bluuebunny/crossref_metadata_2025 huggingface dataset:
Mirror Image Based Three-Dimensional Virtual Surgical Planning and Three-Dimensional Printing Guide System for the Reconstruction of Wide Maxilla Defect Using the Deep Circumflex Iliac Artery Free Flap
Authors: Jang Wan-Hee , Lee Jake Minki , Jang Sam , Kim Hee-Dong , Ahn Kang-Min , Lee Jee-Ho
Published: May 2019

A patient was diagnosed with squamous cell carcinoma of the maxillary sinus and consequently underwent a unilateral total maxillectomy and reconstruction using an anterolateral thigh (ALT) free flap. Soft tissue transplantation without a bone graft at the large maxillary defect site caused a midfacial collapse, which worsened, especially after radiotherapy. The 3-dimensional positioning of the composite flap for wide maxillary reconstruction is aesthetically important. To achieve ideal symmetry and aesthetics, a mirror image was created using the normal contralateral side. Through computer simulation, the function and symmetry of the virtually reconstructed maxilla was evaluated, and the surgical guide was made using a 3D printing system. Based on the prepared surgical guide, a deep circumflex iliac artery (DCIA) free flap was harvested, and its implementation in the reconstruction ultimately led to satisfactory results. Utilization of mirror image based virtual surgical planning and a 3D printing guide is a significantly effective method for maxilla reconstruction with DCIA flaps.
Liver Transplantation Using Uncontrolled Donors After Circulatory Death: A 10-year Single-center Experience
Authors: Jiménez-Romero Carlos , Manrique Alejandro , Calvo Jorge , Caso Óscar , Marcacuzco Alberto , García-Sesma Álvaro , Abradelo Manuel , Nutu Anisa , García-Conde María , San Juan Rafael , Justo Iago
Published: May 2019

Background.

One method for increasing the donor pool for orthotopic liver transplantations (OLTs) is to use uncontrolled donation after circulation death (uDCDs).

Methods.

From January 2006 to December 2016, we performed 75 OLTs using uDCD livers. The control group comprised a sample of 265 OLTs using livers of donations after brain death (DBDs). A comparative study was performed.

Results.

Of 256 potential uDCD donors cannulated, 75 (29.3%) livers were accepted for OLT. The amount of hemoderivatives transfused was significantly higher in the uDCD group. The rate of primary nonfunction was also significantly higher (P = 0.031) in uDCD recipients (8%) than DBD recipients (1.5%). The overall rate of biliary complications was significantly higher (P = 0.001) in uDCD recipients (23 cases, 30.6%) than DBD recipients (28 cases, 10.6%). In the uDCD group, 1-, 3-, and 5-year patient survival rates were 82.7%, 73%, and 71.5%, respectively; in the DBD group, they were 89%, 83.7%, and 78.8%, respectively (P = 0.180). In the uDCD group, 1-, 3-, and 5-year graft survival rates were 73.3%, 65.1%, and 63.6%, respectively; in the DBD group, they were 87.1%, 81.9%, and 76.5%, respectively (P = 0.013). Multivariate analysis showed that independent risk factors for patient and graft survival were intraoperative transfusion of >6 units of packed red blood cell concentrates and recipients who were older than 60 years.

Conclusions.

Although graft survival is significantly lower using uDCD livers, 5-year patient survival in recipients of DBD and uDCD livers is similar. After careful selection, the livers of uDCD can be selectively used for OLT.
Discriminative Ability of Montreal Cognitive Assessment Subtests and Items in Racial and Ethnic Minority Groups
Authors: Milani Sadaf Arefi , Marsiske Michael , Striley Catherine W.
Published: May 2019

Introduction:

The Montreal Cognitive Assessment (MoCA) is a popular screening tool for Mild Cognitive Impairment (MCI). The psychometric properties of the MoCA have not been widely examined in minority groups. We aimed to analyze the discriminate ability of subtests and items by race and ethnicity given gold-standard clinical diagnosis of cognitive status.

Methods:

We analyzed data from the National Alzheimer Coordinating Center Uniform Data Set March 2018 data freeze. Stepwise regression was used to determine which subtests predicted cognitive status (normal cognition, MCI, or dementia), by race/ethnicity. Item discrimination and difficulty was calculated by race/ethnicity and cognitive status.

Results:

In our sample (n=3895), with an average age of 69.7, 80.7% were non-Hispanic white, 15.0% were non-Hispanic black, and 4.2% were Hispanic. Among non-Hispanic whites all subtests, education, and age predicted clinician diagnosis, while visuospatial/executive, attention, language, delayed recall, and orientation subtests were predictive among non-Hispanic blacks and visuospatial/executive, delayed recall, and orientation subtests and education were predictive among Hispanics. Item discrimination and difficulty varied by race/ethnicity and cognitive status.

