bluuebunny/crossref_metadata_2025 huggingface dataset:
3D Separable 2-layered Elastic Models of the Face for Surgical Planning of Local Flaps
Authors: Okamoto Toyoko , Hirota Yuka , Kimura Yusuke , Senda Erina , Ueda Koichi
Published: July 2018

Reconstruction with the use of local flaps always involves 3 dimensional movements. It is difficult to predict with 3D complex forms stereoscopic changes after local flap operations on the face. We have made 3-dimensional computer-assisted 2-layered elastic models of the face. The surface layer of the model can be detached from the inner layer. By observing the surface model after simulation surgery, it becomes possible to note the distortions caused by the flaps and to determine the tension of each stitch during suturing of the flap. For the simulation surgery, we used our model for a 73-year-old woman with basal cell carcinoma of the nose, selecting the best of several candidate flaps. The time of removal of the stitches could be delayed at the places with high tension. By using these separable 2-layered models of the face, we can choose the best reconstruction method. The actual operation can be performed smoothly, and the best time to remove the stitches can be determined.
INTERNAL LIMITING MEMBRANE PEELING DURING PARS PLANA VITRECTOMY FOR RHEGMATOGENOUS RETINAL DETACHMENT
Authors: Yannuzzi Nicolas A. , Callaway Natalia F. , Sridhar Jayanth , Smiddy William E.
Published: July 2018

Purpose:

To evaluate the visual and potential economic impact of primary internal limiting membrane (ILM) peeling in primary treatment of rhegmatogenous retinal detachment.

Methods:

A PubMed search was performed to extract data regarding the rate of epiretinal membrane formation and the rate of secondary pars plana vitrectomy with membrane peel after repair of rhegmatogenous retinal detachment with or without ILM peeling. Data were aggregated and analyzed in a meta-analysis. This information was used to perform a cost analysis to determine the economic ramifications of primary ILM peeling.

Results:

Six included studies compared the outcomes of eyes receiving pars plana vitrectomy for rhegmatogenous retinal detachment repair with and without primary ILM peel. The cumulative rate of epiretinal membrane formation was 29% (86/295) in the eyes without ILM peel and 3% (8/289) in the eyes with ILM peel. The cumulative rate of secondary pars plana vitrectomy/membrane peel was 16% (22/141) in the eyes without ILM peel and 0% (0/158) in the eyes with ILM peel. The weighted summary point estimate odds ratio was 0.083 (95% confidence interval 0.042–0.164), indicating a statistically significant protective effect across the 6 studies of ILM peeling and the development of epiretinal membrane. Based on published data, the average dollars saved by conducting a primary ILM peel was $615 in a facility setting and $364 in an ambulatory surgical center.

Conclusion:

Published, mainly retrospective, data suggest that primary ILM peel in rhegmatogenous retinal detachment repair may have a significant reduction in the rate of postoperative epiretinal membrane and may lessen the need for secondary pars plana vitrectomy/membrane peel. Furthermore, from an economic perspective, the reduction in the need for secondary surgery may justify the higher cost with primary ILM peel.
5-Flouorouracil Is an Attractive Medical Treatment in Women With Vaginal Intraepithelial Neoplasia: A Meta-Analysis
Authors: Tranoulis Anastasios , Georgiou Dimitra , Laios Alexandros , Theophilou Georgios , Thangavelu Amudha , Hutson Richard Chanellor
Published: July 2018

Objective

In the absence of standard guidelines, the management of vaginal intraepithelial neoplasia (VaIN) remains a field of debate. The aim of this systematic review and meta-analysis was to ascertain the 5-flouorouracil (5-FU) effectiveness in this context.

Materials and Methods

A literature search was conducted throughout the PubMed, EMBASE, SCOPUS, ClinicalTrials.gov, and Cochrane Databases for relevant studies. We computed the summary proportions of women treated for VaIN with 5-FU for the outcomes of complete response and recurrence by random-effects meta-analysis. We also performed a subgroup analysis by computing the summary proportions for complete response among women with high-grade VaIN, persistent disease, and recurrence respectively.

Results

Fourteen observational studies reporting on 358 women included in the study. The study quality was moderate. The summary proportions of women who had complete response after the first 5-FU course were 82.18% (95% CI = 69.80%–88.82%). The summary proportions of women who recurred were 16.42% (95% CI = 7.39%–28.14%). The summary proportions of women with complete response in the high-grade VaIN, persistent disease, and recurrence subgroups were 77.53% (95% CI = 59.90%–91.15%), 53.92% (95% CI = 34.62%–72.61%), and 72.32% (95% CI = 48.12%–91.05%), respectively.

