bluuebunny/crossref_metadata_2025 huggingface dataset:
PSXI-18 Clove oil and cashew nut shell liquid have antibacterial activity against some ruminal Prevotella
Authors: Carvalho Venício M , Avila Vicente A Diaz , Matos Aylle Medeiros , Bonin Edineia , Mendes Amanda T Teixeira , Castilho Ricardo Araújo , Prado Rodolpho Martin Do , Prado Ivanor Nunes do
Published: December 2019

This work was carried out to evaluate in vitro antimicrobial activity of cashew nut shell liquid (CNSL) and clove essential oil (Eugenia caryophyllata) on Prevotella albensis (DSM 11370), Prevotella bryantii (DSM 11371) and Prevotella ruminicola (ATCC® 19189™). The experiments were designed using each bacterium exposed to two different doses (1:500 and 1:5000 g/L on Tween) of either clove oil or CNSL and with six replicates. Bacteria were cultivated on Hobson’s M2 medium in Hungate tubes. Cultures without addition of any oils were considered as control. Antimicrobial activity was evaluated using Spectrophotometer Evolution 201 UV-visible (Thermo Scientific) at 600 nm. Readings were performed at 0, 8, 12 and 24 hours after inoculation. Data were analysed using linear mixed models and NLME Procedure in R software. Both clove oil and CNSL had an inhibitory effect against the tested bacteria. However, each bacterium responded differently to the treatment. Clove oil decreased (P < 0.05) the microbial growth of P. ruminicola (-32% and -31%) when doses 1:500 and 1:5000 were used. However, there was no effect of clove oil P. bryantii and P. albensis. The use of CNSL reduced growth of P. albensis (-38 and -41%), P. bryantii (-44% and 52%) and P. ruminicola (-41 and -52%), when doses 1:500 and 1:5000, respectively. These results demonstrate the effect of clove oils and CNSL to inhibit growth of gram negative ruminal bacteria. These results provide a prospect of the use of both products to modulate the rumen. For example, the Prevotellaceae family is responsible to degrade protein, amino acid deamination and formation of volatile fatty acids in the rumen. Thus, CNSL and clove oils have potential to modulate the ruminal fermentation by having antibacterial activity against gram negative bacteria.
PSXII-11 In vitro fermentative parameters of diets containing increasing inclusions of soybean molasses for sheep
Authors: Arruda Maria Carolina G , Pereira-Junior Sérgio A G , Almeida Marco Túlio C
Published: December 2019

The objective of this study was to evaluate the effects of increasing inclusion of soybean molasses (SM) in sheep diets on in vitro gas production, pH, N-NH3 and VFA. Three ruminally-cannulated adult sheep were used as donors of inoculum. The treatments consisted of diets containing 0, 10, 20 and 30% of SM (DM basis) with forage: concentrate ratio of 20:80. The experimental design was completely randomized with repeated measurements over time (2, 6, 12 and 24 hours). Flasks with a volume of 50 mL were used for incubation. Approximately, 0.2 g of sample, 10 mL of the inoculum and 20 mL of the McDougall buffer solution were added into the flasks. Each time consisted of 6 bottles per treatment and 2 bottles without sample (n = 104). Gas production was measured by a pressure transducer. Concentrations of N-NH3 was determined using micro-Kjeldhal apparatus, and VFA was determined by gas chromatography. The disappearance of DM was evaluated by filtration using nylon bags (50 μm porosity). The data were analyzed using the MIXED procedure of SAS. Orthogonal contrasts were used to determine the linear and quadratic effect of SM inclusion. Total concentration of VFA, pH and gas production per g disappeared (mL/g DM disappeared) had no significant effect (P > 0.05). Gas production per incubated g (mL/g DM incubated), disappearance of DM (%) showed increasing linear effect (P < 0.05), with values of 92.87 to 119.64 and 58.48 to 75.40 for 0 and 30% of SM, respectively. N-NH3 (mg/dL) presented a linear decreasing effect (P < 0.05), ranging from 19.27 to 16.95, for 0 and 30% of SM, respectively. The inclusion up to 30% of SM (DM basis) in sheep diets did not affect in vitro fermentation parameters and did not promote a difference in gas production per g disappeared when compared to other treatments.
PSXII-19 Feed additives association for the rumen fermentation manipulation and reduce production methane in Nellore cattle
Authors: Sene Guilherme , Tropaldi Cristiane , Assumpçao Alice H , Tseu Ramos , Oliveira Júlia , Mendes Isabelle , Junior Flávio Perna , Rodrigues Paulo H
Published: December 2019

