bluuebunny/crossref_metadata_2025 huggingface dataset:
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
Authors: Ahmed Rafsan , Baali Ilyes , Erten Cesim , Hoxha Evis , Kazan Hilal
Published: August 2019

Motivation

Genomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem is to incorporate the fact that genes act together in functional modules. The connectivity knowledge present in existing protein–protein interaction (PPI) networks together with mutation frequencies of genes and the mutual exclusivity of cancer mutations can be utilized to increase the accuracy of identifying cancer driver modules.

Results

We present a novel edge-weighted random walk-based approach that incorporates connectivity information in the form of protein–protein interactions (PPIs), mutual exclusivity and coverage to identify cancer driver modules. MEXCOwalk outperforms several state-of-the-art computational methods on TCGA pan-cancer data in terms of recovering known cancer genes, providing modules that are capable of classifying normal and tumor samples and that are enriched for mutations in specific cancer types. Furthermore, the risk scores determined with output modules can stratify patients into low-risk and high-risk groups in multiple cancer types. MEXCOwalk identifies modules containing both well-known cancer genes and putative cancer genes that are rarely mutated in the pan-cancer data. The data, the source code and useful scripts are available at: https://github.com/abu-compbio/MEXCOwalk.

Supplementary information

Supplementary data are available at Bioinformatics online.
Detection of splicing forgery using differential evolution and wavelet decomposition
Authors: Kashyap Abhishek , Suresh B , Gupta Hariom
Published: August 2019

In this paper, we have proposed a computationally efficient algorithm to detect splicing (copy-create) forgery, our proposed method is developed by using differential evolution and wavelet decomposition, the differential evolution algorithm automatically generates customized parameter values of tampered images, and wavelet decomposition is used to process large-size images under block-based framework. Our proposed method is resilient to distortions, such as the addition of Gaussian noise, scaling and compression of the forged images.
An unusual complication during alcohol septal ablation: severe left anterior descending artery vasospasm causing cardiac arrest: a case report and review of the literature
Authors: Keskin Ömer Faruk , Iyisoy Atila
Published: August 2019

Background

Septal reduction therapy can be considered along the lines of hypertrophic obstructive cardiomyopathy patients who have drug-refractory symptoms. This can be applied either surgical myectomy or either alcohol septal ablation (ASA). Alcohol septal ablation has been performed successfully since the first announcement of ASA in 1995.

Case summary

We present a case report of coronary artery vasospasm that occurred in the left anterior descending artery (LAD) during ASA. We performed ASA via first septal artery. Two cubic centimetre of 99% ethanol was slowly injected and 10 min later balloon was withdrawn. Then the patient felt severe chest pain; his systolic blood pressure went down quickly and fibrillated. We started the cardiopulmonary resuscitation (CPR). After CPR, the rhythm was achieved total 4 min later cardiac arrest but blood pressure was low. Emergent coronary angiography showed that coronary spasm caused severe occlusion in the LAD segment just after the first septal artery and impaired coronary flow nearly totally in the LAD just after septal artery. At that time, we decided to implant a stent due to the patient’s serious condition and a 3.5 × 18 mm drug-eluting stent was implanted. We performed control angiography to patient 3 days later of the procedure and LAD flow was TIMI 3.

Discussion

The causes of LAD occlusion are alcohol leakage, dissection, and vasospasm. It is important to detect the correct reason for appropriate treatment. Alcohol leakage impairs and causes coronary flow disruption; this can cause ventricular wall motion abnormalities. In our case, there was severe spasm in the LAD coronary artery and LAD flow was severely impaired. On echocardiogram, there was no myocardial wall motion abnormality. So alcohol leakage was ruled out. Left anterior descending artery image was not typical dissection. As a result of these findings, we concluded that the cause of LAD occlusion was coronary artery vasospasm.
‘The Nation Rejoices or Mourns’: Literary and Cultural Ambivalences in Wendy Cope’s Making Cocoa for Kingsley Amis (1986)
Authors: Waterman Rory
Published: August 2019

The poet Wendy Cope gained a huge reputation in the early 1980s mainly for a series of witty and incisive parodies, often under the name of her desperate fictional poète maudit Jake Strugnell, and these poems were collected, along with others, in her hugely successful and influential debut collection, Making Cocoa for Kingsley Amis, which appeared in 1986. This book sold almost 200,000 copies, but has been the subject of a very small body of criticism. Many of her contemporary poet-critics were dismissive: in one contemporary review, Peter Riley epitomized a not uncommon reaction when he claimed that no ‘poetic import can be claimed for the book’, and railed against ‘a new audience for poetry, one which must be presumed to have previously fought shy of it as too difficult or too deep’. Certainly, Making Cocoa for Kingsley Amis is not a work of avant garde complexity, but Cope’s debut is not as cosily complacent as such critics indicate. It is in fact highly allusive and resistant to orthodoxies – and was a thorn in the side of the literary and cultural establishment into which she was instantly propelled. This essay assesses the ways in which Cope’s debut collection takes an ambivalent, nuanced, and parodic response to British institutions, and to the orthodoxies of the male-dominated literary world she was entering.
The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins
Authors: Ely Zackery A , Moon Jiyun M , Sliwoski Gregory R , Sangha Amandeep K , Shen Xing-Xing , Labella Abigail L , Meiler Jens , Capra John A , Rokas Antonis
Published: August 2019

Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal–fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins, both across mammals and within humans, we conducted a series of between- and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage- and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
Authors: Douglas Gavin M , Langille Morgan G I
Published: August 2019

High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
Potential Effect of Immunotherapy Agents on Cognitive Function in Cancer Patients
Authors: Joly Florence , Castel Hélène , Tron Laure , Lange Marie , Vardy Janette
Published: August 2019

A paradigm shift is occurring in cancer therapy, where instead of targeting tumor cells, immunotherapy agents (IA) target the immune system to overcome cancer tolerance and to stimulate an antitumor immune response. IA using immune checkpoint inhibitors (CPI) or chimeric antigen receptor T-cells have emerged as the most encouraging approaches to treat cancer patients. CPI are reported to induce moderate-to-severe neurologic immune-related adverse events in less than 1% of patients, whereas chimeric antigen receptor T-cell therapy is associated with frequent neurological toxicities that can be severe or even fatal. Cognitive difficulties have been described following chemotherapy and targeted therapy, but not specifically explored in patients receiving IA. The aim of this review is to establish a picture of the first published studies suggesting some biological and physiopathological effects of IA on cognitive functions among cancer patients. The first results originate from a preclinical study evaluating the role of CPI associated with peripheral radiation on cognitive dysfunction and the recent discovery of the central nervous lymphatic system allowing leukocytes to penetrate the central nervous system. Evaluating possible side effects of IA on cognitive function will be an important challenge for future clinical trials and for better understanding the underlying mechanisms through preclinical animal models.
Beliefs About HPV Vaccine’s Success at Cervical Cancer Prevention Among Adult US Women
Authors: Fokom Domgue Joël , Chido-Amajuoyi Onyema G , Yu Robert K , Shete Sanjay
Published: August 2019

Background

Beliefs are known to be a key determinant in vaccines’ uptake. However, little is known about beliefs surrounding the success of the human papillomavirus (HPV) vaccine in preventing cervical cancer in the United States.

Methods

Data from the Health Information National Trends Survey 5 Cycle 1 (2017) were analyzed for 1851 female respondents aged 18 years and older. Weighted multinomial logistic regression was employed to determine predictors of beliefs in the success of the HPV vaccine in preventing cervical cancer.

Results

Overall, 29.8% of women believed that HPV vaccine is successful in preventing cervical cancer, 6.6% believed it is not successful, and 63.6% did not know if the HPV vaccine is successful. Non-Hispanic blacks (adjusted odds ratio [aOR] = 1.80, 95% confidence interval [CI] = 1.16 to 2.79), women with no more than 12 years of education (aOR = 2.05, 95% CI = 1.17 to 3.60), those who did not know if they were advised by a health-care provider to get an HPV shot within the last 12 months (aOR = 4.19, 95% CI = 1.39 to 12.60), and those unaware of a family cancer history (aOR = 5.17, 95% CI = 1.48 to 18.21) were more likely to not know whether the HPV vaccine prevents cervical cancer. Women younger than 65 years were more likely than elderly to believe that the HPV vaccine is not successful at preventing cervical cancer.

Conclusions

A substantial proportion of US women are uninformed about the HPV vaccine. To accelerate progress in the HPV vaccine’s uptake, future interventions should incorporate educational programs, particularly targeting Non-Hispanic blacks, women with a lower level of education, and those younger than 65 years. Health-care providers’ participation in promotion of patient education about HPV vaccination should also be increased.
Measuring the growth of structure by matching dark matter haloes to galaxies with VIPERS and SDSS
Authors: Granett Benjamin R , Favole Ginevra , Montero-Dorta Antonio D , Branchini Enzo , Guzzo Luigi , de la Torre Sylvain
Published: August 2019

We test the history of structure formation from redshift 1 to today by matching galaxies from the VIMOS Public Extragalactic Redshift Survey (VIPERS) and Sloan Digital Sky Survey (SDSS) with dark matter haloes in the MultiDark, Small MultiDark Planck (SMDPL), N-body simulation. We first show that the standard subhalo abundance matching (SHAM) recipe implemented with MultiDark fits the clustering of galaxies well both at redshift 0 for SDSS and at redshift 1 for VIPERS. This is an important validation of the SHAM model at high redshift. We then remap the simulation time steps to test alternative growth histories and infer the growth index γ = 0.6 ± 0.3. This analysis demonstrates the power of using N-body simulations to forward model galaxy surveys for cosmological inference. The data products and code necessary to reproduce the results of this analysis are available online (https://github.com/darklight-cosmology/vipers-sham).
Machine-assisted Semi-Simulation Model (MSSM): Estimating Galactic Baryonic Properties from Their Dark Matter Using A Machine Trained on Hydrodynamic Simulations
Authors: Jo Yongseok , Kim Ji-hoon
Published: August 2019