Conclusions

This is the first meta-analysis to date to provide a convincing overview of 5-FU efficacy on the VaIN treatment. Albeit a medium risk of bias warrants some caution with interpretation of the results, 5-FU can be an attractive alternative to surgery, especially among young women with multifocal and recurrent disease.
Esophageal varices are not predictive of patient prognosis after surgical resection of hepatocellular carcinoma
Authors: Chang Chung-Yu , Hsieh Wei-Yao , Chau Gar-Yang , Chen Ping-Hsien , Su Chien-Wei , Hou Ming-Chih , Lei Hao-Jan , Huo Teh-Ia , Huang Yi-Hsiang , Lin Han-Chieh , Wu Jaw-Ching
Published: July 2018

Objective

The predictive value of esophageal varices (EV) in determining the patient outcome in hepatocellular carcinoma (HCC) remains unresolved. We aimed to assess the impact of EV on the prognosis of HCC patients after surgical resection.

Materials and methods

We consecutively enrolled 446 treatment-naive HCC patients who underwent surgical resection and esophagogastroduodenoscopy from 2003 to 2015. Prognostic factors were analyzed using the Cox proportional hazards model and a propensity score matching analysis.

Results

A total of 89 (20.0%) HCC patients presented with EV. Compared with those without EV, patients with EV had poorer preservation of liver function and higher rates of cirrhosis in the nontumor part of liver specimens. After a median follow-up period of 34.6 months (25–75 percentiles; 12.8–59.3 months), 130 patients had died. The cumulative 5-year overall survival (OS) rates were 62.3 and 70.6% in patients with and without EV, respectively (P=0.102). A multivariate analysis showed that serum albumin level less than or equal to 4 g/dl (P=0.020), α-fetoprotein level greater than 20 ng/ml (P<0.001), as well as the presence of vascular invasion (P<0.001), but not the presence of EV, were independent risk factors associated with poor OS. Moreover, 67 patients were matched in each group using the one-to-one nearest-neighbor matching method. After matching, the OS rates were comparable between HCC patients with and without EV.

Conclusion

EV is not an independent risk factor predictive of poor prognosis for HCC patients after resection surgery if they have well-preserved liver function.
Expression of HPV-induced DNA Damage Repair Factors Correlates With CIN Progression
Authors: Spriggs Chelsey C. , Blanco Luis Z. , Maniar Kruti P. , Laimins Laimonis A.
Published: July 2018

Human papillomaviruses (HPVs) are DNA viruses with epithelial tropism. High-risk types of HPV are the causative agents of the majority of cervical cancers and are responsible for a number of other anogenital as well as oropharyngeal cancers. The life cycle of HPV is closely linked to the differentiation state of its host cell and is dependent on the activation of specific pathways of the DNA damage response. Several proteins from the ataxia telangiectasia mutated and the ataxia telangiectasia mutated and Rad3-related DNA repair pathways, which are essential for maintaining genomic stability in cells, are upregulated in HPV-positive cells and are required for viral replication. Our studies examine the expression of 5 such DNA repair factors—pCHK2, pCHK1, FANCD2, BRCA1, and H2AX—in cervical specimens from patients diagnosed with low-grade, intermediate-grade, or high-grade lesions. The percentage of cells expressing pCHK2, pCHK1, FANCD2, and BRCA1 is significantly higher in high-grade squamous intraepithelial lesions compared with that of either low-grade squamous intraepithelial lesions or normal tissue, particularly in differentiated cell layers. In addition, the distribution of this staining throughout the epithelium is altered with increasing lesion grade. This study characterizes the expression of pCHK2, pCHK1, FANCD2, H2AX and BRCA1 during cervical cancer progression and provides additional insight into the role of these DNA damage response proteins in viral transformation.
Simple Screening Tool to Help Identify High-Risk Children for Targeted HIV Testing in Malawian Inpatient Wards
Authors: Moucheraud Corrina , Chasweka Dennis , Nyirenda Mike , Schooley Alan , Dovel Kathryn , Hoffman Risa M. ,   on behalf of the EQUIP Innovations Team
Published: July 2018

Background:

To meet global AIDS goals, pediatric HIV diagnosis must be strengthened. Provider-initiated testing and counseling, which is recommended by the WHO, faces persistent implementation challenges in low-resource settings. Alternative approaches are needed.

Setting:

Malawi has achieved high coverage of HIV diagnosis and treatment, but there are gaps among pediatric populations. This study assessed the sensitivity and specificity of a brief screening tool to identify at-risk pediatric patients for targeted HIV testing in Malawi.

Methods:

A tool containing 6 yes/no items was used for children (aged 1–15 years) in the inpatient pediatric wards at 12 hospitals in Malawi (July 2016–July 2017). Questions were based on an established tool, translated to Chichewa, and implemented by HIV diagnostic assistants. All participating children were provided HIV testing and counseling per Ministry of Health guidelines. Analysis estimated the tool's characteristics including sensitivity, specificity, negative, and positive predictive values.

Results:

HIV prevalence among the 8602 participants was 1.1% (n = 90). Children with a screening tool score of 1 had double the odds of being HIV positive than those with a score of 0. Frequent sickness was the most sensitive predictor of HIV status (55.1%), and having a deceased parent was the most specific (96.7%). False classification of HIV-negative status was rare (n = 14) but occurred more often among boys and younger children.

