bluuebunny/crossref_metadata_2025 huggingface dataset:
Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation
Authors: Urano Ryo , Shinoda Wataru , Yoshii Noriyuki , Okazaki Susumu
Published: June 2020

In molecular dynamics (MD) calculations of the free energies of ions and ionic molecules, we often encounter net charged molecular systems where the electrical neutrality condition is broken. This charge causes a problem in the evaluation of long-range Coulombic interactions under periodic boundary conditions. A standard remedy for this problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of Coulombic interactions for such systems including background charge using the fast multipole method (FMM). Furthermore, an efficient scheme is developed to evaluate solute–solvent interaction energies using the FMM, reducing the computational burden for the far-field part. We calculate the hydration free energies of Mg2+, Na+, and Cl− ions dissolved in a neutral solvent using the new expression. The calculated free energies show good agreement with the results obtained using the well-established particle mesh Ewald method. This demonstrates the validity of the proposed expression. This work should make a contribution to highly parallelized MD calculations for large-scale charged systems (particularly, those with over million particles).
All-inorganic cesium lead halide perovskite nanocrystals for solar-pumped laser application
Authors: Masuda Taizo , Zhang Yaohong , Ding Chao , Liu Feng , Sasaki Kiyoto , Shen Qing , Endo Masamori
Published: June 2020

We demonstrate a low-concentrated solar-pumped laser (SPL) with natural sunlight by using an all-inorganic cesium lead halide perovskite (CsPbBrxI3−x) nanocrystal (NC) dispersed in toluene as a sensitizer. The perovskite NCs exhibit substantial advantages for SPL applications because of their broad absorption and narrow photoluminescence (PL) spectra with high quantum yield using inexpensive commercial precursors. We successfully synthesized CsPbBrxI3−x NCs with precisely tuned PL wavelengths from 581 to 612 nm by altering the I/Br ratio to achieve spectral overlap with Nd3+ ions, which have been widely used as a laser medium for SPLs. The measurement results show that the laser output power is highly sensitive to the peak PL wavelength of the NCs, and the highest laser output was obtained at the peak wavelength of 595 nm. Although the synthesized NCs have a wider absorption band, the laser output power obtained was much less than that of an organic dye of rhodamine 6G (R6G). The numerical analyses show that the optimal peak PL wavelength is 10 nm shorter than the absorption peak of Nd3+ ions because of the reflection property of the dichroic mirror coated on the input window. Moreover, we found that the concentration of NCs needs to be optimized in response to the peak PL wavelength. The calculations show that a laser output power 2.7 times greater than that of R6G can be obtained under an optimal peak PL wavelength of 575 nm and a concentration of 24 g/l for the CsPbBrxI3−x NCs.
Breakthrough instruments and products steady-state and time-resolved photoluminescence using the FluoTime 300 spectrometer with a FluoMic add-on
Authors: Ermilov E. , Oelsner C. , Birke F. , Gerber D. , Buschmann V. , Devaux A. , Erdmann R.
Published: June 2020

This report highlights the combination of the FluoTime 300 photoluminescence spectrometer with a FluoMic add-on as a powerful tool for photophysical research and applications, yielding spectral, temporal, and spatial information on a wide range of samples. The steady-state and time-resolved measurement capabilities of this combination are demonstrated reflecting a broad range of applications.
Stuck at home, physicists pivot to combat COVID-19
Authors: Feder Toni
Published: June 2020

Consultations with biologists and medical experts bear fruit.
The transition to family caregiving and its effect on biomarkers of inflammation
Authors: Roth David L. , Haley William E. , Sheehan Orla C. , Huang Jin , Rhodes J. David , Durda Peter , Howard Virginia J. , Walston Jeremy D. , Cushman Mary
Published: June 2020

Significance

Family caregiving has been proposed as a type of chronic stress that may lead to health risks through increased systemic inflammation. However, most previous studies of caregiving and inflammation have used small convenience samples and compared caregivers with poorly characterized noncaregiving controls. In this prospective investigation of 480 participants over a 9-y period, only one of six biomarkers showed a significantly larger increase in persons who became caregivers over that time period compared with noncaregiving controls. The size of this one effect was small, and no biomarker effects were found for a subset of strained spouse caregivers of persons with dementia. The findings are consistent with other population-based studies and suggest minimal systemic inflammation in response to chronic caregiving stress.
Cyclic GMP-AMP synthase promotes the inflammatory and autophagy responses in Huntington disease
Authors: Sharma Manish , Rajendrarao Sumitha , Shahani Neelam , Ramírez-Jarquín Uri Nimrod , Subramaniam Srinivasa
Published: June 2020

