bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of acquisition time on image quality and visibility of Yttrium-90 Positron Emission Tomography: A phantom study
Authors: Thareeboonchai T , Buranatrivedhaya N , Sriwiang W , Charoenphun P , Chuamsaamarkkee K
Published: June 2019

90Y has internal pair production which enables the imaging of this isotope with positron emission tomography (PET). The acquisition time is a crucial factor which strongly influence the image quality due to very small decay branch of this isotope. Hence, the aim of this study was to evaluate the impact of acquisition time on image quality and visibility of 90Y PET. A NEMA IEC body phantom with set of fillable spheres were filled with 90Y to generate a hot lesion to background ratio of 8:1. PET image was acquired by Philips Gemini TF PET/CT scanner with acquisition time per bed varied from 15, 30, 60 and 120 minutes. Image quality was assessed by percentage hot contrast (HC), image noise (CV), signal-to-noise (SNR) ratio and visibility (VS). From a result, hot spheres and their edges were more defined as acquisition time increased. Additionally, SNR and visibility were increased with acquisition time and sphere size as expected but percentage hot contrast was decreased. Thus, this can be explained by the growing of noise at shorter acquisition times and smaller spheres. In conclusion, 90Y PET imaging was feasible but the imaging protocol should be carefully considered particularly in small object.
Classification of urinary stones based on edge detection using semi-automatic threshold
Authors: Fitri L A , Warty Y , Haryanto F , Fauzi U , Latief F D E
Published: June 2019

Urinary stones are commonly differentiated into four types; calcium, struvite, cystine, and uric acid. While two of them, cysteine and struvite, could not be distinguished easily, in fact, they need a different kind of treatments. Significantly, the purpose of this study was to classify of urinary stones based on edge detection using a semi-automatic threshold. Five urinary stones were scanned using eight sources voltage. The source voltage was 65, 75, …, 115 KV. The consistent parameters were set at; 0.20 rotation, 13.89 µm resolution, and 1 mm aluminum. The reconstructed images were quantified in CT Analyser 1.16.4.1. The region of interest (ROI) was a circle with a diameter of 275 pixels as well as the semi-automatic threshold were drawn on the reconstructed image. Based on the Hounsfield unit (HU) analysis, there were three groups of urinary stone on source voltage of 85 KV. The first group (struvite) has consisted of stone number 1 (461.42) and 3 (489.05). The second group (cystine) has consisted of stone number 2 (55.08) and 5 (-233.41). The third group was stone number 4 (634.18). The edge detection using semi-automatic threshold can classify five urinary stones into three types; struvite, cystine, and the other group.
Comparison study between different contrast administration protocols for routine CT thorax examination in two tertiary centres
Authors: Ibrahim NR , Karim NK A. , Shuaib IL , Osman ND , Hashim S , Phuah HF
Published: June 2019

The purpose of this study was to evaluate the degree of contrast enhancement and image quality of computed tomography (CT) thorax examination using different contrast administration protocols. Data was retrospectively collected from 140 patients from two centres; 70 patients (Group A) from Advanced Medical and Dental Institute (IPPT), Universiti Sains Malaysia [19 males, 51 females; mean age ± standard deviation (SD) 53.6 ± 11.2 years; mean weight ± SD 54.04 ± 13.77 kg] using automatic bolus tracking (ABT) with weight-based contrast volume (WBV) administration, and 70 patients (Group B) from Hospital Pulau Pinang (HPP), Ministry of Health Malaysia [24 males, 46 females; mean age ± SD 54.5 ± 13.2 years] using fixed time-delay (FTD) with fixed contrast volume (FV) technique. The degree of enhancement was quantified by measuring Hounsfield unit (HU) values in different arteries and veins, and rated on a 5-point scale (1 = very poor, 5 = excellent) for qualitative assessment. The mean enhancement values in Group B were found to be higher than those in Group A (P < 0.001). There was no statistically significant difference between mean qualitative scores on a 5-point scale in both groups (P = 0.185). A weak correlation was seen between HU values with administered contrast volume (r = 0.1152). Overall, FTD with FV protocol was found to have higher degree of contrast enhancement for routine CT thorax examination. The qualitative assessment showed no significant difference between both protocols although higher mean grading in CT image quality was given by assessors for ABT with WBV technique.
Phantom design for quality control of Positron Emission Tomography/Computed Tomography (PET/CT) imaging
Authors: Mu’minah I A S , Ratianto  , Nurlely  , Soejoko D S
Published: June 2019