Conclusions:

By understanding the psychometric properties of MoCA subtests, we can focus on subtests that have higher discrimination and more diagnostic utility. Subtests should be further evaluated for use in screening of minority individuals.
Patient Stakeholder Versus Physician Preferences Regarding Amyloid PET Testing
Authors: Armstrong Melissa J. , Gronseth Gary S. , Day Gregory S. , Rheaume Carol , Alliance Slande , Mullins C.D.
Published: May 2019

Background:

Patient and caregiver perspectives on amyloid positron emission tomography (PET) use are largely unexplored, particularly as compared with clinician views.

Methods:

We surveyed clinicians, patients, caregivers, and dementia advocates on topics relating to an evidence-based guideline on amyloid PET use. Topic importance was rated on a 9-point scale. Patient stakeholder and clinician views were compared using the Mann-Whitney U test.

Results:

Patient representatives (n=107) rated all survey topics as equal to or more important than clinicians (n=114) except 1 item discussing potential harms of false-positive diagnoses. Differences between patient representative and clinician populations were greatest when comparing the competing values of false-positive and false-negative diagnoses and the value of testing asymptomatic individuals.

Conclusions:

Patients and caregivers emphasized the importance of having a dementia diagnosis and placed more value on testing and outcomes for asymptomatic populations than clinicians. This underscores the importance of research investigating the effect of amyloid PET results on asymptomatic individuals and the need for amyloid PET ordering and disclosure standards.
Recent developments in imaging of epilepsy
Authors: Wiest Roland , Beisteiner Roland
Published: May 2019

Purpose of review

Imaging constitutes one of the key pillars in the diagnostic workup after a first seizure as well as for the presurgical workup in epilepsy. The role of imaging in emergency situations, mainly to support the adequate diagnosis, as well as its role in planning of noninvasive image-guided therapies is less well established. Here, we provide an overview on peri-ictal imaging findings to support differential diagnosis in emergency situations and describe recent attempts toward minimal invasive therapy in the treatment of epilepsy and its comorbidities based on a combination of imaging techniques with ultrasound.

Recent findings

Peri-ictal perfusion changes can differentiate ictal stroke mimics from acute ischemic stroke if focal areas of increased perfusion are depicted by computed tomography or MRI. Postictal perfusion patterns in patients with persisting neurological symptoms are frequently normal and do not reach enough diagnostic sensitivity to differentiate between stroke and its mimics. Noninvasive magnetic resonance-techniques as arterial spin labeling may provide a higher sensitivity, especially in combination with diffusion-weighted and susceptibility-weighted MRI. Imaging guided focused ultrasound (FUS) bears the potential to ablate epileptogenic tissue and allows suppression of epileptic activity. Imaging guided blood–brain-barrier opening with FUS offers new options for local drug administration.

MRI should be considered the method of choice in the differential diagnosis of peri-ictal imaging findings and their differential diagnosis. A combination of various MRI techniques with FUS opens new avenues for treatment of epilepsy.
Spaniel: analysis and interactive sharing of Spatial Transcriptomics data
Authors: Queen Rachel , Cheung Kathleen , Lisgo Steven , Coxhead Jonathan , Cockell Simon
Published: May 2019

Spatial Transcriptomics allows the sequencing of the complete transcriptomes from barcoded regions of intact tissue. The technology has the potential to answer a wide range of biological questions concerning cellular function, but analysis of the data presents a number of challenges which are not met by existing analysis tools. Here we present Spaniel, an R package providing a framework for analysing and sharing Spatial Transcriptomics data.
Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer
Authors: Gatenbee Chandler D. , Baker Ann-Marie , Schenck Ryan O. , Neves Margarida , Hasan Sara Yakub , Martinez Pierre , Cross William C.H. , Jansen Marnix , Rodriguez-Justo Manuel , Sottoriva Andrea , Leedham Simon , Robertson-Tessi Mark , Graham Trevor A. , Anderson Alexander
Published: May 2019

Colorectal cancer develops from its precursor lesion, the adenoma. The immune system is hypothesized to be key in modulating progression, but tumor-immune eco-evolutionary dynamics remain uncharacterized. Here, we demonstrate a key role for immune evasion in the progression of human benign disease to colorectal cancer. We constructed a mathematical model of tumor-immune eco-evolutionary dynamics that predicted ecological succession, from an "immune-hot" adenoma immune ecology rich in T cells to an "immune-cold" carcinoma ecology, deficient in T cells and rich in immunosuppressive cells. Using a cross-sectional cohort of adenomas and carcinomas, we validated this prediction by direct measurement of the tumor-immune ecology using whole-slide 10-marker immunohistochemistry (IHC), and analysis of neoantigen clonal architecture multi-region exome sequencing data. Changes in immune ecology relax selection against antigens with high recognition potentials. This study indicates that immune surveillance represents a key evolutionary bottleneck in the evolution of colon cancer.
Expanded Scope of Practice Fellowships for Radiologists: a Survey of Interest Amongst Current Canadian Radiology Residents
Authors: Barfett Joseph J , Colak Errol , Smith Christopher U , Vlachou Paraskevi , Mnatzakanian Aren , Lin Hui Ming , Bartlett Eric , Moody Alan
Published: May 2019

Rationale and Objectives

Radiology residents acquire a diverse educational experience and skill set, including a general internship year, which may enable the direct management of patients. In order for radiology residents to define new scopes of practice, however, additional fellowship training may in certain instances be warranted.