Significance

Huntington disease (HD) is a genetic disorder caused by glutamine-expansion in the huntingtin (mHTT) protein, which affects motor, psychiatric, and cognitive function, but the mechanisms remain unclear. mHTT is known to induce DNA damage and affect autophagy, both associated with inflammatory responses, but what mediates all these were unknown. Here we report that cGAS, a DNA damage sensor, is highly upregulated in the striatum of a mouse model and HD human patient’s tissue. We found ribosomes, which make proteins, are robustly accumulated on the cGAS mRNA in HD cells. cGAS depletion decreases—and cGAS expression increases—both inflammatory and autophagy responses in HD striatal cells. Thus, cGAS is a therapeutic target for HD. Blocking cGAS will prevent/slow down HD symptoms.
PPARα exacerbates necroptosis, leading to increased mortality in postinfluenza bacterial superinfection
Authors: Tam Vincent C. , Suen Rosa , Treuting Piper M. , Armando Aaron , Lucarelli Ronald , Gorrochotegui-Escalante Norma , Diercks Alan H. , Quehenberger Oswald , Dennis Edward A. , Aderem Alan , Gold Elizabeth S.
Published: June 2020

Significance

Superinfection with bacteria, such as
Staphylococcus aureus,
following influenza leads to increased morbidity and mortality compared to infection with either the bacteria or the virus alone. For example, secondary bacterial infections were responsible for a large percentage of the 50 million deaths caused by the 1918 influenza pandemic. The emergence of antibiotic-resistant strains has increased the threat of these bacteria commonly associated with influenza. We have determined that the increased mortality following superinfection is mediated, in part, by increased cell death in the lungs and have uncovered a molecular circuit that controls this process. A better understanding of the molecular regulation of immunity and cell death may enable the development of preventive and therapeutic treatments for bacterial superinfection.
Maximal fat oxidation capacity is associated with cardiometabolic risk factors in healthy young adults
Authors: Montes‐de‐Oca‐García Adrián , Perez‐Bey Alejandro , Corral‐Pérez Juan , Velázquez‐Díaz Daniel , Opazo‐Díaz Edgardo , Fernandez‐Santos Jorge R. , Rebollo‐Ramos María , Amaro‐Gahete Francisco J. , Cuenca‐García Magdalena , Ponce‐González Jesús‐Gustavo
Published: June 2020

It is unknown whether resting fat oxidation (RFO), maximal fat oxidation (MFO) and FatMax (intensity at which MFO is reached) are related to cardiometabolic risk (CMR). Thus the aim of this study was to examine the association of RFO, MFO and FatMax with CMR. 81 healthy adults (n = 31 women; 22.72 ± 4.40 years) participated in this cross‐sectional study. Glucose and triglycerides were analysed in plasma. Body composition, anthropometry, physical activity, blood pressure (BP) and heart rate measurements were taken. RFO and MFO were determined through indirect calorimetry. Maximal oxygen uptake (VO2max) test was performed until exhaustion after MFO test. The CMR cluster was created from individual CMR factors: waist circumference, body fat percentage, systolic BP, diastolic BP, blood glucose and plasma triglycerides. Groups of high and low MFO and VO2max were created. RFO was not associated with CMR (p < 0.05). FatMax, MFO and VO2max were associated with individual CMR factors as waist circumference (R 2 = 0.144; R 2 = 0.241; R 2 = 0.285; p = 0.001; respectively) and plasma triglycerides (R 2 = 0.111; p = 0.004 and R 2 = 0.130; p = 0.002 and R 2 = 0.093; p = 0.008; respectively) and clustered CMR factors (R 2 = 0.105; p = 0.008 and R 2 = 0.162; p = 0.001 and R 2 = 0.239; p = 0.001; respectively). VO2max was also associated with body fat percentage (R 2 = 0.105; p = 0.003) and diastolic BP (R 2 = 0.083; p = 0.01), even adjusting for sex or age (p < 0.05). Groups with high level of MFO or VO2max obtained lower CMR (p = 0.001), even adjusting for sex or age (p < 0.01). FatMax, MFO and, especially, VO2max are associated with CMR, regardless of age and sex. However, RFO is not associated with CMR.
A polybasic domain in aPKC mediates Par6-dependent control of membrane targeting and kinase activity
Authors: Dong Wei , Lu Juan , Zhang Xuejing , Wu Yan , Lettieri Kaela , Hammond Gerald R. , Hong Yang
Published: June 2020

Mechanisms coupling the atypical PKC (aPKC) kinase activity to its subcellular localization are essential for cell polarization. Unlike other members of the PKC family, aPKC has no well-defined plasma membrane (PM) or calcium binding domains, leading to the assumption that its subcellular localization relies exclusively on protein–protein interactions. Here we show that in both Drosophila and mammalian cells, the pseudosubstrate region (PSr) of aPKC acts as a polybasic domain capable of targeting aPKC to the PM via electrostatic binding to PM PI4P and PI(4,5)P2. However, physical interaction between aPKC and Par-6 is required for the PM-targeting of aPKC, likely by allosterically exposing the PSr to bind PM. Binding of Par-6 also inhibits aPKC kinase activity, and such inhibition can be relieved through Par-6 interaction with apical polarity protein Crumbs. Our data suggest a potential mechanism in which allosteric regulation of polybasic PSr by Par-6 couples the control of both aPKC subcellular localization and spatial activation of its kinase activity.
Mesoscopic interference for metric and curvature & gravitational wave detection
Authors: Marshman Ryan J , Mazumdar Anupam , Morley Gavin W , Barker Peter F , Hoekstra Steven , Bose Sougato
Published: June 2020

