bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation and preliminary characterization of sago flour and semi refined kappa carrageenan-based biocomposite film incorporated with coconut crabs chitosan nanoparticles
Authors: Rasulu H , Praseptiangga D , Joni I M , Ramelan A H
Published: October 2019

The use of nano-sized chitosan natural polymers served as biopolymers containing antimicrobial substances is promising to be utilized as preservatives that could maintain quality and extend the shelf-life of foods.The objective of this research was to evaluate the effect of chitosan coconut crabs nanoparticles (CsCC NPs) incorporation to the sago flour (SF) and semi-refined kappa carrageenan (SRKC) based biocomposite film on their mechanical and barrier properties. The CsCC NPs suspension was prepared by the beads-milling method. The CCCsNPs was incorporated with various concentration (0, 1, 2, 3%) and introduced into 2 g of SF and SRKC (2:1) with the addition of Carboxymethyl Cellulose(CMC) and glycerol (2: 1) as a plasticizer. The results showed that the brightness value (L*) of prepared biocomposite film was at the range of 59.21-60.44. The thickness, tensile strength, and elongation at break of the films were at the range of 0.082-0.172mm, 3.22-8.09 MPa, 18.49-24.25%, respectively, while the water vapor permeability (WVP) of the films were at a range of 3.61-7.99 gm/m2h−1kPa−1. It is indicated that the incorporation of CsCC NPs on the investigated biocomposite film could improve the films’ properties and have enormous potential to be developed as biodegradable active packaging.
Implementation of organic farming system and consumer satisfaction
Authors: Suswadi  , Rahayu E S , Harisudin M , Anantanyu S
Published: October 2019

The research objectives are: (1) to analyse the implementation of organic farming of Boyolali farmers. (2) to find out consumer satisfaction level of organic rice in Surakarta and Boyolali.The research location was determined purposively in Dlingo Village, Boyolali and Surakarta. This research used qualitative method with interactive data analysis model of Miles and Huberman and descriptive analysis. The research resulted in the application of organic farming systems by the farmers in the following ways: (a) the selection of locations not contaminated with chemicals, (b) appropriate local types of rice plant, (c) programming of appropriate crop rotation, (d) processing soil with tools not contaminated with chemicals, (e) intermitten irrigation, (f) use of fermented compost, (g) control of pests with natural enemies and vegetable pesticides, (h) appropriate post-harvest handling, and (i) organic rice marketed with the packaging that attaches the SNI organiklogo. The results of research on the level of consumer satisfaction with organic rice are: (a) the quality of the organic rice is 90.41% meaning that the consumers are satisfied; (b) the availability of the organic rice is 73% meaning that the consumers are satisfied; and (c) the price of the organic rice is 60% meaning that the consumers are dissatisfied.
Analysis of potential featured agriculture commodities and processed products in Sragen Regency
Authors: Setyowati N , Ardianto D T , Khomah I , Widiyanti E
Published: October 2019

This research aimed to identify the mapping of potential featured agricultural commodities and processed products in Sragen Regency. Data analysis used Exponential Comparative Method (ECM) and Borda Method. ECM Method showed that featured agriculture commodities at subdistrict level in Sragen Regency are Paddy, Pomelo Oranges, Corn, Banana Seedlings, Chili, Peanut, Melon, Watermelon, Sugarcane, Cassava, Arrowroot, Soybean, Fish, etc. Borda Method showed that the five featured agriculture commodities in Sragen Regency are Paddy with a value of 13, 600.56; Corn 4, 918.36; Sugar Cane 3, 313.95; Pamelo Orange 1, 466.64; and Peanut 904.64. Borda Method also showed that the featured processed products in the subdistrict level at Sragen Regency are Intip, Processed Fish, Rice, Marneng, Tempe Benguk, Ampyang, Emping Garut, Tofu, Keripik Tempe, Etawa Milk, Cornmeal, and others. Borda Method showed that the fifth rank featured processed products in Sragen Regency are Rice with the value of 7, 530.2; Marneng 1, 683; Emping Garut 1, 241.99; Keripik Tempe 957.65; and Tempe Benguk 713.99. It means that the featured agriculture commodities in Sragen Regency feasible to economic development priority in order to support community economic welfare are Rice, Corn, Garut, Pamelo Orange, and Peanut. Meanwhile, the featured processed products in Sragen Regency feasible to develop are Rice, Marneng, Emping Garut, Keripik Tempe, and Tempe Benguk.
The Influence of Loading Force on Ultrasonic Drilling Garnet Ferrite
Authors: Pei T H , Zhang X F , Wang Q , Zhang T Y , Zhong Y , Zhu Y Y
Published: October 2019

In order to achieve high precision microholes of garnet ferrite, the rotary ultrasonic assisted machining and the tool load matching system were employed. An ultrasonic precise microholes technology experiment platform was built to machine garnet ferrite materials. A series of drilling experiments to machine garnet ferrite were presented in this paper, which were used to explore the influence of cutting force on tool wear. And the holes’ exit aperture and wall surface roughness were applied to be evaluation parameters to explore the effect of loading force on machining quality. As a result, tool wear is aggravates as cutting force increases. And loading force shows different influence tendency on exit aperture size precision and wall surface roughness, the selection of proper loading force does good to control exit aperture size and hole wall surface roughness effictively.
‘The Great Britain of the South’: the Law of Contract in Early Colonial New Zealand
Authors: Swain Warren
Published: October 2019