We present a pipeline to estimate baryonic properties of a galaxy inside a dark matter (DM) halo in DM-only simulations using a machine trained on high-resolution hydrodynamic simulations. As an example, we use the IllustrisTNG hydrodynamic simulation of a (75  h−1Mpc)3 volume to train our machine to predict e.g., stellar mass and star formation rate in a galaxy-sized halo based purely on its DM content. An extremely randomized tree (ERT) algorithm is used together with multiple novel improvements we introduce here such as a refined error function in machine training and two-stage learning. Aided by these improvements, our model demonstrates a significantly increased accuracy in predicting baryonic properties compared to prior attempts — in other words, the machine better mimics IllustrisTNG’s galaxy-halo correlation. By applying our machine to the MultiDark-Planck DM-only simulation of a large (1  h−1Gpc)3 volume, we then validate the pipeline that rapidly generates a galaxy catalogue from a DM halo catalogue using the correlations the machine found in IllustrisTNG. We also compare our galaxy catalogue with the ones produced by popular semi-analytic models (SAMs). Our so-called machine-assisted semi-simulation model (MSSM) is shown to be largely compatible with SAMs, and may become a promising method to transplant the baryon physics of galaxy-scale hydrodynamic calculations onto a larger-volume DM-only run. We discuss the benefits that machine-based approaches like this entail, as well as suggestions to raise the scientific potential of such approaches.
Smaller stellar disc scale lengths in rich environments
Authors: Demers Melanie L , Parker Laura C , Roberts Ian D
Published: August 2019

We investigate the dependence of stellar disc scale lengths on environment for a sample of Sloan Digital Sky Survey Data Release 7 galaxies with published photometric bulge-disc decompositions. We compare disc scale lengths at fixed bulge mass for galaxies in an isolated field environment to galaxies in X-ray rich and X-ray poor groups. At low bulge mass, stellar disc scale lengths in X-ray rich groups are smaller compared to discs in both X-ray poor groups and in isolated field environments. This decrease in disc scale length is largely independent of halo mass, though shows some dependence on group-centric distance. We also find that stellar disc scale lengths are smaller in X-ray rich environments for a subset of star-forming galaxies and for galaxies of different morphological types. We note that disc scale lengths of low mass galaxies are known to have large systematic uncertainties, however we focus on differences between samples with the same measurement biases. Our results show that stellar disc scale lengths depend on X-ray brightness, a tracer of IGM density, suggesting a role for hydrodynamic processes such as ram-pressure stripping and/or starvation.
The Association Between Tobacco Outlet Density and Smoking Among Young People: A Systematic Methodological Review
Authors: Nuyts Paulien A W , Davies Lisa E M , Kunst Anton E , Kuipers Mirte A G
Published: August 2019

Aim

Evidence on the association between tobacco outlet density and proximity and smoking behavior among youth is inconsistent, which may be due to methodological problems in some studies. We assessed the association of outlet density or proximity with smoking behavior among young people while taking into account the methodological quality of studies.

Methods

MEDLINE, EMBASE, and Google Scholar were systematically searched for studies on the relationship between outlet density or proximity and smoking behavior among 12- to 25-year-olds, published between 1997 and 2017. Methodological quality of the included studies was evaluated independently by two reviewers.

Results

Twenty studies were included in the review. The quality assessment identified five primary sources of potential bias: overadjustment for mediators (problems identified in 14 studies), underadjustment for confounders (six studies), poor statistical model fit (four studies), selection bias (three studies), and misclassification of exposure measurements (eight studies). Four studies were of high methodological quality. In studies with relatively high quality, 10 associations were reported, of which seven were nonsignificant, two positive, and one negative. Similarly, the complete body of evidence demonstrated mostly nonsignificant associations, but a larger proportion of positive associations than negative.

Conclusion

Although there is some support for a positive direction, current literature does not provide consistent evidence for a positive association between outlet density and smoking among youth. This is not necessarily due to bias in specific studies, but more to fundamental challenges in study design and exposure measurements. These issues need to be addressed in future studies using more rigorous methods.

