bluuebunny/crossref_metadata_2025 huggingface dataset:
Color and texture analyses of meatballs made from beef, pork, rat, dog meats, and their mixtures
Authors: Tathma F R , Wibowo T , Taufik I M , Cahyadi M
Published: October 2019

The aim of this study was to evaluate color and texture of meatballs made from beef, pork, rat, dog meats, and their mixtures. A total of 32 meatballs have been made and they were grouped into eight treatments containing four meatballs, respectively. Color intensity consisting of lightness(L*), redness (a*), and yellowness (b*) has been tested using chromameter CR-400. Additionally, texture of meatballs consisting hardness, gumminess, springiness, chewiness was analyzed using AMETEX test and calibration instrument. The data obtained from this study was furthermore analyzed using one-way analysis of variance (ANOVA) and the pairwise differences among treatments were tested by Duncan’s multiple range test (DMRT). The results showed that L*, a*, b* were significantly different among treatments (P<0.01). The L* value of dog meat was different with beef, pork, and rat meat. Also, the a* value of beef was similar to pork and significant different with dog and rat meats, while b* value of dog meat was different with other meats. The L*, a*, b* scores in mixture samples consistently represented the average value of color scores of samples consisting various species. Moreover, texture analysis indicated highly significant effect of treatments on hardness, gumminess, springiness, and chewiness (P<0.05). Highest hardness, gumminess, and chewinessscores were found in meatballs made from beefand rat, respectively. In addition, springiness of meatballs was relatively similar among treatments. This study concluded that meatballs made from different species and mixtures had different color and texture. Further study should be conducted to test whether color and texture analysis could be utilized for checking meat-based food adulteration and halalness.
Effect of different solvents and extraction conditions on fiber contents of local corns silk powders
Authors: Haslina  , Praseptiangga D , Bintoro V P , Pujiasmanto B
Published: October 2019

The aim of this study was to optimize the different solvents and extraction conditions on fiber contents of local corn silk powders. Each sample of corn silk powder extract was analyzed by enzymatic method for fiber content including soluble fiber, insoluble fiber and total fiber. Design using Factorial Randomized Block Design (RBD) with 4 factors are local varieties of cornsilk (Bisma, Arjuna and Srikandi Putih), different solvents (water, methanol, ethanol and ethyl acetate), different concentration of solvents ( methanol (60%, 70% and 80%), ethanol (60%, 70% and 80%), ethyl acetate (60%, 70% and 80%) and water), and ratio of material and solvent (1:5 (w/v), 1:10 (w/v), 1:15 (w/v) and 1:20 (w/v)). Response Surface Methodology (RSM) technique for optimum condition determination was used. Results showed that the difference in experimental conditions affects the content of soluble fiber, insoluble fiber, and total fiber produced by optimization analysis using the DX11.0® Program with RSM-Central Composite Design (CCD). In conclusion, Bisma variety, solvent of methanol, concentration of 80% solvent and ratio of (1:20) was selected as the optimum condition of which resulted in soluble fiber content of 0.85%, insoluble fiber of 0.60% and total fiber of 1.45%.
Utilization of carrageenan and chitosan as coating material in phycocyanin encapsulation
Authors: Hadiyanto  , Sutanto H , Suzery M , Adetya N P , Nilamsari A M , Yunanda A
Published: October 2019

Phycocyanin is one of the pigments found in Spirulina platensis. Phycocyanin has potential as natural blue dye and antioxidant. The application of phycocyanin as food ingredient is still limited due to its vulnerability to environment. Microencapsulation can keep phycocyanin from environmental influences such as temperature, light and pH. This research aimed to determine the antioxidant activity of phycocyanin microencapsulation with carrageenan and chitosan coating material caused by the effect of thermal degradation overtime and its influence on the physical characteristics of the microencapsulation. The highest antioxidant activity of 61.48% was found in chitosan coating material that occurred at temperature of 40° with 30 minutes heat treatment.Phycocyanin microcapsule with chitosan has more vibrant blue color compared to carrageenan.Phycocyanin microencapsulation either by using carrageenan or chitosan have functional groups such as alkane, alcohol, ether and ester.
Effect of various heat treatment on physical and chemical characteristics of red rice bran (Oryza nivara L.) Rojolele
Authors: Siswanti  , Anandito R B K , Nurhartadi E , Iskandar B D
Published: October 2019

This research aims to study the effect of various heat treatment on physical and chemical characteristics of red rice bran (Oryza nivara L.) Rojolele. This study used a Completely Randomized Design (CRD) with one-factor variations of heat treatment applied on the bran. The various heat treatments use Oven an hour (80ºC and 100ºC), Microwave maximum temperature (2 and 5 minutes), and Autoclave 1500C (5 and 10 minutes). Results showed that all heat treatment methods decrease L value. The highest moisture level is on heating by microwave for 2 min. There were no significant difference in the level of ash, fat, and antioxidant activity. The FFA content was decreased by all heating treatment. The fenol level with heating with Oven 80ºC an hour was the highest. Among the treatments, Oven an hour at 80ºC is the best method. This method produces red rice bran with characteristics of lightness, water content, ash, fat, protein, total phenol, antioxidant activity, crude fiber, and free fatty acid content respectively 49.78; 5.51%; 8.37%; 27.11%; 10.50%; 0.25%; 75.88%; 9.30%; and 13.48%. Red rice bran Rojolele also contains anthocyanin and thiamin obtained from spectroscopy FTIR.
Household consumption of broilers meat in Kudus Central Java
Authors: Zulkarnain M B , Rahayu W , Antriyandartiand E , Ani S W
Published: October 2019