A compact detector for space-time metric and curvature is highly desirable. Here we show that quantum spatial superpositions of mesoscopic objects could be exploited to create such a detector. We propose a specific form for such a detector and analyse how asymmetries in its design allow it to directly couple to the curvature. Moreover, we also find that its non-symmetric construction and the large mass of the interfered objects, enable the detection gravitational waves (GWs). Finally, we discuss how the construction of such a detector is in principle possible with a combination of state of the art techniques while taking into account the known sources of decoherence and noise. To this end, we use Stern–Gerlach interferometry with masses ∼10−17 kg, where the interferometric signal is extracted by measuring spins and show that accelerations as low as 5 × 10−15  ms−2 Hz−1/2, as well as the frame dragging effects caused by the Earth, could be sensed. The GW sensitivity scales differently from the stray acceleration sensitivity, a unique feature of the proposed interferometer. We identify mitigation mechanisms for the known sources of noise, namely gravity gradient noise, uncertainty principle and electro-magnetic forces and show that it could potentially lead to a metre sized, orientable and vibrational noise (thermal/seismic) resilient detector of mid (ground based) and low (space based) frequency GWs from massive binaries (the predicted regimes are similar to those targeted by atom interferometers and LISA).
Effect of litter size, kidding age, mating weight, and kidding weight on partial cumulative milk yields in G1 Sapera goat
Authors: Anggraeni A , Saputra F , Kumalawati D S , Sumantri C
Published: June 2020

Milk Production of the dairy goat is influenced by genetic and non-genetic factors. Crossbred dairy goat of Sapera (50% Saanen, 50% PE) has been formed by the Indonesian Research Institute for Animal Production (IRIAP). Genetic improvement of milk production is the main trait considered in forming Sapera goat, so the effects of non-genetic factors on milk production should be investigated. Effects of litter size, kidding age, mating weight and kidding weight were examined on weekly cumulative milk yields (week 1-14) in Generation 1 (G1) Sapera goat (28 heads) at RIAP. General Linear Model for unbalanced data was used to study the effects of those four factors, while mean differences among subfactors were tested by the Duncan test. The G1 Sapera does had kidding age, litter size, mating weight, and kidding weight successively 4.22±1.45 yrs old, 2.07±0.55, 49.0±11.43 kg, and 44.4±11.75 kg. Higher litter sizes resulted in more milk yields, but litter size effects decreased by the lengthening lactation. Kidding age at ≥ 5 yrs old produced higher milk yields than the younger does (3 and 4 years old). The mating weight did not affect milk yields, while does having kidding weigh ≥ 70 kg resulted from lower milk than other weights. Considerable variation for various partial cumulative milk yields among G1 Sapera does have a good indication for possible selection on milk production in Sapera dairy goat.
Accessibility of beef cattle farmers for formal financing institutions in Bontomarannu District, Gowa Regency, South Sulawesi
Authors: Yunus E Y , Asnawi A , Amrawaty A A
Published: June 2020

Every beef cattle business owner has certain considerations in choosing the type of financing to run his business. One type of external financing available comes from formal institutional financing, but household-scale beef cattle farms with little livestock ownership make access to financing sources primarily financing from formal institutions difficult. The middle to lower livestock business actors is generally less able to reach formal financial institutions such as banks to obtain additional capital so that this financial market segment is actually filled by non-formal financial institutions such as loans from close relatives, merchants suggesting production and even money lenders. The purpose of this study is to determine the accessibility of household-scale beef cattle business to formal financial institutions. The types of data used in this study are qualitative and quantitative data. The research data was collected through a survey using interview techniques. The results showed that the accessibility of beef cattle breeders to formal financial institutions was relatively low, even to non-formal financial institutions originating from close relatives.
The effect of pumice composition upon transmission loss and impact strength of pumice hybrid composite–coconut fiber/gypsum
Authors: Suardana N P G , Kencanawati C I P K , Sugita I K G , Wardana I G N , Putra I P G R
Published: June 2020

Voice could not be separated from ears, but there is other sound called noise. Soundproofing panel in a room is highly important to hold and absorb sound in order to prevent sound to come and out of the room so the room will be comfortable. The objective of this study is to find the characteristic of transmission loss and the value of impact strength caused by the effect of pumice and gypsum composition. This study used 2 mm pumice combined with coconut fiber in 20% of fiber volume fraction, by using gypsum and glue matrix. The varied composition of this study used two comparisons Gypsum: Pumice: Glue of 1:1:1/2, and 1:2:1/2. Transmission loss was tested by using test equipment (ASTM-E-1050) and Sound Level Master (SL-4011), while the impact strength was tested by using Charpy Impact test equipment (ISO179-2). Result of this study showed that the lowest transmission loss occurred in specimen with composition 1:1:1/2 with value 13.48dB, while the highest transmission loss occurred in specimen with composition 1:2:1/2 with value 25.21dB. The lowest impact strength occurred in specimen with composition 1:2:1/2 with value 4.293kJ/m2, while the highest mean value for impact strength was 5, 534 kJ/m2 which occurred in composition 1:1:1/2.
Mixed convection of single-walled carbon nanotubes in a triangular cavity containing a pentagonal impediment
Authors: Khan Waqar A , Khan Zafar H
Published: June 2020