Conclusions:

A brief screening tool for pediatric inpatients helped target HIV testing in those most at risk in a low-pediatric-prevalence, resource-constrained setting. Future research should include a direct, rigorous comparison with PITC including comparative effectiveness, efficiency, and cost effectiveness.
Associating Liver Partition and Portal Vein Ligation for Staged Hepatectomy for Unresectable Hepatitis B Virus-related Hepatocellular Carcinoma
Authors: Wang Zheng , Peng Yuanfei , Hu Jingwu , Wang Xiaoying , Sun Huichuan , Sun Jian , Shi Yinghong , Xiao Yongsheng , Ding Zhenbing , Yang Xinrong , Tang Min , Tang Zhaoyou , Wang Jiping , Lau Wan Y. , Fan Jia , Zhou Jian
Published: July 2018

Objective:

The aim of the study is to assess the efficacy and safety of associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) in patients with hepatitis B virus-related hepatocellular carcinoma (HCC).

Background:

ALPSS allows curative resection of conventionally-unresectable liver tumors. However, its role in HCC is largely unknown.

Methods:

Consecutive HCC patients who underwent ALPPS at our center between April 2013 and September 2017 were retrospectively studied. The oncological results were compared with patients receiving transcatheter arterial chemoembolization (TACE), and patients undergoing one-stage resection by using propensity score matching (PSM) analysis.

Results:

The median tumor diameter was 13 cm (range: 6–22 cm) in patients with a single tumor (n = 28), whereas the median total tumor diameter was 12 cm (range: 9–31 cm) in patients with multiple tumors (n = 17). After stage-1 ALPPS, the median future liver remnant (FLR) increased by 56.8%. The stage-2 ALPPS was completed in 41 patients (91.1%) after a median of 12 days. The 90-day mortality rate was 11.1% (5/45). The overall survival (OS) rates at 1- and 3-year were 64.2% and 60.2%, whereas the disease-free survival (DFS) rates at 1 and 3 years were 47.6% and 43.9%, respectively. On PSM analysis, the long-term survival of patients undergoing ALPPS was significantly better than those receiving TACE (OS, P = 0.004; DFS, P < 0.0001) and similar to those subjected to one-stage liver resection (OS, P = 0.514; DFS, P = 0.849).

Conclusions:

The long-term survival after ALPPS was significantly better than TACE, and similar to those after one-stage liver resection. ALPPS is a viable treatment option for patients with unresectable HCC in selected patients.
Clinical Importance of Mean Corpuscular Volume as a Prognostic Marker After Esophagectomy for Esophageal Cancer
Authors: Yoshida Naoya , Kosumi Keisuke , Tokunaga Ryuma , Baba Yoshifumi , Nagai Yohei , Miyamoto Yuji , Iwagami Shiro , Iwatsuki Masaaki , Hiyoshi Yukiharu , Ishimoto Takatsugu , Eto Kojiro , Imamura Yu , Watanabe Masayuki , Baba Hideo
Published: July 2018

Objective:

To elucidate the clinical value of mean corpuscular volume (MCV) for prognostic prediction in patients with esophageal cancer who underwent radical esophagectomy.

Background:

High MCV is suggested to be relevant to the incidence and prognosis of several malignancies. However, few studies investigating the correlation between MCV and survival outcome of esophageal cancer have been conducted.

Methods:

This study included 570 patients with esophageal cancer who underwent radical esophagectomy between April, 2005 and December, 2017. Patients were divided into 2 groups according to the standard value of pretreatment MCV: normal (83–99 fL) and high (>99 fL) groups. Clinical backgrounds, short-term outcomes, and prognostic outcomes postesophagectomy were retrospectively compared between the groups.

Results:

Of all patients, 410 (71.9%) had normal MCV, and 160 (28.1%) had high MCV. High MCV was significantly associated with lower body mass index, higher frequency of habitual alcohol and tobacco use, and higher incidence of multiple primary malignancies other than esophageal cancer. High MCV also correlated with higher incidence of postoperative morbidity of the Clavien–Dindo classification ≥II and pulmonary morbidity. Overall survival was significantly worse in patients with high MCV. Multivariate analysis suggested that high MCV was an independent risk factor for worse survival outcome (hazard ratio 1.54, 95% confidence interval 1.098–2.151, P = 0.012).

