recovery supported by science and MAT benefits.

Methods

Twenty-six adult participants with OUD recruited via social media completed all modules and pre/post-assessments within uMAT-R. McNemar’s test was used to compare interest in treatment before and after completing the app, and paired t tests were used to compare MAT attitude scores before and after completing the modules within uMAT-R.

Results

Before viewing uMAT-R, 32% agreed/strongly agreed that they were interested in starting treatment to recover from opioid misuse, compared to 48% after completing uMAT-R. The average scores on the MAT attitudes scale and its Aid to Behavior Change subscale improved from before to after viewing uMAT-R. Among the participants, 88% felt that uMAT-R would be useful to consult when making decisions about recovery.

Conclusions

Our encouraging pilot findings support the use of uMAT-R to help address the current opioid epidemic.
Inference on Causal and Structural Parameters using Many Moment Inequalities
Authors: Chernozhukov Victor , Chetverikov Denis , Kato Kengo
Published: November 2018

This article considers the problem of testing many moment inequalities where the number of moment inequalities, denoted by $p$, is possibly much larger than the sample size $n$. There is a variety of economic applications where solving this problem allows to carry out inference on causal and structural parameters; a notable example is the market structure model of Ciliberto and Tamer (2009) where $p=2^{m+1}$ with $m$ being the number of firms that could possibly enter the market. We consider the test statistic given by the maximum of $p$ Studentized (or $t$-type) inequality-specific statistics, and analyse various ways to compute critical values for the test statistic. Specifically, we consider critical values based upon (1) the union bound combined with a moderate deviation inequality for self-normalized sums, (2) the multiplier and empirical bootstraps, and (3) two-step and three-step variants of (1) and (2) by incorporating the selection of uninformative inequalities that are far from being binding and a novel selection of weakly informative inequalities that are potentially binding but do not provide first-order information. We prove validity of these methods, showing that under mild conditions, they lead to tests with the error in size decreasing polynomially in $n$ while allowing for $p$ being much larger than $n$; indeed $p$ can be of order $\exp (n^{c})$ for some $c > 0$. Importantly, all these results hold without any restriction on the correlation structure between $p$ Studentized statistics, and also hold uniformly with respect to suitably large classes of underlying distributions. Moreover, in the online supplement, we show validity of a test based on the block multiplier bootstrap in the case of dependent data under some general mixing conditions.
Clinical Predictors for Poor Quality of Life in Patients With Covert Hepatic Encephalopathy
Authors: Labenz Christian , Toenges Gerrit , Schattenberg Jörn M. , Nagel Michael , Sprinzl Martin F. , Nguyen-Tat Marc , Zimmermann Tim , Huber Yvonne , Marquardt Jens U. , Galle Peter R. , Wörns Marcus-Alexander
Published: November 2018

Background:

Current EASL/AASLD guidelines recommend treatment of covert hepatic encephalopathy (HE) only in symptomatic patients, for example, in those with impaired quality of life or with affected driving abilities.

Goals:

Because testing for impaired quality of life is time consuming, the aim of the present study was to identify simple clinical predictors for poor quality of life in patients with covert HE (CHE).

Study:

In total, 139 cirrhotic in- and outpatients without a history of overt hepatic encephalopathy were enrolled. Diagnosis of HE grade 1 (HE1) was diagnosed clinically according to the West-Haven Criteria. Critical flicker frequency and the Psychometric Hepatic Encephalopathy Score were used to detect minimal HE (MHE). Chronic Liver Disease Questionnaire was used to assess health-related quality of life (HrQoL).

Results:

CHE was detected in 51 (36.7%) patients. Multivariate analysis identified a history of falls in the previous year (P=0.003) and female gender (P=0.030) as independent predictors of reduced HRQoL in patients with CHE. Comparison of patients with and without a history of falls revealed relevant differences in the subdomains—abdominal symptoms, fatigue, systemic symptoms, emotional functions and worries.

Conclusions:

A history of falls and female gender are associated with impaired HRQoL in patients with CHE. These data indicate that a history of falls should be considered as a treatment indication in patients with CHE to improve HRQoL and ultimately prognosis.
Nomogram for predicting diabetes mellitus after the first attack of acute pancreatitis
Authors: Ma Ji-Hong , Yuan You-Jun , Lin Su-Han , Pan Jing-Ye
Published: November 2018

Background

Diabetes mellitus can occur after acute pancreatitis (AP), but there are currently no tools for evaluating the risk of developing diabetes after an attack of AP. The aim of the study was to develop a nomogram for prediction of new-onset diabetes mellitus after the first attack of AP.