This research was aimed to develop an in-house phantom for quality control (QC) of image quality in PET/CT imaging. Wax and rice powder were mixed to produce tissue-equivalent materials characterized by Hounsfield Unit (HU). The in-house phantom was two circular cylinders with 20 cm in diameter and 10 cm in length which consists of six symmetric vessel pairs with varied diameters of 4.20, 6.20, 8.30, 9.80, 16.30, and 19.00 mm. Each measurement was performed using radioactivity concentrations of 18F-FDG with variation from 1 to 17 µCi/mL Images were displayed with the pixel size of 4 × 4 mm2. Image quality was evaluated in terms of conversion factor between full-width-half-maximum (FWHM) and actual diameter, and a pixel value for local uniformity of each object. Two types of phantoms have been designed which were liver-equivalent material (LEM) and muscle-equivalent material (MEM). HU and electron densities were (74.17 ± 1.48) HU and 3.396 × 1023 electron/m3 for LEM, while (20.27 ± 0.33) HU and 3.461 × 1023 electron/m3 for MEM, respectively. The conversion factor was initially high at 2.240 ± 0.07 for diameter 4.20 mm, falls to 0.99 ± 0.003 for diameter 9.80 mm, slowly decrease up to 0.82 ± 0.01 at diameter 16.30 mm, and then nearly constant at 0.82 with increasing diameter for both phantoms. The in-house phantom could be used to analyse the image quality performance of PET imaging with a tissue-specific material. The phantom design including the development of tissue-surrogate materials, size, and geometrical considerations of the features will be beneficial for innovating QC tools.
Quantitative metrics for assessing IMRT plan conformity: A virtual phantom study
Authors: Soh H S , Langmack K A , Morgan P S , Perkins A C
Published: June 2019

Intensity Modulated Radiation Therapy (IMRT) is a complex form of radiation delivery for the treatment of malignant tumours and other diseases. In IMRT treatment planning, quantitative assessment is crucial to measure and improve the plan quality and treatment delivery. The search for simple and universal quantitative metrics to assess IMRT treatment plan quality has been identified as important, but as yet not entirely successful. The aim of this study was to assess the IMRT treatment plan quality from the perspective of planning conformity. Conformity index (CI) was adopted to quantify the plan conformity. Virtual phantoms were developed for the initial conformity assessment, in order to form a basis for treatment plan inter-comparisons amongst the different IMRT techniques. A series of multi organs at risk (OARs) phantoms was developed to simulate the planning target volume (PTV) and OARs for different configurations. Conformity assessments were undertaken on all the IMRT plans generated using the virtual phantoms. This study has demonstrated the successful development of virtual phantoms to assess objectively and systematically the IMRT treatment plan conformity.
Inter-comparison of phantoms for CT numbers to relative electron density (RED)/physical density calibration and influence to dose calculation in TPS
Authors: Koniarova Irena
Published: June 2019

Six different phantoms (2x CIRS, 1x Agmeco, 1x QUASAR, 1x Gammex, 1x CatPhan) and Varian formulas were used to evaluate their suitability for CT numbers to relative electron density (RED) calibration in the treatment planning system at two centres using two CT scanners. The variability in calibration curve and the influence to dose calculation in the TPS were estimated for 6 MV and 18 MV. The presence of scattering material around inhomogeneities and influence of CT spectra (90 kV, 120 kV, 140 kV) were evaluated. All phantoms were found convenient for calibration except CatPhan where large deviations were observed for dense bone. Phantoms without scatter material around inhomogeneities should be used with caution. Varian formula slightly overestimates calibration curve in the region of 200 - 300 HU. The tolerance level of 10% suggested for RED during commissioning is reasonable as it can cause change in dose of 3% and 1.5% for 6 MV and 18 MV respectively as a very conservative estimate. Calibration curves should be acquired for all scanning protocols with different CT spectra.
Evaluation of image quality and radiation dose in kilovoltage cone beam computed tomography
Authors: Pinsaitong N , Asavaphatiboon S , Tangboonduangjit P
Published: June 2019

This study was to evaluate the image quality and radiation dose of kV-CBCT when varying mAs and reconstruction filter. The radiation dosimetry (CBDIw) and quality control of kV-CBCT image were done. Routine protocols in head, thorax, and pelvis protocols were performed as a reference image. Then the images were acquired with varied mAs, the other parameters were fixed. Each technique was reconstructed with different filter. The image quality in terms of low contrast and high contrast resolution including CBDIw were compared. The result found that the variation of mAs with auto filter affected low contrast resolution, but slightly effect high contrast resolution. When mAs increased, low contrast detectability increased. Decreasing one step of mAs (16.67%) kept in acceptable image quality and reduced about 15% of CBDIw. The smooth filter improved the low contrast resolution, but it decreased the high contrast resolution. While the sharp or ultra-sharp filter improved the high contrast resolution. In conclusion, the changing of mAs affects the low contrast resolution and CBDIW. While the reconstruction filter changed the both of low and high contrast resolution, but no effect to CBDIw. To optimize the image quality and radiation dose of routine protocols, mAs can reduce one step-down.
Occupational radiation dose during fluoroscopy guided interventional procedures at Institut Kanser Negara
Authors: Bohari A , Hashim S , Mustafa S N M
Published: June 2019