Aimed to evaluate the association between essential oils (Next Enhance 300®), exogenous enzymes (Allzyme SSF®), and monensin for the rumen fermentation manipulation, especially reduction of rumen methane in Nellore cattle. Eight cows weighing 480 ± 55 kg and cannulated in the rumen were used in two 4x4 Latin squares, into a 2x2x2 factorial arrangement, which one of the factors being analyzed by the squared effect. The animals fed the same basal diet using a corn silage: concentrate ratio of 60:40. The factors used were: 300 mg/animal/d, 10 g/animal/d, 300 mg/animal/d for essential oils, exogenous enzyme, and monensin, respectively. Each experimental period lasted 26 days. Sixteen days were used for adaptation to the experimental diets, while from D16 to D21 for evaluation of DMI and D22 to evaluate rumen fermentation (0, 3, 6, 9, and 12h after feeding) through the ex situ technique, which consists of incubating ruminal content in conditions similar to those of the rumen allowing the measurement of rumen production (SCFA and methane). Differences were considered significant when P-value was below 0,05 through analysis of variance using mixed procedure. No significant difference (P > 0.05) was observed for DMI Monensin decreased (P < 0.05) the concentration of acetic, butyric and total SCFA. However, the production of acetic acid, propionic acid, total SCFA and acetate:propionate ratio was not altered (P > 0,05). Significant interaction (P < 0.05) between enzyme and monensin was observed for butyric acid production, indicating the enzyme used alone did not alter the production of these acid, but when associated with monensin, a reduction was observed. The enzyme reduced (P < 0.05) methane concentration, and when associated with monensin this reduction was increased. However methane production was not affected (P > 0.05). The feed additives evaluated do not reduce the rumen production of methane, but reduced butyric acid production.
PSXII-15 Fiber content in diets for feedlot lambs: ruminal and cecal pH and short chain fatty acids
Authors: Ferreira Evandro M , Eckermann Nathalia R , Biava Janaina S , Avelino Matheus , Pasqualino Letícia , Martins André S , Limede Arnaldo C , Baggio Marcelo , Cunha Ancelmo , Neto Francisco Montanaro , de Paula Matheus F F V , Pires Alexandre Vaz
Published: December 2019

Fifty-eight Dorper x Santa Inês ram lambs (initial BW 20.7 ± 1.19 kg and 75 ± 10.83 d old) were assigned to a randomized complete block design to evaluate the effects of fiber content on ruminal and cecal pH and SCFA. The treatments were defined by the fiber (“Coastcross” hay) content in diets (CP: 16,12% ± 0.92): 0F: no forage diet (NDF: 10.4%); 5F: 5% of forage (NDF: 12.1%); 10F: 10% of forage (NDF: 15%); 15F: 15% of forage (NDF: 15.5%); 20F: 20% of forage (NDF: 20.8%) and 25F: 25% of forage (NDF: 23.5%). The experiment lasted 89 days, at the end of the experiment the lambs were slaughtered without fasting. The forage inclusion linear decreased ruminal concentration of propionate (0F: 45.4; 5F: 39.7; 10F: 41.5; 15F: 39.4; 20F: 35.3; 25F: 30.5 mM/100mM; P < 0.01) and total SCFA (0F: 106.6; 5F: 96.4; 10F: 84.2; 15F: 90.6; 20F: 63.0; 25F: 71.2 mM; P = 0.01) and increased the ruminal concentration of acetate (0F: 43.4; 5F: 45.3; 10F: 47.8; 15F: 49.8: 20F: 51.8; 25F: 57.2 mM/100mM; P < 0.01). However, there was a quadratic effect on ruminal pH (0F: 5.61; 5F: 5.66; 10F: 5.98; 15F: 6.27; 20F: 6.05; 25F: 5.74; P = 0.01). There was no effect of fiber levels on cecal concentration of acetate, propionate, butyrate and acetate:propionate ratio. Nevertheless, there was a linear decrease in cecal concentration of valerate (0F: 3.28; 5F: 2.35; 10F: 2.39; 15F: 2.64: 20F: 2.12; 25F: 1.80 mM/100mM; P < 0.01) and total SCFA (0F: 173.9; 5F: 165.7; 10F: 153.2; 15F: 155.2; 20F: 139.9; 25F: 128.9 mM; P < 0.01). Similarly to rumen, cecal pH presented a quadratic response (0F: 5.92; 5F: 6.12; 10F: 6.15; 15F: 6.23; 20F: 6.30; 25F: 5.83; P < 0.01). In conclusion, cecal fermentation was different from rumen fermentation. However, pH variation was similar, with higher values for 15F diet.
PSXII-35 Tolerance of fattening cattle to slow release urea
Authors: Devant Maria , Holder Vaughn , Moran Colm
Published: December 2019

The objective of this experiment was to evaluate the tolerance of fattening beef cattle to slow release urea (SRU). Twenty-four growing Holstein bulls were blocked by weight and randomly assigned to one of three treatments: CON (no urea) and SRU (Optigen®, Alltech Inc., KY) at 1% or 3% of the ration. Energy and crude protein levels were maintained in SRU diets by replacing soybean meal with SRU, barley meal and corn meal. Daily feed intake and body weights at d 0, 21 and 42 were registered. Blood was collected on d 0 and 42 for hematologic and biochemical analysis. Intake was analyzed using a linear mixed-effects model with repeated measures with initial body weight as a covariate. Blood data at d 42 were analyzed using a linear model with fixed effect of treatment including data of d 0 as covariate. Intake did not differ among dietary treatments (P > 0.1). Blood hematologic results for all treatments were within normal physiologic ranges. Compared with CON, bulls fed diets with SRU at 1% or 3% had lesser hemoglobin (13.0 vs.12.3, 12.3 g/dL; P = 0.028) and lesser packed cell volume (33.1 vs. 31.1, 31.2%; P = 0.007). Serum albumin concentrations differed between treatments, but values were within normal physiologic range (3.7, 3.4 and 3.6 g/dL, P < 0.01). Total protein values were significantly lesser in SRU containing diets versus CON (6.8 vs. 6.6, 6.5 %; P = 0.031) and slightly under the reference values. Serum ammonia concentrations were well below the toxic limit and did not differ among dietary treatments (P > 0.1). There was no evidence of ammonia toxicity during the study. Feeding SRU appears to be safe and well tolerated when included at up to 3% of the diet in Holstein bulls fed high-concentrate diets during a 6-wks period.
PSXIV-15 Metagenomic sequencing of rumen microorganisms of cattle fed a corn stover-based diet
Authors: Piña-Gónzalez Laura , Miranda-Ríos Juan , Alonso-Morales Rogelio Alejandro , Maya Otoniel , Corona Luis , Márquez-Mota Claudia Cecilia
Published: December 2019