Some nineteenth century writers like the Scottish born poet William Golder, used the term ‘the Great Britain of the south’ as a description of his new home. He was not alone in this characterisation. There were of course other possible perspectives, not least from the Māori point of view, which these British writers inevitably fail to capture. A third reality was more specific to lawyers or at least to those caught up in the legal system. The phrase ‘the Great Britain of the south’ fails to capture the complexity of the way that English law was applied in the early colony. The law administered throughout the British Empire reflected the common law origins of colonial legal systems but did not mean that the law was identical to that in England. Scholars have emphasised the adaptability of English law in various colonial settings. New Zealand contract law of this time did draw on some English precedents. The early lawyers were steeped in the English legal tradition. At the same time, English authorities were used with a light touch. The legal and social framework within which contract law operated was also quite different. This meant, for example, that mercantile juries were important in adapting the law to local conditions. Early New Zealand contract law provides a good example of both the importance of English law in a colonial setting and its adaptability.
Spray Drift from Three Airblast Sprayer Technologies in a Modern Orchard Work Environment
Authors: Kasner Edward J , Fenske Richard A , Hoheisel Gwen A , Galvin Kit , Blanco Magali N , Seto Edmund Y W , Yost Michael G
Published: October 2019

Pesticide spray drift represents an important exposure pathway that may cause illness among orchard workers. To strike a balance between improving spray coverage and reducing drift, new sprayer technologies are being marketed for use in modern tree canopies to replace conventional axial fan airblast (AFA) sprayers that have been used widely since the 1950s. We designed a series of spray trials that used mixed-effects modeling to compare tracer-based drift volume levels for old and new sprayer technologies in an orchard work environment. Building on a smaller study of 6 trials (168 tree rows) that collected polyester line drift samples (n = 270 measurements) suspended on 15 vertical masts downwind of an AFA sprayer application, this study included 9 additional comparison trials (252 tree rows; n = 405 measurements) for 2 airblast tower sprayers: the directed air tower (DAT) and the multi-headed fan tower (MFT). Field-based measurements at mid (26 m) and far (52 m) distances showed that the DAT and MFT sprayers had 4–15 and 35–37% less drift than the AFA. After controlling for downwind distance, sampling height, and wind speed, model results indicated that the MFT [−35%; 95% confidence interval (CI): −22 and −49%; P < 0.001] significantly reduced drift levels compared to the AFA, but the DAT did not (−7%; 95% CI: −19 and 6%; P = 0.29). Tower sprayers appear to be a promising means by which to decrease drift levels through shorter nozzle-to-tree canopy distances and more horizontally directed aerosols that escape the tree canopy to a lesser extent. Substitution of these new technologies for AFA sprayers is likely to reduce the frequency and magnitude of pesticide drift exposures and associated illnesses. These findings, especially for the MFT, may fit United States Environmental Protection Agency’s Drift Reduction Technology (DRT) one-star rating of 25–50% reduction. An ‘AFA buyback’ incentive program could be developed to stimulate wider adoption of new drift-reducing spray technologies. However, improved sprayer technologies alone do not eliminate drift. Applicator training, including proper sprayer calibration and maintenance, and application exclusion zones (AEZs) can also contribute to minimizing the risks of drift exposure. With regard to testing DRTs and establishing AEZs, our study findings demonstrate the need to define the impact of airblast sprayer type, orchard architecture, sampling height, and wind speed.
Clinical Outcomes and Satisfaction following Neuropsychological Assessment for Adults: A Community Hospital Prospective Quasi-Experimental Study
Authors: Lanca Margaret , Giuliano Anthony J , Sarapas Casey , Potter Anya I , Kim Michelle S , West Adrienne L , Chow Clifton M
Published: October 2019

Objective

Patients and other stakeholders generally report high satisfaction with neuropsychological evaluations (NPEs), but no research has examined effects of cognitive, emotional, and other factors that often prompt evaluations. A prospective, quasi-experimental study was conducted to examine self-reported cognitive and psychiatric symptoms, self-efficacy, motivation, and satisfaction following a NPE.

Method

Participants from a neuropsychology clinic who were diagnosed with AD/HD and/or a DSM-IV mood disorder based on a NPE were included, and excluded if diagnosed with dementia or failure on performance validity tests.