Mixed convection of nanofluid (a homogeneous mixture of water and single-walled carbon nanotubes) is investigated numerically in a triangular cavity containing an adiabatic pentagonal obstacle close to the top surface. Analytical models are employed for effective thermophysical properties of nanofluid regarding carbon nanotubes and water. The top wall of the cavity is kept at a higher temperature, while the inclined sidewalls are kept at a lower temperature. A constant magnetic field of intensity B0
is introduced in the momentum equation. The effects of radiation and viscous heating on heat transfer are neglected. The impacts of Richardson number on the dimensionless velocity and temperature are presented graphically in terms of streamlines and isotherms. The Galerkin finite element method with a penalty function is employed to obtain the solution of dimensionless partial differential equations. The numerical results are examined for governing parameters, including volume fraction of carbon nanotubes, Richardson, and Hartmann numbers. It is concluded that the Nusselt number increases with increasing the governing parameters in the presence of an adiabatic pentagonal obstacle.
Hartree theory calculations of quasiparticle properties in twisted bilayer graphene
Authors: Goodwin Zachary A H , Vitale Valerio , Liang Xia , Mostofi Arash A , Lischner Johannes
Published: June 2020

A detailed understanding of interacting electrons in twisted bilayer graphene (tBLG) near the magic angle is required to gain insights into the physical origin of the observed broken symmetry phases. Here, we present extensive atomistic Hartree theory calculations of the electronic properties of tBLG in the (semi-)metallic phase as function of doping and twist angle. Specifically, we calculate quasiparticle properties, such as the band structure, density of states (DOS) and local density of states (LDOS), which are directly accessible in photoemission and tunnelling spectroscopy experiments. We find that quasiparticle properties change significantly upon doping—an effect which is not captured by tight-binding theory. In particular, we observe that the partially occupied bands flatten significantly which enhances the density of states at the Fermi level. We predict a clear signature of this band flattening in the LDOS in the AB/BA regions of tBLG which can be tested in scanning tunneling experiments. We also study the dependence of quasiparticle properties on the dielectric environment of tBLG and discover that these properties are surprisingly robust as a consequence of the strong internal screening. Finally, we present a simple analytical expression for the Hartree potential which enables the determination of quasiparticle properties without the need for self-consistent calculations.
Contingent trade-off decisions with feedbacks in cyclical environments: testing alternative theories
Authors: Railsback Steven F , Harvey Bret C , Ayllón Daniel
Published: June 2020

Many animals make contingent decisions, such as when and where to feed, as trade-offs between growth and risk when these vary not only with activity and location but also 1) in cycles such as the daily light cycle and 2) with feedbacks due to competition. Theory can assume an individual decides whether and where to feed, at any point in the light cycle and under any new conditions, by predicting future conditions and maximizing an approximate measure of future fitness. We develop four such theories for stream trout and evaluate them by their ability to reproduce, in an individual-based model, seven patterns observed in real trout. The patterns concern how feeding in four circadian phases—dawn, day, dusk, and night—varies with predation risk, food availability, temperature, trout density, physical habitat, day length, and circadian cycles in food availability. We found that theory must consider the full circadian cycle: decisions at one phase must consider what happens in other phases. Three theories that do so could reproduce almost all the patterns, and their ability to let individuals adapt decisions over time produced higher average fitness than any fixed behavior cycle. Because individuals could adapt by selecting among habitat patches as well as activity, multiple behaviors produced similar fitness. Our most successful theories base selection of habitat and activity at each phase on memory of survival probabilities and growth rates experienced 1) in the three previous phases of the current day or 2) in each phase of several previous days.
The Cinderella discipline: morphometrics and their use in botanical classification
Authors: Christodoulou Maria D , Clark Jonathan Y , Culham Alastair
Published: June 2020

Between the 1960s and the present day, the use of morphology in plant taxonomy suffered a major decline, in part driven by the apparent superiority of DNA-based approaches to data generation. However, in recent years computer image recognition has re-kindled the interest in morphological techniques. Linear or geometric morphometric approaches have been employed to distinguish and classify a wide variety of organisms; each has strengths and weaknesses. Here we review these approaches with a focus on plant classification and present a case for the combination of morphometrics with statistical/machine learning. There are many classification techniques available for biological analysis and selecting the most appropriate is not trivial. Performance should be evaluated using standardized metrics such as accuracy, sensitivity and specificity. The gathering and storage of high-resolution images, combined with the processing power of desktop computers, makes morphometric approaches practical as a time- and cost-efficient way of non-destructive identification of plant samples.
Homeosis and delayed floral meristem termination could account for abnormal flowers in cultivars ofDelphiniumandAquilegia(Ranunculaceae)
Authors: Espinosa Felipe , Damerval Catherine , Le Guilloux Martine , Deroin Thierry , Wang Wei , Pinedo-Castro Myreya , Nadot Sophie , Jabbour Florian
Published: June 2020

