[Experimental] List of manuscripts available for review volunteers
8 manuscripts available for review volunteers
September 20, 2017
Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.
September 15, 2017
Plant defensins are known for different biological functions such as insect resistance, antibacterial, antifungal and antiviral activities. The role of plant defensins against weevils is based on inhibitor of alpha-amylase activity in weevil gut, therefore, weevils can not digest starch and then die. The low content of Vigna radiata plant defensin 1 (VrPDF1) in mung bean seeds is promted researches to increase the VrPDF1content, in which leads to enhance alpha-amylase inhibition and improve bruchid resistance in mung bean. This article presents the results of overexpression of VrPDF1 gene in transgenic mung bean plants. VrPDF1 gene was successfully transferred into DX22 mung bean cultivar and expressed in T1 generation transgenic mung bean seeds. The extract containing recombinant VrPDF1 protein inhibited alpha-amylase of weevil larvae in its larval stage. The performance of alpha-amylase inhibitor of DX1-3 and DX1-7 transgenic mung bean lines increased by 166.40% and 178.19% respectively, in comparison with non-transgenic plants. The enhancement of alpha-amylase inhibitor ability of rVrPDF1 extracted from transgenic plants is scientifically fundamental to confirm the effectiveness of the application of gene technology in enhancement the ability of mung bean weevil resistance in particular and grain crops in general revenue.
September 14, 2017
Using Smith’s (1986) cognitive-affective model of athletic burnout as guiding framework, the purpose of this study was to examine the relationships among athletes’ life stress, negative thoughts, and burnout; and examine the mediating role of negative thoughts on the life stress-burnout relationship. A total of 300 college student-athletes (males = 174; females = 126, Mage =20.43 yrs, SD = 1.68) completed the College Student-Athletes’ Life Stress Scale (CSALSS; Lu, Hsu, Chan, Cheen, & Kao, 2012), Automatic Thoughts Questionnaire (ATQ; Hollon & Kendall, 1980), and Athlete Burnout Questionnaire (ABQ; Raedeke & Smith, 2001). Correlational analyses found 2 types of life stress and 4 types of negative thoughts correlated with burnout. Also, hierarchical regression analyses found 4 types of negative thoughts partially mediated the life stress-burnout relationship. We concluded that athletes’ negative thoughts play a pivotal role in influencing athletes’ stress and psychological responses. Future study may examine how irrational cognitions influence athletes’ motivation and psychological well-being.
September 6, 2017
Background: The number of oropharyngeal lesions caused by HPV has been increasing in worldwide in the last years. Nonetheless, there is just little evidence relating HPV oropharynx status in healthy oral mucosa and HIV infection. The aim of the present study was to investigate the frequency of oropharynx papillomavirus infection in HIV positive subjects . Methods: A cross sectional study design was performed using samples collected from 100 HIV positive subjects.HPV infection was evaluated by conventional, base-liquid cytology and hybrid capture (HC). Clinical data was also collected to investigate the relation with HPV status. Results: Morphological features didn’t show signs of dysplasia lesion, but atypical squamous cells of undetermined significance (ASC-US) was diagnosed in 2 cases.High and low-risk types of HPV were present in 8% and 16.7% of the total sample. The mean ± dp (maximum-minimum) of the relative ratio light unit (RLU)/cutoff (CO) was 2.94±2.58 (1.09 – 7.87) and 1.61±0.65 (1.07 - 2.8) for high- and low-risk-HPV, respectively. Signs of dysplastic cells were not detected, but atypical squamous cells of undetermined significance (ASC-US) was diagnosed in 2 samples by cytology. Discussion: In spite of HPV oropharynx infection presence in some HIV subjects, neither clinical nor cytological signs suggestive of dysplasia/neoplasia were observed. Hybrid capture was able to detect and characterize HPV infection and may represent a good tool for screening and follow-up of this population.
September 6, 2017
Background: Sclerostin is a canonical Wnt/β-catenin signaling pathway inhibitor. The Wnt/β-catenin signaling pathway is believed to be implicated in the development of arterial stiffness. This study investigated the relationship between sclerostin and carotid–femoral pulse wave velocity (cfPWV) among hypertensive patients. Methods: Fasting blood samples were obtained from 105 hypertensive patients. cfPWV values >10 m/s were used to define the high arterial stiffness group, whereas values ≤ 10 m/s were used to define the low arterial stiffness group. Serum sclerostin levels were quantified using commercially available enzyme-linked immunosorbent assays. Results: Thirty-six hypertensive patients (34.3%) were defined as the high arterial stiffness group. Compared with the low arterial stiffness group, hypertensive patients in the high arterial stiffness group had diabetes mellitus (p = 0.030) and higher age (p < 0.001), systolic blood pressure (SBP, p = 0.013), pulse pressure (p = 0.026), creatinine (p = 0.013), intact parathyroid hormone (iPTH, p = 0.003), and sclerostin levels (p < 0.001) but lower estimated glomerular filtration rate (eGFR, p = 0.014). Multivariate logistic regression analysis of the factors significantly associated with arterial stiffness showed that sclerostin (odds ratio: 1.054, 95% confidence interval (CI): 1.025–1.083, p < 0.001) was still an independent predictor of arterial stiffness in hypertensive patients. Discussion: In this study, older age, higher SBP and pulse pressure, higher serum level of creatinine, iPTH, and sclerostin, whereas lower eGFR values were found in the high arterial stiffness group compared to those in the low arterial stiffness group among the hypertensive patients. Serum sclerostin level is an independent predictor of arterial stiffness after adjusted other significant confounders among hypertensive patients.
August 31, 2017