Results

To examine whether a NPE with an interventional feedback session was associated with outcomes, changes from baseline to post-feedback session were examined with repeated-measures analysis of variance. Pearson correlations determined whether changes in hypothesized mechanisms (i.e., self-efficacy, goal importance and confidence ratings, and use of cognitive strategies) were related to changes in cognitive or psychiatric symptom severity. At follow-up, participants reported reductions in psychiatric (change in Brief Symptom Inventory depression: M = -2.8, SD = 4.4, range = −11 to 8, ${\eta}_p^2$=.30; anxiety: M = 3.2, SD = 6.6, range = −21 to 10, ${\eta}_p^2$ = .20) and cognitive symptoms (change in Multiple Ability Self-Report Questionnaire attention: M = −0.3, SD = 0.5, range = −1.6 to 0.5, ${\eta}_p^2$ = .31; verbal memory: M = −0.3, SD = 0.5, range = −1.1 to 0.5, ${\eta}_p^2$ = .24; language: M = −0.4, SD = 0.4, range = −1.3 to 0.4, ${\eta}_p^2$ = .48), and improved cognition (change in Meta-Memory Questionnaire ability: M = 4.4,SD = 6.2, range = −10 to 16, ${\eta}_p^2$ = .35; contentment: M = 4.3, SD = 4.5, range = −7 to 14, ${\eta}_p^2$ = .49). Participants reported increased self-efficacy for general and evaluation-specific goals. Increased goal-specific self-efficacy was associated with large reductions in psychiatric symptoms.

Conclusions

Participants reported high levels of satisfaction with the NPE. Results support the clinical utility of NPE and feedback, and underscore the importance of individualized goal setting as part of the evaluation process.
CRISPR therapy towards an HIV cure
Authors: Herrera-Carrillo Elena , Gao Zongliang , Berkhout Ben
Published: October 2019

Tools based on RNA interference (RNAi) and the recently developed clustered regularly short palindromic repeats (CRISPR) system enable the selective modification of gene expression, which also makes them attractive therapeutic reagents for combating HIV infection and other infectious diseases. Several parallels can be drawn between the RNAi and CRISPR-Cas9 platforms. An ideal RNAi or CRISPR-Cas9 therapeutic strategy for treating infectious or genetic diseases should exhibit potency, high specificity and safety. However, therapeutic applications of RNAi and CRISPR-Cas9 have been challenged by several major limitations, some of which can be overcome by optimal design of the therapy or the design of improved reagents. In this review, we will discuss some advantages and limitations of anti-HIV strategies based on RNAi and CRISPR-Cas9 with a focus on the efficiency, specificity, off-target effects and delivery methods.
The effect of tissue composition on gene co-expression
Authors: Zhang Yun , Cuerdo Jonavelle , Halushka Marc K , McCall Matthew N
Published: October 2019

Variable cellular composition of tissue samples represents a significant challenge for the interpretation of genomic profiling studies. Substantial effort has been devoted to modeling and adjusting for compositional differences when estimating differential expression between sample types. However, relatively little attention has been given to the effect of tissue composition on co-expression estimates. In this study, we illustrate the effect of variable cell-type composition on correlation-based network estimation and provide a mathematical decomposition of the tissue-level correlation. We show that a class of deconvolution methods developed to separate tumor and stromal signatures can be applied to two component cell-type mixtures. In simulated and real data, we identify conditions in which a deconvolution approach would be beneficial. Our results suggest that uncorrelated cell-type-specific markers are ideally suited to deconvolute both the expression and co-expression patterns of an individual cell type. We provide a Shiny application for users to interactively explore the effect of cell-type composition on correlation-based co-expression estimation for any cell types of interest.
Combining clinical and molecular data in regression prediction models: insights from a simulation study
Authors: De Bin Riccardo , Boulesteix Anne-Laure , Benner Axel , Becker Natalia , Sauerbrei Willi
Published: October 2019

Data integration, i.e. the use of different sources of information for data analysis, is becoming one of the most important topics in modern statistics. Especially in, but not limited to, biomedical applications, a relevant issue is the combination of low-dimensional (e.g. clinical data) and high-dimensional (e.g. molecular data such as gene expressions) data sources in a prediction model. Not only the different characteristics of the data, but also the complex correlation structure within and between the two data sources, pose challenging issues. In this paper, we investigate these issues via simulations, providing some useful insight into strategies to combine low- and high-dimensional data in a regression prediction model. In particular, we focus on the effect of the correlation structure on the results, while accounting for the influence of our specific choices in the design of the simulation study.
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies
Authors: Yang Qingxia , Hong Jiajun , Li Yi , Xue Weiwei , Li Song , Yang Hui , Zhu Feng
Published: October 2019

Unwanted experimental/biological variation and technical error are frequently encountered in current metabolomics, which requires the employment of normalization methods for removing undesired data fluctuations. To ensure the ‘thorough’ removal of unwanted variations, the collective consideration of multiple criteria (‘intragroup variation’, ‘marker stability’ and ‘classification capability’) was essential. However, due to the limited number of available normalization methods, it is extremely challenging to discover the appropriate one that can meet all these criteria. Herein, a novel approach was proposed to discover the normalization strategies that are consistently well performing (CWP) under all criteria. Based on various benchmarks, all normalization methods popular in current metabolomics were ‘first’ discovered to be non-CWP. ‘Then’, 21 new strategies that combined the ‘sample’-based method with the ‘metabolite’-based one were found to be CWP. ‘Finally’, a variety of currently available methods (such as cubic splines, range scaling, level scaling, EigenMS, cyclic loess and mean) were identified to be CWP when combining with other normalization. In conclusion, this study not only discovered several strategies that performed consistently well under all criteria, but also proposed a novel approach that could ensure the identification of CWP strategies for future biological problems.
AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation
Authors: Rawat Puneet , Prabakaran R , Kumar Sandeep , Gromiha M Michael
Published: October 2019

Motivation

Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases, biotechnology and biomaterial sciences. A majority of sequence-structural properties known for their mechanistic roles in protein aggregation do not correlate well with the aggregation kinetics. This limits the practical utility of predictive algorithms.