Materials and Methods

Using the Canadian family medicine Enhanced Skills Program as a model, we conducted a Canada-wide survey of radiology residents to assess interest in additional fellowship training to expand their scope of practice.

Results

Our results indicate that a majority of residents (69.2%) would like to routinely see patients in clinic and more than half (52%) are willing to undergo an additional year of fellowship to enhance their skill set. The most popular choices for such fellowships were sports medicine (22.8%), emergency medicine (19.6%) and vascular medicine (18.5%). In addition, a majority (52.9%) of residents felt capable of offering incidentaloma clinics without additional training beyond their core radiology residency.

Conclusion

Traditional diagnostic and interventional radiology fellowships must be reconsidered to reflect the interests and capabilities of modern radiology trainees. Expansion of training options into the domain of direct patient management will likely prove popular among current residents.
Insect pollination is an ecological process involved in the assembly of the seed microbiota
Authors: Prado Alberto , Marolleau Brice , Vaissière Bernard E. , Barret Matthieu , Torres-Cortes Gloria
Published: May 2019

The assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the vascular tissues of the plant, but also from the flower. Flowers are known to be a hub for microbial transmission between plants and insects. This floral-insect exchange opens the possibility for insect-transmitted bacteria to colonize the ovule and subsequently the seed, and to pass then into the next plant generation. In this study, we evaluated the contribution of insect pollination to the seed microbiota through high-throughput sequencing. Oilseed rape (OSR)Brassica napusflowers were exposed to visits and pollination by honey bees (Apis mellifera) or red mason bees (Osmia bicornis), hand pollination, or autonomous self-pollination (ASP). Sequence analyses revealed that honey bee visitation reduced the bacterial richness and diversity, increased the variability in the seed microbial structure, and introduced bee-associated taxa. In contrast, mason bee pollination had minor effects on the seed microbiota. We highlight the need to consider insect pollination as an ecological process involved in the transmission of bacteria from flower to seeds.

IMPORTANCE

Insect pollinators and flowering plants have a very old mutualistic relationship in which animal mobility is used for the dispersal of pollen. The pollination services provided by insects are extremely important to many natural plant populations as well as agricultural crops. Here we show that while visiting flowers, insect pollinators can disperse bacteria that are able to colonize the developing seed via the flower. Hence, insect pollination participates in the assembly of the seed microbiota, the inoculum for the next plant generation. This novel insight has important implications in terms of re-assessing pollinator services by including microbe transfer.
A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System
Authors: Kingan Sarah B. , Urban Julie , Lambert Christine C. , Baybayan Primo , Childers Anna K. , Coates Brad S. , Scheffler Brian , Hackett Kevin , Korlach Jonas , Geib Scott M.
Published: May 2019

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gbde novogenome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 36-fold coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated withL. delicatula, each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
Isolation and Characterization of ΦGF1, a Morphotype C3 Bacteriophage that InfectsEscherichia coli
Authors: Punil Renzo , Talledo Miguel , Arcondo Mayra , Suárez Katherine , Zumaeta Kattya
Published: May 2019

It has been isolated a lytic bacteriophage specific toEscherichia coli, which can infect at least one different bacterial group. Phage ФGF1 was isolated from a wastewater treatment plant. It is resistant to the effect of chloroform and is stable at 40 and 50 °C. In addition, it is stable in the range of pH 5-8. Its host range is wide, infecting even strains from another genus such asShigella. The one-step growth curve yielded a short latent period of 15 minutes and a burst size of 85 PFU per infected cell. Under the electron microscope, this phage presents the C3 morphotype, extremely rare among members of the Podoviridae family. Phage ФGF1 shows some characteristics that could be considered useful in biocontrol applications againstE. coli. Keywords: Bacteriophage,Escherichia coli, morphotype C3,Podoviridae.

IMPORTANCE

Wastewater throughout the world is a heavy carrier of potential pathogens that live in their environment along with other biological agents, such as bacteriophages, which play a controlling role of the bacterial populations there, as in soil. The description of the diversity of such bacteriophages is of paramount importance since they could be used to intentionally reduce or remove those pathogens from that environment. Our work describes a bacteriophage that lives primarily in this type of water.
Spatial genome re-organization between fetal and adult hematopoietic stem cells
Authors: Chen C , Yu W , Tober J , Gao P , He B , Lee K , Trieu T , Blobel GA , Speck NA , Tan K
Published: May 2019

Fetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs. The functional properties of the HSCs change dramatically during this switch, including their cycling behavior, hematopoietic lineage outputs and proliferation rate. The relationship between three-dimensional (3D) genome organization, epigenomic state, and transcriptome is poorly understood during this critical developmental transition. Here we conducted a comprehensive survey of the 3D genome, epigenome and transcriptome of fetal and adult HSCs in mouse. We found that chromosomal compartments and topologically associating domains (TAD) are largely conserved between fetal and adult HSCs. However, there is a global trend of increased compartmentalization and TAD boundary strength in adult HSCs. In contrast, dynamics of intra-TAD chromatin interactions is much higher and more widespread, involving over a thousand gene promoters and distal enhancers. Such dynamic interactions target genes involved in cell cycle, metabolism, and hematopoiesis. These developmental-stage-specific enhancer-promoter interactions appear to be mediated by different sets of transcription factors in fetal and adult HSCs, such as TCF3 and MAFB in fetal HSCs, versus NR4A1 and GATA3 in adult HSCs. Loss-of-function studies of TCF3 confirms the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. In summary, our data suggest that the fetal-to-adult transition is accompanied by extensive changes in intra-TAD chromatin interactions that target genes underlying the phenotypic differences between fetal and adult HSCs.
Epigenetic Effects of Exposure to Insecticide on Early Differentiation of Mouse Embryonic Stem Cells
Authors: Wang Wenlong , Otsuka Satoshi , Nansai Hiroko , Ito Tomohiro , Abe Kuniya , Nakao Yoichi , Ohgane Jun , Yoneda Minoru , Sone Hideko
Published: May 2019

Increasing evidence indicates that insecticides induce various diseases via DNA methylation. DNA methylation plays an important role during cell differentiation and exhibits its greatest vulnerability to environmental factors during embryogenesis. Therefore, it is important to evaluate the effects on DNA methylation at the early stage of cell differentiation to understand developmental toxicity. However, DNA methylation induced by insecticides and the associated effects on cell differentiation are unclear. In this research, we introduced a high-content approach utilizing mouse embryonic stem cells harboring enhanced green fluorescent protein fused with methyl CpG-binding protein to evaluate global DNA methylation induced by various insecticides. DNA methylation was assessed in 22 genes after pesticide exposure to investigate the relationships with biological processes such as cell cycle, cell apoptosis, and cell differentiation. Exposure to acetamiprid, imidacloprid, carbaryl, ando,p′-DDT increased the granular intensity, indicating their global DNA-methylating effects. Exposure to imidacloprid decreased DNA methylation in genes such as Cdkn2a, Dapk1, Cdh1, Mlh1, Timp3, and Rarb, indicating the potential influence of the DNA methylation pattern on cell differentiation. We developed a promising approach for evaluating global DNA methylation, and our findings suggested that imidacloprid might exhibit developmental effects through DNA methylation pattern.
Rapid evolution of invasive traits facilitates the invasion of common ragweed, Ambrosia artemisiifolia
Authors: Sun Yan , Roderick George K.
Published: May 2019

Invasive alien plants, together with organisms introduced for biological control, are ideal study systems with which to address questions of whether, and how fast, organisms adapt to changing environments. We compared populations of common ragweed, Ambrosia artemisiifolia, from native (USA) and introduced (China) ranges at similar latitudes, together with herbivores introduced for biological control, to understand the rate of evolutionary adaptive response of an invasive plant to novel environments.

Evolution of phenotypic traits associated with invasiveness was assessed by comparing differentiation in quantitative traits (QST) to that of neutral microsatellite genetic loci (FST) and through climate data. A common‐garden experiment estimated quantitative genetic variation associated with competition with grasses and biological control history by beetles.

Three growth traits (height, total and stem biomass) and plasticity associated with additional nutrients were significantly greater in invasive compared to native populations and differed from expectations from genetic drift alone. Native, but not invasive, populations exhibited traits showing evidence of past selection and correlations with climate, consistent with the recent timing of introductions. Competition experiments between invasive populations and a US bunch grass showed reduced competitive ability in populations with a history of biological control that might indicate a trade‐off between competitive ability and herbivore resistance in invasive populations.

Synthesis. Our results demonstrate the rapid rate at which traits favouring invasion can evolve in invasive weeds, such as A. artemisiifolia, but also that adaptation may reflect joint effects of release from specialist herbivores and novel climatic conditions.
Mediterranean Eucalyptus plantations affect small mammal ectoparasites abundance but not individual body condition
Authors: Teixeira Daniela , Carrilho Maílis , Silva Marcelo , Nunes Mónica , Vieira Maria L. , Novo Maria T. , Santos‐Reis Margarida , Rosalino Luís M.
Published: May 2019

Biodiversity is recognizably affected by land conversion for agriculture. However, the assessment of impacts on wildlife often lacks information on populations structure and individuals' condition, allowing only a limited view of the problem. Individual body condition/health can influence animal's reproductive success or survival. Eucalyptus globulus plantations are important forestry systems in Iberia, being the widest forested‐land use in Portugal, which hosts the broadest European E. globulus coverage. We tested Eucalyptus plantations' effects on small mammals' body condition (using the Scaled Mass Index‐SMI as surrogate) and ectoparasite abundance (number of mites, ticks and fleas per host). We applied a Generalized Linear Mixed Model (GLMM) approach for testing the influence of gender, habitat, species, season and understory cover on SMI and ectoparasites abundance. We captured 681 individuals, hosting overall 521 fleas (n = 305), mites (n = 159) and ticks (n = 57). Animal's body condition was not affected by plantations, but was lower for males and higher in spring. However, animals captured in Eucalyptus plantations and spring had higher parasite abundance (namely ticks and fleas), as well as males. Mites results were inconclusive. Body condition patterns seem to be determined by males demanding spatial/reproductive behavior (i.e., wider home‐ranges and search for females), while plantations promote ectoparasites abundance (e.g., induced by habitat disturbance and dilution effect). Results highlight that plantations may have negative effects on wildlife, but the evaluation of anthropic landscapes impact upon wildlife should encompass several bio‐ecological indicators, since the use of a restricted set (e.g., body condition) may induce a biased view.
Comparison of Blood Compatibility in Various Membrane Materials for Continuous Renal Replacement Therapy
Authors: Togo Konomi , Yamamoto Masahito , Imai Motoyuki , Akiyama Keiichi , Yamashita Akihiro C.
Published: May 2019