Conclusions:

Patients with high MCV have various disadvantages in clinical background that can adversely affect both short-term and long-term outcomes after esophagectomy. MCV can become a predictive marker to estimate survival outcome after esophagectomy for esophageal cancer.
Shared environmental effects bias phenotypic estimates of assortative mating in a wild bird
Authors: Class Barbara , Brommer Jon E.
Published: July 2018

Assortative mating is pervasive in wild populations and commonly described as a positive correlation between the phenotypes of males and females across mated pairs. This correlation is often assumed to reflect non-random mate choice based on phenotypic similarity. However, phenotypic resemblance between mates can also arise when their traits respond plastically to a shared environmental effect creating a (within-pair) residual correlation in traits. Using long-term data collected in pairs of wild blue tits and a covariance partitioning approach, we empirically demonstrate that such residual covariance indeed exists and can generate phenotypic correlations (or mask assortative mating) in behavioural and morphometric traits. These findings (i) imply that residual covariance is likely to be common and bias phenotypic estimates of assortative mating, which can have consequences for evolutionary predictions, (ii) call for the use of rigorous statistical approaches in the study of assortative mating, and (iii) show the applicability of one of these approaches in a common study system.
Intercomparison of photogrammetry software for three-dimensional vegetation modelling
Authors: Probst Alexandra , Gatziolis Demetrios , Strigul Nikolay
Published: July 2018

Photogrammetry-based three-dimensional reconstruction of objects is becoming increasingly appealing in research areas unrelated to computer vision. It has the potential to facilitate the assessment of forest inventory-related parameters by enabling or expediting resource measurements in the field. We hereby compare several implementations of photogrammetric algorithms (CMVS/PMVS, CMPMVS, MVE, OpenMVS, SURE and Agisoft PhotoScan) with respect to their performance in vegetation assessment. The evaluation is based on (i) a virtual scene where the precise location and dimensionality of objects is known
a priori
and is thus conducive to a quantitative comparison and (ii) using series of
in situ
acquired photographs of vegetation with overlapping field of view where the photogrammetric outcomes are compared qualitatively. Performance is quantified by computing receiver operating characteristic curves that summarize the type-I and type-II errors between the reference and reconstructed tree models. Similar artefacts are observed in synthetic- and
in situ
-based reconstructions.
Cryptic niche switching in a chemosymbiotic gastropod
Authors: Chen Chong , Linse Katrin , Uematsu Katsuyuki , Sigwart Julia D.
Published: July 2018

Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. ‘Metamorphosis’ broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropodGigantopelta chessoiaexperiences a further, cryptic metamorphosis at body sizes around 5–7 mm.The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term ‘cryptometamorphosis’ to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.
Short-term aerobic training does not improve memory functioning in relapsing remitting multiple sclerosis – a randomized controlled trial
Authors: Baquet L , Hasselmann H , Patra S , Stellmann JP , Vettorazzi E , Engel AK , Rosenkranz S , Poettgen J , Gold SM , Schulz KH , Heesen C
Published: July 2018

Background

Only few aerobic exercise intervention trials specifically targeting cognitive functioning have been performed in MS.

Objective and methods

This randomized controlled trial aimed to determine the effects of aerobic exercise on cognition in relapsing-remitting MS. The primary outcome was verbal memory (Verbal learning and memory test, VLMT). Patients were randomized to an intervention group (IG) program or a waitlist control group (CG). Patients in the IG exercised according to an individually tailored training schedule (with 2-3 sessions per week for 12 weeks). The primary analysis was carried out using the intention-to-treat (ITT) sample with ANCOVA adjusting for baseline scores.

Results

77 RRMS patients were screened and 68 participants randomized (CG n=34; IG n=34). The sample comprised 68% females, had a mean age of 39 years, a mean disease duration of 6.3 years, and a mean EDSS of 1.8. No significant effects were detected in the ITT analysis for the primary endpoint VLMT or any other cognitive measures. Moreover, no significant treatment effects were observed for quality of life, fatigue, or depressive symptoms.

Conclusion

This study failed to demonstrate beneficial effects of aerobic exercise on cognition in RRMS.

The trial was prospectively registered at clinicaltrials.gov (NCT02005237).
Closed-Loop Control of Active Sensing Movements Regulates Sensory Slip
Authors: Biswas Debojyoti , Arend Luke A. , Stamper Sarah A. , Vágvölgyi Balázs P. , Fortune Eric S. , Cowan Noah J.
Published: July 2018

Active sensing involves the production of motor signals for the purpose of acquiring sensory information [1–3]. The most common form of active sensing, found across animal taxa and behaviors, involves the generation of movements—e.g. whisking [4–6], touching [7,8], sniffing [9,10], and eye movements [11]. Active-sensing movements profoundly affect the information carried by sensory feedback pathways [12–15] and are modulated by both top-down goals (e.g. measuring weight vs. texture [1,16]) and bottom-up stimuli (e.g. lights on/off [12]) but it remains unclear if and how these movements are controlled in relation to the ongoing feedback they generate. To investigate the control of movements for active sensing, we created an experimental apparatus for freely swimming weakly electric fish,Eigenmannia virescens, that modulates the gain of reafferent feedback by adjusting the position of a refuge based on real time videographic measurements of fish position. We discovered that fish robustly regulate sensory slip via closed-loop control of active-sensing movements. Specifically, as fish performed the task of maintaining position inside the refuge [17–22], they dramatically up- or down-regulated fore-aft active-sensing movements in relation to a 4-fold change of experimentally modulated reafferent gain. These changes in swimming movements served to maintain a constant magnitude of sensory slip. The magnitude of sensory slip depended on the presence or absence of visual cues. These results indicate that fish use two controllers: one that controls the acquisition of information by regulating feedback from active sensing movements, and another that maintains position in the refuge, a control structure that may be ubiquitous in animals [23,24].
Risk of bias in Cochrane systematic reviews: assessments of risk related to attrition bias are highly inconsistent
Authors: Babic Andrija , Tokalic Ruzica , Cunha João Amílcar Silva , Novak Ivana , Suto Jelena , Vidak Marin , Miosic Ivana , Vuka Ivana , Pericic Tina Poklepovic , Puljak Livia
Published: July 2018