Fluoroscopy-guided interventional (FGI) tends to involve long-term procedures that increase the fluoroscopy time and the dose area product (DAP). Therefore, radiation protection is a major concern for interventional radiology staff. This study signifies the occupational and the radiation doses for interventional radiology staff, in particular, non-physician in order to clarify the current dose level for radiographers and nurses. The occupational doses were compared among interventional radiology staff in Institut Kanser Negara (IKN), Putrajaya, Malaysia where 230 patients underwent FGI procedures were observed in one-year. The occupational doses of interventional radiologist (IR), medical officer (MO), radiographer and nurse were recorded using two optically stimulated luminescence dosimeter (OSLD), one worn over and one under their protective aprons. The occupational dose (effective dose) indicated that the IR, MO, radiographer and nurse with double OSLDs were 9.82, 7.91, 6.42 and 6.02 mSv, respectively. The effective dose of IR, MO, radiographer and nurse were 7.63, 7.91, 6.42, 5.66 mSv, respectively using a single OSLD. It has shown a statistically significant difference in the effective dose of double worn OSLDs and one OSLD of (p < 0.05) for interventional radiology staff. In both methods, IR > MO > radiographer > nurse was the highest effective dose in the interventional radiology staff. However, the occupational dose of single OSLD was found to be lower than double OSLDs. It is highly recommended that interventional radiology staff to use double OSLDs during the FGI procedures in order to determine the occupational dose accurately.
The impact of pitch and modulation factor to Tomotherapy treatment plan optimization for motion target
Authors: Kartutik K. , Wibowo Wahyu E. , Pawiro Supriyanto A.
Published: June 2019

The influence on target motion resulted from the respiratory process, the pitch and modulation factor presented in Tomotherapy. This study was aimed to investigate the effect of motion management using CT-images obtained from the fusion process between the static and dynamic scanning mode on the CIRS Thorax Phantom. The images were created using axial and helical modes which amplitudes were varied from 10 mm, 15 mm, and 20 mm. Then, the organ structures were planned using TomoPlan TPS with the variation of pitch ranging from 0.25 to 0.5, and the modulation factor (MF) in the range 2 to 3. Furthermore, evaluation of radiotherapy planning was performed using dose parameters on target, the organ at risk, homogeneity index (HI), and mean leaf open time (LOT). Target volume for static mode was 3.53 cc, whereas target volume has changed to 10.9 cc, 10.3 cc, 16.1 cc for axial and 6.6 cc, 8.5 cc, 14.9 cc for helical scanning. The HI value obtained was less than 0.07 and lower HI was resulted for a larger MF. It means that the higher modulation factor values will provide a uniform dose distribution to the target and lower dose to the OAR. The greater value of pitch gave the greater mean LOT. The optimum parameters were at the pitch of 0.5 and MF of 3 based on the evaluation of mean LOT and HI. Axial scanning mode provides a larger target volume compared to a helical scanning mode. Therefore, the increment of the target volume in delineating organ should be considered.
Synthesis and characterization of fluoridated hydroxyapatite nano-powder via microwave irradiation method
Authors: Wisnugroho M , Nurlely  , Sari Y W
Published: June 2019

Fluoridated hydroxyapatite (FHA) occur in teeth and form the basis for application as a biomaterial. This work aims to synthesize and analyze the characteristic of FHA nano-powder with different degrees of fluoridation via microwave irradiation method. FHA nano-powder with a chemical formula of Ca10(PO4)6(OH2-x
)F
x
(where degrees of fluoridation, x values were selected equal to 0.7 and 1.3) were synthesized using a mixture of calcium hydroxide, diammonium hydrogen phosphate, and ammonium fluoride solutions by utilizing microwave with the variation of irradiation power. X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and energy dispersive X-ray (EDX) spectroscopy analysis techniques were utilized in order to evaluate the characteristic of synthesized FHA nano-powder. The XRD and FTIR results confirmed highly crystalline FHA powder with the carbonate peaks in the IR spectrum. Using a Scherrer formula, the average crystallite size was found to be 30 nm. The SEM and EDX results indicated various element composition and several morphologies with the lattice parameter increased along with irradiation power. FHA nano-powder could be synthesized via microwave irradiation method. The results from different kind of analysis illustrated that synthesized FHA nano-powder could fulfill the requirement of ASTM F1185-88 for used as biomaterial.
Synthesis and characterization of hydroxyapatite-chitosan composite in situ by microwave irradiation method
Authors: Ersal F M , Nurlely  , Sari Y W
Published: June 2019

Chitosan is a natural polysaccharide which has bioresorbable, biocompatible, and non-toxic properties. The combination between chitosan and hydroxyapatite will form a nanocomposite which improves its mechanical properties and can be applied as a bone implant material. The aim of this work was synthesis and characterization of composite hydroxyapatite-chitosan through in situ way utilized by microwave irradiation with time variation. A composite which was formed by hydroxyapatite and 2% chitosan solution through in situ way were irradiated by 270-watt power for 20-60 minutes with an interval of 10 minutes. The XRD results showed peak hydroxyapatite and chitosan. Meanwhile, the highest crystallite size was found in 50 minutes composite with value 20.87 nm. The FTIR spectroscopy identified the functional group of hydroxyapatite and chitosan (NH). Increase in irradiation time caused reduction of chitosan-based on the existence of NH composition. Highest mass was present at time 20 minutes which means the reduction of mass also occurred with increasing irradiation time. The SEM and EDX results indicated the hydroxyapatite has filled chitosan matrix. The presence of NH cluster proved that microwave irradiation method can be used to synthesize nanocomposites hydroxyapatite and chitosan. Increase in irradiation time caused a reduction of chitosan existence and its mass.
Shifting landscapes: decoupled urban irrigation and greenness patterns during severe drought
Authors: Quesnel Kimberly J , Ajami Newsha , Marx Andrew
Published: June 2019