Implications

Our findings suggest that, although there is some evidence for a positive association, current scientific literature does not provide consistent support to claim an effect of tobacco outlet density or proximity on youth smoking. This underlines the need for more research with improved methodology. There is a need for quasiexperimental studies, in which the outlet density changes substantially, studies measuring the actual exposure of youth to tobacco outlets, and qualitative research on the mechanisms underlying any association.
Effect of supplementing a Saccharomyces cerevisiae fermentation product during a preconditioning period prior to transit on receiving period performance, nutrient digestibility, and antioxidant defense by beef steers
Authors: Deters Erin L , Hansen Stephanie L
Published: August 2019

Forty-eight newly weaned crossbred beef steers from a single-source were used to determine the effects of feeding a Saccharomyces cerevisiae fermentation product (SCFP; NaturSafe, Diamond V) on receiving period performance, nutrient digestibility, and antioxidant defense. Seven days after arrival, steers were stratified by BW (257 ± 18 kg), sorted into pens (n = 1 pen/treatment), and pens assigned to dietary treatments: SCFP at 0 (CON), 12 (SCFP12), 18 (SCFP18), or 0 g·steer−1·d−1 during preconditioning (PRE; days −19 to 0), then 18 g·steer−1·d−1 during receiving (REC; days 0 to 58; CON18). On day −1 BW and blood were collected, steers were loaded onto a semitruck and transported 1,748 km over 19 h. Upon return, steers were weighed, stratified by BW within treatment and sorted into pens with GrowSafe bunks (n = 12 steers/treatment). Steers were weighed on days −1, 0, 29, 30, 57, and 58. Blood was collected from all steers on days −1, 1, and 8 and liver biopsies were performed on all steers on days −20, −3, and 59. Titanium dioxide was included as an indigestible marker in the diet of all steers from days 14 through 29 to determine total tract nutrient digestibility. Data were analyzed as a completely randomized design using ProcMixed of SAS with the fixed effect of treatment. Steer was the experimental unit for REC period variables. Contrast statements compared the linear and quadratic effects of feeding SCFP throughout the trial (CON, SCFP12, and SCFP18) and the effect of supplementation at 18 g·steer−1·d−1 for the entire trial or starting in REC (SCFP18 vs. CON18). Steers fed SCFP12 exhibited the greatest ADG and G:F from days 0 to 30 (quadratic P ≤ 0.04). Total tract digestibility of NDF and ADF was linearly decreased by SCFP (linear P ≤ 0.03). On day −3, SCFP12-fed steers tended to have the greatest liver concentrations of total, oxidized, and reduced glutathione (quadratic P = 0.06). Red blood cell lysate Mn:total-superoxide dismutase activity was 16% greater 1 d posttransit compared with pretransit values (day P ≤ 0.01). Timing of SCFP supplementation (SCFP18 vs. CON18) did not affect any of the variables assessed herein (P ≥ 0.19). Supplementing SCFP at 12 g·steer−1·d−1 tended to affect antioxidant capacity prior to transit and improved early receiving period performance; however, overall receiving period performance was not affected by SCFP supplementation. Further research is necessary to determine the optimal dose and timing of SCFP supplementation for beef cattle.
¡Ojo! What to expect in recruiting and retaining older Latinos in physical activity programs
Authors: Marquez David X , Aguiñaga Susan , Castillo Amparo , Hughes Susan L , Der Ananian Cheryl , Whitt-Glover Melicia C
Published: August 2019

Older Latinos are the fastest growing cohort among older adults in the USA, and their lives are often fraught with comorbidities, such as diabetes and obesity. Strong evidence has demonstrated health benefits of regular physical activity for older adults. In spite of this, older Latinos participate in low levels of physical activity. Interventions designed to increase the physical activity of older Latinos are lacking, yet more are emerging as the number of older Latinos grows. Unfortunately, older Latinos face many impediments to participating in physical activity interventions that researchers are unaware of. The purpose of the current article was to identify barriers that researchers are likely to face in conducting physical activity interventions for older Latinos, highlighting recently identified barriers, and providing barriers we encountered specifically with older Latino adults; and strategies to overcome these barriers to implementation.
A three-dimensional skeleton of Goniopholididae from the Late Jurassic of Portugal: implications for the Crocodylomorpha bracing system
Authors: Puértolas-Pascual E , Mateus O
Published: August 2019

We here describe an articulated partial skeleton of a small neosuchian crocodylomorph from the Lourinhã Formation (Late Jurassic, Portugal). The skeleton corresponds to the posterior region of the trunk and consists of dorsal, ventral and limb osteoderms, dorsal vertebrae, thoracic ribs and part of the left hindlimb. The paravertebral armour is composed of two rows of paired osteoderms with the lateral margins ventrally deflected and an anterior process for a ‘peg and groove’ articulation. We also compare its dermal armour with that of several Jurassic and Cretaceous neosuchian crocodylomorphs, establishing a detailed description of this type of osteoderms.

