bluuebunny/crossref_metadata_2025 huggingface dataset:
Postreflux swallow‐induced peristaltic wave index from pH‐impedance monitoring associates with esophageal body motility and esophageal acid burden
Authors: Rogers Benjamin D. , Rengarajan Arvind , Ribolsi Mentore , Ghisa Matteo , Quader Farhan , Penagini Roberto , de Bortoli Nicola , Mauro Aurelio , Cicala Michele , Savarino Edoardo , Gyawali C. Prakash
Published: August 2020

Background

Postreflux swallow‐induced peristaltic wave (PSPW) on pH‐impedance monitoring and contraction vigor on high‐resolution manometry (HRM) both assess esophageal peristaltic response. We aimed to evaluate relationships between PSPW and esophageal peristalsis on HRM in the context of reflux disease in this multicenter cohort study.

Methods

pH‐impedance and HRM studies performed on patients with persisting reflux symptoms were reviewed from 6 centers (5 in Europe and 1 in US). Total, upright and supine acid exposure time (AET) were evaluated from pH‐impedance studies; PSPW index (PSPWI) and mean nocturnal baseline impedance (MNBI) were calculated using standard methodology. Esophageal body contraction vigor was analyzed using distal contractile integral (DCI), and DCI ratio > 1 between single swallows and multiple rapid swallows (MRS) defined presence of contraction reserve. Student's t test, ANOVA, and linear regression were utilized to investigate relationships between PSPW, contraction vigor, and contraction reserve.

Key Results

Of 296 patients (52.8 ± 0.8 yr, 63% F), median PSPWI was 0.475. Only 24.0% had intact DCI; the remainder had varying degrees of hypomotility. As hypomotility increased, PSPWI and MNBI decreased significantly, while total AET and reflux episodes had an inverse response (P ≤ .002 for each). MRS data were available in 167 (56.4%), 72.5% had contraction reserve. MRS cohorts with normal PSPWI had significantly lower reflux burden compared to low PSPWI, regardless of presence or absence of contraction reserve (P ≤ .001).

Conclusions and Inferences

PSPWI correlates with esophageal hypomotility and reflux burden, and complements clinical reflux evaluation. Intact PSPW is more relevant to esophageal reflux clearance than contraction reserve.
Relating Mori’s Uncanny Valley in generating conversations with artificial affective communication and natural language processing
Authors: Betriana Feni , Osaka Kyoko , Matsumoto Kazuyuki , Tanioka Tetsuya , Locsin Rozzano C.
Published: August 2020

Human beings express affinity (Shinwa‐kan in Japanese language) in communicating transactive engagements among healthcare providers, patients and healthcare robots. The appearance of healthcare robots and their language capabilities often feature characteristic and appropriate compassionate dialogical functions in human–robot interactions. Elements of healthcare robot configurations comprising its physiognomy and communication properties are founded on the positivist philosophical perspective of being the summation of composite parts, thereby mimicking human persons. This article reviews Mori's theory of the Uncanny Valley and its consequent debates, and examines "Uncanny" relations with generating healthcare robot conversational content with artificial affective communication (AAC) using natural language processing. With healthcare robots provoking influential physical composition and sensory expressions, the relations in human–healthcare robot transactive engagements are argued as supportive of the design and development in natural language processing. This implies that maintaining human–healthcare robot interaction and assessing the eeriness situations explained in the Uncanny Valley theory are crucial positions for healthcare robot functioning as a valuable commodity in health care. As such, physical features, language capabilities and mobility of healthcare robots establish the primacy of the AAC with natural language processing as integral to healthcare robot–human healthcare practice.
Flexible Instrumental Variable Distributional Regression
Authors: Briseño Sanchez Guillermo , Hohberg Maike , Groll Andreas , Kneib Thomas
Published: August 2020