Patients and methods

We enrolled 616 patients with first-attack AP. We collected and statistically analyzed demographic data (age, BMI, and duration of hospitalization) and laboratory data (glucose, low-density lipoprotein cholesterol, triglyceride, and cholesterol).

Results

Univariate analysis suggested duration of hospitalization (P=0.0003), BMI (P=0.0059), cholesterol (P=0.0005), triglyceride (P=0.0005), hemoglobin (P=0.0229), and glucose (P<0.001) at admission were significantly associated with newly developed diabetes after the first-attack AP. Multivariate analysis showed that age [odds ratio (OR)=1.01; 95% confidence interval (CI): 1.00–1.03; P=0.045], BMI (OR=1.06; 95% CI: 1.01–1.12; P=0.018), glucose (OR=1.07; 95% CI: 1.02–1.12; P=0.008), triglyceride (OR=1.03; 95% CI: 1.00–1.06; P=0.035), and low-density lipoprotein-cholesterol (OR=1.18; 95% CI: 1.00–1.38; P=0.044) at admission were important predictors.

Conclusion

The nomogram is a potentially clinically useful tool for predicting new-onset diabetes, which is currently clinically unprecedented. This finding is not confined to the patients with severe AP but is also for patients who have recovered from mild AP. The nomogram must to be validated externally.
Overcoming the Challenging Cervix: Identification and Techniques to Access the Uterine Cavity
Authors: Wood Michelle A. , Kerrigan Katherine L. , Burns Megan K. , Glenn Tanya L. , Ludwin Artur , Christianson Mindy S. , Bhagavath Bala , Lindheim Steven R.
Published: November 2018

Importance

Cervical stenosis is a challenging clinical entity that requires prompt identification and management in order to avoid iatrogenic injury at the time of endocervical canal cannulation.

Objective

The aim of this study was to identify cervical stenosis and discuss associated etiologies, risk factors, and review medical and surgical approaches for overcoming cervical stenosis.

Evidence Acquisition

Computerized searches of MEDLINE and PubMed were conducted using the key words “cervix”, “cervical stenosis,” “embryo transfer,” “hysteroscopy complications,” “misoprostol,” and “ultrasound.” References from identified sources were manually searched to allow for a thorough review. Data from relevant sources were compiled to create this review.

Results

Transcervical access to the uterine cavity is frequently required for procedures such as hysteroscopy, dilation and curettage, endometrial biopsy, sonohysterogram, hysterosalpingogram, intrauterine insemination, embryo transfer in those undergoing in vitro fertilization, and insertion of intrauterine devices. These procedures can become complicated when difficult cannulation of the endocervical canal is encountered. Management strategies include preprocedural use of cervical-ripening agents or osmotic dilators, ultrasound guidance, no-touch vaginoscopy, manual dilatation, and hysteroscopic resection of the obstructed endocervical canal.

Conclusions and Relevance

Cervical stenosis is associated with iatrogenic complications that can result in significant patient morbidity. In patients undergoing in vitro fertilization, difficult embryo transfer is associated with lower pregnancy rates. The clinician should carefully consider the patient's menopausal status, risk factors, and symptoms in order to anticipate difficult navigation of the endocervical canal. Various medical and surgical management strategies, including hysteroscopic resection, can be used to overcome the stenotic cervix.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After participating in this activity, the provider should be better able to diagnose cervical stenosis; distinguish associated etiologies and risk factors; and assess appropriate medical and surgical approaches.
Impact of Dry Eye on Prolonged Reading
Authors: Karakus Sezen , Mathews Priya M. , Agrawal Devika , Henrich Claudia , Ramulu Pradeep Y. , Akpek Esen K.
Published: November 2018

SIGNIFICANCE

Patients with dry eye frequently report difficulty with reading. However, the impact of dry eye on reading has not been studied in detail. This study shows the unfavorable effect of dry eye on reading speed and offers mechanisms that may be responsible.

PURPOSE

The purpose of this study was to evaluate the impact of dry eye signs as well as symptoms on both short-duration out-loud and prolonged silent reading.