Results

We analyzed experimental data on 183 unique single point mutations that lead to change in aggregation rates for 23 polypeptides and proteins. Our initial mathematical model obtained a correlation coefficient of 0.43 between predicted and experimental change in aggregation rate upon mutation (P-value <0.0001). However, when the dataset was classified based on protein length and conformation at the mutation sites, the average correlation coefficient almost doubled to 0.82 (range: 0.74–0.87; P-value <0.0001). We observed that distinct sequence and structure-based properties determine protein aggregation kinetics in each class. In conclusion, the protein aggregation kinetics are impacted by local factors and not by global ones, such as overall three-dimensional protein fold, or mechanistic factors such as the presence of aggregation-prone regions.

Availability and implementation

The web server is available at http://www.iitm.ac.in/bioinfo/aggrerate-pred/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Towards a Political Economy of Charging Regimes: Fines, Fees and Force in Uk Immigration Control
Authors: Burnett Jon , Chebe Fidelis
Published: October 2019

Charging regimes and the extraction of revenue are integral components of immigration control in the United Kingdom. However, while these have been analysed in their individual guises, to date, there has been little substantive analysis bringing these regimes together and locating them at the centre of its enquiry. Drawing on data obtained through the Freedom of Information Act 2000, this paper consequently examines the functions of charging regimes as a distinct form of statecraft, focussing its attention on UK Visas and Immigration fees and charges, carrier sanctions, charges related to accessing services and civil penalties administered though immigration enforcement. Analysing their historical roots and their contemporary prevalence, it suggests that they contribute to the political economy of financial power, which has significant implications for understandings of criminalization and immigration enforcement.
Development of a Multiresidue Method for Endocrine-Disrupting Pesticides by Solid Phase Extraction and Determination by UHPLC-MS/MS from Drinking Water Samples
Authors: Liu Shaoying , Huang Xihui , Hu Kejun , Jin Quan , Zhu Guonian
Published: October 2019

A rapid and efficient method based on solid phase extraction and liquid chromatography–tandem mass spectrometry was validated, allowing the determination of the endocrine-disrupting herbicides (acetochlor, alachlor, amitrole and atrazine), fungicides (carbendazim, triadimefon, penconazole and propiconazole), and insecticides (carbaryl and carbofuran) in drinking water. Low method detection limits (0.01–0.64 ng/L) and method quantification limits (0.03–2.13 ng/L) were obtained with satisfactory recoveries and precision for the endocrine-disrupting pesticides. The method was applied for real drinking water samples collected in the area of the city of Hangzhou (Zhejiang, China); the results showed that carbendazim, atrazine and acetochlor were detected in the drinking water samples and acetochlor was the most detected analyte.
The role of patient portals in enhancing self-care in patients with renal conditions
Authors: Hazara Adil M , Durrans Katherine , Bhandari Sunil
Published: October 2019

Web-based portals enable patients to access their electronic health records, including test results and clinical documents, from anywhere with Internet access. Some portals also serve as a means of two-way communication between patients and healthcare professionals and provide a platform for the recording of patient-entered data such as home blood pressure readings. Such systems are designed to encourage patient participation in the management of their condition, and ultimately to increase patient empowerment and self-management, which are associated with improved clinical outcomes. As an example of portal use in patients with renal conditions, we discuss the PatientView portal, which is offered free of cost to patients under the care of renal physicians in the UK. We present an account of its various features and briefly describe the user experience. Previous studies examining the impact of this portal on patient care have been very positive; it appears to be popular among users and overall levels of satisfaction with the service are high. As the use of patient portals increases, we discuss barriers to the more widespread use of portals. We offer suggestions on how the care of patients with renal conditions can be enhanced in the future by further developing the existing features, learning from experiences of other patient portals and providing better integration of portal use into the current model of care.
Differently sized cuckoos pose different threats to hosts
Authors: Yu Jiangping , E Mingju , Sun Wei , Liang Wei , Wang Haitao , Møller Anders Pape
Published: October 2019