Background

An important part of the systematic review methodology is appraisal of the risk of bias in included studies. Cochrane systematic reviews (CSRs) are considered golden standard regarding systematic review methodology, but Cochrane’s instructions for assessing risk of attrition bias are vague, which may lead to inconsistencies in authors’ assessments. The aim of this study was to analyze consistency of judgments and support for judgments of attrition bias in CSRs of interventions published in the Cochrane Database of Systematic Reviews (CDSR).

Methods

We analyzed CSRs published from July 2015 to June 2016 in the CDSR. We extracted data on number of included trials, judgment of attrition risk of bias for each included trial (low, unclear or high) and accompanying support for the judgment (supporting explanation). We also assessed how many CSRs had different judgments for the same supporting explanations.

Results

In the main analysis we included 10292 judgments and supporting explanations for attrition bias from 729 CSRs. We categorized supporting explanations for those judgments into four categories and we found that most of the supporting explanations were unclear. Numerical indicators for percent of attrition, as well as statistics related to attrition were judged very differently. One third of CSR authors had more than one category of supporting explanation; some had up to four different categories. Inconsistencies were found even with the number of judgments, names of risk of bias domains and different judgments for the same supporting explanations in the same CSR.

Conclusion

We found very high inconsistency in methods of appraising risk of attrition bias in recent Cochrane reviews. Systematic review authors need clear guidance about different categories they should assess and judgments for those explanations. Clear instructions about appraising risk of attrition bias will improve reliability of the Cochrane’s risk of bias tool, help authors in making decisions about risk of bias and help in making reliable decisions in healthcare.
Judgments of risk of bias associated with random sequence generation in trials included in Cochrane systematic reviews are frequently erroneous
Authors: Barcot Ognjen , Boric Matija , Pericic Tina Poklepovic , Cavar Marija , Dosenovic Svjetlana , Vuka Ivana , Puljak Livia
Published: July 2018

Background

Purpose of this study was to analyze adequacy of judgments about risk of bias (RoB) for random sequence generation in Cochrane systematic reviews (CSRs) of randomized controlled trials (RCTs).

Methods

Information was extracted from RoB tables of CSRs using automated data scraping. We categorized all comments provided as supports for judgments for RoB related to randomization. We analyzed number and type of various supporting comments and assessed adequacy of RoB judgment for randomization in line with recommendations from the Cochrane Handbook.

Results

We analyzed 10527 RCTs that were included in 729 CSRs. For 5682 RCTs randomization was not described; for the others it was indicated randomization was done using computer/software/internet (N=2886), random number table (N=888), mechanic method (N=366), or it was incomplete/inappropriate (N=303).

Overall, 1194/10125 trials (12%) had erroneous RoB judgment about randomization. The highest proportion of errors was found for trials with high RoB (28%), followed by those with low (19%), or unclear (3%). Therefore, one in eight judgments for the analyzed domain in CSRs was erroneous, and one in three if the judgment was “high risk”.

Conclusion

Cochrane systematic reviews cannot be necessarily trusted when it comes to judgments for risk of bias related to randomized sequence generation.
Cancer eQTLs can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity
Authors: Geeleher Paul , Nath Aritro , Wang Fan , Zhang Zhenyu , Barbeira Alvaro N. , Fessler Jessica , Grossman Robert L. , Seoighe Cathal , Huang R. Stephanie
Published: July 2018

Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we demonstrate a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one-third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts. Deconvolution of tumor eQTLs will help determine how inherited polymorphisms influence cancer risk, development, and treatment response.
Single-cell and neuronal network alterations in an in vitro model of Fragile X syndrome
Authors: Moskalyuk Anastasiya , Kooy R. Frank , Giugliano Michele
Published: July 2018

The Fragile X mental retardation protein (FMRP) is involved in many cellular processes and it regulates synaptic and network development in neurons. Its absence is known to lead to intellectual disability, with a wide range of co-morbidities including autism. Over the past decades, FMRP research focused on abnormalities both in glutamatergic and GABAergic signalling, and an altered balance between excitation and inhibition has been hypothesised to underlie the clinical consequences of absence of the protein. Using FMRP knockout mice, we studied an in vitro model of cortical microcircuitry and observed that the loss of FMRP largely affected the electrophysiological correlates of network development and maturation but caused less alterations in single-cell phenotypes. Using a mathematical model, we demonstrated that the combination of an increased excitation and reduced inhibition describes best predicts our experimental observations during the ex vivo formation of the network connections.
Stable memory and computation in randomly rewiring neural networks
Authors: Acker Daniel , Paradis Suzanne , Miller Paul
Published: July 2018