We tackle two limitations of standard instrumental variable regression in experimental and observational studies: restricted estimation to the conditional mean of the outcome and the assumption of a linear relationship between regressors and outcome. More flexible regression approaches that solve these limitations have already been developed but have not yet been adopted in causality analysis. The paper develops an instrumental variable estimation procedure building on the framework of generalized additive models for location, scale and shape. This enables modelling all distributional parameters of potentially complex response distributions and non-linear relationships between the explanatory variables, instrument and outcome. The approach shows good performance in simulations and is applied to a study that estimates the effect of rural electrification on the employment of females and males in the South African province of KwaZulu-Natal. We find positive marginal effects for the mean for employment of females rates, negative effects for employment of males and a reduced conditional standard deviation for both, indicating homogenization in employment rates due to the electrification programme. Although none of the effects are statistically significant, the application demonstrates the potentials of using generalized additive models for location, scale and shape in instrumental variable regression for both to account for endogeneity and to estimate treatment effects beyond the mean.
Single-machine Integrated Production Preventive Maintenance Scheduling: A Simheuristic Approach
Authors: Abdul Halim Nurul Nadiah , Shariff S. Sarifah Radiah , Zahari Siti Meriam
Published: August 2020

Preventive maintenance (PM) planning becomes a crucial issue in the real world of the manufacturing process. It is important in the manufacturing industry to maintain the optimum level of production and minimize its investments. Thus, this paper focuses on multiple jobs with a single production line by considering stochastic machine breakdown time.  The aim of this paper is to propose a good integration of production and PM schedule that will minimize total completion time. In this study, a hybrid method, which is a genetic algorithm (GA), is used with the Monte Carlo simulation (MCS) technique to deal with the uncertain behavior of machine breakdown time. A deterministic model is adopted and tested under different levels of complexity. Its performance is evaluated based on the value of average completion time. The result clearly shows that the proposed integrated production with PM schedule can reduce the average completion time by 11.68% compared to the production scheduling with machine breakdown time.
Study of the Impact of Environmental Pollution on Efficiency and Sustainable Development using Data Envelopment Analysis
Authors: Hosseini Hamid , Fanati Rashidi Sara , Hamzehee Ali
Published: August 2020

Environmental changes resulting from industrial activity have been occurring for many years, and with the increasing production of greenhouse gases and other pollutants, these changes have played a critical role in global warming. Nowadays, all countries have become aware of the great importance of attention to the environment alongside economic growth. Therefore, they are all after solutions that would allow maximum economic growth with minimum harm to the environment. In the present study, the environmental efficiency of a given system is evaluated using data envelopment analysis (DEA). For this purpose, the economic and environmental dimensions are taken into consideration for each decision-making unit (DMU), with the condition of having undesirable outputs in the environmental dimension. Then, using the concept of “order of efficiency”, an enhanced DEA method is proposed based on weak and strong disposability axioms, which can be used to compare and rank units with undesirable outputs. Next, the capabilities of the proposed approach are demonstrated through an example involving various industries in Iran. Enhanced DEA not only takes more comprehensive input and output sets into account but also monitors the units based on the principles of sustainability.
Deep Learning for Social Media Sentiment Analysis
Authors: Fithriasari Kartika , Jannah Saidah Zahrotul , Reyhana Zakya
Published: August 2020

Social media is used as a tool by many people to express their opinions. Sentiment analysis for social media is very important, as it allows information to be obtained about public opinion on government performance. The goal of this research is to learn about the opinions of Surabaya citizens, using deep learning methods. The data are extracted from the official Twitter accounts of the Surabaya government and a private radio station in Surabaya. The data are grouped into two categories: positive and negative sentiments. This research is conducted in three steps: data pre-processing, sentiment classification, and visualization. Data pre-processing is required before modelling approaches are applied. It is used to transform the unstructured text data into structured data. The data pre-processing consists of case folding, tokenizing, and the removal of stop words. Deep learning methods are then applied to the data. A Backpropagation Neural Network (BNN) and a Convolutional Neural Network (CNN) are used to perform the sentiment classification. The BNN and CNN are compared using various metrics, such as precision, sensitivity, and area under the receiver operating characteristic curve (AUC). A word cloud is then used to visualize the data and find the most frequent words in each class. The results show that the sentiment classification with CNN is better than that with the BNN because the values for the precision, sensitivity and AUC are higher.
Thermoelectric Generator–Integrated Solar Air Heater: A Compact Passive System
Authors: Venkateshwar Kumar , Raihan Mohammad Siddique Abu , Tasnim Syeda , Simha Hari , Mahmud Shohel
Published: August 2020