Worldwide, there is a need to discover new microorganisms that efficiently degrade lignocellulosic complexes that would help to improve the digestibility of low-quality agricultural byproducts. The aim of the study was to evaluate the effects of a corn stover-based diet (CSD) on rumen bacteria. Ruminal fluid of 6 Holstein cows (595 ± 96 kg) was collected during two periods. During first period, animals were consuming a diet based on corn silage and oat hay (DB), mineral premix and water ad libitum (50:50, DM). In second period, animals were provided a CSD (100% DM), mineral premix and water ad libitum for 45 days. Ruminal fluid was collected through esophageal tube, filtered and stored at -80°C until DNA extraction. Rumen microorganisms were identified by sequencing the 16SrRNA gene using the Illumina Miseq platform and primers for V3 and V4 regions. Data were analyzed by QIIME 1.9. Analysis of variance was performed for a completely randomized design using the MIXED procedure of SAS 9.1. The taxonomic affiliation showed that both populations were mainly composed of Firmicutes, Bacteroidetes and Proteobacteria. The most abundant bacteria species in both diets were Ruminococcus flavefaciens, Prevotella copri, Prevotella ruminicola, Fibrobacter succinogenes, Bacillus coagulans, Bacteroides uniformis and Selenomonas ruminantium. Feeding a CSD, increased the relative abundance of Prevotella ruminicola (from 6.1 to 20.9%, P < 0.01), Streptococcus luteciae (from 0.05 to 0.78%, P < 0.01), Clostridium aminophilum (0.45 to 3.1%, P < 0.01), Selenomonas ruminantium (5.2 to 21.8%, P < 0.02) and Pantoea agglomerans (0.7 to 3.9%, P < 0.01) and decreased Propionibacterium acnes (0.7 to 0.1%, P < 0.02) and Bacteroides ovatus (0.9 to 0.1%, P < 0.01). Feeding cattle with a diet with a more lignified forage like CSD led to the proliferation of bacteria such as Prevotella ruminicula, Streptococcus luteciae, Clostridium aminophilum, Selenomonas ruminantium and Pantoea agglomerans.
PSX-26 Levels of forage and narasin inclusion on rumen fermentation in feedlot lambs
Authors: Sardinha Lairana A , Polizel Daniel M , Miszura Alexandre A , Limede Arnaldo C , Barroso José P R , Martins André S , Oliveira Gabriela B , Ferreira Evandro M , Eckermann Nathalia R , Vaz Pires Alexandre
Published: December 2019

The objective of this study was to determine the effects of forage levels and narasin inclusion in diets on the rumen parameters in feedlot lambs. Forty-four lambs were allotted in a randomized complete block design, defined by initial body weight, in a 2x2 factorial arrangement. The first factor was forage inclusion (10 or 20% of coastcross hay, DM basis) and the second factor was narasin (0 or 13 ppm). The experimental diets were isonitrogenous (17.4%, DM basis). At the end of the experimental period, the lambs were slaughtered without fasting, and the rumen fluid was collected to determinate pH and short chain fatty acid (SCFA). Data were analyzed using the MIXED procedure of SAS and the LSMEANS option was used to obtain the means. The effects were considered significant when P < 0.05. There was an interaction between hay and narasin on the molar proportion of propionate (P = 0.02) and the acetate:propionate ratio (P < 0.01). Narasin inclusion in diets containing 20% forage increased propionate (25.4 vs 37.1 mM/100mM; P = 0.02); however, there was no effect in diets containing 10% forage (35.9 ± 1.75 mM/100Mm). Consequently, the narasin decreased acetate:propionate ratio in diets containing 20% forage (2.57 vs 1.42; P < 0.01), and no effect was observed 10% forage diets (1.40 ± 0.14). The inclusion of narasin increased the total SCFA (86.2 vs 115.4 mM; P < 0.01), ruminal pH (6.26 vs 6.49; P = 0.05) and decreased acetate (55.6 vs 47.6 mM/100mM; P < 0.01). The inclusion of 20% forage increased acetate when compared with 10% hay (54.99 vs 48.19 mM/100mM; P < 0.01) and the pH ruminal (6.25 vs 6.49; P = 0.04). The experimental diets did not affect the butyrate. In summary, the narasin inclusion and forage levels content change rumen parameters in feedlot lambs.
Cyberbullying Perpetration and Victimization in Youth: A Meta-Analysis of Longitudinal Studies
Authors: Marciano Laura , Schulz Peter J , Camerini Anne-Linda
Published: December 2019