Broilers meat is one of protein intake sources from meat in Indonesia, but the consumption still very low compared to the standard set by Food and Agriculture Organization (FAO). This study investigates the pattern of animal food consumption, examines the determinants of broilers meat consumption and analyzes the demand elasticity in the household. This study uses Panel Data Analysis with Random Effect Model to estimate the factors influencing broilers meat consumption. The determinants are the number of family members, household income, the price of broilers meat, egg, rice, beef, fish, and the residential area. The results show that the most influential factor is the price of broilers meat, with inelastic demand elasticity.
Farming occupation in the views of farmer families in rural area
Authors: Widiyanti E , Karsidi R , Wijaya M , Utari P
Published: October 2019

As main actors in food production system, farmers receive much of the world’s attention due to the food crisis phenomenon happening all over the world. However, the attention to small-scale farmers tends to be neglected, especially regarding to the crisis of farmer regeneration. Thus it is interesting to understand how small-scale farmers and their families think of farming occupations. To comprehend the meanings underlying the farmer families’ views on farming occupations, the researchers applied Hebert Blumer’s symbolic interactionism in descriptive qualitative study using paradigm construction. The data were collected by interviews with a number of farmers and their families in Tegalmade Village, Mojolaban District, Sukoharjo Regency. The results showed that there are different views among older generation (farmers) and younger generation (farmers’ children). The identified views were positive, neutral and negative. The differences in their views are caused by different interaction processes, leading to different action orientations. The young generation has positive views when interacting with their families and youth community engaged in agriculture especially in agriculture entrepreneurship. These positive views result in action orientations to work on the farming occupations. The older generation has positive views when interacting with fellow farmers, views that they want to continue to make farming as their main livelihood.
Using Deep Neural Networks to Predict the Tensile Property of Ceramic Matrix Composites Based on Incomplete Small Dataset
Authors: Xiang GAO , Guanghui LI , Rong TAN , Leijiang YAO
Published: October 2019

It has been a hot spot in the area of material science that how to design an experiment to produce a kind of ceramic matrix composites (CMCs) which possesses ideal performances. An approach is to build models with data from previous experiments recorded in published papers and predict the experiment parameters needed by the ideal CMCs. According to the database of CMCs funded by the National Material Genome Engineering, 8 factors were considered to affect the tensile property of CMCs, which were the basis, the reinforcement fiber type, the reinforcement fiber volume content, the perform type, the porosity, the interface type, the interface thickness and the density. Among the data we collected from papers, however, only few of pieces contained all the 8 factors, most were incomplete, some of them even lacked multiple factors. This paper’s work mainly researched how to take advantage of the incomplete data to build an effective model to predict the tensile property of CMCs. We proposed a model to predict the tensile property of CMCs based on a 1-D convolution neural network (CNN), the training data of which were all from papers. To decrease the influences of the incompleteness of data, we tried several methods to process the missing data, such as the mean imputation, the K-Means clustering imputation, the Hot-Deck Imputation and the regression imputation. The results showed that the regression imputation with a dual-hidden-layer feedforward network performed better and improved the performance of the CNN tensile property prediction model.
Mechanism and Research on Preparation of AlN Powder by Carbon Thermal Reduction Method
Authors: Wang L Y , Zhang N
Published: October 2019

The alumina and activated carbon used as raw materials were prepared by chemical precipitation method. The uniformed aluminum nitride precursor was synthesized by mechanical mixing process. The effects of nitride temperature and time on the diameter of the particle were studied in detail. Ultrafined aluminum nitride powder was prepared by carbon-thermal reduction method. The results show that the precursor has better activity and nitride reaction proceeds rapidly. The complete conversion can be got at 1600°C for 2h. After calcination, it can be seen from the XRD graph that the powder with uniform size distribution has high AlN content.
A Reliable Defect Detection Method for Patterned Wafer Image Using Convolutional Neural Networks with the Transfer Learning
Authors: Lee Ji-Hee , Lee Jee-Hyong
Published: October 2019