METHODS

This study included 116 patients with clinically significant dry eye, 39 patients with dry eye symptoms only, and 31 controls, 50 years or older. After the Ocular Surface Disease Index (OSDI) questionnaire, objective testing of dry eye (tear film stability studies, Schirmer's test, and ocular surface staining) was performed. Total OSDI score and two subscores (vision related and discomfort related) were calculated. A short-duration out-loud reading test and a 30-minute sustained silent reading test were performed. Reading speed for each test was calculated as words per minute (wpm) and compared across the three groups.

RESULTS

Patients with clinically significant dry eye read slower than controls measured with sustained silent reading test (240 vs. 272 wpm, P = .04), but not with short-duration out-loud reading test (146 vs. 153 wpm, P = .47). Patients with dry eye symptoms only did not have slower reading speed measured using either reading test as compared with controls. However, vision-related OSDI subscore independently was associated with slower reading speed (P = .02). Multivariable regression models demonstrated that each 1-point (between 0 and 6) increase in corneal staining score led to a 10-wpm decrease in sustained silent reading speed (P = .01).

CONCLUSIONS

This study demonstrates a significant negative impact of dry eye (particularly presence of corneal staining) on prolonged reading. Prolonged reading task may serve as an objective clinically relevant test to measure the impact of dry eye on vision-related quality of life.
7 T Magnetic Resonance Spectroscopic Imaging in Multiple Sclerosis
Authors: Heckova Eva , Strasser Bernhard , Hangel Gilbert J. , Považan Michal , Dal-Bianco Assunta , Rommer Paulus S. , Bednarik Petr , Gruber Stephan , Leutmezer Fritz , Lassmann Hans , Trattnig Siegfried , Bogner Wolfgang
Published: November 2018

Objectives

The aim of this study was to assess the utility of increased spatial resolution of magnetic resonance spectroscopic imaging (MRSI) at 7 T for the detection of neurochemical changes in multiple sclerosis (MS)–related brain lesions.

Materials and Methods

This prospective, institutional review board–approved study was performed in 20 relapsing-remitting MS patients (9 women/11 men; mean age ± standard deviation, 30.8 ± 7.7 years) after receiving written informed consent. Metabolic patterns in MS lesions were compared at 3 different spatial resolutions of free induction decay MRSI with implemented parallel imaging acceleration: 2.2 × 2.2 × 8 mm3; 3.4 × 3.4 × 8 mm3; and 6.8 × 6.8 × 8 mm3 voxel volumes, that is, matrix sizes of 100 × 100, 64 × 64, and 32 × 32, respectively. The quality of data was assessed by signal-to-noise ratio and Cramér-Rao lower bounds. Statistical analysis was performed using Wilcoxon signed-rank tests with correction for multiple testing.

Results

Seventy-seven T2-hyperintense MS lesions were investigated (median volume, 155.7 mm3; range, 10.8–747.0 mm3). The mean metabolic ratios in lesions differed significantly between the 3 MRSI resolutions (ie, 100 × 100 vs 64 × 64, 100 × 100 vs 32 × 32, and 64 × 64 vs 32 × 32; P < 0.001). With the ultra-high resolution (100 × 100), we obtained 40% to 80% higher mean metabolic ratios and 100% to 150% increase in maximum metabolic ratios in the MS lesions compared with the lowest resolution (32 × 32), while maintaining good spectral quality (signal-to-noise ratio >12, Cramér-Rao lower bounds <20%) and measurement time of 6 minutes. There were 83% of MS lesions that showed increased myo-inositol/N-acetylaspartate with the 100 × 100 resolution, but only 66% were distinguishable with the 64 × 64 resolution and 35% with the 32 × 32 resolution.

Conclusions

Ultra-high-resolution MRSI (~2 × 2 × 8 mm3 voxel volume) can detect metabolic alterations in MS, which cannot be recognized by conventional MRSI resolutions, within clinically acceptable time.
Refining interaction search through signed iterative Random Forests
Authors: Kumbier Karl , Basu Sumanta , Brown James B. , Celniker Susan , Yu Bin
Published: November 2018