Because hemofilters used for continuous renal replacement therapy contact with blood over a prolonged period during treatments, platelet activation may occur stronger. The purpose of this study is to clarify the blood compatibility in three hemofilters mostly used in Japan. We compared the blood compatibility of the two polysulfone (AEF: Asahi Kasei Medical Co., Tokyo, Japan and SHG: Toray Medical Co., Ltd., Tokyo, Japan) and one polymethylmethacrylate membranes (CH: Toray Medical Co., Ltd.). First, test blood was collected from healthy volunteers. Subsequently, the blood was circulated by a roller pump at the rate of 100 mL/min. We measured the platelet counts and platelet factor 4 (PF4). The platelet counts at 48 h in polymethylmethacrylate membrane were significantly less than that in polysulfone membranes. Levels of the PF4 after the circulation were 978.5 ± 200.0 ng/dL with AEF, 863.0 ± 233.9 ng/dL with SHG and 1780.0 ± 465.1 ng/dL with CH, respectively. Hemofilters with polysulfone membranes showed less platelet activation. It was inferred that the amount of PVP, the smoothness of the membrane surface, and the inner diameter of the hollow fiber affect the blood compatibility in the hemofilter.
One‐vector CRISPR/Cas9 genome engineering of the industrial fungus Ashbya gossypii
Authors: Jiménez Alberto , Muñoz‐Fernández Gloria , Ledesma‐Amaro Rodrigo , Buey Rubén M. , Revuelta José L.
Published: May 2019

The filamentous fungus Ashbya gossypii is currently used for the industrial production of vitamin B2. Furthermore, the ability of A. gossypii to grow using low‐cost substrates together with the inexpensive downstream processing makes this fungus an attractive biotechnological chassis. Indeed, the production in A. gossypii of other high‐added value compounds such as folic acid, nucleosides and biolipids has been described. Hence, the development of new methods to expand the molecular toolkit for A. gossypii genomic manipulation constitutes an important issue for the biotechnology of this fungus. In this work, we present a one‐vector CRISPR/Cas9 system for genomic engineering of A. gossypii. We demonstrate the efficiency of the system as a marker‐less approach for nucleotide deletions and substitutions both with visible and invisible phenotypes. Particularly, the system has been validated for three types of genomic editions: gene inactivation, the genomic erasure of loxP scars and the introduction of point mutations. We anticipate that the use of the CRISPR/Cas9 system for A. gossypii will largely contribute to facilitate the genomic manipulations of this industrial fungus in a marker‐less manner.
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Authors: Weilguny Lukas , Kofler Robert
Published: May 2019

Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
Declining use of radical prostatectomy and pelvic lymphadenectomy despite more robotics: National population data over 15 years
Authors: Roberts Matthew J. , Papa Nathan , Perera Marlon , Joshi Andre , Scott Susan , Bolton Damien , Lawrentschuk Nathan , Yaxley John
Published: May 2019

Aim

To describe national surgical patterns of prostate cancer (PCa) care considering radical prostatectomy with or without pelvic lymphadenectomy and consideration of robotic‐assisted techniques.

Methods

Retrospective analysis of publicly accessible Medicare claims data was performed for the period 2001–2016 and included patients undergoing radical prostatectomy with or without pelvic lymphadenectomy relative to total and PCa‐specific populations among men aged 45–84 years. Proportion of cases performed robotically was considered.

Results

Total procedures performed increased from 2001, peaked in 2009 and subsequently decreased until 2016. Since 2009, the age‐specific rate of surgery in men aged 75–84 increased by 2.3‐fold, whereas the rates for men aged 55–64 and 45–54 reduced by 44% and 55%, respectively. Rates of concurrent pelvic lymphadenectomy fell until 2009 with subsequent stabilization (ratio 1.05–1.14) through to 2016. Significant regional practice patterns were observed, as was an increasing trend toward a robotic‐assisted laparoscopic approach, comprising more than 80% of radical prostatectomies in 2016.

