bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
Authors: Conte Matthew A , Joshi Rajesh , Moore Emily C , Nandamuri Sri Pratima , Gammerdinger William J , Roberts Reade B , Carleton Karen L , Lien Sigbjørn , Kocher Thomas D
Published: April 2019

Background

African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.

Results

We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (~2–28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage.

Conclusion

This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
What Happens After a Positive Screen for Depression and Posttraumatic Stress Disorder in the Outpatient Burn Clinic?
Authors: Carmean Melissa , Grigorian Areg , Stefan Julie , Godes Natalya , Burton Kimberly , Joe Victor C
Published: April 2019

Multiple reports have demonstrated a wide prevalence of both depression and posttraumatic stress disorder (PTSD) within 1 year of burn injury. The purpose of this study is to determine outcomes of burn patients after a positive outpatient screen for depression or PTSD at an American Burn Association-verified burn center. All patients who screened positive were offered referral for psychologic and/or psychiatric counseling. Rescreening was performed with a goal of approximately 6 months. A total of 445 patients were enrolled with 91 (20.6%) screening positive for depression and 59 (13.4%) for PTSD. TBSA burned was associated with a positive screen for depression (P = .008) and PTSD (P = .012) while electrical injury was associated with a positive screen for depression (P = .029). Rescreening was done in 15.5% with 23% rescreening positive for depression and 15% for PTSD. The study validated the need for early screening and referral for psychologic and/or psychiatric counseling in this population.
Cost-Utility of Early Breast Cancer Surveillance in Survivors of Thoracic Radiation-Treated Adolescent Hodgkin Lymphoma
Authors: Furzer Jill , Tessier Lauren , Hodgson David , Cotton Cecilia , Nathan Paul C , Gupta Sumit , Pechlivanoglou Petros
Published: April 2019

Background

Adolescent women treated for Hodgkin lymphoma (HL) are at increased risk of breast cancer (BC). We evaluate the cost-utility of eight high-risk BC surveillance strategies for this population, including the Children’s Oncology Group guideline of same-day annual mammography and magnetic resonance imaging (MRI) beginning at age 25 years.

Methods

A discrete event simulation model was used to simulate the life histories of a cohort of 500 000 25-year-old women treated for HL at age 15 years. We estimated BC incidence and mortality, life expectancy, quality-adjusted life-years (QALYs), health-care costs, and the relative cost-utility (incremental cost-utility ratio [ICUR]) under the eight assessed surveillance strategies. One-way sensitivity analysis enabled modeling of uncertainty evaluation. A publicly funded health-care payer perspective was adopted.

Results

Costs across the eight screening strategies ranged from $32 643 to $43 739, whereas QALYs ranged from 24.419 to 24.480. In an incremental cost-effectiveness analysis, annual mammography beginning at age 25 years was associated with an ICUR of $43 000/QALY gained, annual MRI beginning at age 25 years with a switch to annual mammography at age 50 years had an ICUR of $148 000/QALY, and annual MRI beginning at age 25 years had an ICUR of $227 222/QALY. Among all assessed surveillance strategies, the differences in life expectancy were small.

Conclusions

Current high-risk BC surveillance guidelines do not reflect the most cost-effective strategy in survivors of adolescent HL. The results suggest that groups at high risk of BC may require high-risk surveillance guidelines that reflect their specific risk profile.
Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer
Authors: Li Na , McInerny Simone , Zethoven Magnus , Cheasley Dane , Lim Belle W X , Rowley Simone M , Devereux Lisa , Grewal Norah , Ahmadloo Somayeh , Byrne David , Lee Jue Er Amanda , Li Jason , Fox Stephen B , John Thomas , Antill Yoland , Gorringe Kylie L , James Paul A , Campbell Ian G
Published: April 2019

Background

Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer.

Methods

RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation.

Results

A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency.

Conclusions

This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
Intensity-modulated radiotherapy for cervical esophageal squamous cell carcinoma without hypopharyngeal invasion: dose distribution and clinical outcome
Authors: Ishida Yuichi , Sakanaka Katsuyuki , Fujii Kota , Itasaka Satoshi , Mizowaki Takashi
Published: April 2019