Background. A substitution effect occurs when patients substitute Medical Cannabis (MC) for another drug. Three lines of evidence: 1) patient self-report; 2) ecological examination of reduced opioid overdoses in states that legalized MC; and 3) medical expenditures, are consistent with patients reducing their opioid use after starting MC. Further, a prior investigation (Piper et al. 2017a) found that over three-quarters (76.7%) of New England dispensary members, most with chronic pain, reported reducing their use of opioids after starting MC and two-fifths (42.0%) decreased their use of alcohol. This finding is of interest because existing pharmacotherapies for Alcohol Use Disorders (AUD) have very limited efficacy. There is also a preclinical evidence base that manipulating the endocannabinoid neurotransmitter system can modify alcohol consumption. The objective of this exploratory study was to identify any factors which differentiate alcohol substituters from those that do not modify their alcohol use after starting MC (non-substituters).

Methods. Among a large sample of dispensary patients (N=1,477), the majority with chronic pain, that completed a 77-item online survey, 7.4% indicated that they regularly consumed alcohol. Comparisons were made to identify any demographic or health history characteristics which differentiated alcohol substituters (N = 47) from non-substituters (N = 65). Respondents selected from among a list of 37 diseases and health conditions (e.g. diabetes, high blood pressure, chronic pain, sleep disorder) and the total number was calculated. Variability was expressed as the standard deviation and p < .05 was considered statistically significant.

Results. Substituters were more likely to be employed (68.1%) than non-substituters (51.1%, p < .05). Substituters also reported having more health conditions and diseases (3.3 + 2.0) than non-substituters (2.4 + 1.4, p < .05). Substituters and non-substituters were indistinguishable in terms of sex, age, or prior drug history.

Discussion. This small, descriptive and exploratory study offers some insights into the profile of patients whose self-reported alcohol intake decreased following initiation of MC. Alcohol substituters had more other health conditions but also were more likely to be employed which may indicate that they fit a social drinker profile. Additional prospective or controlled research into the alcohol substitution effect following MC with a sample with more advanced alcohol misuse or an AUD may be warranted.

August 18, 2017
This study examined whether being aware of the repetition of stimuli in a simple numerosity task could aid the development of automaticity. The numerosity task used in this study was a simple counting task. Thirty-four participants were divided into two groups. One group was instructed that the stimuli would repeat many times throughout the experiment. The results showed no significant differences in the way automatic processing developed between the groups. Similarly, there was no correlation between the point at which automatic processing developed and the point at which participants felt they benefitted from the repetition of stimuli. These results suggest that extra-trial features of a task may have no effect on the development of automaticity, a finding consistent with the instance theory of automatisation.
August 2, 2017
We describe the \textsc{Coefficient-Flow} algorithm for calculating the bounding chain of an $(n-1)$--boundary on an $n$--manifold-like simplicial complex $S$. We prove its correctness and show that it has a computational time complexity of $O(|S^{(n-1)}|)$ (where $S^{(n-1)}$ is the set of $(n-1)$--faces of $S$). We estimate the big-$O$ coefficient which depends on the dimension of $S$ and the implementation. We present an implementation, experimentally evaluate the complexity of our algorithm, and compare its performance with that of solving the underlying linear system.

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