Hole-nesting tits Parus spp. have been classified as “unsuitable” hosts for cuckoo parasitism because cuckoos cannot enter a cavity if the entrance is too small. However, Chinese tits could reject alien eggs and egg ejection rate increased with the local diversity of parasitic cuckoo species. Antiparasitic behavior among Chinese tits may have evolved due to greater size variation among sympatric cuckoo species. This raises the question of whether differently sized parasitic cuckoos pose different threats to Chinese tits. A green-backed tit Parus monticolus population that is sympatric with Asian emerald cuckoo Chrysococcyx maculatus (eme-cuckoo, small-sized parasite) and common cuckoo Cuculus canorus (com-cuckoo, large-sized parasite), and a cinereous tit P. cinereus population that is only sympatric with com-cuckoo were chosen as study organisms. We observed behavioral response and recorded alarm calls of the 2 tit species to eme-cuckoo, com-cuckoo, chipmunk Tamias sibiricus (a nest predator) and dove Streptopelia orientalis (a harmless control), and subsequently played back alarm calls to conspecific incubating females. In dummy experiments, both tit species performed intense response behavior to chipmunk, but rarely responded strongly to the 3 avian species. In playback experiments, both tit species responded strongly to conspecific chipmunk alarm calls, but rarely responded to dove alarm calls. The intensity of response of incubating female green-backed tits to eme-cuckoo and com-cuckoo alarm calls were similar to that of chipmunk alarm calls, while the intensity to eme-cuckoo alarm calls was higher than the intensity to dove alarm calls which was similar to that of com-cuckoo alarm calls. In contrast, few female cinereous tits responded to eme-cuckoo and com-cuckoo alarm calls. These findings indicated that the threat level of eme-cuckoo was slightly greater than that of com-cuckoo for sympatric green-backed tits, but not for allopatric cinereous tits.
Mechanisms of mitral regurgitation after percutaneous mitral valve repair with the MitraClip
Authors: Ikenaga Hiroki , Makar Moody , Rader Florian , Siegel Robert J , Kar Saibal , Makkar Raj R , Shiota Takahiro
Published: October 2019

Aims

We sought to find the morphological mechanisms of recurrent mitral regurgitation (MR) after MitraClip procedure using 3D transoesophageal echocardiography (TOE).

Methods and results

Of 478 consecutive patients treated with the initial MitraClip procedure, 41 patients who underwent repeat mitral valve (MV) transcatheter or surgical intervention for recurrent MR were retrospectively reviewed. Using 3D-TOE, we investigated morphological changes of MV leading to repeat MV intervention. Aetiology of MR at the index intervention was primary in 24 (59%) and secondary in 17 (41%) patients. In the primary MR group, worsening leaflet prolapse at the clip site caused recurrent MR in 12 (50%) patients, while 7 (29%) patients had a leaflet tear at the clip site. Acute single leaflet device detachment was seen in four patients and one patient had recurrent MR between the plug and the clip. In secondary MR, left ventricular (LV)/left atrial dilation caused recurrent MR in 13 (76%) patients. Significant increase in the LV end-diastolic volume and tenting height were observed from post-index procedure to repeat intervention (LV end-diastolic volume; from 205 to 237 ml, P < 0.001, tenting height; from 0.8 to 1.3 cm, P < 0.001). New emergent leaflet prolapse/flail was seen in 3 (18%) patients, suggesting iatrogenic MR.

Conclusion

Mechanisms of recurrent MR after MitraClip procedure varied and depended on the underlying MV pathology: in primary MR, worsening mitral leaflet prolapse and in secondary MR, progressive LV dilation with worsening tenting were the main causes of recurrent MR.
Computed tomography follow-up identifies radically treatable new primaries after resection for lung cancer
Authors: Mitchell Jenny , Benamore Rachel , Gleeson Fergus , Belcher Elizabeth
Published: October 2019

OBJECTIVES

The optimal imaging programme for the follow-up of patients who have undergone resection of primary lung cancer is yet to be determined. We investigated the incidence and patterns of new and recurrent malignancy after resection for early-stage lung cancer in patients enrolled into a computed tomography (CT) follow-up programme.

METHODS

We reviewed the outcomes of consecutive patients who underwent CT follow-up after resection of early-stage primary lung cancer at the Oxford University Hospitals NHS Foundation Trust, between 2013 and 2017.

RESULTS

Four hundred and sixty-six consecutive patients underwent resection of primary lung cancer between 1 January 2013 and 31 March 2017. Three hundred and thirty-one patients (71.0%) were enrolled in CT follow-up. The median follow-up was 98 weeks (range 26–262). Sixty patients (18.2%) were diagnosed with programme-detected malignancy. Recurrence was diagnosed in 36 patients (10.9%), new primary lung cancer in 16 patients (4.8%) and non-lung primary tumours in 8 patients (2.4%). A routine CT scan identified the majority of new primary lung cancers (84.2%) and those with disease recurrence (85.7%). The majority of programme-detected malignancies were radically treatable (55%). The median survival of programme-detected cancers was 92.4 versus 23.0 weeks for patients with clinically detected tumours (P < 0.0001). Utilizing the CT scout image as a surrogate for chest X-ray, the sensitivity of this modality was 16.95% (8.44–28.97%) and specificity was 89.83% (79.17–96.18%). Negative likelihood ratio was 0.92 (0.8–1.07).