Cyberbullying perpetration (CP) and victimization (CV) are prevalent issues in adolescent development. However, previous meta-analyses focused only on cross-sectional findings. The present study aims to meta-analytically summarize 56 longitudinal studies on CP, CV, and related factors in children and adolescents. Forty meta-analyses on CP and CV as both predictors and outcomes of person-related, Internet activity-related, and contextual factors were performed. Additional moderator analyses took into account study design, sample population, and quality of the studies. Results highlight reciprocal longitudinal effects among CP, CV, and both traditional bullying and victimization: CP causes externalizing problem behaviors over time, whereas CV constitutes a risk factor of internalizing problems, such as depression and anxiety. Conversely, behavioral problems and increased Internet use predict involvement in CP, while depression, anxiety, and Internet use also predict CV over time. Further longitudinal research is needed to provide empirical evidence on understudied concepts.
The Purposes of Starvation
Authors: Conley Bridget , de Waal Alex
Published: December 2019

Mass starvation has throughout history been mis-categorized as a natural phenomenon, or an unfortunate side-effect of conflict and political oppression. The numbers and names of the victims fade into the background, blurred traces of the horrors of history. Yet, this is both an inaccurate understanding of starvation crimes and an injustice to victims. Mass starvation is a process of deprivation that occurs when actors impede the capacity of targeted persons to access the means of sustaining life. In this article, we introduce key features of starvation and note that many of the acts that create conditions of mass starvation are already prohibited under different provisions of international law. We introduce the term ‘starvation crimes’ to capture how these separately criminalized acts, when perpetrated over a long duration can create mass starvation. Implicit in ‘starvation crimes’ is that starvation is produced by leaders’ decisions and serves political, military or economic goals. We discuss nine objectives that can be furthered through mass starvation, offering historical examples to illustrate each. They include: (i) extermination or genocide; (ii) control through weakening a population; (iii) gaining territorial control; (iv) flushing out a population; (v) punishment; (vi) material extraction or theft; (vii) extreme exploitation; (viii) war provisioning; and (ix) comprehensive societal transformation.
Pollen Resources Used by Two Species of Stingless Bees (Meliponini) in a Tropical Dry Forest of Southern Ecuador
Authors: Gaona Fernando P , Guerrero Anthony , Gusmán Elizabeth , Espinosa Carlos Iván
Published: December 2019

Pollinators are crucial for ecosystem functionality; however, little is known about the plant species used by some of these, such as stingless bees. In this study, for the first time, pollen resources used by Melipona mimetica Cockerell (Hymenoptera: Apidae: Meliponini) and Scaptotrigona sp. Moure (Hymenoptera: Apidae: Meliponini) were identified through analysis of corbicular pollen found on worker bees in a dry forest in southern Ecuador. In total, 68 pollen types were identified belonging to 31 botanical families. The most represented plant families were Fabaceae (16%), Malvaceae (7%), and Boraginaceae (7%). Both stingless bee species exhibited a polylectic behavior, with an average of 16 pollen types collected by individual bees. Differences in abundances of pollen types collected by each species indicated distinct uses for these two bee species.
Detection of Amblyomma mixtum (Acari: Ixodidae) in Germany on a Human Traveler Returning From Cuba
Authors: Chitimia-Dobler Lidia , Schaper Sabine , Mansfeld Peter , Gonschorrek Joachim , Bröker Michael , Nava Santiago
Published: December 2019

The importation of exotic ticks to Germany on infested humans is rarely reported. Here we describe the detection of an Amblyomma mixtum nymph harboring Rickettsia amblyommatis by a tourist returning from a holiday trip to Cuba. Tick infestation may be neglected by tourists. Therefore, careful anamnesis and diagnosis should be carried out when tourists return from tropical and subtropical countries suffering from nonspecific symptoms, such as fever and malaise.
Successful management of severe coronoid process hyperplasia in a patient with mucopolysaccharidosis VI: a case report
Authors: Khadembaschi Darius , Arvier John , Beech Nicholas , Dolan David , McGill Jim
Published: December 2019

Mucopolysaccharidoses are a group of rare lysosomal storage diseases caused by a deficiency of enzymes, which breakdown glycosaminoglycans, with consequent dysfunction of affected tissues. Mandibular coronoid hyperplasia, with associated trismus, has been recently described as a feature of the craniofacial abnormalities seen in these patients. However, the details of the surgical and post-operative management of these patients have not been previously documented. This case describes the successful management of severe trismus from coronoid process hyperplasia in a 14-year-old male, utilising an extra-oral approach for bilateral coronoidectomies and removal of exophytic zygomatic bone, followed by immediate and long-term physiotherapy. An improvement of mandibular opening from 8 to 45 mm has been maintained at 18 months post operation.
The influence of metagalactic ultraviolet background fluctuations on the high-redshift Lyα forest
Authors: Meiksin Avery
Published: December 2019

Under the assumption that galaxies and quasi-stellar objects (QSOs) dominate the metagalactic ultraviolet (UV) background, it is shown that at high redshifts, fluctuations in the UV background are dominated by QSO shot noise and have an autocorrelation length of a few to several comoving Mpcs, depending on the bright end of the QSO luminosity function. The correlations create long-range spatial coherence in the neutral hydrogen fraction. Using a semi-analytic model, it is demonstrated that the coherence may account for the broad distribution in effective optical depths measured in the Lyα forest spectra of background QSOs, for line-of-sight segments of comoving length $50\, h^{-1}$ Mpc at redshifts 5 < z < 6. Capturing the fluctuations in a numerical simulation requires a comoving box size of ∼1 Gpc, although a box half this size may be adequate if sufficient random realizations of the QSO population are performed.
The use of particle distributions in Solar system small body dynamics
Authors: Kastinen Daniel
Published: December 2019