In the semiconductor manufacturing process, wafer inspection images have valuable information on defects and wafer yield. It is worthy to analysis these images and there are many algorithms for this. Whenever new product designs are introduced, the algorithms are used to detect defects. Most new product designs have new types of defects. Hence, it is important to update the algorithms to cope with new types of defects. To update the algorithms, engineers collect the data and adjust a parameter values, such as threshold, to detect defects. It is time-consuming to collect enough data and only a knowledgeable engineer can find an appropriate parameter value. However, there is always a lack of engineer resources and time in the manufacturing industry. Due to these reasons, many algorithms can’t be used reliably and have disappeared. Therefore, we propose the advanced method to update an algorithm easily using a deep learning model. Deep learning models achieve high accuracy with less engineer knowledge than traditional algorithms. But it also needs a lot of data to train the model, so we apply an advanced method of updating with a small amount of data in a short time. This is called as transfer learning. Once we train a deep learning model with high accuracy, we can update the model with a small amount of data. Transfer learning uses the information gained during the training. As a result, we make a model that is easy to update with high accuracy. In the experiments, we obtained 99% accuracy with sufficient training data. To update the model for the new data, we did transfer learning and got 97% accuracy. It was lower, but we only used 10% of the training data and 5% of the training time. Also, the accuracy we have obtained is enough to be used for defect analysis. Our approach outperformed and executed faster than traditional algorithms.
Serial Ottawa 3DY assessments to detect delirium in older emergency department community dwellers
Authors: Yadav Krishan , Boucher Valérie , Carmichael Pierre-Hugues , Voyer Philippe , Eagles Debra , Pelletier Mathieu , Gouin Émilie , Daoust Raoul , Vu Thien Tuong Minh , Berthelot Simon , Émond Marcel
Published: October 2019

Background

delirium is associated with increased morbidity and mortality among older emergency department (ED) patients. When using physician gestalt, delirium is missed in the majority of patients. The Ottawa 3DY (O3DY) has been validated to detect cognitive dysfunction among older ED patients.

Objectives

to determine the sensitivity and specificity of serial O3DY assessments to detect delirium in older ED patients.

Design

a prospective observational multicenter cohort study.

Setting

four Quebec EDs.

Participants

independent or semi-independent older patients (age ≥ 65 years) with an ED stay of at least 8 hours that required hospitalisation.

Measurements

eligible patients were evaluated using serial O3DY assessments at least 6 hours apart. The primary outcome was delirium after at least 8 hours in the ED. The reference standard for delirium assessment was the confusion assessment method (CAM). The sensitivity and specificity of the serial O3DY to detect delirium were calculated.

Results

we enrolled 301 patients (mean age 77 years, 49.5% male, 3.0% with a history of mild dementia). Thirty patients (10.0%) were CAM positive for delirium. Patients had a median of three O3DY assessments. Serial O3DY evaluations to detect delirium among patients with at least one abnormal O3DY had a sensitivity of 86.7% (95% confidence interval—CI 69.3–96.2%) and a specificity of 44.3% (95%; CI 38.3–50.4%).

Conclusion

serial O3DY testing demonstrates good sensitivity as a screening tool to detect delirium among older adult patients with prolonged ED lengths of stay. Emergency physicians should consider the use of the serial O3DY over clinician gestalt to improve delirium detection.
Population-Level Sexual Mixing According to HIV Status and Preexposure Prophylaxis Use Among Men Who Have Sex With Men in Montreal, Canada: Implications for HIV Prevention
Authors: Wang Linwei , Moqueet Nasheed , Lambert Gilles , Grace Daniel , Rodrigues Ricky , Cox Joseph , Lachowsky Nathan J , Noor Syed W , Armstrong Heather L , Tan Darrell H S , Burchell Ann N , Ma Huiting , Apelian Herak , Knight Jesse , Messier-Peet Marc , Jollimore Jody , Baral Stefan , Hart Trevor A , Moore David M , Mishra Sharmistha
Published: October 2019

Using cross-sectional survey data (Engage, 2017–2018) from 1,137 men who have sex with men, ≥16 years old, in Montreal, we compared observed human immunodeficiency virus (HIV) seroconcordance in previous-6-months’ sexual partnerships with what would have been observed by chance if zero individuals serosorted. Of 5 recent partnerships where both individuals were HIV-negative, we compared observed concordance in preexposure prophylaxis (PrEP) use with the counterfactual if zero individuals selected partners based on PrEP use. We estimated the concordance by chance using a balancing-partnerships approach assuming proportionate mixing. HIV-positive respondents had a higher proportion of HIV-positive partners (66.4%, 95% confidence interval (CI): 64.0, 68.6) than by chance (23.9%, 95% CI: 23.1, 24.7). HIV-negative respondents (both on and not on PrEP) had higher proportions of HIV-negative partners (82.9% (95% CI: 81.1, 84.7) and 90.7% (95% CI: 89.6, 91.7), respectively) compared with by chance (76.1%, 95% CI: 75.3, 76.9); however, those on PrEP had a higher proportion of HIV-positive partners than those not on PrEP (17.1% (95% CI: 15.3, 18.9) vs. 9.3% (95% CI: 8.3, 10.4). Those on PrEP also had a higher proportion of partners on PrEP among their HIV-negative partners (50.6%, 95% CI: 42.5, 58.8) than by chance (28.5%, 95% CI: 27.5, 29.4). The relationship between PrEP and sexual-mixing patterns demonstrated by less population-level serosorting among those on PrEP and PrEP-matching warrants consideration during PrEP roll-out.
Hitting the brakes: pathological subthalamic nucleus activity in Parkinson’s disease gait freezing
Authors: Georgiades Matthew J , Shine James M , Gilat Moran , McMaster Jacqueline , Owler Brian , Mahant Neil , Lewis Simon J G
Published: October 2019