Hypopharyngeal invasion would be a key finding in determining the extent of the irradiation fields in patients with cervical esophageal squamous cell carcinoma (CESCC). This study aimed to investigate the clinical outcomes of chemoradiotherapy using simultaneous integrated boost intensity-modulated radiotherapy (SIB-IMRT) omitting upper cervical lymph nodal irradiation in CESCC without hypopharyngeal invasion, and the dosimetric superiority of SIB-IMRT to 3D conformal radiotherapy (3DCRT). We retrospectively identified 21 CESCC patients without hypopharyngeal invasion [clinical Stage I/II/III/IV (M1LYM); 3/6/5/7] (UICC-TNM 7th edition) who underwent chemoradiotherapy using SIB-IMRT between 2009 and 2015. SIB-IMRT delivered 60 Gy to each primary tumor and the metastatic lymph nodes, and 48 Gy to elective lymph nodal regions, including Levels III and IV of the neck, supraclavicular, and upper mediastinal lymphatic regions, in 30 fractions. The overall survival rate, locoregional control rate, and initial recurrence site were evaluated. 3DCRT plans were created to perform dosimetric comparisons with SIB-IMRT. At a median follow-up of 64.5 months, the 5-year locoregional control and overall survival rates were 66.7% and 53.4%, respectively. Disease progressed in eight patients: all were locoregional progressions and no patients developed distant progression including upper cervical lymph nodal regions as initial recurrence sites. The planning study showed SIB-IMRT improved target coverage without compromising the dose to the organs at risk, compared with 3DCRT. In conclusion, omitting the elective nodal irradiation of the upper cervical lymph nodes was probably reasonable for CESCC patients without hypopharyngeal invasion. Locoregional progression remained the major progression site in this population.
The O star hinterland of the Galactic starburst, NGC 3603
Authors: Drew J E , Monguió M , Wright N J
Published: April 2019

The very bright and compact massive young cluster, NGC 3603, has been cited as an example of a starburst in the Milky Way and compared with the much-studied R136/30 Doradus region in the Large Magellanic Cloud. Here we build on the discovery by Mohr-Smith et al. of a large number of reddened O stars around this cluster. We construct a list of 288 candidate O stars with proper motions (PMs), in a region of sky spanning 1.5 × 1.5 deg2 centred on NGC 3603, by cross-matching the Mohr-Smith et al. catalogue with Gaia DR2. This provides the basis for a first comprehensive examination of the PMs of these massive stars in the halo of NGC 3603, relative to the much better studied central region. We identify up to 11 likely O star ejections – 8 of which would have been ejected between 0.60 and 0.95 Myr ago (supporting the age of ∼1 Myr that has been attributed to the bright cluster centre). Seven candidate ejections are arranged in a partial ring to the south of the cluster core spanning radii of 9–18 arcmin (18–36 pc if the cluster is 7 kpc away). We also show that the cluster has a halo of a further ∼100 O stars extending to a radius of at least 5 arcmin, adding to the picture of NGC 3603 as a scaled down version of the R136/30 Dor region.
Is There a Need for a 6-Month Postradiosurgery Magnetic Resonance Imaging in the Treatment of Vestibular Schwannoma?
Authors: Perry Avital , Graffeo Christopher S , Carlstrom Lucas P , Hughes Joshua D , Peris-Celda Maria , Cray Nealey M , Pollock Bruce E , Link Michael J
Published: April 2019

BACKGROUND

Stereotactic radiosurgery (SRS) is a common treatment modality for vestibular schwannoma (VS), with a role in primary and recurrent/progressive algorithms. At our institution, routine magnetic resonance imaging (MRI) is obtained at 6 and 12 mo following SRS for VS.

OBJECTIVE

To analyze the safety and financial impact of eliminating the 6-mo post-SRS MRI in asymptomatic VS patients.

METHODS

A prospectively maintained SRS database was retrospectively reviewed for VS patients with 1 yr of post-treatment follow-up, 2005 to 2015. Decisions at 6-mo MRI were binarily categorized as routine follow-up vs clinical action—defined as a clinical visit, additional imaging, or an operation as a direct result of the 6-mo study.

RESULTS

A total of 296 patients met screening criteria, of whom 53 were excluded for incomplete follow-up and 8 for NF-2. Nine were reimaged prior to 6 mo due to clinical symptoms. Routine 6-mo post-SRS MRI was completed by 226 patients (76% of screened cohort), following from which zero instances of clinical action occurred. When scaled using national insurance database-derived financials—which estimated the mean per-study charge for MRI of the brain with and without contrast at $1767—the potential annualized national charge reduction was approximated as $1 611 504.