Floral mutants display various deviant phenotypes and, as such, they are appropriate material with which to address the origin and the building of morphological variation. To identify the pivotal developmental stages at which floral variation may originate and to infer the putative associated genetic causes, we studied abnormal flowers in nine cultivars of Aquilegia and Delphinium of Ranunculaceae, a family displaying a high range of floral diversity. Wild-type flowers of the two genera are pentamerous and spurred, but they differ in their overall symmetry (actinomorphy vs. zygomorphy). Floral morphology of their cultivars at different developmental stages up to anthesis was observed, and the putative identity of the perianth organs and vascularization was inferred. Our results show that in the floral mutants in both genera, phyllotaxis was generally conserved, whereas floral organization, vascularization and symmetry were modified. Most of the morphological and anatomical deviations impacted the perianth, including organ number, identity and (spur) elaboration, and also led to the formation of mosaic organs. We hypothesized that the phenotypes of floral mutants in Aquilegia and Delphinium result from genetic alterations affecting frontiers between sets of organs of different identity, homeosis and length of floral meristem activity.
The role of women in managing waste banks and supporting waste management in local communities
Authors: Asteria Donna , Herdiansyah Herdis
Published: June 2020

This paper aims to describe women’s role with active participation in waste management within their communities. The environmental awareness education of citizens combined with the application of the ‘4Rs’ principle (reduce, reuse, recycle, and replant) is necessary to develop waste banks to resolve the issue of waste. Waste bank management is predicted to be the best solution for the municipal waste management and increases the public’s awareness of recycling household waste as a waste management strategy. An increase in awareness begins at the community level. Women can be as social capital in community with the capacity to move the community through their active role in waste management activities. This study considered citizens in Karang Resik, Tasikmalaya, West Java, Indonesia and used the emancipatory participation methods of counselling, educating, and training. The results showed that the presence of a waste bank educated residents to be disciplined in managing their waste and provided extra income from waste collection. Moreover, it strengthened the social cohesion for women within the community. This study shows that local female administrators in family welfare empowerment programmes can be used as role models for other women and can provide a significant impact on waste management.
Genomic Determination of Relative Risks forClostridioides difficileInfection From Asymptomatic Carriage in Intensive Care Unit Patients
Authors: Worley Jay , Delaney Mary L , Cummins Christopher K , DuBois Andrea , Klompas Michael , Bry Lynn
Published: June 2020

Background

Clostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood.

Methods

We identified asymptomatic C. difficile carriage among 1897 ICU patients using rectal swabs from an existing ICU vancomycin-resistant enterococci (VRE) surveillance program. C. difficile isolates from VRE swabs, and from C. difficile–positive stool samples, were genome sequenced. Spatial-temporal data from hospital records assessed genomically identified clusters for potential transmission events.

Results

Genomic analyses identified a diverse set of strains in infected patients and asymptomatic carriers. A total of 7.4% of ICU patients asymptomatically carried C. difficile; 69% of isolates carried an intact toxin locus. In contrast, 96% of C. difficile stool isolates were toxin encoding. CDI rates in asymptomatic carriers of toxin-encoding strains were 5.3% versus 0.57% in noncarriers. The relative risk for CDI with asymptomatic carriage of a toxin-encoding strain was 9.32 (95% confidence interval, 3.25–26.7). Genomic identification of clonal clusters supported analyses for asymptomatic transmission events, with spatial-temporal overlaps identified in 13 of 28 cases.

Conclusions

Our studies provide the first genomically confirmed assessments of CDI relative risk from asymptomatic carriage of toxin-encoding strains and highlight the complex dynamics of asymptomatic transmission in ICUs. Asymptomatic carriers are an active reservoir of C. difficile in the nosocomial environment. C. difficile screening can be implemented within existing HAI surveillance programs and has the potential to support infection-control efforts against this pathogen.
Pattern of recurrence of pN2 non-small-cell lung cancer: should postoperative radiotherapy be reconsidered?
Authors: Nakagawa Kazuo , Yoshida Yukihiro , Yotsukura Masaya , Watanabe Shun-ichi
Published: June 2020

OBJECTIVES

The prognosis of patients with mediastinal lymph node (LN) metastasis (pN2 stage III disease) is still unsatisfactory. Both systemic and local recurrence should be prevented after curative surgery. The aim of this study was to explore the pattern of recurrence in patients with completely resected pN2 non-small-cell lung cancer (NSCLC) in the era of adjuvant chemotherapy.