Conclusion

Since the peak in 2009, radical prostatectomy is performed less in men <65 years and more in men ≥65 years. An increasing proportion of cases omit concurrent pelvic lymphadenectomy and are performed robotically.
Aid vs. “Aid”: Foreign Aid in Mao‐Era China's Public Diplomacy
Authors: Atkinson Joel
Published: May 2019

Historicising Chinese foreign‐aid thinking has become indispensable given China's increasing global role. This article examines a key aspect of this context: the Great Leap Forward and the emerging Sino‐Soviet split period (1958‐1961). The Peking Review is utilised as a window into official aid‐related discourses of the time. The article is organized around an aid vs. “aid” rhetorical and conceptual symmetry within the magazine. Aid is ultimately what Mao Zedong and other leaders intend audiences to code as pro‐development and prestigious. The greater the unreciprocated cost to the donor and the higher the embodied technology, the more helpful and prestigious the donor. At the same time, the more ideologically correct the recipient or donor, the greater its relative prestige in the equation. An ideologically correct recipient such as China deserves more help but needs it less, and accrues more prestige even as it gives comparatively less aid. “Aid” is the reverse image of aid in that it is harmful rather than helpful. But instead of being the opposite of prestigious, “aid” is powerful in a predatory, paper tiger‐like way. While this discourse reflects parochial concerns of the period, the underlying concepts are likely to continue to influence contemporary Chinese aid thinking and practices.
Collateral Consequences for Juveniles in the Justice System: Change in Perceptions after an Educational Intervention
Authors: Janssen Jennica , Wagage Suraji , Cole Lindsey M. , Gale‐Bentz Elizabeth , Goldstein Naomi E. S.
Published: May 2019

There is a dearth of empirical research investigating public awareness or perceptions of the impact of collateral consequences of juvenile justice system involvement on youths’ lives. The current study recruited 555 Pennsylvania residents through Amazon Mechanical Turk to participate in a brief, educational intervention on collateral consequences of system involvement. Participants read a short vignette about a hypothetical youth who was adjudicated delinquent in Pennsylvania, answered 20 knowledge‐based questions, and provided pre‐ and postintervention ratings of the impact the delinquency finding would have on the youth's life in the short term and in the long term. Results of linear mixed model analysis revealed significant fixed effects of both phase (pre‐post educational intervention), b = .62, p < .001, 95% CI [.47, .78] and timing (before the youth turns age 18 and after the youth turns age 18), b = –.98, p < .001, 95% CI [–1.18, –.78], on impact ratings (i.e., how big an impact a juvenile adjudication will have on the youth's life). Participants provided incorrect responses to approximately half of collateral consequences, indicating a gap in knowledge. Findings from the current study can inform targeted intervention efforts to increase public awareness of the consequences of juvenile justice system involvement.
The epidemiology of bacille Calmette–Guérin infections after bladder instillation from 2002 through 2017: a nationwide retrospective cohort study
Authors: Larsen Emilie S. , Nordholm Anne C. , Lillebaek Troels , Holden Inge K. , Johansen Isik S.
Published: May 2019

Objective

To describe incidence and clinical characteristics of bacille Calmette–Guérin (BCG) infections after BCG bladder instillation amongst patients with non‐muscle‐invasive bladder cancer in Denmark.

Patients and methods

We conducted a nationwide register‐based cohort study in Denmark between 2002 through 2017. Patients with BCG infection were identified by cross‐linking data from the Danish National Hospital Registry on patients treated with BCG instillations and patients diagnosed with tuberculosis according to the International Classification of Diseases 10, and data obtained from International Reference Laboratory of Mycobacteriology. Hospital records were reviewed for clinical information.

Results

During the study period, 6753 patients (5281 men; mean [SD] age 71.1 (0.1) years) received BCG instillations, of which 66 patients (1%) developed BCG infections. There were no differences in age or Charlson Comorbidity Index between the patients in the study population stratified by BCG infection. The median (interquartile range) time from first BCG instillation until symptoms of BCG infection was 169.5 (38–585) days. Extrapulmonary localisation of BCG infections (37 patients, 56.1%) was significantly more frequent than pulmonary BCG infections (20 patients, 30.3%; P < 0.001). The most common extrapulmonary localisation was the genitourinary tract (29 patients, 78.4%).

Conclusion

BCG infections after bladder instillation are rare, mainly affect male patients, and are most frequently extrapulmonary. BCG infections should be suspected despite a long time span between occurrence of symptoms and prior bladder instillation.
Genomic classifiers for treatment selection in newly diagnosed prostate cancer
Authors: Fine Noam David , LaPolla Fred , Epstein Matthew , Loeb Stacy , Dani Hasan
Published: May 2019

Objectives

To review systematically the literature on genomic tests for prostate cancer (PCa) and to evaluate the current state of the evidence on their use in patients with newly diagnosed PCa.

Methods

We conducted a systematic review by searching PubMed, Embase, Cochrane Central and conference abstracts from the American Urological Association, published between 2010 and 2018. Studies evaluating Prolaris, Oncotype Dx and Decipher assays were assessed for inclusion by two authors. Studies were excluded if the results were derived from surgical specimens rather than biopsy specimens. A meta‐analysis was not performed owing to significant variations in methodologies, definitions and outcome measures.