The neurobiology of gait freezing in Parkinson’s disease is poorly understood and therapies are largely ineffective. Using a virtual reality task to elicit freezing intra-operatively during implantation of DBS electrodes, Georgiades et al. identify pathological subthalamic nucleus activity associated with freezing onset and discernible from that of volitional stopping.
Reduced Microstructural Lateralization in Males with Chronic Schizophrenia: A Diffusional Kurtosis Imaging Study
Authors: McKenna Faye , Babb James , Miles Laura , Goff Donald , Lazar Mariana
Published: October 2019

Decreased brain lateralization is considered a trait marker of schizophrenia. Whereas reductions in both functional and macrostructural gray matter laterality in schizophrenia are well established, the investigation of gray matter microstructural lateralization has so far been limited to a small number of ex vivo studies, which limits the understanding of neurobiological substrates involved and development of adequate treatments. The aim of the current study was to assess in vivo gray matter microstructure lateralization patterns in schizophrenia by employing the diffusion kurtosis imaging (DKI)–derived mean kurtosis (MK) metric. MK was calculated for 18 right-handed males with chronic schizophrenia and 19 age-matched healthy control participants in 46 bilateral gray matter regions of interest (ROI). Microstructural laterality indexes (μLIs) were calculated for each subject and ROI, and group comparisons were conducted across regions. The relationship between μLI values and performance on the Wisconsin Card Sorting Test (WCST) was also evaluated. We found that compared with healthy controls, males with chronic schizophrenia had significantly decreased μLI across cortical and subcortical gray matter regions, which was correlated with poorer performance on the WCST. Our results suggest the ability of DKI-derived MK to capture gray matter microstructural lateralization pathology in vivo.
A Neural Mechanism of Cue-Outcome Expectancy Generated by the Interaction Between Orbitofrontal Cortex and Amygdala
Authors: Takei Kenji , Fujita Kazuhisa , Kashimori Yoshiki
Published: October 2019

Taste perception is important for animals to take adequate nutrients and avoid toxins for their survival. Appetitive and aversive behaviors are produced by value evaluation of taste and taste expectation caused by other sensations. The value evaluation, coupled with a cue presentation, produces outcome expectation and guides flexible behaviors when the environment is changed. Experimental studies demonstrated distinct functional roles of basolateral amygdala (ABL) and orbitofrontal cortex (OFC) in value evaluation and adaptive behavior. ABL is involved in generating a cue–outcome association, whereas OFC makes a contribution of generating a cue-triggered expectation to guide adaptive behavior. However, it remains unclear how ABL and OFC form their functional roles, with the learning of adaptive behavior. To address this issue, we focus on an odor discrimination task of rats and develop a computational model that consists of OFC and ABL, interacting with reward and decision systems. We present the neural mechanisms underlying the rapid formation of cue–outcome association in ABL and late behavioral adaptation mediated by OFC. Moreover, we offer 2 functions of cue-selective neurons in OFC: one is that the activation of cue-selective neurons transmits value information to decision area to guide behavior and another is that persistent activity of cue-selective neurons evokes a weak activity of taste-sensitive OFC neurons, leading to cue-outcome expectation. Our model further accounts for ABL and OFC responses caused by lesions of these areas. The results provide a computational framework of how ABL and OFC are functionally linked through their interactions with the reward and decision systems.
Multisensory interactions underlying flavor consumption in rats: the role of experience and unisensory component liking
Authors: Elliott Victoria E , Maier Joost X
Published: October 2019

The mechanisms by which taste and odor are combined in determining food choice behavior are poorly understood. Previous work in human subjects has yielded mixed results, potentially due to differences in task context across studies, and a lack of control over flavor experience. Here, we used rats as a model system to systematically investigate the role of experience and unisensory component liking in the multisensory interactions underlying consumption behavior. We demonstrate that taste–smell mixture consumption is best explained by a linear average of component liking. The observed pattern of results was not dependent on prior experience with specific taste–smell combinations, and unique for multisensory as opposed to unisensory mixture consumption. The results are discussed with respect to existing models of flavor integration, and a maximum-likelihood integration model previously described for multisensory judgments in other systems.
National Trends in Incidence of Purulent Skin and Soft Tissue Infections in Patients Presenting to Ambulatory and Emergency Department Settings, 2000–2015
Authors: Fritz Stephanie A , Shapiro Daniel J , Hersh Adam L
Published: October 2019

Nationally representative data from 2000–2015 demonstrated a rise in the incidence of outpatient visits for skin infections, peaking in 2010–2013, followed by a plateau. While cephalexin was the most frequently prescribed antibiotic at the beginning, trimethoprim-sulfamethoxazole was most frequently prescribed by the end of the study period.
Effects of a medium cut-off (Theranova®) dialyser on haemodialysis patients: a prospective, cross-over study
Authors: Cozzolino Mario , Magagnoli Lorenza , Ciceri Paola , Conte Ferruccio , Galassi Andrea
Published: October 2019

Background

Despite significant advances in haemodialysis (HD) in recent decades, current dialysis techniques are limited by inadequate removal of uraemic solutes such as middle molecules and protein-bound uraemic toxins. Novel medium cut-off (MCO) membrane or ‘expanded haemodialysis’ (HDx) provides diffusive removal of conventional and large middle molecular weight uraemic toxins, with marginal albumin leak.