Urban outdoor water conservation and efficiency offer high potential for demand-side management, but irrigation, greenness, and climate interlinks must be better understood to design optimal policies. To identify paired transitions during drought, we matched parcel-level water use data from smart, dedicated irrigation meters with high-spatial resolution, multispectral aerial imagery. We examined changes across 72 non-residential parcels using potable or recycled water for large landscape irrigation over four biennial summers (2010, 2012, 2014, and 2016) that encompassed a historic drought in California. We found that despite little change in irrigation levels during the first few years of the drought, parcel greenness deteriorated. Between summers 2010 and 2014, average parcel greenness decreased −61% for potable water irrigators and −56% for recycled water irrigators, providing evidence that vegetation could not reach its vigor from wetter, cooler years as the drought intensified with abnormally high temperatures. Between summers 2014–2016 as drought severity lessened, irrigation rates decreased significantly in line with high drought saliency, but greenness rebounded ubiquitously, on average +110% for potable water irrigators and +62% for recycled water irrigators, demonstrating climate-driven vegetation recovery as evaporation and plant evapotranspiration rates decreased. Transitions were similar for customers with both potable and recycled water; vegetation changes were dominated by the overarching climatic regime. As irrigation cannot always overcome drought conditions, which will become more severe under climate change, to maintain vegetation health, utilities and urban planners should consider the tradeoffs between providing green spaces and water scarcity. This includes evaluating the roles of climate-appropriate landscaping and adaptive reallocation of potable and recycled water resources to enhance water security. By addressing emerging themes in urban water management through analysis of data from forthcoming water metering and aerial imagery technologies, this research provides a unique perspective on water use, greenness, and drought linkages.
Assessment of core and lower limb muscles for static/dynamic balance in the older people: An ultrasonographic study
Authors: Özkal Özden , Kara Murat , Topuz Semra , Kaymak Bayram , Bakı Aysun , Özçakar Levent
Published: June 2019

Background

sufficient research has not been conducted to determine the role of core and lower limb muscles in providing balance in older people.

Objective

to investigate the relationships between the thickness of core/lower limb muscles and static/dynamic balance in older people.

Methods

the study included a total of 68 older people (≥ 65 years) and 68 gender-matched young subjects, aged 20–40 years. Balance, knee proprioception sense, regional and total muscle measurements and grip strength were assessed using a force platform system, isokinetic dynamometer, ultrasound imaging, bioelectrical impedance analysis and Jamar dynamometer, respectively.

Results

all the static (postural sway) parameters were higher and all the dynamic (limits of stability) parameters were lower in the older adults compared to the young adults (all P<0.05). The diaphragm was thicker and all the other muscles (except for multifidus and tibialis anterior) were thinner in the older group (all P<0.05). A higher error of knee proprioception sense was determined at 45 and 70 degrees in the older subjects (both P<0.001). According to the multivariate analyses, significant predictors for balance were age, gender, height, and rectus femoris, vastus intermedius and diaphragm muscle thicknesses in the older group, and age, gender, height, grip strength, and rectus abdominis, internal oblique, longissimus, tibialis anterior and soleus muscle thicknesses in the young group (all P<0.05).

Conclusions

the thickness of core/lower limb muscles are important determinants of balance in both older and young adults. These findings could provide a strong rationale for strengthening specific (abdominal and quadriceps) muscles to prevent falls and regional sarcopenia, and to improve posture/balance in the older population.

Clinical trial registration number

NCT03791047

Ethics committee approval

Hacettepe University Non-interventional Clinical Research Ethics Board. Decision number:GO 18/506-39
Mortality Risks Associated With Dual– and Poly–Tobacco-Product Use in the United States
Authors: Choi Kelvin , Inoue-Choi Maki , McNeel Timothy S , Freedman Neal D
Published: June 2019

Increasing numbers of adults in the United States use more than 1 tobacco product. Most use cigarettes in combination with other tobacco products. However, little is known about the all-cause and cancer-specific mortality risks of dual– and poly–tobacco-product use. We examined these associations by pooling nationally representative data from the 1991, 1992, 1998, 2000, 2005, and 2010 National Health Interview Surveys (n = 118,144). Mortality information was obtained through linkage to the National Death Index. Cigarette smokers who additionally used other tobacco products smoked as many if not more cigarettes per day than exclusive cigarette smokers. Furthermore, cigarette smokers who additionally used other tobacco products had mortality risks that were as high as and sometimes higher than those of exclusive cigarette smokers. As tobacco use patterns continue to change and diversify, investigators in future studies need to carefully assess the impact of noncigarette tobacco products on cigarette use and determine associated disease risks.
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data
Authors: Ye Chengzhong , Speed Terence P , Salim Agus
Published: June 2019

Motivation

Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed it affects the validity of the statistical analyses. Despite this, few current methods for differential expression (DE) analysis of scRNA-seq data explicitly model the process that gives rise to the dropout events. We develop DECENT, a method for DE analysis of scRNA-seq data that explicitly and accurately models the molecule capture process in scRNA-seq experiments.