Advances in supervised learning have enabled accurate prediction in biological systems governed by complex interactions among biomolecules. However, state-of-the-art predictive algorithms are typically “black-boxes,” learning statistical interactions that are difficult to translate into testable hypotheses. The iterative Random Forest (iRF) algorithm took a step towards bridging this gap by providing a computationally tractable procedure to identify the stable, high-order feature interactions that drive the predictive accuracy of Random Forests (RF). Here we refine the interactions identified by iRF to explicitly map responses as a function of interacting features. Our method, signed iRF (s-iRF), describes “subsets” of rules that frequently occur on RF decision paths. We refer to these “rule subsets” as signed interactions. Signed interactions share not only the same set of interacting features but also exhibit similar thresholding behavior, and thus describe a consistent functional relationship between interacting features and responses. We describe stable and predictive importance metrics (SPIMs) to rank signed interactions in terms of their stability, predictive accuracy, and strength of interaction. For each SPIM, we definenull importance metricsthat characterize its expected behavior under known structure. We evaluate our proposed approach in biologically inspired simulations and two case studies: predicting enhancer activity and spatial gene expression patterns. In the case of enhancer activity, s-iRF recovers one of the few experimentally validated high-order interactions and suggests novel enhancer elements where this interaction may be active. In the case of spatial gene expression patterns, s-iRF recovers all 11 reported links in the gap gene network. By refining the process of interaction recovery, our approach has the potential to guide mechanistic inquiry into systems whose scale and complexity is beyond human comprehension.
First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis
Authors: Afonso Luana Ferreira , Amaral Danielle , Uliano-Silva Marcela , Torres André Luiz Quintanilha , Simas Daniel Reis , Rebelo Mauro de Freitas
Published: November 2018

Background

Protiumspecies produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.

Results

Here we present (i) the first draft genome of an endemic tree of the Brazil’s Atlantic Rainforest (Mata Atlântica),Protium kleiniiCuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resin’s volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenesα-terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resin’s volatile fraction identified four monoterpenes: terpinolene, limonene,α-pinene andα-phellandrene.

Conclusion

These results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.
Patterns and mechanisms of diminishing returns from beneficial mutations
Authors: Wei Xinzhu , Zhang Jianzhi
Published: November 2018

Diminishing returns epistasis causes the benefit of the same advantageous mutation smaller in fitter genotypes, and is frequently observed in experimental evolution. However, its occurrence in other contexts, environment-dependence, and mechanistic basis are unclear. Here we address these questions using 1005 sequenced segregants generated from a yeast cross. Under each of 47 examined environments, 66-92% of tested polymorphisms exhibit diminishing returns epistasis. Surprisingly, improving environment quality also reduces the benefits of advantageous mutations even when fitness is controlled for, indicating the necessity to revise the global epistasis hypothesis. We propose that diminishing returns originates from the modular organization of life where the contribution of each functional module to fitness is determined jointly by the genotype and environment and has an upper limit, and demonstrate that our model predictions match empirical observations. These findings broaden the concept of diminishing returns epistasis, reveal its generality and potential cause, and have important evolutionary implications.
Source-sink dynamics could sustain HIV epidemics in rural communities in sub-Saharan Africa: the case of Malawi
Authors: Okano Justin T. , Sharp Katie , Palk Laurence , Blower Sally
Published: November 2018

Background:

Approximately 25.5 million individuals are infected with HIV in sub-Saharan Africa (SSA). Epidemics in this region are generalized, show substantial geographic variation in prevalence, and are driven by heterosexual transmission; populations are highly mobile. We propose that generalized HIV epidemics should be viewed as a series of micro-epidemics occurring in multiple connected communities. Using a mathematical model, we test the hypothesis that travel can sustain HIV micro-epidemics in communities where transmission is too low to be self-sustaining. We use Malawi as a case study.

Methods:

We first conduct a mapping exercise to visualize geographic variation in HIV prevalence and population-level mobility. We construct maps by spatially interpolating georeferenced HIV-testing and mobility data from a nationally representative population-level survey: the 2015-16 Malawi Demographic and Health Survey. To test our hypothesis, we construct a novel HIV epidemic model that includes three transmission pathways: resident-to-resident, visitor-caused and travel-related. The model consists of communities functioning as “sources” and “sinks”. A community is a source if transmission is high enough to be self-sustaining, and a sink if it is not.

Results:

HIV prevalence ranges from zero to 27%. Mobility is high, 27% of the population took a trip lasting at least a month in the previous year. Prevalence is higher in urban centers than rural areas, but long-duration travel is higher in rural areas than urban centers. We show that a source-community can sustain a micro-epidemic in a sink-community, but only if specific epidemiological and demographic threshold conditions are met. The threshold depends upon the level of transmission in the source- and sink-communities, as well as the relative sizes of the two communities. The larger the source than the sink, the lower transmission in the source-community needs to be for sustainability.