Our brains must maintain a representation of the world over a period of time much longer than the typical lifetime of the biological components producing that representation. For example, recent research suggests that dendritic spines in the adult mouse hippocampus are transient with an average lifetime of approximately 10 days. If this is true, and if turnover is equally likely for all spines, approximately 95-percent of excitatory synapses onto a particular neuron will turn over within 30 days; however, a neuron’s receptive field can be relatively stable over this period. Here, we use computational modeling to ask how memories can persist in neural circuits such as the hippocampus and visual cortex in the face of synapse turnover. We demonstrate that Hebbian learning during replay of pre-synaptic activity patterns can integrate newly formed synapses into pre-existing memories. Further, we find that Hebbian learning during replay is sufficient to stabilize the receptive fields of hippocampal place cells in a model of the grid-cell-to-place-cell transformation in CA1 and of orientation-selective cells in a model of the center-surround-to-simple-cell transformation in V1. We also ask how synapse turnover affects memory in Hopfield networks with CA3-like, auto-associative properties. We find that attractors of Hopfield networks are remarkably stable if learning occurs during network reactivations. Together, these data suggest that a simple learning rule, correlative Hebbian plasticity of synaptic strengths, is sufficient to preserve neural representations in the face of synapse turnover, even in the absence of Hebbian structural plasticity.
TnClone: high-throughput clonal analysis using Tn5-mediated library construction and de novo assembly
Authors: Hwang Byungjin , Heo Sunghoon , Cho Namjin , Bang Duhee
Published: July 2018

A typical molecular cloning procedure requires Sanger sequencing for validation, which becomes cost-prohibitive and labour-intensive for large-scale clonal analysis of genotype-phenotype studies. Here we present a Tn5-mediated clonal analysis platform TnClone, which uses next-generation sequencing (NGS) to rapidly and cost-effectively analyze a large number of clones. We also developed a user-friendly graphical user interface and have provided general guidelines for conducting validation experiments. Using TnClone, we achieved more than 20-fold cost reduction compared with the cost incurred using conventional Sanger sequencing and detected low-frequency mutant clones (~10%) in mixed samples. We tested our programme and achieved 99.4% sensitivity. Our platform provides rapid turnaround with minimal hands-on time for secondary evaluation as NGS technology continues to evolve.
Regeneration of dopaminergic neurons in adult zebrafish depends on immune system activation and differs for distinct populations
Authors: Caldwell Lindsey J. , Davies Nick O. , Cavone Leonardo , Mysiak Karolina S. , Semenova Svetlana A. , Panula Pertti , Armstrong J. Douglas , Becker Catherina G. , Becker Thomas
Published: July 2018

Adult zebrafish regenerate neurons in their brain, but the extent and variability of this capacity is unclear. Here we ask whether loss of various dopaminergic neuron populations is sufficient to trigger their functional regeneration. Genetic lineage tracing shows that specific diencephalic ependymo-radial glial progenitor cells (ERGs) give rise to new dopaminergic (Th+) neurons. Ablation elicits an immune response, increased proliferation of ERGs and increased addition of new Th+ neurons in populations that constitutively add new neurons, e.g. diencephalic population 5/6. Inhibiting the immune response attenuates neurogenesis to control levels. Boosting the immune response enhances ERG proliferation, but not addition of Th+ neurons. In contrast, in populations in which constitutive neurogenesis is undetectable, e.g. the posterior tuberculum and locus coeruleus, cell replacement and tissue integration are incomplete and transient. This is associated with loss of spinal Th+ axons, as well as permanent deficits in shoaling and reproductive behaviour. Hence, dopaminergic neuron populations in the adult zebrafish brain show vast differences in regenerative capacity that correlate with constitutive addition of neurons and depend on immune system activation.
Identifying Lineage-specific Targets of Darwinian Selection by a Bayesian Analysis of Genomic Polymorphisms and Divergence from Multiple Species
Authors: Zhao Shilei , Zhang Tao , Liu Qi , Liu Yongming , Wu Hao , Su Bing , Shi Peng , Chen Hua
Published: July 2018

We present a method that jointly analyzes the polymorphism and divergence sites in genomic sequences of multiple species to identify the genes under positive or negative selection and pinpoints the occurrence time of selection to a specific lineage of the species phylogeny. This method integrates population genetics models using the Bayesian Poisson random field framework and combines information over all gene loci to boost the power to detect selection. The method provides posterior distributions of the fitness effects of each gene along with parameters associated with the evolutionary history, including the species divergence times and effective population sizes of external species. A simulation is performed, and the results demonstrate that our method provides accurate estimates of these population genetic parameters.