These features are present in crocodylomorphs with a closed paravertebral armour bracing system. The exceptional 3D conservation of the specimen, and the performance of a micro-CT scan, allowed us to interpret the bracing system of this organism to assess if previous models were accurate. The characters observed in this specimen are congruent with Goniopholididae, a clade of large neosuchians abundant in most semi-aquatic ecosystems from the Jurassic and Early Cretaceous of Laurasia. However, its small size, contrasted with the sizes observed in goniopholidids, left indeterminate whether it could have been a dwarf or juvenile individual. Future histological analyses could shed light on this.
Genome Sequence Data of Six Isolates of Phytophthora capsici from Mexico
Authors: Reyes-Tena Alfredo , Huguet-Tapia José C. , Lamour Kurt H. , Goss Erica M. , Rodríguez-Alvarado Gerardo , Vázquez-Marrufo Gerardo , Santillán-Mendoza Ricardo , Fernández-Pavía Sylvia P.
Published: August 2019

Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.
ARID1A knockdown triggers epithelial‐mesenchymal transition and carcinogenesis features of renal cells: role in renal cell carcinoma
Authors: Somsuan Keerakarn , Peerapen Paleerath , Boonmark Wanida , Plumworasawat ikanya , Samol Ratirath , Sakulsak Natthiya , Thongboonkerd Visith
Published: August 2019

Down‐regulation/mutation of AT‐rich interactive domain 1A (ARID1A), a novel tumor suppressor gene, has been reported in various cancers. Nevertheless, its role in renal cell carcinoma (RCC) remained unclear and underinvestigated. We thus evaluated carcinogenesis effects of ARID1A knockdown in nonmalignant Madin‐Darby canine kidney (MDCK) renal cells using small interfering RNA (siRNA) against ARID1A (siARID1A). The siARID1A‐transfected cells had decreased cell death, increased cell proliferation, and cell cycle shift (from G0/G1 to G2/M) compared with those transfected with controlled siRNA (siControl). Additionally, the siARID1A‐transfected cells exhibited epithelial‐mesenchymal transition (EMT) shown by greater spindle index, increased mesenchymal markers (fibronectin/vimentin), and decreased epithelial markers (E‐cadherin/zonula occludens‐1). Moreover, the siARID1A‐transfected cells had increases in migratory activity, nuclear size, self‐aggregated multicellular spheroid size, invasion capability, chemoresistance (to docetaxel), Snail family transcriptional repressor 1 expression, and TGF‐β1 secretion. All of these siARID1A‐knockdown effects on the carcinogenic features were reproducible in malignant RCC (786‐O) cells, which exhibited a higher degree of carcinogenic phenotypes compared with the nonmalignant MDCK cells. Finally, immunohistochemistry showed obvious decrease in ARID1A protein expression in human RCC tissues (n = 23) compared with adjacent normal renal tissues (n = 23). These data indicate that ARID1A down‐regulation triggers EMT and carcinogenesis features of renal cells in vitro, and its role in RCC could be proven in human tissues.—Somsuan, K., Peerapen, P., Boonmark, W., Plumworasawat, S., Samol, R., Sakulsak, N., Thongboonkerd, V. ARID1A knockdown triggers epithelial‐mesenchymal transition and carcinogenesis features of renal cells: role in renal cell carcinoma. FASEB J. 33, 12226‐12239 (2019). www.fasebj.org
Mass lesions of the myometrium: interpretation and management of unexpected pathology
Authors: Porter Anne E. , Kho Kimberly A. , Gwin Katja
Published: August 2019

Purpose of review

Uterine leiomyomas are the most common benign uterine smooth muscle tumors. On the basis of imaging, these masses are often presumed to be benign conventional leiomyomas and surgical excision is a common treatment choice. After myomectomy or hysterectomy for presumed leiomyomas, the surgical pathology report may reveal an unexpected diagnosis of another type of mesenchymal tumor. These can range from a variant of benign smooth muscle tumors to smooth muscle tumors of uncertain malignant potential to malignant sarcomas. This review describes these variant pathologies and reviews data on recurrence risk and postoperative management.

Recent findings

The majority of benign smooth muscle tumors will be classified as leiomyomas. Cellular, bizarre nuclei, mitotically active, epitheliod, myxoid, and dissecting are all terms that describe pathologic variants of benign leiomyomas. Smooth muscle tumors of uncertain malignant potential contain both benign and malignant features and should be referred to Gynecologic Oncology for follow-up. Leiomyosarcomas and low-grade endometrial stromal sarcomas may present preoperatively as benign tumors but are malignant with a high risk of recurrence and should be referred to Gynecologic Oncology.

We advocate for the continued benefits of minimally invasive procedures in appropriately selected patients. Despite these measures, unexpected pathologic diagnoses can occur and should be managed appropriately.
Computerized Approach to Facial Transplantation: Evolution and Application in 3 Consecutive Face Transplants
Authors: Ramly Elie P. , Kantar Rami S. , Diaz-Siso J. Rodrigo , Alfonso Allyson R. , Rodriguez Eduardo D.
Published: August 2019

Background:

Face transplant (FT) candidates present with unique anatomic and functional defects unsuitable for autologous reconstruction, making the accurate design and transplantation of patient-specific allografts particularly challenging. In this case series, we present our computerized surgical planning (CSP) protocol for FT.