Solar air heater is a promising, economically viable, and matured technology for space heating and drying applications. One of the primary reasons for the limited usage of a solar air heater in developing countries is the unavailability of continuous electricity supply. Although the solar air heater is theoretically passive, practically electrical energy is required to achieve a steady airflow. Therefore, the unreliability of electricity forces people to rely on firewood for heat during the cold weather, which has severe effects on health and climate change. In the present work, the potential of thermoelectric generators (TEGs) to meet the electrical energy requirement of a solar air heater is studied. Two configurations, each with three different numbers of stages of TEGs, are analyzed. The effect of the integration of TEGs on the thermal performance of solar air heater is analyzed alongside the comparison between the electrical energy required by solar air heaters and electrical energy generated upon the integration of TEGs. A numerical model is developed in matlab and validated using the experimental results. One of the designs meets the electrical energy requirement of the fan in a wide operational range but lowers the process heat generation by approximately 1–6.25%. The electrical energy generated by the other design falls short of demand posed by the system in most operating range. However, the thermal energy generation is marginally higher compared to that of the conventional solar air heater.
Enhanced Recovery From Naturally Fractured Gas Reservoirs With Seismic Vibrations
Authors: Zare Khadijeh , Mahiyar Hojjat , Ghaedi Mojtaba
Published: August 2020

Water level rising in fracture networks of a naturally fractured gas reservoir is extremely challenging and can significantly decrease the ultimate recovery due to reservoir heterogeneity. Although capillary drainage and gravity force can enhance the displacement of gas recovery from matrix to fracture, these forces may not be so effective in mobilizing a large amount of trapped gas through the matrix. So called, the use of seismic wave can be suggested as a low cost and environmentally friendly enhanced method compared with the other conventional enhanced methods. This article is aimed to examine the ability of seismic vibration in generating an efficient driving force for moving the remaining gas into the fracture which, to the best of the author’s knowledge, has not been reported so far. To this end, an in-house numerical simulator has been developed to investigate this enhanced recovery method and also to evaluate the effect of wave characteristics as well as rock properties on the ultimate recovery. The governing equations are solved numerically using finite difference approach and the accuracy of these equations was compared with a commercial simulator for verification. The results are very encouraging and show substantial gas recovery enhancement by applying seismic waves. Our investigation also shows that this stimulation method is more efficient at lower frequencies and also in higher permeable matrix and fractures.
Inverse Optimal Boundary Tracking Control and Observer Design for a One-Link Rotating Flexible Arm
Authors: Do K. D.
Published: August 2020

A new design of an inverse optimal boundary control law is first proposed to force a one-link rotating flexible arm with a tip mass subject to bounded disturbances to track a reference model. The proposed boundary control law ensures global practical exponential stability of the tracking error system and is optimal in the sense that it minimizes a cost functional that appropriately penalizes both the tracking errors and the boundary control without having to solve a Hamilton–Jacobi–Bellman equation. Based on the above boundary control development, an observer-control approach is proposed to design a new inverse optimal observer that globally practically exponentially estimates the one-link rotating flexible arm's states using only measurements at the actuated boundary.
Quantitative Assessment of Rectal Washout With Irrigation and Aspiration
Authors: Ishimaru Kei , Sato Mitsunori , Akita Satoshi , Watanabe Katsuya , Kawamoto Takayasu , Kuwabara Jun , Tanigawa Kazufumi , Nakagawa Yusuke , Kikuchi Satoshi , Tatsuta Kyosuke , Yoshida Motohira , Koga Shigehiro , Watanabe Yuji
Published: August 2020

Local recurrence of rectal cancer is defined as any evidence of relapse within the small pelvis after surgical resection of the primary tumor. After removal of a rectal tumor, necrotic cellular debris and viable exfoliated cancer cells are present in the rectal lumen; using saline or povidone-iodine solution, many surgeons perform rectal washout beyond an occlusive clamp to remove these exfoliated malignant cells, which may lead to local recurrence. A meta-analysis showed that intraoperative rectal washout at the surgical anastomosis site can reduce the risk of local recurrence after rectal cancer resection. Therefore, intraluminal lavage is useful to prevent local recurrence. Although intraoperative rectal washing is considered to be important, there is probably room for improvement on this method. We described the idea of a new transanal irrigation and aspiration system for small rectal contents. The aim of this research was to investigate the effect of a new rectal washout system using a chemiluminescent imaging system. We attempted to evaluate and compare the washout efficiency between this new system and the conventional irrigation system using a cylindrical rectum model. Our results implied that, at the same volume of solution, the irrigation–aspiration rectal washout system was more effective than the irrigation washout system. This new rectal washout system was easy to use and allowed a good washout. To the best of our knowledge, this was the first report that evaluated the efficacy of a rectal washout system using quantitative data.
Detection of some amino acids with modulation-doped and surface-nanoengineered GaAs Schottky P-I-N diodes
Authors: Alkhidir Tamador , Abi Jaoude Maguy , Gater Deborah L. , Alpha Christopher , Isakovic A. F.
Published: August 2020