Results

A total of 729 articles were retrieved in our initial search. After removing duplicates (270) and excluding articles deemed not relevant (432), 21 full‐text articles were deemed suitable for inclusion in the present analysis. The full‐text articles comprised eight studies on Prolaris, eight studies on Oncotype Dx and five studies on Decipher. For each genomic test we extracted data regarding the risks of adverse pathology, biochemical recurrence, metastasis and PCa‐specific mortality.

Conclusion

The results of genomic tests that use biomarkers derived from prostate biopsy can be used in conjunction with clinicopathological variables to improve our ability to risk‐stratify patients with newly diagnosed PCa. Additional data are needed on the impact of using these tests on long‐term patient outcomes and their cost‐effectiveness.
Design, synthesis, and antimicrobial activities of novel functional peptides against Gram‐positive and Gram‐negative bacteria
Authors: Lee Ping‐Chien , Chu Chia‐Chun , Tsai Yi‐Je , Chuang Ya‐Chu , Lung Feng‐Di
Published: May 2019

The extensive use of antibiotics in medicine results in the multidrug resistance of bacteria, making the development of new antimicrobial agents an urgent need. Antimicrobial peptides (AMPs) are considered as a new class of antibiotic with characteristics including an ability to kill target cells rapidly and a broad spectrum of activity. We have developed a potent antimicrobial peptide MAP‐0403 (MIC = 5 μM), but it exhibited a high hemolytic side‐effect (70.7%). To reduce its hemolytic effect and increase antimicrobial activity, three peptides derivatives of MAP‐0403 (J‐1, J‐2, and J‐3) were designed, synthesized by solid phase synthesis, purified by RP‐HPLC, and characterized by MALDI‐TOF MS. Structure–activity relationships of these peptides were studied by using circular dichroism and antimicrobial assays. The percentage of helical structure in J‐1, J‐2, and J‐3 was lower than that of MAP‐0403. The antimicrobial activity of J‐1 was the same as that of MAP‐0403 (MIC = 5 μM), J‐2 exhibited the highest activity (MIC = 2.5 μM), while J‐3 showed decreased activity (MIC = 10 μM). Compared to MAP‐0403, J‐2 showed significantly reduced hemolytic effect (3.4%), while J‐1 and J‐3 showed slightly decreased hemolytic effect (46.2%, 55.6%, respectively). Peptide J‐2 was discovered as a novel and potent antimicrobial agents.
Labial soft tissue contour dynamics following immediate implants and immediate provisionalization of single maxillary incisors: A 1‐year prospective study
Authors: Tian Jiehua , Wei Donghao , Zhao Yijiao , Di Ping , Jiang Xi , Lin Ye
Published: May 2019

Background

Soft tissue dynamics in the esthetic zone are gaining increasing attention in recent years. Emerging intraoral scanning technology allows easier capture of soft tissue contours.

Purpose

To quantitatively assess the time‐dependent contour alterations of labial soft tissue following single immediate implants and immediate provisionalization (IIPP) in maxillary incisors via intraoral scanning.

Materials and Methods

This was a prospective cohort study. Thirty eligible consecutive patients were included and received immediate replacement of a failure maxillary single incisor. A screw‐retained immediate restoration was delivered for each patient. Subsequently, the anterior maxillary region was scanned by an intraoral scanning system at four time points: preoperation (baseline, BL), 3 months (3 m), 6 months (6 m), and 12 months (12 m). The Standard Tessellation Language files were exported to a dedicated software and superimposed for visual analysis. At 3, 6, and 12 months, the mid‐facial mucosa level (ML) was assessed, and the precise three‐dimensional (3D) configuration of the altered volume was calculated and reconstructed for visual analysis. Furthermore, quantitative analysis of the reconstructed morphology was performed using the following parameters: mean change in thickness (△d), mesio‐distal width (w), coronal‐apical height (h), and horizontal and vertical position of the thickest point represented by coordinates (x, z).

Result

Twenty‐seven of thirty enrolled patients were finally available for analysis at the 1‐year follow‐up. In general, the frontal view of the reconstructed volume exhibited a crescent shape. The mid‐facial ML change at 3, 6, and 12 months was −0.05 ± 0.36 mm, −0.03 ± 0.32 mm, and −0.24 ± 0.37 mm, respectively (P = .012). The mean change in thickness at 3 months (△d3m), 6 months (△d6m), and 12 months (△d12m) was 0.50 ± 0.19 mm, 0.59 ± 0.21 mm, and 0.62 ± 0.22 mm, respectively (P <.001). At 12 months, nine patients had a △d less than 0.5 mm. The mean △d3 m/△d12 m and △d6 m/△d12 m was 0.81 ± 0.17 and 0.96 ± 0.13. The w, h, x, and z results showed no significant differences during the 1‐year observation (P = .126, P = .324, P = .635, P = .263). At 12 months, w, h, x, and z were 11.57 ± 1.77 mm, 6.46 ± 2.01 mm, 0.03 ± 1.43 mm, and 2.16 ± 0.65 mm, respectively.