Methods:

CSP, computer-aided design and manufacturing, intraoperative navigation, and intraoperative computerized tomography have been successfully incorporated into a comprehensive protocol. Three consecutive FTs were performed. CSP and postoperative results were compared using computerized tomography–derived cephalometric measurements, and the literature was reviewed.

Results:

Two full and 1 partial FT were successfully performed using the CSP protocol. CSP facilitated the execution of FT with minor angular and translational cephalometric variations on immediate postoperative imaging. Our evolving experience was accompanied by a decreased reliance on cadaveric simulation, from 10 mock transplants and a research procurement before the senior author’s first clinical FT (2012) to 6 mock transplants and no research procurement before the third FT (2018). Operative time was significantly reduced from 36 to 25 hours, as was the need for major orthognathic surgical revision. This reflects the learning curve and variable case complexity, but it is also representative of improved planning and execution, complemented by the systematic incorporation of CSP into FT.

Conclusions:

A CSP protocol allows for refinement of operative flow, technique, and outcomes in partial and full FT. Standards for functional and esthetic outcomes are bound to evolve with the field’s growth, and computerized planning and execution offer a reproducible approach to FT through objective quality assurance.
Corneal Biomechanical Evaluation After Conventional Corneal Crosslinking With Oxygen Enrichment
Authors: Wang Jia , Wang Lijun , Li Zhiwei , Wang Yu Meng , Zhu Kaimin , Mu Guoying
Published: August 2019

Purpose:

To assess corneal biomechanical changes after conventional corneal crosslinking (CXL), with and without oxygen enrichment.

Methods:

Sixty fresh porcine corneas were randomly divided into group 1 (control), group 2 (conventional CXL), and group 3 (conventional CXL in a high-oxygen environment during ultraviolet A [UVA] irradiation). After crosslinking, a 5-mm wide corneal strip was extracted using a double-bladed knife from 12 to 6'o clock. The Young's modulus of each strip was determined by stress–strain measurements. A comparison between the three groups was performed with a one-way analysis of variance.

Results:

At 4% strain, the Young's modulus of the corneas in groups 1, 2, and 3 were: 0.68±0.20 megapascal (MPa), 1.01±0.23 MPa, and 1.12±0.24 MPa, respectively. The Young's modulus values for groups 2 and 3 showed no statistical significance (P>0.05), However, both groups 2 and 3 were significantly higher than group 1 (P<0.05). At 6% strain, the Young's modulus of the corneas in groups 1, 2, and 3 were: 0.97±0.21, 1.35±0.25, and 1.64±0.44 MPa, respectively, and at 8% strain, the Young's modulus was: 1.29±0.26, 1.72±0.45, 2.20±0.74 MPa, respectively. At 6% and 8% strain, the Young's modulus for the corneas in group 3 was significantly higher than those in both group 1 and group 2 (P<0.05).

Conclusions:

Increasing oxygen concentration during UVA irradiation may improve the efficacy of conventional CXL.
Communication Under Pressure
Authors: Jones Lindsay , Cline Genieveve J. , Battick Kentlee , Burger Kristina J. , Amankwah Ernest K.
Published: August 2019

Effective communication in health care is a mainstay of patient safety and staff perception of a healthy work environment. A quasi-experimental study was conducted to assess the impact of a course on staff perceptions of communication. A Wilcoxon signed-ranks test indicated a statistically significant difference between pre and post scores for the self-assessment component of the Heathy Work Environment Instrument (p = .0005); coworker assessments revealed borderline statistical significance (p = .056).
Long-term Fecal Incontinence, Recurrence, Satisfaction, and Regret After the Transobturator Postanal Sling Procedure
Authors: Winkelman William D. , Demtchouk Veronica O. , Brecher Liza G. , Erlinger Adrienne P. , Modest Anna M. , Rosenblatt Peter L.
Published: August 2019

Objectives

The objective of this study was to assess long-term outcomes after the transobturator postanal sling (TOPAS) procedure for the treatment of fecal incontinence. Long-term recurrence, satisfaction and regret after transobturator postanal sling procedure support the ongoing use of this procedure for patients with fecal incontinence.

Methods

Both a retrospective review of medical records and a prospective telephone survey were conducted. For the retrospective review of medical records, all patients who underwent the TOPAS procedure at our institution were eligible. Medical records were reviewed to assess for symptom resolution, retreatment, and complications. For the prospective telephone survey, patients who were conversant in English and had a valid contact information were eligible and were asked to complete questions on satisfaction, the Patient Global Impression of Improvement, the Wexner Symptom Severity Score, the Fecal Incontinence Qualify of Life Scale, and the modified Decision Regret Scale.