Most current techniques for analyzing amino acids require substantial instrumentation and significant sample preprocessing. In this study, we designed, fabricated, and tested a scalable diode-based microdevice that allows for direct sensing of amino acids. The device is based on modulation-doped GaAs heterostructure with a Schottky contact on one side. The relatively high mobility and relatively small dielectric constant of GaAs are naturally helpful in this problem. We also paid attention to a proper etching procedure allowing for substantial modification of the surface properties, thereby further boosting the sensing performance. Transport data (I-V, differential conductance) are presented for three qualitatively different classes of amino acids (i.e., nonpolar with aliphatic R-group, polar uncharged R-group, and charged R-group) with glycine, cysteine, and histidine as specific examples, respectively. The conductance for the GaAs-amino acid interface measured using a scanning tunneling microscope (STM) was previously reported to have distinct spectral features. In this paper, we show that measuring the differential conductance of a GaAs diode, whose surface is in direct contact with an aqueous solution of amino acid, is a simple methodology to access useful information, previously available only through sophisticated and equipment-demanding STM and molecular electronics approaches. Density functional theory calculations were used to examine which adsorption processes were likely responsible for the observed surface conductance modification. Last, in future and ongoing work, we illustrate how it might be possible to employ standard multivariate data analysis techniques to reliably identify distinct (95%) single amino acid specific features in near-ambient differential conductance data.
How hair deforms steel
Authors: Roscioli Gianluca , Taheri-Mousavi Seyedeh Mohadeseh , Tasan Cemal Cem
Published: August 2020

A hair-splitting way to get dull

Razors eventually become dull after shaving even though the blade is about 50 times harder than the hair. Whereas edge rounding and brittle cracking of a blade's hard coating were thought to be responsible, a detailed microstructural investigation by Roscioli
et al.
shows a different mechanism. A combination of out-of-plane bending, microstructural heterogeneity, and asperities—microscopic chips along the smooth edge—sometimes caused fracture to occur if the conditions lined up. This fracture originated at the hair-edge asperity interface and created chipping that dulled a blade faster than other processes.

Science
, this issue p.
689
COVID-19 in Africa: Dampening the storm?
Authors: Mbow Moustapha , Lell Bertrand , Jochems Simon P. , Cisse Badara , Mboup Souleymane , Dewals Benjamin G. , Jaye Assan , Dieye Alioune , Yazdanbakhsh Maria
Published: August 2020

The dampened course of COVID-19 in Africa might reveal innovative solutions
Ribosome-Mediated Attenuation of
vga
(A) Expression Is Shaped by the Antibiotic Resistance Specificity of Vga(A) Protein Variants
Authors: Vimberg Vladimir , Cavanagh Jorunn Pauline , Novotna Michaela , Lenart Jakub , Nguyen Thi Ngoc Bich , Vesela Jana , Pain Maria , Koberska Marketa , Balikova Novotna Gabriela
Published: August 2020

Vga(A) protein variants confer different levels of resistance to lincosamides, streptogramin A, and pleuromutilins (LS
A
P) by displacing antibiotics from the ribosome. Here, we show that expression of
vga
(A) variants from
Staphylococcus haemolyticus
is regulated by
cis
-regulatory RNA in response to the LS
A
P antibiotics by the mechanism of ribosome-mediated attenuation. The specificity of induction depends on Vga(A)-mediated resistance rather than on the sequence of the riboregulator.
Achromobacter
Infections and Treatment Options
Authors: Isler Burcu , Kidd Timothy J. , Stewart Adam G. , Harris Patrick , Paterson David L.
Published: August 2020

Achromobacter
is a genus of nonfermenting Gram-negative bacteria under order
Burkholderiales
. Although primarily isolated from respiratory tract of people with cystic fibrosis,
Achromobacter
spp. can cause a broad range of infections in hosts with other underlying conditions. Their rare occurrence and ever-changing taxonomy hinder defining their clinical features, risk factors for acquisition and adverse outcomes, and optimal treatment.
Achromobacter
spp.
The Alternative Sigma Factor SigB Is Required for the Pathogenicity of Bacillus thuringiensis
Authors: Henry Stéphanie , Lereclus Didier , Slamti Leyla
Published: August 2020