Results

We show that DECENT demonstrates improved DE performance over existing DE methods that do not explicitly model dropout. This improvement is consistently observed across several public scRNA-seq datasets generated using different technological platforms. The gain in improvement is especially large when the capture process is overdispersed. DECENT maintains type I error well while achieving better sensitivity. Its performance without spike-ins is almost as good as when spike-ins are used to calibrate the capture model.

Availability and implementation

The method is implemented as a publicly available R package available from https://github.com/cz-ye/DECENT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Toward Control? The Prospects and Challenges of Typhoid Conjugate Vaccine Introduction
Authors: Carey Megan E , Diaz Zoey I , Broadstock Martin , Bailey Roderick , Bentsi-Enchill Adwoa D , Larson Heidi J
Published: June 2019

With a newly World Health Organization (WHO)–prequalified typhoid conjugate vaccine (TCV), Gavi funding for eligible countries, and a WHO policy recommendation for TCV use, now is the time for countries to introduce TCVs as part of an integrated typhoid control program, particularly in light of the increasing burden of antimicrobial resistance. Continued vaccine development efforts will lead to secure supply of low-cost vaccines, and ongoing vaccine studies will provide critical vaccine performance data and inform optimal deployment strategies, in both routine use and in outbreak settings. TCV programs should include thoughtful communication planning and community engagement to counter vaccine hesitancy.
Increased wave action promotes muscle performance but increasing temperatures cause a tenacity–endurance trade-off in intertidal snails (Nerita atramentosa)
Authors: Clayman Samuel , Seebacher Frank
Published: June 2019

Concurrent increases in wave action and sea surface temperatures increase the physical impact on intertidal organisms and affect their physiological capacity to respond to that impact. Our aim was to determine whether wave exposure altered muscle function in intertidal snails (Nerita atramentosa) and whether responses to wave action and temperature are plastic, leading to compensation for altered environmental conditions. We show that field snails from exposed shores had greater endurance and vertical tenacity than snails from matched protected shores (n = 5 pairs of shores). There were no differences in muscle metabolic capacities (strombine/lactate dehydrogenase, citrate synthase and cytochrome c oxidase activities) between shore types. Maximum stress (force/foot area) produced by isolated foot muscle did not differ between shore types, but foot muscle from snails on exposed shores had greater endurance. A laboratory experiment showed that vertical tenacity was greater in animals acclimated for 3 weeks to cool winter temperatures (15 C) compared to summer temperatures (25 C), but endurance was greater in snails acclimated to 25°C. Acclimation to water flow that mimicked wave action in the field increased vertical tenacity but decreased endurance. Our data show that increased wave action elicits a training effect on muscle, but that increasing sea surface temperature can cause a trade-off between tenacity and endurance. Ocean warming would negate the beneficial increase in tenacity that could render snails more resistant to acute impacts of wave action, while promoting longer term resistance to dislodgment by waves.
A human embryonic stem cell reporter line for monitoring chemical-induced cardiotoxicity
Authors: Tsai Su-Yi , Ghazizadeh Zaniar , Wang Hou-Jun , Amin Sadaf , Ortega Francis A , Badieyan Zohreh Sadat , Hsu Zi-Ting , Gordillo Miriam , Kumar Ritu , Christini David J , Evans Todd , Chen Shuibing
Published: June 2019

Aims 

Human embryonic stem cells (hESCs) can be used to generate scalable numbers of cardiomyocytes (CMs) for studying cardiac biology, disease modelling, drug screens, and potentially for regenerative therapies. A fluorescence-based reporter line will significantly enhance our capacities to visualize the derivation, survival, and function of hESC-derived CMs. Our goal was to develop a reporter cell line for real-time monitoring of live hESC-derived CMs.

Methods and results 

We used CRISPR/Cas9 to knock a mCherry reporter gene into the MYH6 locus of hESC lines, H1 and H9, enabling real-time monitoring of the generation of CMs. MYH6:mCherry+ cells express atrial or ventricular markers and display a range of cardiomyocyte action potential morphologies. At 20 days of differentiation, MYH6:mCherry+ cells show features characteristic of human CMs and can be used successfully to monitor drug-induced cardiotoxicity and oleic acid-induced cardiac arrhythmia.

Conclusion 

We created two MYH6:mCherry hESC reporter lines and documented the application of these lines for disease modelling relevant to cardiomyocyte biology.
IL-12 and Mucosal CD14+ Monocyte-Like Cells Induce IL-8 in Colonic Memory CD4+ T Cells of Patients With Ulcerative Colitis but not Crohn’s Disease
Authors: Chapuy Laurence , Bsat Marwa , Rubio Manuel , Sarkizova Sisi , Therrien Amélie , Bouin Mickael , Orlicka Katarzina , Weber Audrey , Soucy Geneviève , Villani Alexandra-Chloé , Sarfati Marika
Published: June 2019

Background and Aims

CD14+ mononuclear phagocytes [MNPs] and T cells infiltrate colon in ulcerative colitis [UC]. Here we investigated how CD14+ MNPs and the cytokines they produce shape the colonic effector T cell profile.

Methods

Colonic or mesenteric lymph node [mLNs] CD4+ T cells isolated from UC or Crohn’s disease [CD] patients were stimulated with cytokines or autologous CD14+ MNPs. Cytokine expression was assessed by intracytoplasmic staining and multiplex ELISA. Unsupervised phenotypic multicolour analysis of colonic CD14+ MNPs was performed using the FlowSOM algorithm.