Methods

This prospective, open-label, controlled, cross-over pilot study compared HDx (novel MCO membrane Theranova® 400) and conventional HD in 20 prevalent HD patients. Biochemical, dialysis adequacy and safety measures (adverse events, infections and hospitalization frequency) were recorded. Ten patients underwent conventional HD high-flux dialyser and 10 patients underwent HDx for 3 months, and the patients then switched and received the other treatment for a further 3 months.

Results

Treatment with HDx was associated with a significant reduction in serum albumin concentration [median (interquartile range) reduction −0.45 g/dL (−0.575 to −0.05); P = 0.025]. However, median albumin levels were ≥3.5 g/dL and no patients had clinical symptoms of hypoalbuminaemia or needed intravenous albumin administration. The number of infections was lower in patients treated with HDx (n = 7/19) compared with patients treated with HD (n = 14/20; P = 0.03). Patients treated with HDx had reduced levels of interleukin (IL)-1β (from 0.06 ± 0.02 pg/mL versus 0.28 ± 0.18 pg/mL with HD) and IL-6 (6.45 ± 1.57 pg/mL versus 9.48 ± 2.15 pg/mL), while tumour necrosis factor-α levels remain unchanged.

Conclusions

This study demonstrates that the chronic use of the novel MCO dialyser Theranova® appears to be safe and well-tolerated, without serious side effects or hypoalbuminaemia, as well as fewer infections. These results need to be confirmed in larger randomized clinical trials.
Translation as Creative Process: Elaine Feinstein’s Marina Tsvetaeva
Authors: Impens Florence
Published: October 2019

This essay sheds new light on Elaine Feinstein’s Selected Poems by Marina Tsvetaeva (1971). This publication was crucial, not only in introducing Tsvetaeva to a larger Anglophone audience, but also in influencing Feinstein’s career. Its importance is the more remarkable, as Feinstein was then neither a Russian specialist nor a translator. Using archival material, the essay shows, first, how Feinstein’s versions of Tsvetaeva’s poems present a personal perspective on the Russian writer, echoing Feinstein’s poetic concerns at the turn of the 1970s and, second, how she used these drafts to test new creative possibilities that could be harnessed for her own future practice. More broadly, this is a case study of the links between literary translation and creative writing, when the poet has no previous knowledge of the source language.
Preoperative and intraoperative argatroban as anticoagulant for bridging a patient with heparin-induced thrombocytopaenia to lung transplantation
Authors: Oh Dong Kyu , Kim Dong Kwan , Choi Sehoon , Hong Sang-Bum
Published: October 2019

A 65-year-old male was bridged to lung transplantation with veno-venous extracorporeal membrane oxygenation (ECMO). After experiencing heparin-induced thrombocytopaenia, heparin was replaced with argatroban. After 24 days, bilateral sequential lung transplantation was performed with argatroban anticoagulation. Intraoperative argatroban doses ranged between 0.4 and 0.6 μg/kg/min, resulting in activated clotting time of 169–216 s and activated partial thromboplastin time of 45–75 s. The patient was weaned from ECMO immediately after lung transplantation, and no bleeding or thrombotic complications were observed. He was discharged home on postoperative day 140.
Effects of atrial natriuretic peptide on renal function during cardiopulmonary bypass: a randomized pig model
Authors: Kolsrud Oscar , Damén Tor , Nygren Andreas , Ricksten Sven-Erik , Tholén Maria , Hjärpe Anders , Laffin Anna , Dellgren Göran
Published: October 2019

OBJECTIVES

Acute kidney injury is a well-known complication after cardiac surgery and cardiopulmonary bypass (CPB). In this experimental animal study, we evaluated the effects of atrial natriuretic peptide (ANP) on renal function, perfusion, oxygenation and tubular injury during CPB.

METHODS

Twenty pigs were blindly randomized to continuous infusion of either ANP (50 ng/kg/min) or placebo before, during and after CPB. Renal blood flow as well as cortical and medullary perfusion was measured. Blood was repeatedly sampled from the renal vein. Glomerular filtration rate was measured by infusion clearance of 51Cr-EDTA.

RESULTS

Glomerular filtration rate was higher (P < 0.001), whereas renal blood flow or renal oxygen delivery was not affected by ANP during CPB. Renal oxygen consumption did not differ between groups during CPB, whereas renal oxygen extraction was higher in the ANP group (P = 0.03). Urine flow and sodium excretion were higher in the ANP group during CPB. Blood flow in the renal medulla, but not in the cortex, dropped during CPB, an effect that was not seen in the animals that received ANP.