CONCLUSION

For clinically stable VS, 6-mo post-SRS MRI does not contribute significantly to management. We recommend omitting routine MRI before 12 mo, in patients without new or progressive neurological symptoms. If extrapolated nationally to the more than 100 active SRS centers, thousands of patients would be spared an inconvenient, nonindicated study, and national savings in health care dollars would be on the order of millions annually.
Clinical Outcomes of Stereotactic Radiosurgery for Cerebral Arteriovenous Malformations in Pediatric Patients: Systematic Review and Meta-Analysis
Authors: Börcek Alp Özgün , Çeltikçi Emrah , Aksoğan Yiğit , Rousseau Matthew John
Published: April 2019

BACKGROUND

Arteriovenous malformations (AVMs) in pediatric patients exhibit remarkable differences in terms of management and outcomes. Owing to a paucity of relevant data pertaining to AVMs in pediatric patients, special interest and investigation are required for an improved understanding of the available evidence by clinicians.

OBJECTIVE

To determine the clinical outcomes of single-session stereotactic radiosurgery (SRS) for AVMs in pediatric patients.

METHODS

A systematic literature review was performed to identify studies that reported the outcomes of SRS for AVMs in pediatric patients. Data pertaining to variables such as obliteration rate, post-SRS new hemorrhage rate, post-SRS new neurological deficit rate, and mortality rate were extracted and analyzed using meta-analysis techniques.

RESULTS

Based on pooled data from 20 studies with 1212 patients, single-session SRS resulted in complete obliteration in 65.9% (95% confidence interval [CI], 60.5%-71.1%; I2 = 66.5%) patients. Overall complication rate (including new hemorrhage, new neurodeficit, and mortality) was 8.0% (95% CI, 5.1%-11.5%; I2 = 66.4%). Post-SRS new neurological deficit rate was 3.1% (95% CI, 1.3%-5.4%; I2 = 59.7%), and post-SRS hemorrhage rate was 4.2% (95% CI, 2.5%-6.3%; I2 = 42.7%). There was no significant difference between studies disaggregated by treatment method (Gamma Knife [Elekta AB] vs other), treatment year (before year 2000 vs after year 2000), median AVM volume reported (≥3 vs <3 cm3), median dose reported (≥20 vs <20 Gy), or follow-up period (≥36 vs <36 mo).

CONCLUSION

Single-SRS is a safe treatment alternative that achieves high obliteration rates and acceptable complication rates for AVMs in pediatric patients.
IMPACT ON ABSORBED DOSE RATE IN AIR IN KANTO REGION BY FUKUSHIMA DAIICHI NUCLEAR POWER PLANT ACCIDENT
Authors: Inoue K , Arai M , Tsuruoka H , Saito K , Fujisawa M , Nakazawa S , Veerasamy N , Fukushi M
Published: April 2019

Absorbed dose rates in air were measured for the whole area of the Kanto region in 2015, 2016 and 2017 (n = 31 147). The mean absorbed dose rates in air for each prefecture measured by car-borne surveys were from 44 to 67 nGy h−1 (13–289 nGy h−1). The absorbed dose rate in air from artificial radionuclides (134Cs + 137Cs) measured by fixed-point observation (n = 507) was from 1 to 14 nGy h−1 (0–105 nGy h−1), and meaning that the contribution ratios of 134Cs and 137Cs were 3–22%. The deposited location of artificial radionuclides was less than 1000 m from ground level and depended on the topography, wind direction and precipitation field.
NATURAL RADIONUCLIDES IN AGRICULTURAL PLANTS FROM NORTHERN THAILAND
Authors: Kritsananuwat R , Kranrod C , Chanyotha S , Ploykrathok T , Sriploy P
Published: April 2019

Thailand is predominantly an agricultural country. The Northern Region occupies the second largest cultivated land area in the country. To establish baseline data for future environmental monitoring, seventy-nine plant samples including vegetables, fruits and tobaccos and their relevant soils were collected from the major plantation zones of Northern Thailand. Activity concentrations of natural radionuclides in the samples were determined using gamma-ray spectrometry technique. The median activity concentrations of 226Ra and 228Ra in the soil samples were higher than worldwide value, while as those of 40K were comparable with worldwide value. There was a large variation and non-uniform distribution in the soil samples. The activity concentrations of 226Ra, 228Ra and 40K in the plant samples varied widely within plants and between species and were very low compared to their relevant soils. A decreasing trend of their activity concentration has been observed in the order leaf > stem > rhizome/root (as found in galangal); and leaf > stalk/stem (as found in lemongrass).
INTERCOMPARISON EXPERIMENT AND UNCERTAINTY ANALYSIS OF THREE MEASUREMENT METHODS FOR RADON PROGENY AT NIM
Authors: Wang Yunxiang , Zhang Lei , Yang Zhijie , Guo Qiuju , Liang Juncheng
Published: April 2019