Results

Among CD14+CD64+HLA-DR+SIRPα + MNPs, only the pro-inflammatory cytokine-producing CD163− subpopulation accumulated in inflamed UC colon and promoted mucosal IL-1β-dependent Th17, Th17/Th1, Th17/Th22 but not Th1 responses. Unsupervised phenotypic analysis of CD14+CD64+ MNPs segregated CD163− monocyte-like cells and CD163+ macrophages. Unexpectedly, IL-12, IL-1β and CD163−, but not CD163+, cells induced IL-8 expression in colonic CD4+ T cells, which co-expressed IFN-γ and/or IL-17 in UC and not CD. The CD163− monocyte-like cells increased the frequency of IL-8+IL-17+/−IFN-γ +/− T cells through IL-1β and IL-12. Finally, colonic IL-8+ T cells co-expressing GM-CSF, TNF-α and IL-6 were detected ex vivo and, promoted by IL-12 in the mucosa and mLNs in UC only.

Conclusions

Our findings established a link between monocyte-like CD163− MNPs, IL-12, IL-1β and the detection of colonic memory IL-8-producing CD4+ T cells, which might all contribute to the pathogenesis of UC.
It is a medical emergency! Act fast: a case report of painless aortic dissection
Authors: Yanamadala Anusha , Kumar Sanjay , Lichtenberg Robert
Published: June 2019

Background

A painless presentation of aortic dissection is rare in about 5% of cases. A few case reports discussed about involvement of coronary arteries causing bradycardia. In our case, we are presenting a rare presentation of aortic dissection with initial presentation as bradycardia without involvement of coronary arteries and without cardiac symptoms.

Case summary

A 56-year-old man with history of hypertension presented with acute onset of altered mental status and right hand numbness. Initial vital signs were remarkable for bradycardia with heart rate 36/min. Physical exam was only significant for decreased sensation for light touch on right hand. Electrocardiogram showing marked sinus bradycardia. Initial computed tomography (CT) head did not show any acute abnormalities. On Day 2, patient complained of new weakness in left upper extremity. On exam, he had dysmetria, left upper extremity drift and cold to touch. Blood pressure was significantly different in both arms with 141/83 mmHg on right and 44/23 mmHg on left. He underwent immediate CT angiography chest showing Type 1 aortic dissection with extension into the brachiocephalic artery and right common carotid artery (RCCA) with thrombosis in RCCA. Patient was emergently taken for surgical repair of aortic dissection and resuspension of aortic valve.

Discussion

In our case, the initial presentation of aortic dissection included isolated sinus bradycardia without cardiac symptoms and no evidence for atrioventricular block. The mechanism may have been involvement in the arterial supply of the carotid body receptors. Patients with coexisting symptoms such as bradycardia and neurological deficits should be evaluated for aortic dissection.
Electrically vs. imaging-guided left ventricular lead placement in cardiac resynchronization therapy: a randomized controlled trial
Authors: Stephansen Charlotte , Sommer Anders , Kronborg Mads Brix , Jensen Jesper Møller , Nørgaard Bjarne Linde , Gerdes Christian , Kristensen Jens , Jensen Henrik Kjærulf , Fyenbo Daniel Benjamin , Bouchelouche Kirsten , Nielsen Jens Cosedis
Published: June 2019

Aims

To test in a double-blinded, randomized trial whether the combination of electrically guided left ventricular (LV) lead placement and post-implant interventricular pacing delay (VVd) optimization results in superior increase in LV ejection fraction (LVEF) in cardiac resynchronization therapy (CRT) recipients.

Methods and results

Stratified according to presence of ischaemic heart disease, 122 patients were randomized 1:1 to LV lead placement targeted towards the latest electrically activated segment identified by systematic mapping of the coronary sinus tributaries during CRT implantation combined with post-implant VVd optimization (intervention group) or imaging-guided LV lead implantation by cardiac computed tomography venography, 82Rubidium myocardial perfusion imaging and speckle tracking echocardiography targeting the LV lead towards the latest mechanically activated non-scarred myocardial segment (control group). Follow-up was 6 months. Primary endpoint was absolute increase in LVEF. Additional outcome measures were changes in New York Heart Association class, 6-minute walk test, and quality of life, LV reverse remodelling, and device related complications. Analysis was intention-to-treat. A larger increase in LVEF was observed in the intervention group (11 ± 10 vs. 7 ± 11%; 95% confidence interval 0.4–7.9%, P = 0.03); when adjusting for pre-specified baseline covariates this difference did not maintain statistical significance (P = 0.09). Clinical response, LV reverse remodelling, and complication rates did not differ between treatment groups.