Discussion:

Our results support our hypothesis, and suggest that it may be rather easy for large urban communities to sustain HIV micro-epidemics in small rural communities; this may be occurring in northern Malawi. Visitor-generated and travel-related transmission may also be sustaining micro-epidemics in rural communities in other SSA countries with highly-mobile populations. It is essential to consider mobility when developing HIV elimination strategies.
Genetic loss of the ubiquitin ligase RNF126, an AID interacting partner and modifier, affects strand targeting during somatic hypermutation of antibody genes
Authors: Economos Nicholas , Delker Rebecca K , Stavropoulos Pete , Papavasiliou F. Nina
Published: November 2018

Activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) in B lymphocytes by catalyzing the introduction of deoxyuracil: deoxyguanine mismatches into the DNA of the transcribed Ig locus. Repair pathways then process these mismatches to produce point mutations in the Ig variable region or double-stranded DNA breaks in the switch region followed by deletional recombination. It has been suggested that post-translational modifications on AID mediate a number of these different decisions, ranging from global targeting (Ig vs the genome), local targeting (variable vs switch region; transcribed vs non-transcribed strand) as well as process-appropriate DNA repair. Here we demonstrate that absence of RNF126, an E3 ligase shown to mono-ubiquitylate AID, results in a specific strand targeting defect in SHM, producing substantial G>C bias; strickingly, loss of RNF126 was also associated with tandem indels within the variable region (JH4 intron) but only a slight increase in the types of chromosomal translocations that are characteristic of deregulated AID. Conversely, these findings suggest that mono-ubiquitination of AID, likely in situ, is necessary for the proper removal of the protein from the non-transcribed strand, thus producing both optimal patterns of SHM and also limiting the number of indels within the target locus.
Classification of naturally evoked compound action potentials in peripheral nerve spatiotemporal recordings
Authors: Koh Ryan G. L. , Nachman Adrian I. , Zariffa José
Published: November 2018

Peripheral neural signals have the potential to provide the necessary motor, sensory or autonomic information for robust control in many neuroprosthetic and neuromodulation applications. However, developing methods to recover information encoded in these signals is a significant challenge. We introduce the idea of using spatiotemporal signatures extracted from multi-contact nerve cuff electrode recordings to classify naturally evoked compound action potentials (CAP). 9 Long-Evan rats were implanted with a 56-channel nerve cuff on the sciatic nerve. Afferent activity was selectively evoked in the different fascicles of the sciatic nerve (tibial, peroneal, sural) using mechano-sensory stimuli. Spatiotemporal signatures of recorded CAPs were used to train three different classifiers. Performance was measured based on the classification accuracy, F1-score, and the ability to reconstruct original firing rates of neural pathways. The mean classification accuracies, for a 3-class problem, for the best performing classifier was 0.686 ± 0.126 and corresponding mean F1-score was 0.605 ± 0.212. The mean Pearson correlation coefficients between the original firing rates and estimated firing rates found for the best classifier was 0.728 ± 0.276. The proposed method demonstrates the possibility of classifying individual naturally evoked CAPs in peripheral neural signals recorded from extraneural electrodes, allowing for more precise control signals in neuroprosthetic applications.
Premovement suppression of corticospinal excitability may be a necessary part of movement preparation
Authors: Ibáñez J. , Hannah R. , Rocchi L. , Rothwell J.C.
Published: November 2018

In a warned reaction time (RT) task, corticospinal excitability (CSE) decreases in task-related muscles at the time of the imperative signal (preparatory inhibition). Because RT tasks emphasise speed of response, it is impossible to distinguish whether preparatory inhibition reflects a mechanism preventing premature reactions, or whether it is an inherent part of movement preparation. We used transcranial magnetic stimulation (TMS) to study CSE changes preceding RT movements and movements that were either self-paced (SP) or performed at predictable times to coincide with an external event (PT). Results show that CSE changes over a similar temporal profile in all cases, suggesting that preparatory inhibition is a necessary state in planned movements allowing the transition between rest and movement. Additionally, TMS given shortly before the times to move speeded the onset of movements in both RT and SP contexts, suggesting that their initiation depends on a form of trigger that can be conditioned by external signals. On the contrary, PT movements do not show this effect, suggesting the use of a mechanistically different triggering strategy. This relative immunity of PT tasks to be biased by external events may reflect a mechanism that ensures priority of internal predictive signals to trigger movement onset.
A novel model plant to study the light control of seed germination
Authors: Mérai Zsuzsanna , Graeber Kai , Wilhelmsson Per , Ullrich Kristian K. , Arshad Waheed , Grosche Christopher , Tarkowská Danuše , Turečková Veronika , Strnad Miroslav , Rensing Stefan A. , Leubner-Metzger Gerhard , Scheid Ortrun Mittelsten
Published: November 2018