An intercomparison experiment of three radon progeny measurement methods, based on alpha spectrometry (Kerr method), alpha–beta spectrometry and liquid scintillation counter (LSC method), was carried out in the standard radon chamber at NIM. Both the consistency and the uncertainty analysis of three different methods were studied in detail. Results show that, at the EEC level of 4000 Bq/m3, the uncertainties of the alpha–beta spectrometry, LSC method and Kerr method were 3.78%, 6.41% and 9.46%, respectively, which are mainly contributed by detection efficiency uncertainty, measuring time uncertainty and counting statistical uncertainty in sequence. The comparison results at different concentration levels show that the measurement values of three methods are consistent within the error range of 3%. The alpha–beta spectrometry can be used as a reference standard method to achieve the simultaneous measurement of RaA, RaB, RaC concentrations and EEC in the radon chamber.
Hybridization between sympatric hammerhead sharks in the western North Atlantic Ocean
Authors: Barker Amanda M. , Adams Douglas H. , Driggers William B. , Frazier Bryan S. , Portnoy David S.
Published: April 2019

Hybridization between closely related species has been documented across a wide range of taxa but has not been well studied in elasmobranchs. Hammerhead sharks have drawn global conservation concern because they experience some of the highest mortality rates among sharks when interacting with fisheries. Here we report on the detection of hybrids between the globally distributed scalloped hammerhead (Sphyrna lewini) and recently described Carolina hammerhead (S. gilberti) which are only known from the western Atlantic Ocean. Using a genomics approach, 10 first-generation hybrids and 15–17 backcrosses were detected from 554 individuals. The identification of backcrosses demonstrates hybrids are viable, and all backcrosses but one involved a scalloped hammerhead. All hybrids but one possessed Carolina hammerhead mtDNA, indicating sex-biased gene flow between species. Repeated hybridization and backcrossing with scalloped hammerheads could lead to the loss of endemic Carolina hammerheads.
Unveiling tipping points in long-term ecological records from
Sphagnum
-dominated peatlands
Authors: Lamentowicz Mariusz , Gałka Mariusz , Marcisz Katarzyna , Słowiński Michał , Kajukało-Drygalska Katarzyna , Dayras Milva Druguet , Jassey Vincent E. J.
Published: April 2019

Unveiling past tipping points is a prerequisite for a better understanding of how individual species and entire ecosystems will respond to future climate change. Such knowledge is key for the implementation of biodiversity conservation. We identify the relationships between peatland vegetation and hydrological conditions over the past 2000 years using plant macrofossils, testate amoebae-based quantitative hydrological reconstructions and
Sphagnum
-moss functional traits from seven Polish peatland records. Using threshold indicator taxa analysis, we discovered that plant community composition strongly converged at a water level of
ca
11.7 cm, indicating a community-level tipping point. We identified 45 plant taxa that showed either an increase or a decrease in their relative abundance between 8 and 17 cm of water-level depth. Our analysis of
Sphagnum
community traits further showed that
Sphagnum
functional diversity was remarkably stable over time despite
Sphagnum
species sensitivity to hydrological conditions. Our results suggest that past hydrological shifts did not influence major functions of the
Sphagnum
community, such as photosynthetic capacity, growth and productivity, owing to species replacement with a similar functional space. Although further studies including trait plasticity will be required, our findings suggest that the capacity of the
Sphagnum
community to gain carbon remained stable despite hydrological changes.
Stephen William Hawking CH CBE. 8 January 1942—14 March 2018
Authors: Carr Bernard J. , Ellis George F. R. , Gibbons Gary W. , Hartle James B. , Hertog Thomas , Penrose Roger , Perry Malcolm J. , Thorne Kip S.
Published: April 2019

Stephen Hawking's contributions to the understanding of gravity, black holes and cosmology were truly immense. They began with the singularity theorems in the 1960s followed by his discovery that black holes have an entropy and consequently a finite temperature. Black holes were predicted to emit thermal radiation, what is now called Hawking radiation. He pioneered the study of primordial black holes and their potential role in cosmology. His organization of and contributions to the Nuffield Workshop in 1982 consolidated the picture that the large-scale structure of the universe originated as quantum fluctuations during the inflationary era. Work on the interplay between quantum mechanics and general relativity resulted in his formulation of the concept of the wavefunction of the universe. The tension between quantum mechanics and general relativity led to his struggles with the information paradox concerning deep connections between these fundamental areas of physics.