Conclusion

Electrically guided CRT implantation appeared non-inferior to an imaging-guided strategy considering the outcomes of change in LVEF, LV reverse remodelling and clinical response. Larger long-term studies are warranted to investigate the effect of an electrically guided CRT strategy.
Development of de novo resistance in Salmonella Typhimurium treated with antibiotic combinations
Authors: Dawan Jirapat , Uddin Md Jalal , Ahn Juhee
Published: June 2019

This study was designed to evaluate the evolution of antibiotic resistance in Salmonella enterica serovar Typhimurium treated with the combination of antibiotics. The experimental evolution of antibiotic resistance of S. Typhimurium was evaluated either under single antibiotic (kanamycin, KAN; penicillin, PEN; erythromycin, ERY) or in combination of two antibiotics (KAN + PEN or KAN + ERY) as measured by fractional inhibitory concentrations (FICs), stepwise resistance selection, cross-resistance evaluation, resistance fitness and relative gene expression. KAN + PEN and KAN + ERY showed the synergistic effect against S. Typhimurium (FIC index < 0.5). KAN + ERY delayed the induction of de novo mutations in S. Typhimurium. The cross-resistance of S. Typhimurium to all antibiotics except ERY and tetracycline was observed in KAN and PEN alone. The fitness cost was lower in single antibiotic treatments than combinations. The highest relative fitness was 0.91 in PEN, followed by KAN (0.84) and ERY (0.78), indicating the low fitness costs in single antibiotic treatments. The overexpression of efflux pump-related genes (acrA and acrB), outer membrane-related gene (ompC) and adherence-related gene (csgD) were observed in the single antibiotic treatments. Our results suggest that KAN + PEN and KAN + ERY could be used as a potential therapeutic treatment by decreasing the evolution of antibiotic resistance in S. Typhimurium and reusing conventional antibiotics.
Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling
Authors: Lozano-Fernandez Jesus , Giacomelli Mattia , Fleming James F , Chen Albert , Vinther Jakob , Thomsen Philip Francis , Glenner Henrik , Palero Ferran , Legg David A , Iliffe Thomas M , Pisani Davide , Olesen Jørgen
Published: June 2019

The relationships of crustaceans and hexapods (Pancrustacea) have been much discussed and partially elucidated following the emergence of phylogenomic data sets. However, major uncertainties still remain regarding the position of iconic taxa such as Branchiopoda, Copepoda, Remipedia, and Cephalocarida, and the sister group relationship of hexapods. We assembled the most taxon-rich phylogenomic pancrustacean data set to date and analyzed it using a variety of methodological approaches. We prioritized low levels of missing data and found that some clades were consistently recovered independently of the analytical approach used. These include, for example, Oligostraca and Altocrustacea. Substantial support was also found for Allotriocarida, with Remipedia as the sister of Hexapoda (i.e., Labiocarida), and Branchiopoda as the sister of Labiocarida, a clade that we name Athalassocarida (=”nonmarine shrimps”). Within Allotriocarida, Cephalocarida was found as the sister of Athalassocarida. Finally, moderate support was found for Hexanauplia (Copepoda as sister to Thecostraca) in alliance with Malacostraca. Mapping key crustacean tagmosis patterns and developmental characters across the revised phylogeny suggests that the ancestral pancrustacean was relatively short-bodied, with extreme body elongation and anamorphic development emerging later in pancrustacean evolution.
Wartime Rupture and Reconfiguration in French Family Life: Experience and Legacy
Authors: Dodd Lindsey
Published: June 2019

‘Wartime Rupture and Reconfiguration in French Family Life: Experience and Legacy’, by Lindsey Dodd Family separation is a widespread consequence of war, particularly war which targets civilian populations. This article draws on oral history narratives recorded by the author with French people who became child evacuees or refugees in France during the Second World War. All ended up in the département of the Creuse, in central France, hosted by people with whom they had no previous connection. Experiences of family rupture and reconfiguration have been considered by psychologists, but rarely by historians. As children live their lives mainly in the domestic sphere, close examination of their wartime worlds gives insight into the indirect effects of conflict on the youngest members of society. I argue that the experience of the Second World War must be understood as profound and lasting, even among those who did not experience combat, persecution or aggression directly. My case studies complicate understandings of family separation as a wholly negative experience for children in war, without compromising sensitivity to the nuances of individual difference. And I show the power of subjective retrospective sources to reveal the legacy of war inside commemorative actions situated well below national levels, which go unacknowledged in studies focused on the ‘collective’ or ‘cultural’ memory of the period.
Developmental and Evolutionary Allometry of the Mammalian Limb Skeleton
Authors: Cooper Kimberly L
Published: June 2019

The variety of limb skeletal proportions enables a remarkable diversity of behaviors that include powered flight in bats and flipper-propelled swimming in whales using extremes of a range of homologous limb architectures. Even within human limbs, bone lengths span more than an order of magnitude from the short finger and toe bones to the long arm and leg bones. Yet all of this diversity arises from embryonic skeletal elements that are each a very similar size at formation. In this review article, I survey what is and is not yet known of the development and evolution of skeletal proportion at multiple hierarchical levels of biological organization. These include the cellular parameters of skeletal elongation in the cartilage growth plate, genes associated with differential growth, and putative gene regulatory mechanisms that would allow both covariant and independent evolution of the forelimbs and hindlimbs and of individual limb segments. Although the genetic mechanisms that shape skeletal proportion are still largely unknown, and most of what is known is limited to mammals, it is becoming increasingly apparent that the diversity of bone lengths is an emergent property of a complex system that controls elongation of individual skeletal elements using a genetic toolkit shared by all.
The Road to Nonprofit Diversity and Inclusion
Authors: Walker Vernetta
Published: June 2019

Leadership at the board and executive levels across the nonprofit sector remains predominantly composed of white individuals, despite an increasingly diverse society. Research documents distinct benefits associated with diversity and inclusion, but efforts to move the dial have fallen short. This article explores how voluntary associations can prioritize racial/ethnic equity in their governance and provides specific steps for the examination of culture, practices, and processes required to operationalize change.