CONCLUSIONS

CT follow-up of surgically treated primary lung cancer patients identifies malignancy at a stage where radical treatment is possible in the majority of patients. Chest X-ray follow-up may not be of benefit following lung cancer resection.
Follow-up after biventricular repair of the hypoplastic left heart complex
Authors: IJsselhof Rinske J , Duchateau Saniyé D R , Schouten Rianne M , Freund Matthias W , Heuser Jörg , Fejzic Zina , Haas Felix , Schoof Paul H , Slieker Martijn G
Published: October 2019

OBJECTIVES

In hypoplastic left heart complex patients, biventricular repair is preferred over staged-single ventricle palliation; however, there are too few studies to support either strategy. Therefore, we retrospectively characterized our patient cohort with hypoplastic left heart complex after biventricular repair to measure left-sided heart structures and assess our treatment strategy.

METHODS

Patients with hypoplastic left heart complex who had biventricular repair between 2004 and 2018 were retrospectively reviewed. Operative results were evaluated and echocardiographic mitral valve (MV) and aortic valve (AoV) dimensions, left ventricular length and left ventricular internal diastolic diameter (LVIDd) were measured preoperatively and during follow-up after 0.5, 1, 3, 5 and 10 years.

RESULTS

In 32 patients, the median age at surgery was 10 (interquartile range 5.0) days. The median follow-up was 6.19 (interquartile range 6.04) years. During the 10-year follow-up, the mean Z-scores increased from −2.82 to −1.49 and from −2.29 to 0.62 for MV and AoV, respectively. Analysis of variance results with post hoc paired t-tests showed that growth of left-sided heart structures was accelerated in the first year after repair, but was not equal, with the MV lagging behind the AoV (P = 0.033), resulting in significantly smaller MV Z-scores compared with AoV Z-scores at 10-year follow-up (P < 0.001). There were 2 (6%) early deaths. The major adverse events occurred in 4 (13%) patients. The surgical or catheter-based reintervention was required in 14 (44%) patients.

CONCLUSIONS

The growth rate of heart structures was most prominent during the first year after biventricular repair with lower growth rate of the MV compared with the AoV.
A risk model to predict 2-year survival after VATS lobectomy for non-small-cell lung cancer
Authors: Tan Hui Xian , Drake Benjamin Cooper , Chaudhuri Nilanjan , Kefaloyannis Manos , Milton Richard , Papagiannopoulos Kostas , Tcherveniakov Peter , Brunelli Alessandro
Published: October 2019

OBJECTIVES

We sought to identify the risk factors associated with mortality post-video-assisted thoracoscopic surgery (VATS) lobectomy over a 2-year period.

METHODS

Analysis was performed using a sample from an institutionally maintained database. All lobectomies for non-small-cell lung cancer from April 2014 to March 2018 started with VATS approach and with a complete follow-up were included (n = 732). Several clinical variables were screened using the Cox univariate analysis for their association with 2-year survival. Those with a P-value <0.1 were included in a Cox proportional hazard model.

RESULTS

After multivariable analysis, the following variables showed significant association with 2-year survival: age >75 [hazard ratio (HR) 1.527, P = 0.043], carbon monoxide lung diffusion capacity <70 (HR 1.474, P = 0.061), body mass index (BMI) <18.5 (HR 2.628, P = 0.012), American Society of Anesthesiologist Physical Status >2 (HR 1.518, P = 0.047), performance status >1 (HR 1.822, P = 0.032) and male gender (HR 2.700, P < 0.001). A score of 2 was assigned to the male gender and BMI <18.5, with all other variables assigned a score of 1. Each patient was scored and placed into their risk class. A Kaplan–Meier estimate for 2-year survival was calculated for each class. These were collapsed into the following 3 classes of risk based on their similar 2-year survival: class A (score 0) 97%, 95% CI 88–99, class B (score 1–3) 84%, 95% CI 80–88, class C (score > 3) 66%, 95% CI 57–74.

CONCLUSION

Our scoring system can serve as an adjunct to a clinician’s experience in risk-stratifying patients during multidisciplinary tumour board discussion and the shared decision-making process.
Uptake and detection rate of a stepwise cardiometabolic disease detection program in primary care—a cohort study
Authors: Stol Daphne M , Hollander Monika , Badenbroek Ilse F , Nielen Mark M J , Schellevis François G , de Wit Niek J
Published: October 2019

Background

Early detection and treatment of cardiometabolic diseases (CMD) in high-risk patients is a promising preventive strategy to anticipate the increasing burden of CMD. The Dutch guideline ‘the prevention consultation’ provides a framework for stepwise CMD risk assessment and detection in primary care. The aim of this study was to assess the outcome of this program in terms of newly diagnosed CMD.

Methods

A cohort study among 30 934 patients, aged 45–70 years without known CMD or CMD risk factors, who were invited for the CMD detection program within 37 general practices. Patients filled out a CMD risk score (step 1), were referred for additional risk profiling in case of high risk (step 2) and received lifestyle advice and (pharmacological) treatment if indicated (step 3). During 1-year follow-up newly diagnosed CMD, prescriptions and abnormal diagnostic tests were assessed.