These achievements were all accomplished following the diagnosis during the early years of Stephen's studies as a post-graduate student in Cambridge that he had incurable motor neuron disease—he was given two years to live. Against all the odds, he lived a further 55 years. The distinction of his work led to many honours and he became a major public figure, promoting with passion the needs of disabled people. His popular best-selling book,
A brief history of time
, made cosmology and his own work known to the general public world-wide. He became an icon for science and an inspiration to all.
Incorporating intraspecific variation into dental microwear texture analysis
Authors: Arman Samuel D. , Prowse Thomas A. A. , Couzens Aidan M. C. , Ungar Peter S. , Prideaux Gavin J.
Published: April 2019

Dental microwear texture analysis (DMTA) quantifies microscopic scar or wear patterns left on teeth by different foods or extraneous ingested items such as grit. It can be a powerful tool for deducing the diets of extinct mammals. Here we investigate how intraspecific variation in the dental microwear of macropodids (kangaroos and their close relatives) can be used to maximize the dietary signal inferable from an inherently limited fossil record. We demonstrate significant intraspecific variation for every factor considered here for both scale-sensitive fractal analysis and International Organization for Standardization surface texture analysis variables. Intraspecific factors were then incorporated into interspecific (dietary) analyses through the use of Linear Mixed Effects modelling, incorporating Akaike's Information Criterion to compare models, and testing models through independent cross-validation. This revealed that for each DMTA variable only a small number of intraspecific factors need to be included to improve differentiation between species. Includingspecimenas a random factor accounted for stochastic inter-individual variation, andfacet, incorporated effects of sampling location. Intraspecific effects ofecoregion, microscope, toothposition andwearwere often but not universally important. We conclude that models of microwear data that include intraspecific variation can improve the resolution of dietary reconstructions.
A stochastic game model of searching predators and hiding prey
Authors: Alpern Steve , Gal Shmuel , Lee Viciano , Casas Jérôme
Published: April 2019

When the spatial density of both prey and predators is very low, the problem they face may be modelled as a two-person game (called a ‘search game’) between one member of each type. Following recent models of search and pursuit, we assume the prey has a fixed number of heterogeneous ‘hiding’ places (for example, ice holes for a seal to breathe) and that the predator (maybe polar bear) has the time or energy to search a fixed number of these. If he searches the actual hiding location and also successfully pursues the prey there, he wins the game. If he fails to find the prey, he loses. In this paper, we modify the outcome in the case that he finds but does not catch the prey. The prey is now vulnerable to capture while relocating with risk depending on the intervening terrain. This generalizes the original games to a stochastic game framework, a first for search and pursuit games. We outline a general solution and also compute particular solutions. This modified model now has implications for the question of when to stay or leave the lair and by what routes. In particular, we find the counterintuitive result that in some cases adding risk of predation during prey relocation may result in more relocation. We also model the process by which the players can learn about the properties of the different hiding locations and find that having to learn the capture probabilities is favourable to the prey.
Is breast implant-associated anaplastic large cell lymphoma a hazard of breast implant surgery?
Authors: Fitzal Florian , Turner Suzanne D. , Kenner Lukas
Published: April 2019

Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) may occur after reconstructive or aesthetic breast surgery. Worldwide, approximately 1.7 million breast implant surgeries are performed each year. To date, over 500 cases of BIA-ALCL have been reported around the world, with 16 women having died. This review highlights the most important facts surrounding BIA-ALCL. There is no consensus regarding the true incidence rate of BIA-ALCL as it varies between countries, is probably significantly under-reported and is difficult to estimate due to the true number of breast prostheses used largely being unknown. BIA-ALCL develops in the breast mostly as a seroma surrounding the implant, but contained within the fibrous capsule, or more rarely as a solid mass that can become invasive infiltrating the chest wall and muscle, in some instances spreading to adjacent lymph nodes, in these cases having a far worse prognosis. The causation of BIA-ALCL remains to be established, but it has been proposed that chronic infection and/or implant toxins may be involved. What is clear is that complete capsulectomy is required for treatment of BIA-ALCL, which for early-stage disease leads to cure, whereas chemotherapy is needed for advanced-stage disease, whereby improved results have been reported with the use of brentuximab. A worldwide database for BIA-ALCL and implants should be supported by local governments.
Use of the counter selectable marker PheS* for genome engineering in Staphylococcus aureus
Authors: Schuster Christopher F. , Howard Sophie A. , Gründling Angelika
Published: April 2019

The gold standard method for the creation of gene deletions in

Staphylococcus aureus

is homologous recombination using allelic exchange plasmids with a temperature-sensitive origin of replication. A knockout vector that contains regions of homology is first integrated into the chromosome of