METHODS

We investigated 337 patients with completely resected cN0-1 and pN2 NSCLC from 2005 to 2016 at National Cancer Center Hospital, Japan. The patterns of recurrence were compared between patients who were managed by observation alone and those with adjuvant chemotherapy. In patients with regional LN recurrence, the pattern and site of recurrence were also explored.

RESULTS

There were 195 (58.5%) men and 142 (41.5%) women with a mean age of 63.2 years. Fifty-five (16.3%) patients developed only regional LN recurrence, 116 (32.6%) patients developed only distant recurrence and 65 (19.3%) patients developed both regional LN recurrence and distant recurrence. The difference in the pattern of recurrence between patients with observation alone and those with adjuvant chemotherapy was not statistically significant (P = 0.145). As for the pattern of regional LN recurrence, 68 (20.2%) patients had LN recurrence inside the systematic nodal dissection area.

CONCLUSIONS

Regional LN recurrence was observed in >30% of patients with completely resected pN2 NSCLC. About 20% of patients had recurrence inside the systematic nodal dissection area. Postoperative radiotherapy might be considered as an additional treatment strategy for these patients.
Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans
Authors: González-Robles Arturo , González-Lázaro Mónica , Lagunes-Guillén Anel Edith , Omaña-Molina Maritza , Lares-Jiménez Luis Fernando , Lares-Villa Fernando , Martínez-Palomo Adolfo
Published: June 2020

Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins—which are essential for peroxisome biogenesis, proliferation, and protein import—are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
Eight decades of adaptive changes in herring reproductive investment: the joint effect of environment and exploitation
Authors: Claireaux Marion , dos Santos Schmidt Thassya C , Olsen Esben Moland , Slotte Aril , Varpe Øystein , Heino Mikko , Enberg Katja
Published: June 2020

Reproductive investment is a central trait for population dynamics and productivity. Fishing and environmental variations are major drivers affecting population structure, dynamics, and adaptation of life-history and behavioural traits. However, those factors are often considered independently, and few studies take into account their joint effect. In this study, we investigate the contribution of environment, fishing pressure, and intra-specific competition to variation in the reproductive investment of the Norwegian spring-spawning herring (Clupea harengus), a stock that has been fished for centuries, and monitored for decades. Reproductive investment and post-spawning weight were affected differently by growth rate (measured as mean age-at-length), sea surface temperature, North Atlantic Oscillation, and spawning stock biomass in periods with no fishing, unselective fishing, and low but size-selective fishing. We hypothesize that those changes can be explained by direct effects of exploitation such as age truncation and changes in migration patterns. Our results highlight how fishing, by affecting population-level dynamics, can modify the impact of environmental variations on life-history traits.
Changes in growth and migration patterns of sea trout before and after the introduction of Atlantic salmon farming
Authors: Eldøy Sindre Håvarstein , Ryan D , Roche W K , Thorstad E B , Næsje T F , Sjursen A D , Gargan P G , Davidsen J G
Published: June 2020

Marine growth has strong implications for reproductive potential and ultimate fitness of sea trout. Hence, the effects of anthropogenic factors on marine growth are important when evaluating population responses and implementing management measures. Temporal changes in growth patterns of sea trout from three Norwegian and two Irish watercourses were examined, covering time spans of 25–65 years. Elemental chemistry Ba:Ca profiles and visual reading of fish scales were used to estimate smolt length and lifetime growth after first sea entry. Reduced growth after the first sea entry coincided with periods of nearby (<14 km) salmon-farming activity in impacted watersheds in both countries. Increased Ba:Ca levels were also recorded during these periods, likely indicating reduced residency in marine habitats caused by premature return to freshwater and estuaries. An increase in estimated length at first sea entry coinciding with salmon-farming activity, for groups of fish sampled after sea migration, suggests a size-selective marine mortality, with the smallest individuals experiencing a larger mortality.
Stable asymmetric spike equilibria for the Gierer–Meinhardt model with a precursor field
Authors: Kolokolnikov Theodore , Paquin-Lefebvre Frédéric , Ward Michael J
Published: June 2020

Precursor gradients in a reaction-diffusion system are spatially varying coefficients in the reaction kinetics. Such gradients have been used in various applications, such as the head formation in the Hydra, to model the effect of pre-patterns and to localize patterns in various spatial regions. For the 1D Gierer–Meinhardt (GM) model, we show that a non-constant precursor gradient in the decay rate of the activator can lead to the existence of stable, asymmetric and two-spike patterns, corresponding to localized peaks in the activator of different heights. These stable, asymmetric patterns co-exist in the same parameter space as symmetric two-spike patterns. This is in contrast to a constant precursor case, for which asymmetric spike patterns are known to be unstable. Through a determination of the global bifurcation diagram of two-spike steady-state patterns, we show that asymmetric patterns emerge from a supercritical symmetry-breaking bifurcation along the symmetric two-spike branch as a parameter in the precursor field is varied. Through a combined analytical-numerical approach, we analyse the spectrum of the linearization of the GM model around the two-spike steady state to establish that portions of the asymmetric solution branches are linearly stable. In this linear stability analysis, a new class of vector-valued non-local eigenvalue problem is derived and analysed.
Blood Bacterial Profiles Associated With Human Immunodeficiency Virus Infection and Immune Recovery
Authors: Serrano-Villar Sergio , Sanchez-Carrillo Sergio , Talavera-Rodríguez Alba , Lelouvier Benjamin , Gutiérrez Carolina , Vallejo Alejandro , Servant Florence , Bernadino José I , Estrada Vicente , Madrid Nadia , Gosalbes María José , Bisbal Otilia , de Lagarde María , Martínez-Sanz Javier , Ron Raquel , Herrera Sabina , Moreno Santiago , Ferrer Manuel
Published: June 2020