The extraterrestrial material, called meteoroids, that constantly enters the Earth’s atmosphere gives us a unique opportunity to examine the motion and population of small bodies in the Solar system. This exploration requires simulating the motion of these particles. Currently, only the timing of meteoroids encountering the Earth is well predicted by such simulations, while other parameters are uncertain. This can be remedied by proper stochastic representation and estimation using a sufficient number of samples. We propose methods to both represent simulations in a stochastic manner and to improve sampling using Importance Sampling. We also demonstrate these methods practically with a test model. Using the test model resulted in an error reduction by a factor of 3 without increase in computation time. Thus, we validated that these techniques can be implemented on and are compatible with Solar system small body dynamics models. Based on these results we predict that when properly implemented on a larger and more complex model, Importance Sampling can improve sampling numbers by several orders of magnitude without increasing computation time, depending on the simulation in question. The methods presented here bring advantages such as; greatly reduced estimation errors, fitting models without re-running simulations, model comparisons without sample variations, circumventing unknown properties using invariant measures, representing large particle numbers without additional errors. This methodology has wide application possibility and will enable larger, more reliable and reusable simulations of dynamical astronomy.
Momentum injection by clustered supernovae: testing subgrid feedback prescriptions
Authors: Gentry Eric S , Madau Piero , Krumholz Mark R
Published: December 2019

Using a 1D Lagrangian code specifically designed to assess the impact of multiple, time-resolved supernovae (SNe) from a single-star cluster on the surrounding medium, we test three commonly used feedback recipes: delayed cooling (e.g. used in the gasoline-2 code), momentum-energy injection (a resolution-dependent transition between momentum-dominated feedback and energy-dominated feedback used, e.g. in the fire-2 code), and simultaneous energy injection (e.g. used in the EAGLE simulations). Our work provides an intermediary test for these recipes: we analyse a setting that is more complex than the simplified scenarios for which many were designed, but one more controlled than a full galactic simulation. In particular, we test how well these models reproduce the enhanced momentum efficiency seen for an 11 SN cluster simulated at high resolution (0.6 pc; a factor of 12 enhancement relative to the isolated SN case) when these subgrid recipes are implemented in low resolution (20 pc) runs. We find that: (1) the delayed cooling model performs well – resulting in 9 times the momentum efficiency of the fiducial isolated SN value – when SNe are clustered and 1051 erg are injected per SN, while clearly overpredicting the momentum efficiency in the single SN test case; (2) the momentum-energy model always achieves good results, with a factor of 5 boost in momentum efficiency; and (3) injecting the energy from all SNe simultaneously does little to prevent overcooling and greatly underproduces the momentum deposited by clustered SNe, resulting in a factor of 3 decrease in momentum efficiency on the average.
Spectral library of age-benchmark low-mass stars and brown dwarfs
Authors: Manjavacas E , Lodieu N , Béjar V J S , Zapatero-Osorio M R , Boudreault S , Bonnefoy M
Published: December 2019

In recent years, some extremely red brown dwarfs have been discovered. They were believed to have a low surface gravity, but many of their spectral characteristics are similar to those of high-surface-gravity brown dwarfs, showing that the spectral characteristics of young brown dwarfs are poorly understood. We aim to test surface-gravity indicators in late-M and early-L brown dwarf spectra using data obtained with the X-shooter spectrograph at the Very Large Telescope. We select a benchmark sample of brown dwarf members of Chamaeleon I (∼2 Myr), Upper Scorpius (5−10 Myr), the Pleiades (132 ± 27 Myr) and Praesepe (590−790 Myr) with well-constrained ages and similar metallicities. We provide a consistent spectral classification of the sample in the optical and in the near-infrared. We measure the equivalent widths of their alkali lines, finding that they have a moderate correlation with age, especially for objects with spectral types M8 and later. We use spectral indices defined in the literature to estimate surface gravity, finding that their gravity assignment is accurate for 75 per cent of our sample. We investigate the correlation between red colour and age, finding that after ∼10 Myr, the colour does not change significantly for our sample with spectral types M6.0–L3.0. In this case, the red colours might be associated with circumstellar discs, ring structures, extinction, or viewing angle. Finally, we calculate the bolometric luminosity, and J and K bolometric corrections for our sample. We find that six objects are overluminous compared with other members of the same association. These objects are flagged as binary candidates by the Gaia survey.
De novo diploid genome assembly for genome-wide structural variant detection
Authors: Zhang Lu , Zhou Xin , Weng Ziming , Sidow Arend
Published: December 2019

Detection of structural variants (SVs) on the basis of read alignment to a reference genome remains a difficult problem. De novo assembly, traditionally used to generate reference genomes, offers an alternative for SV detection. However, it has not been applied broadly to human genomes because of fundamental limitations of short-fragment approaches and high cost of long-read technologies. We here show that 10× linked-read sequencing supports accurate SV detection. We examined variants in six de novo 10× assemblies with diverse experimental parameters from two commonly used human cell lines: NA12878 and NA24385. The assemblies are effective for detecting mid-size SVs, which were discovered by simple pairwise alignment of the assemblies’ contigs to the reference (hg38). Our study also shows that the base-pair level SV breakpoint accuracy is high, with a majority of SVs having precisely correct sizes and breakpoints. Setting the ancestral state of SV loci by comparing to ape orthologs allows inference of the actual molecular mechanism (insertion or deletion) causing the mutation. In about half of cases, the mechanism is the opposite of the reference-based call. We uncover 214 SVs that may have been maintained as polymorphisms in the human lineage since before our divergence from chimp. Overall, we show that de novo assembly of 10× linked-read data can achieve cost-effective SV detection for personal genomes.
Examining Procedural Unfairness and Credibility Findings in the UK Asylum System
Authors: Campbell John R
Published: December 2019