S. aureus

by a single crossover event selected for at high temperatures (non-permissive for plasmid replication) and antibiotic selection. Next, the second crossover event is encouraged by growth without antibiotic selection at low temperature, leading at a certain frequency to the excision of the plasmid and the deletion of the gene of interest. To detect or encourage plasmid loss, either a beta-galactosidase screening method or, more typically, a counterselection step is used. We present here the adaptation of the counter-selectable marker pheS*, coding for a mutated subunit of the phenylalanine tRNA synthetase, for use in

S. aureus
. The PheS* protein variant allows for the incorporation of the toxic phenylalanine amino acid analogue para-chlorophenylalanine (PCPA) into proteins and the addition of 20–40 mM PCPA to rich media leads to drastic growth reduction for

S. aureus

and supplementing chemically defined medium with 2.5–5 mM PCPA leads to complete growth inhibition. Using the new allelic exchange plasmid pIMAY*, we delete the magnesium transporter gene mgtE in

S. aureus

USA300 LAC* (SAUSA300_0910/SAUSA300_RS04895) and RN4220 (SAOUHSC_00945) and demonstrate that cobalt toxicity in

S. aureus

is mainly mediated by the presence of MgtE. This new plasmid will aid the efficient and easy creation of gene knockouts in

S. aureus

.
Rhinovirus 2A is the predominant protease responsible for instigating the early block to gene expression encountered in infected cells
Authors: Smart David , Filippi Irene , Smalley Benjamin , Davies Donna , McCormick Christopher J.
Published: April 2019

Human rhinoviruses express 2 cysteine proteases, 2A and 3C, that are responsible for viral polyprotein processing. Both proteases also suppress host gene expression by inhibiting mRNA transcription, nuclear export and cap-dependent translation. However, the relative contribution that each makes in achieving this goal remains unclear. In this study we have compared both the combined and individual ability of the 2 proteases to shut downin cellulogene expression using a novel dynamic reporter system. Our findings show that 2A inhibits host gene expression much more rapidly than 3C. By comparing the activities of a representative set of proteases from the three different Human Rhinovirus (HRV) species, we also find variation in the speed at which host gene expression is suppressed. Our work highlights the key role that 2A plays in early suppression of the infected host cell response and shows that this can be influenced by natural variation in the activity of this enzyme.
Nanoaperture fabrication via colloidal lithography for single molecule fluorescence imaging
Authors: Jamiolkowski Ryan M. , Chen Kevin Y , Fiorenza Shane A. , Tate Alyssa M. , Pfeil Shawn H. , Goldman Yale E.
Published: April 2019

In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100-300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.
IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis
Authors: Chen Yun-Ching , Suresh Abhilash , Underbayev Chingiz , Sun Clare , Singh Komudi , Seifuddin Fayaz , Wiestner Adrian , Pirooznia Mehdi
Published: April 2019

In single-cell RNA-seq analysis, clustering cells into groups and differentiating cell groups by marker genes are two separate steps for investigating cell identity. However, results in clustering greatly affect the ability to differentiate between cell groups. We develop IKAP – an algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets, we demonstrate IKAP improves identification of major cell types and facilitates cell ontology curation.
dropClust2: An R package for resource efficient analysis of large scale single cell RNA-Seq data
Authors: Sinha Debajyoti , Sinha Pradyumn , Saha Ritwik , Bandyopadhyay Sanghamitra , Sengupta Debarka
Published: April 2019

DropClust leverages Locality Sensitive Hashing (LSH) to speed up clustering of large scale single cell expression data. It makes ingenious use of structure persevering sampling and modality based principal component selection to rescue minor cell types. Existing implementation of dropClust involves interfacing with multiple programming languagesviz. R, python and C, hindering seamless installation and portability. Here we present dropClust2, a complete R package that’s not only fast but also minimally resource intensive. DropClust2 features a novel batch effect removal algorithm that allows integrative analysis of single cell RNA-seq (scRNA-seq) datasets.

Availability and implementation

dropClust2 is freely available athttps://debsinha.shinyapps.io/dropClust/as an online web service and athttps://github.com/debsin/dropClustas an R package.
Establishing insect community composition using metabarcoding of soil samples, and preservative ethanol and homogenate from Malaise trap catches: surprising inconsistencies between methods
Authors: Marquina Daniel , Esparza-Salas Rodrigo , Roslin Tomas , Ronquist Fredrik
Published: April 2019

DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several alternative approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different sampling methods – homogenized Malaise trap samples (homogenate), preservative ethanol from the same samples, and soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is quite distinct from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol, with some exceptions that could be related to taxon-specific traits. For soil samples, highly degenerate COI primers pick up large amounts of non-target DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in MOTU content was found between the trap and the soil samples. Our results demonstrate that no metabarcoding approach is all-comprehensive in itself. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.
What, if anything, is the true neurophysiological significance of “rotational dynamics”?
Authors: Lebedev Mikhail A. , Ossadtchi Alexei , Mill Nil Adell , Armengol Urpí Núria , Cervera Maria R. , Nicolelis Miguel A.L.
Published: April 2019

Back in 2012, Churchland and his colleagues proposed that “rotational dynamics”, uncovered through linear transformations of multidimensional neuronal data, represent a fundamental type of neuronal population processing in a variety of organisms, from the isolated leech central nervous system to the primate motor cortex. Here, we evaluated this claim using Churchland’s own data and simple simulations of neuronal responses. We observed that rotational patterns occurred in neuronal populations when (1) there was a temporal shift in peak firing rates exhibited by individual neurons, and (2) the temporal sequence of peak rates remained consistent across different experimental conditions. Provided that such a temporal order of peak firing rates existed, rotational patterns could be easily obtained using a rather arbitrary computer simulation of neural activity; modeling of any realistic properties of motor cortical responses was not needed. Additionally, arbitrary traces, such as Lissajous curves, could be easily obtained from Churchland’s data with multiple linear regression. While these observations suggest that temporal sequences of neuronal responses could be visualized as rotations with various methods, we express doubt about Churchland et al.’s exaggerated assessment that such rotations are related to “an unexpected yet surprisingly simple structure in the population response”, which “explains many of the confusing features of individual neural responses.” Instead, we argue that their approach provides little, if any, insight on the underlying neuronal mechanisms employed by neuronal ensembles to encode motor behaviors in any species.
Characterizing macroinvertebrate community composition and abundance in freshwater tidal wetlands of the Sacramento-San Joaquin Delta
Authors: Hartman Rosemary , Sherman Stacy , Contreras Dave , Furler Alison , Kok Ryan
Published: April 2019

Restored tidal wetlands may provide important food web support for at-risk fish species in the Sacramento-San Joaquin Delta (Delta) of California, including Delta Smelt (Hypomesus transpacificus) and Chinook Salmon (Oncorhynchus tshawytscha). Since many tidal wetland restoration projects are planned or have recently been constructed in the Delta, understanding the diversity and variability of wetland invertebrates that are fish prey items is of increasing importance. During this study, two different invertebrate sampling techniques were tested (leaf packs and sweep nets) in four habitat types within three different wetland sites to evaluate which sampling technique provided the most reliable metric of invertebrate abundance and community composition. Sweep nets provided a better measure of fish food availability than leaf packs and were better able to differentiate between habitat types. Generalized linear models showed submerged and floating vegetation had higher abundance and species richness than channel habitats or emergent vegetation. Permutational multivariate analysis of variance showed significantly different communities of invertebrates in different habitat types and in different wetlands, and point-biserial correlation coefficients found a greater number of mobile taxa associated with sweep nets. There were more taxa associated with vegetated habitats than channel habitats, and one region had more taxa associated with it than the other two regions. These results suggest that restoration sites that contain multiple habitat types may enhance fish invertebrate prey diversity and resilience. However, the effect of habitat diversity must be monitored as restoration sites develop to assess actual benefits to at-risk fish species.
The significance of proximityin cluster initiatives
Authors: Lis Anna Maria
Published: April 2019

Purpose

The purpose of this paper is to analyse relations between geographical and competence proximity and development of cooperation in cluster initiatives.

Design/methodology/approach

The research was based on an original theoretical concept referring to the trajectory of the development of cooperative relations in cluster initiatives. The research was carried out in mid-2017, in four purposefully selected cluster initiatives. The research sample was 132 cluster enterprises. The main research strategy involved non-experimental models; the basic method of data collection was an online questionnaire.

Findings

The results indicated that the role of geographical and competence proximity depends on the level of cooperation in a cluster initiative. In both these dimensions, proximity was important during the initial stage of cluster development: to start cooperation between the members, however, when more mature forms of cooperation were undertaken, the factor of common location was not so crucial any longer. It was also recommended to maintain some competence distance between the partners.

Research limitations/implications

The main limitations referred to the static character of the data, the use of original measurement tools, which had not been tested before, the small and little differentiated research sample and the subjective nature of the research. The above-mentioned limitations should be viewed as a starting point for further empirical research.

Practical implications

Knowledge on the significance of geographical and competence proximity at various levels of cooperation in clusters is valuable for efficient management of a cluster and for higher competitiveness that it can achieve.