To adapt to changing and potentially hostile environments, bacteria can activate the transcription of genes under the control of alternative sigma factors, such as SigB, a master regulator of the general stress response in several Gram-positive species. Bacillus thuringiensis is a Gram-positive spore-forming invertebrate pathogen whose life cycle includes a variety of environments, including plants and the insect hemocoel or gut. Here, we assessed the role of SigB during the infectious cycle of B. thuringiensis in a Galleria mellonella insect model. We used a fluorescent reporter coupled to flow cytometry and showed that SigB was activated in vivo. We also showed that the pathogenicity of the ΔsigB mutant was severely affected when inoculated via the oral route, suggesting that SigB is critical for B. thuringiensis adaptation to the gut environment of the insect. We could not detect an effect of the sigB deletion on the survival of the bacteria or on their sporulation efficiency in the cadavers. However, the gene encoding the pleiotropic regulator Spo0A was upregulated in the ΔsigB mutant cells during the infectious process.

IMPORTANCE Pathogenic bacteria often need to transition between different ecosystems, and their ability to cope with such variations is critical for their survival. Several Gram-positive species have developed an adaptive response mediated by the general stress response alternative sigma factor SigB. In order to understand the ecophysiological role of this regulator in Bacillus thuringiensis, an entomopathogenic bacterium widely used as a biopesticide, we sought to examine the fate of a ΔsigB mutant during its life cycle in the natural setting of an insect larva. This allowed us, in particular, to show that SigB was activated during infection and that it was required for the pathogenicity of B. thuringiensis via the oral route of infection.
Regulation of DNA Binding and High-Order Oligomerization of the DnaB Helicase Loader
Authors: Matthews Lindsay A. , Simmons Lyle A.
Published: August 2020

DnaB is an essential primosomal protein that coloads the replicative helicase in many Gram-positive bacteria, including several human pathogens. Although DnaB is tetrameric in solution, it is from a protein family whose members can oligomerize into large complexes when exposed to DNA. It is currently unknown how DNA binding by DnaB is regulated or how these interactions induce changes in its oligomeric state. Here, we investigated DNA binding by DnaB from Bacillus subtilis and the critical human pathogen Staphylococcus aureus. We found that B. subtilis DnaB binds double-stranded DNA as a tetramer; however, M13mp18 single-stranded DNA induces high-order oligomerization. Mutating a conserved motif at the C-terminal end of DnaB stimulates single-stranded DNA binding, suggesting that conformational changes in this region regulate DNA substrate preferences. S. aureus DnaB could also be induced to form high-order oligomers with either M13mp18 or PhiX174 single-stranded DNA. Therefore, oligomeric shifts in DnaB are tightly controlled and this activity is conserved between B. subtilis and a pathogenic species.

IMPORTANCE DnaB is a replicative helicase loader involved in initiating DNA replication in many bacterial species. We investigated the binding preferences of DnaB for its DNA substrate and determined that the C-terminal end of the protein plays a critical role in controlling DNA interactions. Furthermore, we found that DNA binding in general did not trigger changes to the oligomeric state of DnaB, but rather, certain types of single-stranded DNA substrates specifically induced DnaB to self-assemble into a large complex. This indicates that the structure of DNA itself is an important regulatory element that influences the behavior of DnaB. Importantly, these observations held for both Bacillus subtilis and the pathogenic species Staphylococcus aureus, demonstrating conserved biochemical functions of DnaB in these species.
Modeling Borna Disease Virus
In Vitro
Spread Reveals the Mode of Antiviral Effect Conferred by an Endogenous Bornavirus-Like Element
Authors: Kim Kwang Su , Yamamoto Yusuke , Nakaoka Shinji , Tomonaga Keizo , Iwami Shingo , Honda Tomoyuki
Published: August 2020