This article addresses a key problem confronted by immigration judges (IJs) in their assessment of the asylum claims of unaccompanied asylum-seeking children – who are often not allowed to speak or participate in their own hearings – namely the manner in which asylum legal procedure is intertwined with an IJ’s decision to refuse the claim on the basis of adverse credibility. This article has three linked aims: to examine research that looks at how IJs decide credibility; to set out an ethnographic approach to better understand IJs’ decision-making; and to argue that asylum tribunals need to adopt appropriate guidelines.
True nutrient and amino acid digestibility of dog foods made with human-grade ingredients using the precision-fed cecectomized rooster assay1
Authors: Oba Patrícia M , Utterback Pamela L , Parsons Carl M , Swanson Kelly S
Published: December 2019

For a pet diet to be labeled as human-grade, every ingredient and the finished food must be stored, handled, processed, and transported according to the current good manufacturing practices for human edible foods. Human-grade dog foods are now available and increasing in popularity, but little research has been conducted to test the digestibility of these foods. For this reason, the objective of this experiment was to determine the true nutrient and amino acid (AA) digestibilities of dog foods formulated with human-grade ingredients using the precision-fed cecectomized rooster assay. Six commercial dog foods were tested, including the Beef & Russet Potato (BRP), Chicken & White Rice (CWR), Fish & Sweet Potato (FSP), Lamb & Brown Rice (LBR), Turkey & Whole Wheat Macaroni (TWM), and Venison & Squash (VSR) formulas provided by Just Food For Dogs LLC (Irvine, CA). Before analysis, all foods were lyophilized and ground. A precision-fed rooster assay using cecectomized roosters was conducted to determine the true nutrient digestibility and standardized AA digestibilities of the foods tested. Conventional roosters were used to determine the nitrogen-corrected true metabolizable energy (TMEn) of the foods. All animal procedures were approved by the University of Illinois Institutional Animal Care and Use Committee prior to experimentation. The substrates and rooster excreta were analyzed for macronutrient and AA composition. All data were analyzed using the Mixed Models procedure of SAS (version 9.4; SAS Institute, Cary, NC). In general, all foods tested were highly digestible. Dry matter digestibility was similar among CWR, LBR, and TWR foods, and greater (P < 0.0001) than that of FSP and VSR foods. Organic matter digestibility was highest (P = 0.0002) for CWR and lowest (P = 0.0002) for VSR. For the majority of indispensable AA, digestibilities were greater than 85%, with some being greater than 90%. TMEn was higher (P < 0.0001) for BRP than the other foods, which were similar to one another. Also, TMEn values were much higher than what would be estimated by using modified Atwater factors and often above the predictive equations for metabolizable energy (ME) recommended by the National Research Council or by using Atwater factors. Although statistical differences were observed among foods, they all performed well and the foods tested had very high AA digestibilities. Additionally, the TMEn data suggest that existing methods and equations for ME prediction underestimate the energy content of the foods tested.
Protection of telomeres 1 (POT1) of Pinus tabuliformis bound the telomere ssDNA
Authors: Luo Mei , Teng Xiaotong , Wang Bing , Zhang Jiaxue , Liu Yadi , Liu Di , Li Hui , Lu Hai
Published: December 2019

Protection of telomeres 1 (POT1) is a telomeric protein that binds to the telomere single-stranded (ss) region. It plays an essential role in maintaining genomic stability in both plants and animals. In this study, we investigated the properties of POT1 in Pinus tabuliformis Carr. (PtPOT1) through electrophoretic mobility shift assay. PtPOT1 harbored affinity for telomeric ssDNA and could bind plant- and mammalian-type ssDNA sequences. Notably, there were two oligonucleotide/oligosaccharide binding (OB) folds, and OB1 or OB2 alone, or both together, could bind ssDNA, which is significantly different from human POT1. Based on our data, we hypothesized that the two OB folds of PtPOT1 bound the same ssDNA. This model not only provides new insight into the ssDNA binding of PtPOT1 but also sheds light on the functional divergence of POT1 proteins in gymnosperms and humans.
TDIF overexpression in poplars retards internodal elongation and enhances leaf venation through interaction with other phytohormones
Authors: Yue Jing , Yang Heyu , Yang Shaohui , Wang Jiehua
Published: December 2019

As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-related (CLE) peptide family, tracheary element differentiation inhibitory factor (TDIF) plays crucial roles in vascular meristem maintenance by promoting cell proliferation and inhibiting xylem cell differentiation. In Populus trichocarpa, six TDIF-encoding genes are all expressed in vascular tissues, and in Arabidopsis PtTDIFpro:GUS lines, the expression driven by PtTDIF promoters were predominantly detected in stem vascular bundles, initiating leaves and leaf veins. Although exogenous application of two poplar TDIF peptides did not evidently affect the shoot growth in vitro, overexpression of PtTDIF genes in hybrid poplar severely retarded the internodal elongation by upregulating the expression of GA2ox and GA20ox genes and thus decreasing the level of endogenous gibberellins (GAs), which phenotypic defect could be rescued by exogenously applied GA3. In addition, TDIF overexpression unexpectedly induced a more complex venation pattern in poplar leaves, which was underpinned by the elevated expression of WOX4 and WOX13 genes. Upon TDIF treatment, the DR5:GUS poplar leaves revealed a higher GUS activity and in TDIF-overexpressing leaves, the transcript abundances of several PIN-FORMED (PIN) genes, especially that of PIN1, were increased, which implied an integration of TDIF and auxin in mediating this process. Collectively, data of this work presented novel activities of TDIF involved in internode elongation and leaf vein formation, thus revealing the divergent functions of TDIF in perennial tree species from those in annual herbaceous Arabidopsis.
Zika virus infection in asymptomatic persons in Myanmar, 2018
Authors: Ngwe Tun Mya Myat , Hmone Saw Wut , Soe Aung Min , Luvai Elizabeth , Nwe Khine Mya , Inoue Shingo , Buerano Corazon C , Thant Kyaw Zin , Morita Kouichi
Published: December 2019