Timing of seed germination is crucial for seed plants and coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce andArabidopsis thalianahave documented a strict requirement for light to initiate germination and identified many receptors, signalling cascades, and hormonal control elements. In contrast, seed germination of several other plants is inhibited by light, but the molecular basis of this converse response is unknown. We describeAethionema arabicum(Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as it comprises accessions with natural variation between light-sensitive and light-neutral responses. Inhibition is independent of light wavelength and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination as in Arabidopsis, but transcriptome comparisons of light- and dark-exposedAethionema arabicumseeds revealed that expression of genes for key regulators upon light exposure undergo converse changes, resulting in antipodal hormone regulation. This illustrates that similar modular components of a pathway in light-inhibited, light-neutral and light requiring germination among the Brassicaceae have been assembled by evolution to produce divergent pathways, likely as adaptive traits.

Highlight

In contrast to light requirement for Arabidopsis seed germination, germination of severalAethionema arabicumaccessions is inhibited by light, due to antipodal transcriptional regulation of hormone balance.
Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history
Authors: Ceballos Francisco C. , Hazelhurst Scott , Ramsay Michele
Published: November 2018

The study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups1). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These homozygosity cold and hotspots harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to the health of extant populations.
Comprehensive and quantitative analysis of white and brown adipose tissue by shotgun lipidomics
Authors: Grzybek Michal , Palladini Alessandra , Alexaki Vasileia I , Surma Michal A. , Simons Kai , Chavakis Triantafyllos , Klose Christian , Coskun Ünal
Published: November 2018

Shotgun lipidomics enables an extensive analysis of lipids from tissues and fluids. Each specimen requires appropriate extraction and processing procedures to ensure good coverage and reproducible quantification of the lipidome. Adipose tissue (AT) has become a research focus with regard to its involvement in obesity-related pathologies. However, the quantification of the AT lipidome is particularly challenging due to the predominance of triacylglycerides, which elicit high ion suppression of the remaining lipid classes. We present a new and validated method for shotgun lipidomics of AT, which tailors the lipid extraction procedure to the target specimen and features high reproducibility with a linear dynamic range of at least 4 orders of magnitude for all lipid classes. Utilizing this method, we observed tissue-specific and diet-related differences in three AT types (brown, gonadal, inguinal subcutaneous) from lean and obese mice. Brown AT exhibited a distinct lipidomic profile with the greatest lipid class diversity and responded to high-fat diet by altering its lipid composition, which shifted towards that of white AT. Moreover, diet-induced obesity promoted an overall remodelling of the lipidome, where all three AT types featured a significant increase in longer and more unsaturated triacylglyceride and phospholipid species.

The here presented method facilitates reproducible systematic lipidomic profiling of AT and could be integrated with further –omics approaches used in (pre-)clinical research, in order to advance the understanding of the molecular metabolic dynamics involved in the pathogenesis of obesity-associated disorders.
The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 inArabidopsis thaliana
Authors: Scholz Sebastian , Pleßmann Janys , Hüttl Regina , Wassmer Katrin , Enugutti Balaji , Schneitz Kay
Published: November 2018

Tissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood. We have previously identified the Arabidopsis AGCVIII-class protein kinase UNICORN (UCN) as a central regulator of this process. Plants lackingUCNactivity show spontaneous formation of ectopic multicellular protrusions in integuments and malformed petals indicating thatUCNsuppresses uncontrolled growth in those tissues. In the current model UCN regulates planar growth of integuments in part by directly repressing the putative transcription factor ABERRANT TESTA SHAPE (ATS). Here we report on the identification of3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1(PDK1) as a novel factor involved inUCN-mediated growth control. PDK1 constitutes a basic component of signaling mediated by AGC protein kinases throughout eukaryotes. ArabidopsisPDK1is implied in stress responses and growth promotion. Here we show that loss-of-function mutations inPDK1suppress aberrant growth in integuments and petals ofucnmutants. Additional genetic, in vitro, and cell biological data support the view that UCN functions by repressing PDK1. Furthermore, our data indicate thatPDK1is indirectly required for deregulated growth caused byATSoverexpression. Our findings support a model proposing that UCN suppresses ectopic growth in integuments through two independent processes: the attenuation of the protein kinase PDK1 in the cytoplasm and the repression of the transcription factor ATS in the nucleus.

Author Summary

Plant organs, such as petals or roots, are composites of distinct cell layers. As a rule, cells making up a layer, for example the epidermis, the outermost layer of a tissue, divide “within the plane” of the layer. This cellular behavior results in the two-dimensional sheet-like or planar growth of the cell layer. The mechanism orchestrating such a growth pattern is poorly understood. In particular, it is unclear how uncontrolled and “out-of-plane” growth is avoided. Here we provide insight into this process. Our data indicate that higher than normal activity of a central regulator of growth and stress responses results in wavy and malformed petals and in protrusion-like aberrant outgrowths in the tissue that will develop into the seed coat. It is therefore important to keep this factor in check to allow proper formation of those tissues. We further show that a protein called UNICORN attenuates the activity of this regulator thereby ensuring the sheet-like growth of young petals or the developing seed coat.
Neural distinctiveness declines with age in auditory cortex and is associated with auditory GABA levels
Authors: Lalwani Poortata , Gagnon Holly , Cassady Kaitlin , Simmonite Molly , Peltier Scott , Seidler Rachael D. , Taylor Stephan F. , Weissman Daniel H. , Polk Thad A.
Published: November 2018

Neural activation patterns in the ventral visual cortex in response to different categories of visual stimuli (e.g., faces vs. houses) are less selective, or distinctive, in older adults than in younger adults, a phenomenon known as age-related neural dedifferentiation. Previous work in animals suggests that age-related reductions of the inhibitory neurotransmitter, gamma aminobutyric acid (GABA), may play a role in this age-related decline in neural distinctiveness. In this study, we investigated whether neural dedifferentiation extends to auditory cortex and whether individual differences in GABA are associated with individual differences in neural distinctiveness in humans. 20 healthy young adults (ages 18-29) and 23 healthy older adults (over 65) completed a functional magnetic resonance imaging (fMRI) scan, during which neural activity was estimated while they listened to foreign speech and music. GABA levels in the auditory, ventrovisual and sensorimotor cortex were estimated in the same individuals in a separate magnetic resonance spectroscopy (MRS) scan. Relative to the younger adults, the older adults exhibited both (1) less distinct activation patterns for music vs. speech stimuli and (2) lower GABA levels in the auditory cortex. Also, individual differences in auditory GABA levels (but not ventrovisual or sensorimotor GABA levels) predicted individual differences in neural distinctiveness in the auditory cortex in the older adults. These results demonstrate that age-related neural dedifferentiation extends to the auditory cortex and suggest that declining GABA levels may play a role in neural dedifferentiation in older adults.

Significance Statement

Prior work has revealed age-related neural dedifferentiation in the visual cortex. GABA levels also decline with age in several parts of the human cortex. Here, we report that these two age-related changes are linked; neural dedifferentiation is associated with lower GABA levels in older adults. We also show that age-related neural dedifferentiation extends to auditory cortex, suggesting that it may be a general feature of the aging brain. These findings provide novel insights into the neurochemical basis of age-related neural dedifferentiation in humans and also offer a potential new avenue for investigating age-related declines in central auditory processing.
The lipid phosphatase-like protein PLPPR1 increases cell adhesion by modulating RhoA/Rac1 activity
Authors: Iweka Chinyere Agbaegbu , Tilve Sharada , Mencio Caitlin , Katagiri Yasuhiro , Geller Herbert M
Published: November 2018

Phospholipid Phosphatase-Related Protein Type 1 (PLPPR1) is a member of a family of lipid phosphatase related proteins, integral membrane proteins characterized by six transmembrane domains. PLPPR1 is enriched in the brain and recent data indicate potential pleiotropic functions in several different contexts. An inherent ability of PLPPR1 is to induce membrane protrusions, and we have previously reported that members within this family may act in concert. However, the mechanism by which PLPPR1 produces these actions is not yet understood. Here, we report that exogenous expression of PLPPR1 reduces cell motility and increases cell adhesion to the ECM substrate by altering cytoskeletal dynamics and modulating RhoA and Rac1 activity through association with RhoGDI. This signaling also allows overexpression of PLPPR1 to overcome the inhibitory activity of CSPGs and LPA on neurites. Together, these results establish a novel signaling pathway for the PLPPR1 protein.