Results

Twelve thousand seven hundred and thirty-eight patients filled out the risk score of which 865, 6665 and 5208 had a low, intermediate and high CMD risk, respectively. One thousand seven hundred and fifty-five high-risk patients consulted the general practitioner, in 346 of whom a new CMD was diagnosed. In an additional 422 patients a new prescription and/or abnormal diagnostic test were found.

Conclusions

Implementation of the CMD detection program resulted in a new CMD diagnosis in one-fifth of high-risk patients who attended the practice for completion of their risk profile. However, the potential yield of the program could be higher given the considerable number of additional risk factors—such as elevated glucose, blood pressure and cholesterol levels—found, requiring active follow-up and presumably treatment in the future.
Effect of temperature, pH, physical and chemical factors on germination rate of the chlamydospores of the nematophagous fungus Duddingtonia flagrans
Authors: Wang Bobo , Zhang Nan , Gong Peng-tao , Li Jianhua , Yang Ju , Zhang Xichen , Cai Kuizheng
Published: October 2019

This study mainly investigated the effects of environmental factors on the germination/dormancy, sporulation and resistance of Duddingtonia flagrans chlamydospores. Results showed that the germination temperature of chlamydospores was >10°C and ≤35°C. After the chlamydospores were treated at −20, −40 and −80°C for 12–24 h, they still had the ability to germinate. The chlamydospores germinated at pH 3–13 but did not germinate at pH 1–2 and pH 14. The chlamydospores could tolerate ultraviolet rays for 720 min, but visible light irradiation for 24 h significantly reduced their germination rate. The chlamydospores did not germinate under anaerobic conditions. After the chlamydospores were cultured on water agar (WA) containing 5, 10 and 20% NaCl, their germination rate was significantly inhibited. Once NaCl was removed, the chlamydospores almost completely recovered their germination ability. Among the nine kinds of additives used in the study, 0.3% arginine significantly promoted spore germination (P < 0.05) but 1% trehalose and 1% glycerine significantly inhibited spore germination during incubation from 24 h to 48 h (P < 0.05). This work indicated that D. flagrans chlamydospores are highly resistant to environmental variations and so could be used for biocontrol of animal parasites.
Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma
Authors: Liu Qi , Lin Deng , Li Mingkun , Gu Zhenglong , Zhao Yiqiang
Published: October 2019

Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.
Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen
Authors: Feurtey Alice , Stevens Danielle M , Stephan Wolfgang , Stukenbrock Eva H
Published: October 2019

Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.
Soluble Blood Markers of Mucosal Healing in Inflammatory Bowel Disease: The Future of Noninvasive Monitoring
Authors: Nardone Olga Maria , Shivaji Uday Nagesh , Ferruzza Vittoria , Ghosh Subrata , Iacucci Marietta
Published: October 2019

The traditional management of inflammatory bowel disease (IBD) based on symptom control is not considered valid anymore by most specialists in this field, and a new paradigm called “treat to target” has been introduced. This is based on the assessment of disease activity using objective measures. The identification of noninvasive biomarkers is crucial to diagnosis and monitor IBD because frequent endoscopic examinations are costly and uncomfortable for the patient. In this review, we focus on blood markers that may be able to assess mucosal healing (MH) in IBD and recent advances in this area. Introduction of commercial panel to predict MH opens the way for further developments so that colonoscopy or fecal markers may be avoided in some patients. This may also permit frequent monitoring for therapeutic response and achieve MH. It is a challenging area of research to identify a panel of biomarkers that may reflect inflammation and healing to serve as a surrogate of MH.
Inflammatory Pouch Conditions Are Common After Ileal Pouch Anal Anastomosis in Ulcerative Colitis Patients
Authors: Kayal Maia , Plietz Michael , Rizvi Anam , Radcliffe Marlana , Riggs Alexa , Yzet Clara , Tixier Emily , Trivedi Parth , Ungaro Ryan C , Khaitov Sergey , Sylla Patricia , Greenstein Alexander , Frederic Colombel Jean , Dubinsky Marla C
Published: October 2019

Background

Total proctocolectomy (TPC) with ileal pouch anal anastomosis (IPAA) is the gold standard surgery for ulcerative colitis (UC) patients with medically refractory disease. The aim of this study was to report the rates and risk factors of inflammatory pouch conditions.

Methods

This was a retrospective review of UC or IBD unspecified (IBDU) patients who underwent TPC with IPAA for refractory disease or dysplasia between 2008 and 2017. Pouchoscopy data were used to calculate rates of inflammatory pouch conditions. Factors associated with outcomes in univariable analysis were investigated in multivariable analysis.

Results

Of the 621 patients more than 18 years of age who underwent TPC with IPAA between January 2008 and December 2017, pouchoscopy data were available for 386 patients during a median follow-up period of 4 years. Acute pouchitis occurred in 205 patients (53%), 60 of whom (30%) progressed to chronic pouchitis. Cuffitis and Crohn's disease–like condition (CDLC) of the pouch occurred in 119 (30%) patients and 46 (12%) patients, respectively. In multivariable analysis, female sex was associated with a decreased risk of acute pouchitis, and pre-operative steroid use and medically refractory disease were associated with an increased risk; IBDU was associated with chronic pouchitis; rectal cuff length ≥2 cm and medically refractory disease were associated with cuffitis; age 45–54 at colectomy was associated with CDLC. Rates of pouch failure were similar in chronic pouchitis and CDLC patients treated with biologics and those who were not.