The proposed method is applied to genomic sequences of humans, chimpanzees, gorillas and orangutans, and a spatial and temporal map is constructed of the natural selection that occurred during the evolutionary history of the four Hominidae species. In addition to FOXP2 and other known genes, we identify a new list of lineage-specific targets of Darwinian selection. The positively selected genes in the human lineage are enriched in pathways of gene expression regulation, immune system, metabolism etc. Interestingly, some pathways, such as gene expression, are significantly enriched with positively selected genes, whereas other pathways, such as metabolism, are enriched with both positively and negatively selected genes. Our analysis provides insights into Darwinian evolution in the coding regions of humans and great apes and thus serves as a basis for further molecular and functional studies.
Transitions in interaction landscapes of multidrug combinations
Authors: Kang Tina Manzhu , Østman Bjørn , Cruz-Loya Mauricio , Ann Lozano Natalie , Damoiseaux Robert , Savage Van M. , Yeh Pamela J.
Published: July 2018

Drug combinations are a promising strategy to increase killing efficiency and to decrease the likelihood of evolving resistance. A major challenge is to gain a detailed understanding of how drugs interact in a dose-specific manner, especially for interactions involving more than two drugs. Here we introduce a direct and intuitive visual representation that we term “interaction landscapes”. We use these landscapes to clearly show that the interaction type of two drugs typically transitions smoothly from antagonism to no interaction to synergy as drug doses increase. This finding contradicts prevailing assumptions that interaction type is always the same. Our results, from 56 interaction landscapes, are derived from all possible three-drug combinations among 8 antibiotics, each varied across a range of 7 concentrations and applied to a pathogenic Escherichia coli strain. Such comprehensive data and analysis are only recently possible through implementation of an automated high-throughput drug-delivery system and an explicit mathematical framework that disentangles pairwise versus three-way as well as net (any effect) versus emergent (requiring all three drugs) interactions. Altogether, these landscapes partly capture and encapsulate selective pressures that correspond to different dose regions and could help optimize treatment strategies. Consequently, interaction landscapes have profound consequences for choosing effective drug-dose combinations because there are regions where small changes in dose can cause large changes in pathogen killing efficiency and selective pressure.
Improving accuracy of conceptual cost estimation using MRA and ANFIS in Indonesian building projects
Authors: Jumas Dwifitra , Mohd-Rahim Faizul Azli , Zainon Nurshuhada , Utama Wayudi P.
Published: July 2018

Purpose

The purpose of this paper is to develop a conceptual cost estimation (CCE) model for building project by using a pragmatic approach, which is a mix of tools drawn from multiple regression analysis (MRA) and adaptive neuro-fuzzy inference system (ANFIS), to improve the accuracy of cost estimation at an early stage.

Design/methodology/approach

This paper presents a set of MRA and integrating MRA with ANFIS or MRANFIS. A simultaneous regression analysis was developed to determine the main cost factors from 12 variables as input variables in the ANFIS model. Cost data from 78 projects of state building in West Sumatra, Indonesia were used to indicate the advantages of the proposed model.

Findings

The result shows that the proposed model, MRANFIS, has successfully improved the mean absolute percent error (MAPE) by 2.8 percent from MRA of 10.7–7.9 percent for closeness of fit to the model data and by 3.1 percent from MRA of 9.8–6.7 percent for prediction performance to the new data.

Research limitations/implications

Because the significant variables are different for each building type, the model may be not appropriate for other buildings depending on the characteristics of building. The models can be used and analyzed based on the own historical project data for each case so that the model can be applied.

Originality/value

The study thus provides better accuracy of CCE at an early stage for state building projects in West Sumatra, Indonesia by using the integrated model of MRA and ANFIS.
Cellular automata-based approach for digital image scrambling
Authors: Jeelani Zubair , Qadir Fasel
Published: July 2018

Purpose

The purpose of this paper is to investigate two-dimensional outer totalistic cellular automata (2D-OTCA) rules other than the Game of Life rule for image scrambling. This paper presents a digital image scrambling (DIS) technique based on 2D-OTCA for improving the scrambling degree. The comparison of scrambling performance and computational effort of proposed technique with existing CA-based image scrambling techniques is also presented.

Design/methodology/approach

In this paper, a DIS technique based on 2D-OTCA with von Neumann neighborhood (NvN) is proposed. Effect of three important cellular automata (CA) parameters on gray difference degree (GDD) is analyzed: first the OTCA rules, afterwards two different boundary conditions and finally the number of CA generations (k) are tested. The authors selected a random sample of gray-scale images from the Berkeley Segmentation Data set and Benchmark, BSDS300 (www2.eecs.berkeley.edu/Research/Projects/CS/vision/bsds/) for the experiments. Initially, the CA is setup with a random initial configuration and the GDD is computed by testing all OTCA rules, one by one, for CA generations ranging from 1 to 10. A subset of these tested rules produces high GDD values and shows positive correlation with the k values. Subsequently, this sample of rules is used with different boundary conditions and applied to the sample image data set to analyze the effect of these boundary conditions on GDD. Finally, in order to compare the scrambling performance of the proposed technique with the existing CA-based image scrambling techniques, the authors use same initial CA configuration, number of CA generations, k=10, periodic boundary conditions and the same test images.