Results

A total of 134 patients met the inclusion criteria for the retrospective medical record review. Patients were followed in clinic for a median of 24.0 months (interquartile range, 6.0–53.0). Overall, 75.4% reported improvement in fecal incontinence. There were 37 (27.6%) who required subsequent treatment for fecal incontinence. There were 67 patients eligible for the prospective telephone survey, of whom 46 (68.7%) agreed to participate. Median time between surgery and the telephone survey was 63.5 months (interquartile range, 36.0–98.0). Among these participants, 54.3% were satisfied and 60.9% would recommend the procedure to someone else. No adverse events were identified with long-term follow-up.

Conclusions

Our findings suggest that the TOPAS procedure remains a safe and effective therapy for the treatment of fecal incontinence with favorable long-term outcomes.
Wind loads on open truss structures: applications of blockage to historic transporter bridges
Authors: Carter A. J. , Taylor P. H. , Santo H. , Blakeborough A.
Published: August 2019

The overall aim of this study is to compare and contrast the design of the two remaining working examples of early twentieth-century transporter bridges in the UK, namely, those at Newport and Middlesbrough. With the aid of modern finite-element analysis, the behaviour of the structures under loading is investigated, likely modes of failure determined and the efficiency of each structure evaluated. The important horizontal load component due to wind at the exposed locations of the bridges is examined using ‘current blockage’, ideas transferred from recent work on wave–current–structure interaction for space-frame structures in offshore engineering.

This article is part of the theme issue ‘Environmental loading of heritage structures’.
Prevalence estimate of blood doping in elite track and field at the introduction of the Athlete Biological Passport
Authors: Faiss Raphael , Saugy Jonas , Zollinger Alix , Robinson Neil , Schütz Frédéric , Saugy Martial , Garnier Pierre-Yves
Published: August 2019

In elite sport, the Athlete Biological Passport (ABP) was invented to tackle cheaters by monitoring closely changes in biological parameters, flagging atypical variations. The haematological module of the ABP was indeed adopted in 2011 by the International Association of Athletics Federations (IAAF). This study estimates the prevalence of blood doping based on haematological parameters in a large cohort of track & field athletes measured at two international major events (2011 & 2013 IAAF World Championships) with a hypothesized decrease in prevalence due to the ABP introduction.

A total of 3683 blood samples were collected and analysed from all participating athletes originating from 209 countries. The estimate of doping prevalence was obtained by using a Bayesian network with seven variables, as well as “doping” as a variable mimicking doping with low-doses of recombinant human erythropoietin (rhEPO), to generate reference cumulative distribution functions (CDFs) for the Abnormal Blood Profile Score (ABPS) from the ABP.

Our results from robust haematological parameters indicate an estimation of an overall blood doping prevalence of 18% in average in endurance athletes (95% Confidence Interval (C.I.) 14-22%). A higher prevalence was observed in female athletes (22%, C.I. 16-28%) than in male athletes (15%, C.I. 9-20%). In conclusion, this study presents the first comparison of blood doping prevalence in elite athletes based on biological measurements from major international events that may help scientists and experts to use the ABP in a more efficient and deterrent way.

What are the new findings ?

This study presents the first comparison of blood doping prevalence in elite track & field athletes based on biological measurements from major international events

Our results from robust haematological parameters indicate an estimation of an overall blood doping prevalence of 18% in average in endurance athletes.

The confidence intervals for blood doping prevalence range from 9-28% with wide discrepancies between certain countries.

How might it impact on clinical practice in the near future

The further development of the Athlete Biological Passport with a careful monitoring of biological parameters still represents the most consistent approach to thwart athletes using undetectable prohibited substances or methods.

This study describes a method to define blood doping prevalence with the analysis of robust haematological parameters

Estimates of doping prevalence in subpopulations of athletes may represent a valuable tool for the antidoping authorities to perform a risk assessment in their sport.
Self-reported sleep relates to hippocampal atrophy across the adult lifespan – results from the Lifebrain consortium
Authors: Fjell Anders M. , Sørensen Øystein , Amlien Inge K. , Bartrés-Faz David , Bros Didac Maciá , Demuth Ilja , Drevon Christian A , Düzel Sandra , Ebmeier Klaus P. , Idland Ane-Victoria , Kietzmann Tim C. , Kievit Rogier , Kühn Simone , Lindenberger Ulman , Mowinckel Athanasia M , Nyberg Lars , Price Darren , Sexton Claire E. , Solé-Padullés Cristina , Pudas Sara , Sederevicius Donatas , Suri Sana , Wagner Gerd , Watne Leiv Otto , Westerhausen René , Zsoldos Enikő , Walhovd Kristine B.
Published: August 2019

Background

Poor sleep is associated with multiple age-related neurodegenerative and neuropsychiatric conditions. The hippocampus plays a special role in sleep and sleep-dependent cognition, and accelerated hippocampal atrophy is typically seen with higher age. Hence, it is critical to establish how the relationship between sleep and hippocampal volume loss unfolds across the adult lifespan.