CONCLUSIONS

ANP improved renal function during CPB. Despite impaired renal oxygenation, ANP did not cause tubular injury, suggesting a renoprotective effect of ANP during CPB. Also, CPB induced a selectively reduced blood flow in the renal medulla, an effect that was counteracted by ANP.
Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers
Authors: Fillinger Lucas , Hug Katrin , Griebler Christian
Published: October 2019

Several studies have analyzed biogeographic distribution patterns of microbial communities across broad spatial scales. However, it is often unclear to what extent differences in community composition across different regions are caused by dispersal limitation or selection, and if selection is caused by local environmental conditions alone or additional broad-scale region-specific factors. This is especially true for groundwater environments, which have been understudied in this context relative to other non-subsurface habitats. Here, we analyzed microbial community composition based on exact 16S rRNA amplicon sequence variants (ASVs) from four geographically separated aquifers located in different regions along a latitudinal transect of ∼700 km across Germany. Using a combination of variation partitioning and ecological null models revealed that differences in microbial community composition were mainly the product of selection imposed by local environmental conditions and to a smaller but still significant extent dispersal limitation and drift across regions. Only ∼23% of the total variation in microbial community composition remained unexplained, possibly due to underestimated effects of dispersal limitation among local communities within regions and temporal drift. No evidence was found for selection due to region-specific factors independent of local environmental conditions.
Free fatty acids promote transformation efficiency of yeast
Authors: Duan Xingpeng , Ma Xiaojing , Li Shengying , Zhou Yongjin J
Published: October 2019

High transformation efficiency is essential in genetic engineering for functional metabolic analysis and cell factory construction, in particular in construction of long biosynthetic pathways with multiple genes. Here, we found that free fatty acid (FFA)-overproducing strain showed higher transformation efficiency in Saccharomyces cerevisiae. We then verified that external supplementation of FFAs, to the culture media for competent cell preparation, improved yeast transformation efficiency significantly. Among all tested FFAs, 0.5 g/L C16:0 FFA worked best on promoting transformation of S. cerevisiae and Komagataella phaffii (previously named as Pichia pastoris). Furthermore, C16:0 FFA improved the assembly efficiency of multiple DNA fragments into large plasmids and genome by 100%, which will facilitate the construction and optimization of multigene-containing long pathways.
On enzymatic remodeling of IgG glycosylation; unique tools with broad applications
Authors: Sjögren Jonathan , Lood Rolf , Nägeli Andreas
Published: October 2019

The importance of IgG glycosylation has been known for many years not only by scientists in glycobiology but also by human pathogens that have evolved specific enzymes to modify these glycans with fundamental impact on IgG function. The rise of IgG as a major therapeutic scaffold for many cancer and immunological indications combined with the availability of unique enzymes acting specifically on IgG Fc-glycans have spurred a range of applications to study this important post-translational modification on IgG. This review article introduces why the IgG glycans are of distinguished interest, gives a background on the unique enzymatic tools available to study the IgG glycans and finally presents an overview of applications utilizing these enzymes for various modifications of the IgG glycans. The applications covered include site-specific glycan transglycosylation and conjugation, analytical workflows for monoclonal antibodies and serum diagnostics. Additionally, the review looks ahead and discusses the importance of O-glycosylation for IgG3, Fc-fusion proteins and other new formats of biopharmaceuticals.
Derived Equivalences for Symplectic Reflection Algebras
Authors: Losev Ivan
Published: October 2019

In this paper we study derived equivalences for symplectic reflection algebras. We establish a version of the derived localization theorem between categories of modules over these algebras and categories of coherent sheaves over quantizations of $\mathbb{Q}$-factorial terminalizations of the symplectic quotient singularities. To do this we construct a Procesi sheaf on the terminalization and show that the quantizations of the terminalization are simple sheaves of algebras. We will also sketch some applications to the generalized Bernstein inequality and to perversity of wall crossing functors.
Computer-Mediated Communication in the Age of Communication Visibility
Authors: Treem Jeffrey W , Leonardi Paul M , van den Hooff Bart
Published: October 2019

This article argues that a distinctive aspect of computer-mediated communication (CMC) is the way it can make communication visible to others in ways that were previously impractical. We propose a theory of communication visibility that recognizes its multidimensional nature: resulting from activities that make communication visible, efforts by actors to see communication, and a sociomaterial context that influences possibilities for visibility. The different dimensions of communication visibility are explored as they relate to possibilities for action with CMC, and the ability of third-parties to view communication between others. Centering communication visibility in the study of CMC compels scholars to ask new questions regarding the interdependence of active, strategic efforts to make communication more or less visible to others, and the ways in which communication is assessed by observers. To facilitate ongoing research we offer an agenda for incorporating communication visibility into the study of contemporary and future forms of CMC.
Decay of Thermal Tolerance in Queensland Fruit Fly Eggs (Bactrocera tryoni, Diptera: Tephritidae) Following Non-Lethal Heat Hardening
Authors: Brown S D J , Jamieson L E , Laidlaw W G , de Silva N , Waddell B C
Published: October 2019