PLPPR1 increases cell adhesion and decreases cell motility by modulating RhoA and Rac1 activation through its association with RhoGDI.
Phenomenological and numerical analysis of power evolution and bunching in single-pass X-ray FELs
Authors: Zhukovsky K. , Kalitenko A.
Published: November 2018

The harmonic power and bunching evolution in X-ray single-pass free-electron lasers (FELs) is modelled and the harmonic generation in a phase-shifted two-frequency FEL is explored. The advanced phenomenological FEL model, which is validated numerically and experimentally, is employed. The model accounts for major losses for each harmonic individually; it is compared with reported experimental data and with PERSEO numerical simulations, which are performed here for a variety of experiments. The latter cover the radiation wavelength range 0.15–300 nm. The phenomenological description is based on a few key FEL parameters: electron beam section, current, energy and its spread and divergence. The model is employed for modelling harmonic bunching and power evolution in a phase-shifted X-ray FEL with a two-frequency undulator, where lower harmonics with numbers less than nth are suppressed by the electron–photon phase shift of kπ/n, k = 2, 4, …, between the undulator sections. The benefits of the two-frequency phase-shifted FEL are highlighted. FEL-induced energy spread is shown to be three times lower than in a FEL without the phase-shift. The high-power harmonic and sub-harmonic radiation in such a FEL is demonstrated. In particular, powerful ∼14 GW X-ray radiation at λ5 = 0.15 nm from electrons with energy of 5.47 GeV and beam current ∼3.66 kA is possible in a two-frequency phase-shifted FEL at 30 m; this constitutes half of a FEL length where a common planar undulator radiates the same wavelength and power at the fundamental harmonic. Moreover, about a three times lower energy spread is induced by the dominant fifth harmonic, and the harmonic power can be thousands of times higher than in a common planar undulator FEL.
Eating habits of Polish university students depending on the direction of studies and gender
Authors: Kowalska Anna Sylwia , Tarnowska Agnieszka
Published: November 2018

Purpose

The purpose of this paper is to evaluate the eating habits of students in the field of management and engineering of food products compared to students from faculties not related to food science. Furthermore, another aim is to conduct gender-wise assessment to determine the type of eating habit, i.e., careful or binge eating.

Design/methodology/approach

The research involved 400 students from all years of study. The survey was conducted in 2017–2018 and the selection of the sample was intentional. The research used a questionnaire form. Additionally, χ2 test was performed to assess the statistical independence of characteristics.

Findings

It is found that most students who pledge proper nutrition are women. The majority of respondents ate 3–4 meals in day and regular consumption of breakfast was declared among 42 percent of respondents. The consumption of sweet snacks between meals is reaffirmed by the half of the respondents. Students of the food sciences more often than others believed that they eat healthier and more regularly, although students of non-food directions most often declared intake of five or more meals a day.

Research limitations/implications

An important limitation of the conducted study is a relatively small research sample. It consisted of university students from one of the largest academic centers in Poland. The results cannot be generalized to all students in this country. In the future, a similar survey should be conducted on a larger scale and cover all similar fields of management and engineering of food products in Poland. In addition, it would be worth expanding the research and examine graduates who found employment in the food industry.

Practical implications

The results of the conducted research are a good source of information on the differences in the way of feeding studying women and men. While such studies are not very revealing, the comparison between students in food and non-food fields can be considered a novelty. The described results can be used by the students themselves, but above all, by the authorities of universities conducting food science programs.

Social implications

The students do not eat properly which can lead to nutritional deficiencies and can deteriorate mental and physical endurance damaging overall health.

Originality/value

The described research is important due to the observed deteriorating eating habits and growing overweight of young adults in developed countries like Poland. They show that education of food technologists, even at the academic level, does not always allow to avoid mistakes in their own nutrition.