There are a variety of professional societies and associations, also known as business leagues, established under the Internal Revenue Code. To be exempt, these organizations must be devoted to improving an industry or profession, as distinguished from performing particular services for individuals, and when successful they serve to improve the economic and social well-being of the entire nation.
How People Judge the Usability of a Desktop Graphic User Interface at Different Time Points: Is there Evidence for Memory Decay, Recall Bias or Temporal Bias?
Authors: Boyd Kyle , Bond Raymond , Vertesi Attila , Dogan Huseyin , Magee Justin
Published: June 2019

The System Usability Scale (SuS) survey is a widely respected tool for measuring usability. Generally, a SuS score is administered directly after a usability test to assess the usability and user experience of digital products. However, some researchers have used SuS as a survey as part of longitudinal ‘in the wild’ trials where SuS is often completed some period after the trial. The aim of this research was to determine if a participant’s memory of a product’s usability would change if a SuS survey was administered at different times after a test. Hence, we sought to understand if recalling the usability of a digital technology was affected by temporal bias or memory decay. This paper includes results and findings from two studies, study 1 involved evaluating a web application and study 2 involved evaluating a virtual learning environment. Collectively the two studies had 212 participants (n = 212). The findings conclude that there is no significant change of the user’s recollection of the usability of digital product as evidenced by an analysis of users who completed multiple SuS surveys over a short term period of 3 weeks or over an extended period of time of 6 months.

RESEARCH HIGHLIGHTS

The system usability scale is used to test for memory decay and temporal bias in judging the user experience of technologies at different time points. 212 participants took part in two studies ranging from 3 weeks to 6 months. There is no evidence that there is a temporal bias or memory decay when users complete a SuS survey at the two different time points of 3 weeks and 6 months.
Cost-aware active learning for named entity recognition in clinical text
Authors: Wei Qiang , Chen Yukun , Salimi Mandana , Denny Joshua C , Mei Qiaozhu , Lasko Thomas A , Chen Qingxia , Wu Stephen , Franklin Amy , Cohen Trevor , Xu Hua
Published: June 2019

Objective

Active Learning (AL) attempts to reduce annotation cost (ie, time) by selecting the most informative examples for annotation. Most approaches tacitly (and unrealistically) assume that the cost for annotating each sample is identical. This study introduces a cost-aware AL method, which simultaneously models both the annotation cost and the informativeness of the samples and evaluates both via simulation and user studies.

Materials and Methods

We designed a novel, cost-aware AL algorithm (Cost-CAUSE) for annotating clinical named entities; we first utilized lexical and syntactic features to estimate annotation cost, then we incorporated this cost measure into an existing AL algorithm. Using the 2010 i2b2/VA data set, we then conducted a simulation study comparing Cost-CAUSE with noncost-aware AL methods, and a user study comparing Cost-CAUSE with passive learning.

Results

Our cost model fit empirical annotation data well, and Cost-CAUSE increased the simulation area under the learning curve (ALC) scores by up to 5.6% and 4.9%, compared with random sampling and alternate AL methods. Moreover, in a user annotation task, Cost-CAUSE outperformed passive learning on the ALC score and reduced annotation time by 20.5%–30.2%.

Discussion

Although AL has proven effective in simulations, our user study shows that a real-world environment is far more complex. Other factors have a noticeable effect on the AL method, such as the annotation accuracy of users, the tiredness of users, and even the physical and mental condition of users.

Conclusion

Cost-CAUSE saves significant annotation cost compared to random sampling.
Stage-Specific and Seasonal Induction of the Overwintering Morph of Spotted Wing Drosophila (Diptera: Drosophilidae)
Authors: Leach Heather , Stone Jaclyn , Van Timmeren Steven , Isaacs Rufus
Published: June 2019

Drosophila suzukii Matsumura (Diptera: Drosophilidae) is currently a major pest management challenge in berry and cherry production. This species has a winter morph phenotype with longer wings and increased melanization associated with survival in colder conditions. Measurements of wing morphology in Michigan D. suzukii collected during 2016 and 2017 showed that induction of this morph began in September and increased into December, correlated with decreasing temperature and day length. Importantly, we found that wing length increases along a continuous scale and there is overlap between the two morph types. We tested whether temperature or photoperiod elicited this phenotypic change using a factorial design with each preadult lifestage held at 10 or 25°C and 16:8 or 8:16 L:D. Our results support temperature as the main driver of transition to the winter morph for all immature stages. Comparing the reproductive capacity of winter morph flies in cold conditions and when previously acclimated to warm conditions, flies with the acclimation experience laid comparable numbers of eggs as the summer morphs at 25°C, indicating that winter morphs can reproduce after surviving cold periods. These results highlight the ability of D. suzukii to adapt to changing temperature conditions, allowing it to survive cold and also exploit warmer periods to build populations when conditions allow.