Quarantine disinfestation treatments for Queensland fruit fly (Bactrocera tryoni (Froggatt)) have been developed which use high temperatures to kill preimaginal life stages within fruit prior to export. However, thermal tolerance of individuals can be increased if they are exposed to elevated temperatures before disinfestation treatment. The rate that this thermal conditioning decays after exposure, and the effect of temperature on this decay process, were investigated. Eggs of B. tryoni were exposed to a nonlethal hot water treatment at 38°C for 15 min, 1 or 3 h, then held in air at 25°C for times ranging from 15 min to 12 h, before being exposed to hot water disinfestation at 46°C for various times. From each of these cohorts, the lethal time for 99% mortality (LT99) was calculated. The LT99 of B. tryoni eggs increased with longer conditioning times at 38°C. For each conditioning time, the LT99 decreased with longer delay periods at 25°C prior to disinfestation. The rate of decrease was greatest during the first hour of delay, after which the rate of decrease slowed and tended toward zero. This induction and decay was modeled using a double-exponential equation. These experiments show that thermal conditions prior to disinfestation, and the time delay before the procedure commences, both influence the response of the insect to the disinfestation treatment. These results have implications for the specification of postharvest quarantine treatments, which are usually expressed only in terms of a fruit-center target temperature.
Can skilled immigration raise innovation? Evidence from Canadian Cities
Authors: Blit Joel , Skuterud Mikal , Zhang Jue
Published: October 2019

We examine the effect of changes in skilled-immigrant population shares in 98 Canadian cities on per capita patents. The Canadian case is of interest because its ‘points system’ is viewed as a model of skilled immigration policy. Our estimates suggest that the impact of increasing the university-educated immigrant share on patenting rates is modest at best and unambiguously smaller than the impact of skilled immigrants in the USA. We find larger effects of Canadian science, engineering, technology or mathematics (STEM)-educated immigrants employed in STEM jobs, but this impact is limited because only one-third of Canadian STEM-educated immigrants are employed in STEM jobs, compared with two-fifths of native-born Canadians and one-half of US immigrants. Our findings suggest that for most countries, skilled immigration is unlikely to be a panacea for sluggish innovation and that the US experience may be exceptional.
Prognostic value of risk stratification using blood parameters for nivolumab in Japanese patients with metastatic renal-cell carcinoma
Authors: Yamamoto Yoshiaki , Matsuyama Hideyasu , Matsumoto Hiroaki , Sakano Shigeru , Fuji Nakanori , Oba Kazuo , Yamamoto Mitsutaka , Kamiryo Yoriaki , Hiragino Takeshi , Nagao Kazuhiro , Takai Kimio , Aoki Akihiko
Published: October 2019

Background

Nivolumab is a standard treatment for previously treated advanced renal-cell carcinoma. However, nivolumab is effective in only a limited number of patients; therefore, we evaluated the prognostic value of several biomarkers, including inflammation-based prognostic scores and changes in these scores following nivolumab treatment in Japanese patients with metastatic renal-cell carcinoma.

Methods

We retrospectively reviewed the medical records of 65 patients with previously treated metastatic renal-cell carcinoma and who received nivolumab. Inflammation-based prognostic scores, including neutrophil/lymphocyte ratio, platelet/lymphocyte ratio, lymphocyte/monocyte ratio, and Glasgow prognostic score before and 6 weeks after the treatment were recorded. Categorical variables influencing disease-specific survival were compared using Cox proportional-hazards regression models.

Results

Univariate analysis showed that Memorial Sloan-Kettering Cancer Center risk score (P = 0.0052), lactate dehydrogenase (P = 0.0266), lymphocyte/monocyte ratio (P = 0.0113), and platelet/lymphocyte ratio (P = 0.0017) had a significant effect on disease-specific survival. Multivariate analyses showed that platelet/lymphocyte ratio and lactate dehydrogenase were found to be independent prognostic factors for disease-specific survival (P = 0.0008, risk ratio (RR) = 7.95, 95% confidence interval, 2.16–51.64 and P = 0.0123, RR = 3.92, 95% confidence interval, 1.37–10.80, respectively). The combination of platelet/lymphocyte ratio and lactate dehydrogenase was the most significant prognostic biomarker in metastatic renal-cell carcinoma (P < 0.0001). Changes in lymphocyte/monocyte ratio and platelet/lymphocyte ratio in response to nivolumab were significant prognostic factors for disease-specific survival (P < 0.0001 and P = 0.0477, respectively).