Originality/value

The research study contributes to the literature, which refers to the question of proximity in clusters through the analysis of relations between geographical and competence proximity and development of cooperation in cluster initiatives. The results of the research point out that the role of geographical and competence proximity evolves with the development of cooperation in cluster initiatives.
Olfactory cues and purchase behavior: consumer characteristics as moderators
Authors: Sandell Kaisa
Published: April 2019

Purpose

This study aims to examine the relationship between consumer characteristics and the effectiveness of olfactory cues on purchase behavior.

Design/methodology/approach

The theories of the effects of consumer decision-making, olfaction and sensory marketing on purchase behavior are applied using loyalty card data collected through an experiment. These data are analyzed using quantitative methods.

Findings

The presence of an olfactory cue has a positive impact on purchase behavior, as measured by product-category sales. Results indicate that in sales promotion, olfactory cues are most efficient in men who have hedonistic or quality-oriented decision-making styles.

Research limitations/implications

This paper is the first to study the effectiveness of olfactory cues on purchase behavior when the interactions between the individual characteristics of consumers are considered. The study broadens extant frameworks of sensory marketing by placing the consumer in the central position as the processor of sensory cues. The work pioneers the integration of consumer’s decision-making style (CDMS) as one of the moderating factors in the process.

Practical implications

The results encourage retailers and practitioners to consider CDMS – and not only gender or age – when using olfactory cues in sales promotions. Hopefully, this paper will inspire retailers to think of the more psychological aspects of consumer behavior and decision-making when planning their loyalty card systems.

Originality/value

This paper is the first to study the effectiveness of olfactory cues on purchase behavior when the interactions between the individual characteristics of consumers are considered. Addressing the decision-making style in addition to demographics is a novel approach, contrasting with earlier studies that merely focused on olfactory acuity.
Numerical investigations on particle separation in dynamic separators
Authors: Appadurai Arun , Raghavan Vasudevan
Published: April 2019

Purpose

Dynamic separator is an equipment having a rotor and static vanes and is used to separate solids from gas-solids flow based on size. Particle separation in a dynamic separator happens due to complex interchanges between multiple forces exerted in the separation zone. Currently, there is only limited knowledge concerning the working principles of separation. This paper aims to systematically study a dynamic separator using numerical models to get insights into particle separation.

Design/methodology/approach

The Lagrangian–Eulerian formulation is used to simulate gas-solid flow. Multiple frames of reference using stage interpolation are used to account for rotation. Periodic symmetry in the equipment is exploited to create a simplified numerical model. The predictions from the numerical model are compared against available experimental data.

Findings

The numerical results indicate that only when particle collision is included, the separation efficiency trend from the experiment is matched by numerical predictions. Further, it is shown that at the same range of rotor speeds where numerical results predict increased separation efficiency, the solid pressure due to particle collision also reaches its maximum value. The gas flow and particle behavior in the separator are explained in detail.

Originality/value

The importance of particle collision in separation is interesting because traditionally, particle separation is assumed to be influenced by three forces, namely, centrifugal force, drag force and gravity. The numerical results, however, point to the contribution by particle collision, in addition to the above three forces.
Supply chain integration in omni-channel retailing: a logistics perspective
Authors: Song Guang , Song Shaohua , Sun Luoyi
Published: April 2019

Purpose

The purpose of this paper is to apply resource-based theory to identify the relationships between logistics integration capability, supply chain integration (SCI), and performance in the context of omni-channel retailing (OCR).

Design/methodology/approach

An empirical study was conducted based on a mixed methodology that integrates survey research and focus group. In total, 243 retailers in China have been surveyed to examine the hypotheses of the proposed conceptual model, and focus group discussion has been applied to interpret the results and identify the critical concerns on the implementation of omni-channel (OC) strategy.

Findings

This study reveals that the information integration capability and organization integration capability in logistics management significantly affects SCI, while the integrated supply chain has a greater significant influence on financial performance than operational performance to OC retailers. Moreover, a firm’s characteristics can be regarded as contextual factors influencing performance in OCR.

Research limitations/implications

The authors obtained valuable insights for both academics and practitioners based on the findings. On the one hand, this is an early attempt to empirically study SCI of OCR, revealing the importance of a firm’s nature in the performance. Therefore, this study fills a current research gap. On the other hand, this research provides top managers of OC retailers, particularly supply chain managers, the awareness of the importance of improving of organizational integration and human-resource management capability. Additionally, this study proposes future research based on its limitations.

Originality/value

SCI is investigated in the context of OCR from a logistics perspective. Moreover, this study reveals that the human-resource management and organization management are the main concerns in the implementation of OCR.