Background

Zika virus (ZIKV) is a mosquito-borne flavivirus. Outbreaks of ZIKV infection have occurred in Africa, Southeast Asia, the Pacific Islands, the Americas and the Caribbean. Although most ZIKV infections are asymptomatic, cases of neurological manifestations have been described. The aim of the present study was to identify the prevalence of ZIKV infection among the asymptomatic persons in Myanmar in 2018.

Methods

A total of 284 serum samples from apparently healthy persons were collected from Yangon, Myanmar in 2018. They were analysed for ZIKV infection by immunoglobulin M (IgM) capture enzyme-linked immunosorbent assay (ELISA), IgG indirect ELISA, 50% focus reduction neutralization test, real-time reverse transcription polymerase chain reaction (RT-PCR) and conventional RT-PCR.

Results

Of the 284 apparently healthy persons, 31.3% were positive for the presence of IgM against ZIKV and 94.3% were positive for anti-flavivirus IgG. Among the ZIKV IgM-positive samples, we confirmed ZIKV infection in 15.8% of asymptomatic persons by neutralization test and real-time RT-PCR.

Conclusions

We conclude that ZIKV infection was increasing among asymptomatic persons in the same area in Myanmar during 2018 compared with 2017. It is highly recommended to strengthen the surveillance system for ZIKV to prevent possible outbreaks.
The Hahnemann University Hospital Closure and What Matters: A Department Chair’s Perspective
Authors: Hamilton Richard J.
Published: December 2019

The closure of Hahnemann University Hospital, which was announced on June 26, 2019, resulted in the most significant graduate medical education displacement in history, sending over 550 residents to new institutions within a month of the announcement. Over 2,000 physicians, nurses, and staff lost their jobs. While seemingly predictable in retrospect, the closure came as a cataclysmic event to all involved. In this Invited Commentary, a department chair reflects on the lessons learned from these unprecedented circumstances. These lessons cover areas that are not a typical concern for faculty who are focused on teaching their trainees, but are worthy of their attention. Corporate and organizational structure, leadership, and financing of the hospital were critical determining characteristics of the failure. The roles that the Accreditation Council for Graduate Medical Education and the Centers for Medicare and Medicaid Services played in this event were key stabilizers. However, examining their roles in this event offers opportunities to play a more active role in future events and alter how the next massive displacement unfolds, possibly preserving teaching programs. Highly competitive health systems should rethink noncollaborative strategies before allowing struggling institutions to succumb to market forces. Finally, a commitment by a hospital to the mission of academic medicine is a sacred trust with the faculty, trainees, and patients that it serves. It should not be undertaken by any enterprise that is not well resourced and equipped with the knowledge and expertise to meet this most serious of commitments.
Re-visioning Academic Medicine Through a Constructionist Lens
Authors: Rees Charlotte E. , Crampton Paul E.S. , Monrouxe Lynn V.
Published: December 2019

Constructionism in academic medicine matters. It encourages educators and researchers to question taken-for-granted assumptions, paying close attention to socially and historically contingent meanings. In this Invited Commentary, the authors explain what constructionism is; examine its ontological, epistemological, and axiological underpinnings; and outline its common methodologies and methods. Although constructivism favors the individual, constructionism privileges the social as the controlling force behind the construction of meaning. Where micro-constructionism attends to the minutiae of language, macro-constructionism focuses on broader discourses reproduced through material and social practices and structures. While social constructionists might situate themselves at any point on the relativist–realist continuum, many constructionists focus on constructionism as epistemology (the nature of knowledge) rather than ontology (the nature of reality). From an epistemological standpoint, constructionism asserts that how we come to know the world is constructed through social interaction. Constructionism thus values language, dialogue, and context, in addition to internal coherence between epistemology, methodology, and methods. Constructionism similarly values the concepts of dependability, authenticity, credibility, confirmability, reflexivity, and transferability. It also embraces the researcher–researched relationship. Given the privileging of language, qualitative methodologies and methods are key in constructionism, with constructionist-type questions focusing on how people speak. Here, the authors encourage the reader to develop an understanding of constructionism to re-vision academic medicine through a constructionist lens.
Internal Medicine Resident Professionalism Assessments: Exploring the Association With Patients’ Overall Satisfaction With Their Hospital Stay
Authors: Ratelle John T. , Halvorsen Andrew J. , Mandrekar Jay , Sawatsky Adam P. , Reed Darcy A. , Beckman Thomas J.
Published: December 2019

Purpose

Successful training of internal medicine (IM) residents requires accurate assessments. Patients could assess IM residents in a hospital setting, but medical educators must understand how contextual factors may affect assessments. The objective was to investigate relationships between patient, resident, and hospital-encounter characteristics and the results of patient assessments of IM resident professionalism.