Conclusions

The combination of platelet/lymphocyte ratio and lactate dehydrogenase may be a potential biomarker for estimating disease-specific survival in Japanese patients with metastatic renal-cell carcinoma treated by nivolumab.
Prospective observational study on the safety of an original fiducial marker insertion for radiotherapy in gynecological cancer by a simple method
Authors: Sekii Shuhei , Tsujino Kayoko , Kubota Hikaru , Yamaguchi Satoshi , Kosaka Kengo , Miyazaki Shuichiro , Sulaiman Nor Shazrina , Matsumoto Yoko , Ota Yosuke , Soejima Toshinori , Sasaki Ryohei
Published: October 2019

Our observational study aimed to verify the safety of our original titanium fiducial markers in gynecological cancer by using a simple insertion method. We prospectively evaluated the safety in patients with gynecological cancer who had undergone our insertion procedure of the titanium markers. The decision to implant a titanium marker was at the discretion of each radiation oncologist. The fiducial markers were manufactured by severing ligating clips for surgery into 3–6 mm pieces and were sterilized thereafter. We inserted an 18-gauge injection needle containing the marker before the marker was extruded by a 22-gauge Cattelan needle or shape memory alloy wire into the tumor or tissues close to the tumor. Severe complications within 3 months after implantation were scored according to the National Cancer Institute’s Common Terminology Criteria for Adverse Events version 4.0. Between August 2016 and December 2018, we enrolled 46 patients. Of 46, 44 underwent implantation. The median age was 58.5 years. The most common primary site was the cervix. Two patients experienced detachment of the markers after implantation. No Grade 3 or higher level of complications was observed. Our simple insertion technique for original titanium fiducial markers was well-tolerated.
Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA
Authors: Delaby Marie , Panis Gaël , Viollier Patrick H
Published: October 2019

Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, first activates promoters in late S-phase and then mysteriously switches to different target promoters in G1-phase. We uncovered a highly conserved determinant in the DNA-binding domain (DBD) of CtrA uncoupling this promoter switch. We also show that it reprograms CtrA occupancy in stationary cells inducing a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in a critical residue within the core DBD imposes opposing developmental phenotypes and transcriptional activities of CtrA and a proximal residue can direct CtrA towards activation of the dispersal (G1-phase) program. Hence, we propose that this conserved determinant in the CtrA primary structure dictates promoter reprogramming during the growth transition in other alpha-proteobacteria that differentiate from replicative cells into dispersal cells.
PhaSePro: the database of proteins driving liquid–liquid phase separation
Authors: Mészáros Bálint , Erdős Gábor , Szabó Beáta , Schád Éva , Tantos Ágnes , Abukhairan Rawan , Horváth Tamás , Murvai Nikoletta , Kovács Orsolya P , Kovács Márton , Tosatto Silvio C E , Tompa Péter , Dosztányi Zsuzsanna , Pancsa Rita
Published: October 2019

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.
VISDB: a manually curated database of viral integration sites in the human genome
Authors: Tang Deyou , Li Bingrui , Xu Tianyi , Hu Ruifeng , Tan Daqiang , Song Xiaofeng , Jia Peilin , Zhao Zhongming
Published: October 2019

Virus integration into the human genome occurs frequently and represents a key driving event in human disease. Many studies have reported viral integration sites (VISs) proximal to structural or functional regions of the human genome. Here, we systematically collected and manually curated all VISs reported in the literature and publicly available data resources to construct the Viral Integration Site DataBase (VISDB, https://bioinfo.uth.edu/VISDB). Genomic information including target genes, nearby genes, nearest transcription start site, chromosome fragile sites, CpG islands, viral sequences and target sequences were integrated to annotate VISs. We further curated VIS-involved oncogenes and tumor suppressor genes, virus–host interactions involved in non-coding RNA (ncRNA), target gene and microRNA expression in five cancers, among others. Moreover, we developed tools to visualize single integration events, VIS clusters, DNA elements proximal to VISs and virus–host interactions involved in ncRNA. The current version of VISDB contains a total of 77 632 integration sites of five DNA viruses and four RNA retroviruses. VISDB is currently the only active comprehensive VIS database, which provides broad usability for the study of disease, virus related pathophysiology, virus biology, host–pathogen interactions, sequence motif discovery and pattern recognition, molecular evolution and adaption, among others.
Understanding the binding specificities of mRNA targets by the mammalian Quaking protein
Authors: Sharma Monika , Sharma Shakshi , Alawada Apoorv
Published: October 2019

Mammalian Quaking (QKI) protein, a member of STAR family of proteins is a mRNA-binding protein, which post-transcriptionally modulates the target RNA. QKI protein possesses a maxi-KH domain composed of single heterogeneous nuclear ribonucleoprotein K homology (KH) domain and C-terminal QUA2 domain, that binds a sequence-specific QKI RNA recognition element (QRE), CUAAC. To understand the binding specificities for different mRNA sequences of the KH-QUA2 domain of QKI protein, we introduced point mutations at different positions in the QRE resulting in twelve different mRNA sequences with single nucleotide change. We carried out long unbiased molecular dynamics simulations using two different sets of recently updated forcefield parameters: AMBERff14SB+RNAχOL3 and CHARMM36 (with CMAP correction). We analyzed the changes in intermolecular dynamics as a result of mutation. Our results show that AMBER forcefields performed better to model the interactions between mRNA and protein. We also calculated the binding affinities of different mRNA sequences and found that the relative order correlates to the reported experimental studies. Our study shows that the favorable binding with the formation of stable complex will occur when there is an increase of the total intermolecular contacts between mRNA and protein, but without the loss of native contacts within the KH-QUA domain.