Human immunodeficiency virus (HIV) infection impairs mucosal immunity and leads to bacterial translocation, fueling chronic inflammation and disease progression. While this is well established, questions remain about the compositional profile of the translocated bacteria, and to what extent it is influenced by antiretroviral therapy (ART). Using 16S ribosomal DNA targeted sequencing and shotgun proteomics, we showed that HIV increases bacterial translocation from the gut to the blood. HIV increased alpha diversity in the blood, which was dominated by aerobic bacteria belonging to Micrococcaceae (Actinobacteria) and Pseudomonadaceae (Proteobacteria) families, and the number of circulating bacterial proteins was also increased. Forty-eight weeks of ART attenuated this phenomenon. We found that enrichment with Lactobacillales order, and depletion of Actinobacteria class and Moraxellaceae and Corynebacteriacae families, were significantly associated with greater immune recovery and correlated with several inflammatory markers. Our findings suggest that the molecular cross talk between the host and the translocated bacterial products could influence ART-mediated immune recovery.
The Practices of Evaluating Entitlements: Rethinking “Reputation” in International Politics
Authors: Sundaram Sasikumar S
Published: June 2020

How do reputations work in international politics? The dominant frameworks in international relations scholarship argue that reputation is subservient to real interest or past actions do not influence observers’ behavior in anarchy, and inconsistent reputational beliefs are irrational among policymakers who have miscalculated their interests. These substantialist accounts are problematic in the light of taking political practices seriously. I argue that reputations work within communities of practice through a tripartite process involving actor's entitlement claims, audiences’ relational evaluation of such claims, and the actor's performance to secure entitlements in issue-specific interactions. I illustrate the analytical usefulness of this conceptualization against conventional accounts by studying Brazil's multiple reputational concerns in the issue area of humanitarian crises in the post–Cold War period. The framework offered in the article has a wider relevance for examining how reputations work across states, for example, in India and China, and in different issue areas by foregrounding normative appraisals of each other by community members in distinct reputational games. It also sets the stage for further examination of the intersection of reputational practices upon other social capital such as status.
Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract
Authors: Janssen Axel B , van Hout Denise , Bonten Marc J M , Willems Rob J L , van Schaik Willem
Published: June 2020

Background

Colistin is an antibiotic that targets the LPS molecules present in the membranes of Gram-negative bacteria. It is used as a last-resort drug to treat infections with MDR strains. Colistin is also used in selective decontamination of the digestive tract (SDD), a prophylactic therapy used in patients hospitalized in ICUs to selectively eradicate opportunistic pathogens in the oropharyngeal and gut microbiota.

Objectives

To unravel the mechanisms of acquired colistin resistance in Gram-negative opportunistic pathogens obtained from SDD-treated patients.

Results

Routine surveillance of 428 SDD-treated patients resulted in 13 strains with acquired colistin resistance (Escherichia coli, n = 9; Klebsiella aerogenes, n = 3; Enterobacter asburiae, n = 1) from 5 patients. Genome sequence analysis showed that these isolates represented multiple distinct colistin-resistant clones but that colistin-resistant strains within the same patient were clonally related. We identified previously described mechanisms that lead to colistin resistance, i.e. a G53 substitution in the response regulator PmrA/BasR and the acquisition of the mobile colistin resistance gene mcr-1.1, but we also observed novel variants of basR with an 18 bp deletion and a G19E substitution in the sensor histidine kinase BasS. We experimentally confirmed that these variants contribute to reduced colistin susceptibility. In a single patient, we observed that colistin resistance in a single E. coli clone evolved through two unique variants in basRS.

Conclusions

We show that prophylactic use of colistin during SDD can select for colistin resistance in species that are not intrinsically colistin resistant. This highlights the importance of continued surveillance for strains with acquired colistin resistance in patients treated with SDD.
Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages
Authors: Rodríguez-Rubio Lorena , Serna Carlos , Ares-Arroyo Manuel , Matamoros Bosco R , Delgado-Blas Jose F , Montero Natalia , Bernabe-Balas Cristina , Wedel Emilia F , Mendez Irene S , Muniesa Maite , Gonzalez-Zorn Bruno
Published: June 2020

Objectives

To investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particles

Methods

Several databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT–PCR and Southern blotting.