Findings

The experimental results are evaluated and analyzed using GDD parameter and then compared with existing techniques. The technique results in better GDD values with 2D-OTCA rule 171 when compared with existing techniques. The CPU running time of the proposed algorithm is also considerably small as compared to existing techniques.

Originality/value

In this paper, the authors focused on using von Neumann neighborhood (NvN) to evolve the CA for image scrambling. The use of NvN reduced the computational effort on one hand, and reduced the CA rule space to 1,024 as compared to about 2.62 lakh rule space available with Moore neighborhood (NM) on the other. The results of this paper are based on original analysis of the proposed work.
Job characteristics, employee well-being, and job performance of public sector employees in Malaysia
Authors: Johari Johanim , Mohd Shamsudin Faridahwati , Fee Yean Tan , Yahya Khulida Kirana , Adnan Zurina
Published: July 2018

Purpose

The purpose of this paper is to examine the structural relationships between the job itself (i.e. job characteristics), employee well-being and job performance in light of the new administrative reform called the Government Transformation Program in Malaysia that stresses on measurable performance outputs.

Design/methodology/approach

A total of 208 public sector employees from various public agencies and departments in the northern region of Peninsular Malaysia were surveyed. Some of the agencies that took part in the study include state departments, the fishery department, agriculture-related agencies and the rural development agency.

Findings

The authors observed that feedback positively influenced employee well-being, which served as a significant mediator in the relationship between feedback and job performance. The results indicated that 26.4 percent of the variance that explained employee well-being was accounted for by the different characteristics of a job. The authors also demonstrated that employee well-being accounted for 41.8 percent of job performance.

Research limitations/implications

The authors recommended that public sector managers consider the element of feedback and enhance employee well-being to improve job performance.

Originality/value

This study offers an insight into the effect of perceived changes in the job itself on employee well-being and subsequent job performance in light of government reforms.
Defecting wine club members: an exploratory study
Authors: Newton Sandra K. , Nowak Linda I. , Kelkar Mayuresh
Published: July 2018

Purpose

The purpose of this study is to investigate the range of explanations for why wine club members defect and move on.

Design/methodology/approach

This quantitative research study uses data from US wine consumers, gathered through an online survey of 399 former wine club members who had quit their membership in the recent past. Consistent with literature on customer churn rates in subscription markets, data are analyzed using descriptive statistics, factor analysis, hierarchical multiple regression and analysis of variance.

Findings

The results reported by respondents indicate that higher levels of perceived product quality, fair value in pricing, variety seeking and commitment to customer service at the beginning and at the end of a wine club membership lead to higher levels of customer satisfaction and a desire to recommend the club to others even after quitting. Though variety seeking is more commonplace among experienced wine drinkers, the good news for wineries is that consumers are more likely to recommend a wine club to others if at least a year has passed after they decided to quit.

Practical implications

The results provide implications for wine club managers seeking to improve wine club retention with suggested means for mitigating the rate of customer attrition.

Originality/value

This paper presents original research addressing a variety of reasons why wine club members quit. The extant research has found that factors such as product quality, fair pricing, service commitments and variety-seeking behavior affect members’ satisfaction with their wine club, as well as their desire to recommend it to others. The authors have attempted to combine all these factors into a single study to gain insight into wine club members’ switching behavior, and to find out what the wineries can do to improve customer loyalty.
The communicative power of an extreme territory – the Italian island of Pantelleria and its passito wine
Authors: Ingrassia Marzia , Altamore Luca , Columba Pietro , Bacarella Simona , Chironi Stefania
Published: July 2018

Purpose

This paper aims to examine how Pantelleria’s wineries communicate the extreme territory of Pantelleria through its passito wine and whether this may be a value added for consumers. Specifically examines which dimensions of communication are effectively used by wineries to stimulate, in wine consumers, emotions that link passito wine with the territory of Pantelleria.

Design/methodology/approach

All websites of wineries producing passito wine in Pantelleria were analyzed using the adaptation, goal-attainment, integration and latent pattern maintenance (AGIL) scheme for measuring communication dimensions.

Findings

Results suggest that wineries and stakeholders should apply territory-based marketing strategies to add value to passito wine, the symbol of the island. Synergistically, Pantelleria, through the use of its symbolic product, may enhance its touristic activities. This approach provides useful elements to evaluate the potential of communication in other regions with extreme agriculture, with other agro-food products to promote, due to the replicability of the method.

Research limitations/implications

A limitation of this study is the application of the AGIL method to a population of wineries located in a small wine region; however, regions where heroic agriculture is practiced are generally small.

Practical implications

The findings demonstrate a unique approach that provides an alternative form of wine communication strategy, in which the extreme territory becomes the communication tool of the product linked to it, adding value, regardless of the brand, while, simultaneously, the product becomes the symbol of the territory.

Originality/value

It contributes to the literature by providing the first application of the AGIL scheme to the wine sector, and it shows a new approach for communication strategies in wine marketing.