Conclusion

During the 1‐year observation following single IIPP treatment in maxillary incisors, the labial soft tissue contour showed a continuous alteration resulting in a mean change in thickness of 0.62 mm that occurred mainly in the first 3 months and tended to be relatively stable after 6 months, while the crescent‐like shape, width, height, and thickest point position of the alteration volume remained stable after 3 months. No advanced mid‐facial recession was observed.
Crop research, biotech canola, and innovation policy in Canada: Challenges, opportunities, and evolution
Authors: Malla Stavroula , Brewin Derek G.
Published: May 2019

Increased investment in agricultural research could contribute to sustainable development goals and benefit farmers, consumers, the environment, and the economy. This paper provides recent evidence and a critical assessment of the evolving Canadian canola crop development and innovation policy and compares it to the wheat and pulse sectors that differ in degree of biotechnology adoption, seeded acreage, intellectual property rights, and private sector involvement. This study also assesses how crop characteristics and technological changes affect future optimal public policy. A number of innovation policies are discussed that could stimulate further growth within the crop sector.
The accuracy of static vs. dynamic computer‐assisted implant surgery in single tooth space: A randomized controlled trial
Authors: Kaewsiri Dechawat , Panmekiate Soontra , Subbalekha Keskanya , Mattheos Nikos , Pimkhaokham Atiphan
Published: May 2019

Objectives

The aim of this RCT was to compare the accuracy of implant placement between static and dynamic computer‐assisted implant surgery (CAIS) systems in single tooth space.

Materials and methods

A total of 60 patients in need of a single implant were randomly assigned to two CAIS groups (Static n = 30, Dynamic n = 30) and implants were placed by one surgeon. Preoperative CBCT was transferred to implant planning software to plan the optimal implant position. Implants were placed using either stereolithographic guide template (Static CAIS) or implant navigation system (Dynamic CAIS). Postoperative CBCT was imported to implant planning software, and deviation analysis with the planned position was performed. Primary outcomes were the deviation measurements at implant platform, apex, and angle of placement. Secondary outcome was the distribution of the implant deviation into each 3D direction.

Results

The mean deviation at implant platform and implant apex in the static CAIS group was 0.97 ± 0.44 mm and 1.28 ± 0.46 mm, while that in the dynamic CAIS group was 1.05 ± 0.44 mm and 1.29 ± 0.50 mm, respectively. The angular deviation in static and dynamic CAIS group was 2.84 ± 1.71 degrees and 3.06 ± 1.37 degrees. None of the above differences between the two groups reached statistical significance. The deviation of implants toward the mesial direction in dynamic CAIS group was significantly higher than that of the static CAIS (p = 0.032).

Conclusions

Implant placement accuracy in single tooth space using dynamic CAIS appear to be the same to that of static CAIS. (Thai Clinical Trials Registry TCTR20180826001).
Neural activity in the periaqueductal gray and other specific subcortical structures is enhanced when a selective serotonin reuptake inhibitor selectively prevents seizure‐induced sudden death in the DBA/1 mouse model of sudden unexpected death in epilepsy
Authors: Kommajosyula Srinivasa P. , Faingold Carl L.
Published: May 2019

Objective

Sudden unexpected death in epilepsy (SUDEP) is a critical issue in epilepsy, and DBA/1 mice are a useful animal model of this devastating epilepsy sequela. The serotonin hypothesis for SUDEP proposes that modifying serotonergic function significantly alters susceptibility to seizure‐induced respiratory arrest (S‐IRA). Agents that enhance serotonergic function, including a selective serotonin reuptake inhibitor, fluoxetine, selectively prevent S‐IRA in DBA/1 mice. This study examined fluoxetine‐induced changes in brain activity using manganese‐enhanced magnetic resonance imaging (MEMRI) to reveal sites in the DBA/1 mouse brain where fluoxetine acts to prevent S‐IRA.

Methods

DBA/1 mice were subjected to audiogenic seizures (Sz) after saline or fluoxetine (45 mg/kg, intraperitoneal) administration. Control DBA/1 mice received fluoxetine or saline, but Sz were not evoked. A previous MEMRI study established the regions of interest (ROIs) for Sz in the DBA/1 mouse brain, and the present study examined MEMRI differences in the ROIs of these mouse groups.

Results

The neural activity in several ROIs was significantly increased in fluoxetine‐treated DBA/1 mice that exhibited Sz but not S‐IRA when compared to the saline‐treated mice that exhibited both Sz and respiratory arrest. These structures included the periaqueductal gray (PAG), amygdala, reticular formation (sensorimotor‐limbic network), Kölliker‐Fuse nucleus, facial‐parafacial group (respiratory network), and pontine raphe. Of these ROIs, only the PAG showed significantly decreased neural activity with saline pretreatment when seizure‐induced respiratory arrest occurred as compared to saline treatment without seizure.

Significance

The PAG is known to play an important compensatory role for respiratory distress caused by numerous exigent situations in normal animals. The pattern of fluoxetine‐induced activity changes in the present study suggests that PAG may be the most critical target for fluoxetine's action to prevent seizure‐induced sudden death. These findings have potential clinical importance, because there is evidence of anomalous serotonergic function and PAG imaging abnormalities in human SUDEP.