Results

Multicopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number.

Conclusions

Multicopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.
High prevalence and risk factors of multiple antibiotic resistance in patients who fail first-line Helicobacter pylori therapy in southern China: a municipality-wide, multicentre, prospective cohort study
Authors: Lyu Tao , Cheung Ka Shing , Ni Li , Guo Jiaqi , Mu Pei , Li Yinpeng , Yang Qiu , Yu Xiqiu , Lyu Zhiwu , Wu Jianwei , Guo Haijian , Leung Wai K , Seto Wai-Kay
Published: June 2020

Background

We aimed to study the prevalence of secondary antibiotic resistance of Helicobacter pylori in southern China and its risk factors, particularly geographical and socio-economic factors.

Methods

This was a municipality-wide, multicentre, prospective cohort study involving five major hospitals. Patients aged ≥18 years who failed first-line bismuth-based quadruple anti-H. pylori therapy between September 2016 and February 2018 were recruited. Participants underwent upper gastrointestinal endoscopy with biopsy from the antrum and body for H. pylori culture and antimicrobial susceptibility testing for six antibiotics (clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline and furazolidone). Patients with failure of H. pylori culture were excluded. Participants completed a questionnaire profiling 22 potential risk factors of H. pylori infection and antibiotic resistance, including medical, social, household and birthplace factors.

Results

A total of 1113 patients failed first-line therapy, with successful H. pylori culture in 791 (71.1%) [male = 433 (54.7%); median age = 43 years]. Secondary resistance rates of dual antibiotics (clarithromycin + metronidazole and levofloxacin + metronidazole) and triple antibiotics (clarithromycin + levofloxacin + metronidazole) were 34.0%, 38.7% and 17.8%, respectively. Risk factors for clarithromycin + metronidazole resistance were history of ≥2 courses of H. pylori therapies [adjusted OR (aOR) = 1.71; 95% CI = 1.17–2.54], ≥3 household members (aOR = 2.00; 95% CI = 1.07–3.90) and family history of gastric cancer (aOR = 1.85; 95% CI = 1.18–2.85). Risk factors for levofloxacin + metronidazole resistance were age ≥40 years (aOR = 1.94; 95% CI = 1.37–2.75), lower gross domestic product per capita (aOR = 0.29; 95% CI = 0.10–0.80) and higher number of doctors/10 000 population (aOR = 1.59; 95% CI = 1.07–2.39). A higher human development index was of borderline significance (aOR = 2.79; 95% CI = 0.97–8.70).

Conclusions

The rates of secondary resistance of H. pylori to multiple antibiotics were high in southern China. Certain population-level risk factors were associated with levofloxacin + metronidazole resistance.
A Fast GC-MS-Based Method for Efficacy Assessment of Natural Anti-Oxidants for Inhibiting Lipid Oxidation
Authors: Janssen Hans-Gerd , Gah Carmen , Steenbergen Herrald , Rosing Ed , Spraul Martin
Published: June 2020

Background

For health reasons it is preferred to prepare food products with edible fats and oils that are high in unsaturated fatty acids. Unfortunately, these unsaturated acids are susceptible to lipid oxidation and the addition of natural antioxidants, e.g., rosemary extracts, etc. is needed.

Objective

To assess the efficacy of natural oxidation inhibition strategies, fast, yet realistic, and objective methods are needed to study oxidation inhibition.

Methods

A model system consisting of salt and sunflower oil is proposed as a model for dry soups and sauces. Hexanal formation is studied using fast GC-MS as a quantitative indicator for lipid oxidation.

Results

A fast GC-MS method using a short, 6-m 150 µm inner-diameter column was developed that allowed elution of hexanal within approximately 20 s, with a total run time of 2 min. The GC method has quantification limits below 1 ppm and is hence much more sensitive than the human nose.

Conclusions

The new accelerated method with hexanal read-out was successfully applied in a study to identify spices and herbs mixtures that can act as natural inhibitors of lipid oxidation. The fast GC-MS method is extremely stable and allowed the analysis of thousands of samples with very little maintenance.

Highlights

With the right mixture of spices and herbs, lipid oxidation can be delayed more than 100 times as compared to non-stabilized systems.
A maxillary ameloblastic fibrosarcoma tumor: a rare case report from Syria
Authors: Soltany Amjad , Asaad Ghazal , Daher Rami , Dayoub Mouhannad , Khalil Ali , Alshehabi Zuheir
Published: June 2020

Ameloblastic fibrosarcoma (AFS) is a rare, aggressive malignant odontogenic tumor. AFS is seen most frequently in second and third decades of life. We are reporting a case of a low grade AFS in a 21-year-old male complaining of a painless swelling in the right side of the maxilla. The patient was treated with surgical excision followed by radiotherapy, which is considered the most effective approach for most of soft tissue sarcomas. AFS has a high-reported recurrence rate (up to 37%); therefore, long-term surveillance for recurrence is crucial.