Methods

Self-reported sleep measures and MRI-derived hippocampal volumes were obtained from 3105 cognitively normal participants (18-90 years) from major European brain studies in the Lifebrain consortium. Hippocampal volume change was estimated from 5116 MRIs from 1299 participants, covering up to 11 years. Cross-sectional analyses were repeated in a sample of 21390 participants from the UK Biobank.

Results

The relationship between self-reported sleep and age differed across sleep items. Sleep duration, efficiency, problems, and use of medication worsened monotonously with age, whereas subjective sleep quality, sleep latency, and daytime tiredness improved. Women reported worse sleep in general than men, but the relationship to age was similar. No cross-sectional sleep – hippocampal volume relationships was found. However, worse sleep quality, efficiency, problems, and daytime tiredness were related to greater hippocampal volume loss over time, with high scorers showing on average 0.22% greater annual loss than low scorers. Simulations showed that longitudinal effects were too small to be detected as age-interactions in cross-sectional analyses.

Conclusions

Worse self-reported sleep is associated with higher rates of hippocampal decline across the adult lifespan. This suggests that sleep is relevant to understand individual differences in hippocampal atrophy, but limited effect sizes call for cautious interpretation.
History biases reveal novel dissociations between perceptual and metacognitive decision-making
Authors: Benwell Christopher S.Y. , Beyer Rachael , Wallington Francis , Ince Robin A. A.
Published: August 2019

Human decision-making and self-reflection often depend on context and internal biases. For instance, decisions are often influenced by preceding choices, regardless of their relevance. It remains unclear how choice history influences different levels of the decision-making hierarchy. We employed analyses grounded in information and detection theories to estimate the relative strength of perceptual and metacognitive history biases, and to investigate whether they emerge from common/unique mechanisms. Though both perception and metacognition tended to be biased towards previous responses, we observed novel dissociations which challenge normative theories of confidence. Different evidence levels often informed perceptual and metacognitive decisions within observers, and response history distinctly influenced 1st (perceptual) and 2nd (metacognitive) order decision-parameters, with the metacognitive bias likely to be strongest and most prevalent in the general population. We propose that recent choices and subjective confidence represent heuristics which inform 1st and 2nd order decisions in the absence of more relevant evidence.
A solution to the learning dilemma for recurrent networks of spiking neurons
Authors: Bellec Guillaume , Scherr Franz , Subramoney Anand , Hajek Elias , Salaj Darjan , Legenstein Robert , Maass Wolfgang
Published: August 2019

Recurrently connected networks of spiking neurons underlie the astounding information processing capabilities of the brain. But in spite of extensive research, it has remained open how they can learn through synaptic plasticity to carry out complex network computations. We argue that two pieces of this puzzle were provided by experimental data from neuroscience. A new mathematical insight tells us how these pieces need to be combined to enable biologically plausible online network learning through gradient descent, in particular deep reinforcement learning. This new learning method – callede-prop– approaches the performance ofBPTT(backpropagation through time), the best known method for training recurrent neural networks in machine learning. In addition, it suggests a method for powerful on-chip learning in novel energy-efficient spike-based hardware for AI.
Perceiving structure in unstructured stimuli: Implicitly acquired prior knowledge impacts the processing of unpredictable transitional probabilities
Authors: Kóbor Andrea , Horváth Kata , Kardos Zsófia , Nemeth Dezso , Janacsek Karolina
Published: August 2019

It is unclear how implicit prior knowledge is involved and remains persistent in the extraction of the statistical structure underlying sensory input. Therefore, this study investigated whether the implicit knowledge of 2ndorder transitional probabilities characterizing a stream of visual stimuli impacts the processing of unpredictable transitional probabilities embedded in a similar input stream. Young adults (N= 50) performed a four-choice reaction time (RT) task that consisted of structured and unstructured blocks. In the structured blocks, more probable and less probable short-range nonadjacent transitional probabilities were present. In the unstructured blocks, the unique combinations of the short-range transitional probabilities occurred with equal probability; therefore, they were unpredictable. All task blocks were visually identical at the surface level. While one-half of the participants completed the structured blocks first followed by the unstructured blocks, this was reversed in the other half of them. The change in the structure was not explicitly denoted, and no feedback was provided on the correctness of each response. Participants completing the structured blocks first showed faster RTs to more probable than to less probable short-range transitional probabilities in both the structured and unstructured blocks, indicating the persistent effect of prior knowledge. However, after extended exposure to the unstructured blocks, they updated this prior knowledge. Participants completing the unstructured blocks first showed the RT difference only in the structured blocks, which was not constrained by the preceding exposure to unpredictable stimuli. The results altogether suggest that implicitly acquired prior knowledge of predictable stimuli influences the processing of subsequent unpredictable stimuli. Updating this prior knowledge seems to require a longer stretch of time than its initial acquisition.