Method

The authors performed a prospective cohort study of postgraduate year 1 (PGY-1) IM residents and their patients at 4 general medicine inpatient teaching services at Mayo Clinic Hospital–Rochester, Saint Marys Campus in Rochester, Minnesota, from July 1, 2015, through June 30, 2016. Patient assessments of resident professionalism were adapted from validated instruments. Multivariable modeling with generalized estimating equations was used to determine associations between patient assessment scores and characteristics of residents, residents’ clinical performance and evaluations (including professionalism assessments in other settings), patients, and hospital encounters and to account for repeated assessments of residents.

Results

A total of 409 patients assessed 72 PGY-1 residents (mean [SD], 5.7 [3.0] patient assessments per resident). In the multivariable model, only the highest rating out of 5 levels for overall satisfaction with hospital stay was significantly associated with patient assessment scores of resident professionalism (β [SE], 0.80 [0.08]; P < .001). Hospitalized patients’ assessment scores of resident professionalism were not significantly correlated with assessment scores of resident professionalism in other clinical settings.

Conclusions

Hospitalized patients’ assessment scores of in-hospital resident professionalism were strongly correlated with overall patient satisfaction with hospital stay but were not correlated with resident professionalism in other settings. The limitations of patient evaluations should be considered before incorporating these evaluations into programs of assessment.
A Quality Improvement Project to Improve the Use of Mother's Own Milk (MOM) With Precision Oropharyngeal Therapy
Authors: Wetzel Christine M. , Davis Lisa , Grohler Nikki , Oprondek David , Ruff Debra , Lowery Kaci , Heuer Jessica , Mullvain Maddi , Wolff Jessica
Published: December 2019

Background:

Bioprotective properties of mother's own milk (MOM) support the use of targeted MOM administration methods, including oropharyngeal therapy (OPT) with MOM, which may mimic the protective effects of swallowed amniotic fluid, thereby improving infant health outcomes.

Purpose:

To increase the use of MOM-OPT in premature infants in the first week of life.

Methods:

Quality improvement methods were used to implement precision dosing of OPT.

Results:

After changing processes and replacing the colostrum immune therapy practice with longer-term precision OPT, the percentage of ordered doses administered to infants in the first week of life increased from 24% to 64%. There was also a 15% increase in very low birth-weight infants who received MOM (from 50% to 65%) at discharge. There were no reported adverse events related to OPT administration.

Implications for Practice:

Replacing the unit's short-term colostrum immune therapy protocol with the longer-term precision OPT increased the number of doses given in the first week of life and increased the number of very low birth-weight infants discharged receiving MOM.

Implications for Research:

Researchers should consider studying the reported positive effects of OPT related to infant response (positive oral stimulation, reduction in oral aversion, and improved oral feeding skills), parent participation in care, and maternal milk expression behaviors (longer milk expression duration).
Maternal and Neonatal Morbidity After 4 and 6 Hours of Protracted Active Labor in Nulliparous Term Pregnancies
Authors: Govindappagari Shravya , Greene Naomi , Burwick Richard , Wong Melissa S. , Gregory Kimberly D.
Published: December 2019

OBJECTIVE:

To evaluate whether women with protracted active phase labor longer than 6 hours have an increased risk of adverse maternal and neonatal outcomes after the implementation of new labor management guidelines.

METHODS:

This was a retrospective study of nulliparous, term, singleton, vertex deliveries at Cedars Sinai Medical Center from August 2016 to September 2017. Women were included if they progressed to active phase labor, defined by cervical dilation of 6 cm or more. Women then were divided into three groups based on the time course of cervical change between 6 and 10 cm: 1) normal active phase: cervical change 1 cm or more within 4 hours throughout active labor; 2) mildly protracted active phase: cervical change 1 cm or less over 4–6 hours; and 3) very protracted active phase: cervical change 1 cm or less over 6 hours. Rate of change was assessed between cervical examinations. Primary outcome was a composite of maternal morbidity by study group. Secondary outcome was a composite of neonatal morbidity. We hypothesized that women with very protracted active phase had higher rates of adverse outcomes when compared with normal active phase. Regression analyses were performed to compare maternal and neonatal outcomes by study group.

RESULTS:

There were 2,559 deliveries, of which 2,378 (90.8%) were vaginal deliveries. Composite maternal and neonatal morbidity was higher with longer labor. Maternal morbidity—very protracted active phase (42.0%) compared with normal active phase (22.6%) adjusted odds ratio (aOR) 2.15 (95% CI 1.62–2.86); mildly protracted active phase (39.5%) compared with normal active phase (22.6%) aOR 2.18 (95% CI 1.67–2.84). Neonatal morbidity: very protracted active phase (19.8%) compared with normal active phase (13.8%) aOR 1.38 (95% CI 0.98–1.96); mildly protracted active phase (19.4%) compared with normal active phase (13.8%) aOR 1.44; (95% CI 1.04–1.99). Composite maternal and neonatal morbidity was not different between mildly protracted and very protracted groups.

CONCLUSION:

Composite maternal morbidity was greater in women with cervical change consistent with mildly protracted (4–6 hours) and very protracted (more than 6 hours) labor compared with cervical change in the normal active phase (less than 4 hours) group. However, composite maternal and neonatal morbidity was not different between mildly protracted and very protracted groups.