Conclusions

Inflammatory pouch conditions are common. Biologic use for chronic pouchitis and CDLC does not impact the rate of pouch failure.
Ensemble modelling in descriptive epidemiology: burden of disease estimation
Authors: Bannick Marlena S , McGaughey Madeline , Flaxman Abraham D
Published: October 2019

Ensemble modelling is a quantitative method that combines information from multiple individual models and has shown great promise in statistical machine learning. Ensemble models have a theoretical claim to being models that make the ‘best’ predictions possible. Applications of ensemble models to health research have included applying ensemble models like the super learner and random forests to epidemiological prediction tasks. Recently, ensemble methods have been applied successfully in burden of disease estimation. This article aims to provide epidemiologists with a practical understanding of the mechanisms of an ensemble model and insight into constructing ensemble models that are grounded in the epidemiological dynamics of the prediction problem of interest. We summarize the history of ensemble models, present a user-friendly framework for conceptualizing and constructing ensemble models, walk the reader through a tutorial of applying the framework to an application in burden of disease estimation, and discuss further applications.
Behavior of unconfined and CFRP confined rubberized concrete
Authors: Tufail Rana Faisal , Feng Xiong , Zahid Muhammad
Published: October 2019

The use of rubberized concrete (RuC) is an effective environmental approach to reduce the amount of scrap tires around the world. However, there are serious concerns regarding the compressive strength of RuC. This article investigates the use of externally bonded carbon fiber reinforced polymer (CFRP) jackets on RuC to develop a novel high strength and deformable CFRP confined RuC. In this study, 66 RuC cylinders were cast with 0, 10, 20, 30, 40 and 50% fine or coarse rubber to replace mineral aggregates. The RuC cylinders were then confined with one, two or three layers of CFRP jackets. The results indicated 208% high lateral strains in unconfined RuC as compared to the conventional concrete. CFRP jacketing was highly effective for enhancing the compressive strength and deformation capacity of RuC, where high compressive strength enhancement of 52 MPa and deformation capacity (317% axial strain) was achieved. The confined compressive strength test results were compared with the strength models to assess their validity for CFRP confined RuC. An analysis-oriented strength model was developed to predict the axial compressive strength of RuC confined by CFRP jackets. Overall, this study demonstrated the potential of using CFRP-confined RuC as a new structural material with improved strength and deformation.
Amino acid composition and digestible amino acid content in animal protein by-product meals fed to growing pigs1
Authors: Kerr Brian J , Urriola Pedro E , Jha Rajesh , Thomson John E , Curry Shelby M , Shurson Gerald C
Published: October 2019

An industry survey and animal experiment were conducted to evaluate the amino acid (AA) compositional variability and standardized ileal digestibility (SID) of AA in animal protein by-products fed to growing pigs. Animal protein by-product meals (212) were categorized into 8 groupings (blood meal, chicken by-product meal, chicken meal, feather meal, meat and bone meal, meat meal, poultry by-product meal, and poultry meal) and analyzed for total AA. Amino acid analysis among (e.g., Lys in blood meal averaged 9.20% compared with 2.31% for feather meal, DM basis) and within (e.g., Lys range of 1.54% in blood meal and 1.44% in feather meal, DM basis) the by-product classifications varied as expected, but on average the total AA values were similar to that reported in the literature. For the determination of the SID of AA, 15 barrows (average initial and final BW of 31.6 and 78.7 kg, respectively) were fitted with a T-cannula in the distal ileum and allotted to 15 diets over nine 7-d periods, resulting in 9 replications per diet. Pigs were fed a basal diet based on soybean meal and dehulled-degermed corn, 13 diets containing 17.5% animal protein by-product meal to partially replace a portion of the soybean meal and dehulled-degermed corn in the basal diet, or a N-free diet. Pigs were re-allotted to diets based on minimizing the number to times that the N-free diet would precede or follow feeding either of the blood or feather meal diets because of concern with inadequate diet consumption, as well as to prevent diets from being re-fed to the same pig during the next or subsequent periods. Values for the apparent ileal AA digestibility of each diet were determined, adjusted to SID based upon the endogenous AA losses determined by feeding the N-free diet, and the SID of AA in each animal protein by-product meal calculated using the difference procedure. The SID of AA varied among (e.g., SID of Lys averaged 91% in chicken meal but 47% in feather meal) and within (e.g., SID of Lys in three meat and bone meals was 80%, 71%, and 54%) the animal protein by-product meals, as would be expected and are consistent with variation reported in the literature. Overall, the data provide total AA composition for 212 samples and SID of AA for 13 samples of animal protein by-product meals, including data on their variability, which is critical for their use in feed formulation programs.