Accumulating evidence suggests that some endogenous viral elements (EVEs), including endogenous retroviruses and endogenous nonretroviral virus elements, have acquired functions in the host as a result of long-term coevolution. Recently, an endogenous bornavirus-like element (itEBLN) found in the ground squirrel genome has been shown to have antiviral activity against exogenous bornavirus infection. In this study, we first quantified bornavirus spread in cultured cells and then calculated the antiviral activity of itEBLN on bornavirus infection. The calculated antiviral activity of itEBLN suggests its suppression of multiple processes in the viral life cycle. To our knowledge, this is the first study quantifying the antiviral activity of EVEs and speculating on a model of how some EVEs have acquired antiviral activity during host-virus arms races.
Probing the Structure of the HIV-1 Envelope Trimer Using Aspartate Scanning Mutagenesis
Authors: Das Raksha , Datta Rohini , Varadarajan Raghavan
Published: August 2020

In most crystal structures of the soluble ectodomain of the HIV-1 Env trimer, some residues in the fusion and N-heptad repeat regions are disordered. Whether this is true in the context of native, functional Env on the virion surface is not known. This knowledge may be useful for stabilizing Env in its prefusion conformation and will also help to improve understanding of the viral entry process. Burial of the charged residue Asp in a protein structure is highly destabilizing. We therefore used Asp scanning mutagenesis to probe the burial of apparently disordered residues in native Env and to examine the effect of mutations in these regions on Env stability and conformation as probed by antibody binding to cell surface-expressed Env, CD4-induced shedding of HIV-1 gp120, and viral infectivity studies. Mutations that prevent shedding can potentially be used to stabilize native-like Env constructs for use as vaccine immunogens.
Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature
Authors: Kempher Megan L. , Tao Xuanyu , Song Rong , Wu Bo , Stahl David A. , Wall Judy D. , Arkin Adam P. , Zhou Aifen , Zhou Jizhong
Published: August 2020

Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium,
Desulfovibrio vulgaris
Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.
Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex during Red Blood Cell Invasion by Plasmodium falciparum Merozoites
Authors: More Kunal R. , Kaur Inderjeet , Giai Gianetto Quentin , Invergo Brandon M. , Chaze Thibault , Jain Ravi , Huon Christéle , Gutenbrunner Petra , Weisser Hendrik , Matondo Mariette , Choudhary Jyoti S. , Langsley Gordon , Singh Shailja , Chitnis Chetan E.
Published: August 2020

Invasion of red blood cells (RBCs) by
Plasmodium falciparum
merozoites is a complex process that is regulated by intricate signaling pathways. Here, we used phosphoproteomic profiling to identify the key proteins involved in signaling events during invasion. We found changes in the phosphorylation of various merozoite proteins, including multiple kinases previously implicated in the process of invasion. We also found that a phosphorylation-dependent multiprotein complex including signaling kinases assembles during the process of invasion. Disruption of this multiprotein complex impairs merozoite invasion of RBCs, providing a novel approach for the development of inhibitors to block the growth of blood-stage malaria parasites.
Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth
Authors: Miller John I. , Techtmann Stephen , Joyner Dominique , Mahmoudi Nagissa , Fortney Julian , Fordyce James A. , GaraJayeva Nargiz , Askerov Faig S. , Cravid Claudio , Kuijper Maarten , Pelz Oliver , Hazen Terry C.
Published: August 2020

Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.
Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut
Authors: Lebov Jarrett F. , Schlomann Brandon H. , Robinson Catherine D. , Bohannan Brendan J. M.
Published: August 2020

Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of
Shewanella oneidensis
through the intestines of larval zebrafish (
Danio rerio
). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.
The Ndr/LATS Kinase Cbk1 Regulates a Specific Subset of Ace2 Functions and Suppresses the Hypha-to-Yeast Transition in Candida albicans
Authors: Wakade Rohan S. , Ristow Laura C. , Stamnes Mark A. , Kumar Anuj , Krysan Damian J.
Published: August 2020

The
r
egulation of
A
ce2 and
m
orphogenesis (RAM) pathway is a key regulatory network that plays a role in many aspects of
C. albicans
pathobiology. In addition to characterizing the transcriptional effects of this pathway, we discovered that Cbk1 and Ace2, a key RAM pathway regulator-effector pair, mediate a specific set of the overall functions of the RAM pathway. We have also discovered a new function for the Cbk1-Ace2 axis: suppression of the hypha-to-yeast transition. Very few regulators of this transition have been described, and our data indicate that maintenance of hyphal morphogenesis requires suppression of yeast phase growth by Cbk1-regulated Ace2.
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Authors: McDaniel Elizabeth A. , Peterson Benjamin D. , Stevens Sarah L. R. , Tran Patricia Q. , Anantharaman Karthik , McMahon Katherine D.
Published: August 2020

Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the
Deltaproteobacteria
,
Firmicutes
, and
Euryarchaeota.
Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.
Supplemental Material: Evaluating the Shinumo-Sespe drainage connection: Arguments against the “old” (70–17 Ma) Grand Canyon models for Colorado Plateau drainage evolution
Authors: Karlstrom K.E. , al. et
Published: August 2020

Table S1: Rotations of measured paleomagnetic paleopoles to test the error introduced by measuring inclinations relative to cross bedding of different orientations instead of horizontal bedding. Table S2: Detrital zircon data used in this study. Table S3: Quantitative comparison results from DZstats.
The Cologne rebubbling study: a reappraisal of 624 rebubblings after Descemet membrane endothelial keratoplasty
Authors: Siebelmann Sebastian , Kolb Katharina , Scholz Paula , Matthaei Mario , Franklin Jeremy , Händel Alexander , Schrittenlocher Silvia , Hayashi Takahiko , Guell Jose L , Bachmann Björn , Cursiefen Claus
Published: August 2020

Background/Aims

To analyse graft detachments prior to rebubbling, the influence of rebubbling on the postoperative outcome after Descemet membrane endothelial keratoplasty (DMEK) and the need for rebubbling on the contralateral eye.

Methods

In this retrospective cohort study, out of 1541 DMEKs, optical coherence tomography scans and clinical records of 499 eyes undergoing rebubbling after DMEK at the University Hospital of Cologne, Cologne, Germany, were examined. Main Outcome measures were (a) number, localisation and size of graft detachments; (b) influence of rebubbling/s on postoperative outcome after 12 months; and (c) rebubbling risk of the contralateral eye after DMEK.

Results

Mean number of detachment areas was 2.02±0.9. Mean lateral diameter of all detachments was 4534.76±1920.83 μm. Mean axial diameter was 382.53±282.02 μm. Detachments were equally distributed over all regions of the cornea. Best spectacle corrected visual acuity ( BSCVA) after 12 months was 0.197±0.23 logarithm of the minimum angle of resolution, endothelial cell density (ECD) was 1575.21±397.71 cells/mm2 and mean central corneal thickness (CCT) was 566.37±68.11 μm. BSCVA, CCT, ECD or endothelial cell loss of all rebubbled patients were not influenced by the number of rebubblings or the time between DMEK and rebubbling. Of the rebubbled patients, which received a DMEK subsequently on the other eye, 193 (58.8%) also received a rebubbling, which was significantly higher, when compared to the overall rebubbling rate of 32.3% (p=0.000).

Conclusions

The overall number of rebubblings has no influence on the postoperative outcome after DMEK, if a rebubbling becomes necessary. Patients who received a rebubbling on one eye have an elevated risk for a rebubbling on the fellow eye.
Cross-sectional study of Australian medical student attitudes towards older people confirms a four-factor structure and psychometric properties of the Australian Ageing Semantic Differential
Authors: Wilson Mark , Tran Yvonne , Wilson Ian , Kurrle Susan E
Published: August 2020

Objectives

The Australian Ageing Semantic Differential (AASD) survey was developed to quantify medical student attitudes towards older people. The purpose of this study is to examine psychometric properties of the survey and confirm its factor structure of four composites.

Design

A cross-sectional study.

Setting

Three medical schools in three Australian states: Victoria, Western Australia and South Australia.

Participants

Third-year or fourth-year medical students (n=188, response rate=79%).

Outcome measures

In the previous AASD study, exploratory factor analysis supported a four-factor model consisting of ‘Instrumentality’ (I), ‘Personal Appeal’ (PA), ‘Experience’ (E) and ‘Sociability’ (S). Congeneric one-factor confirmatory factor analysis (CFA) were used to examine model fit for factors using a new student sample (n=188).

Psychometric properties of survey items and factors.

Post-hoc analysis of pooled data from this study and earlier AASD study (n=509).

Results

Indices of fit (Comparative Fit Index (CFI), Tucker-Lewis Index (TLI), root mean square error of approximation (RMSEA), standardised root mean square residual (SRMR)) for data to the factor model were: PA adequate fit (CFI=0.94, TLI=0.89, RMSEA=0.11 and SRMR=0.05), I good fit (CFI=0.99, TLI=0.99, RMSEA=0.04 and SRMR=0.03), S good fit (CFI=0.98, TLI=0.95, RMSEA=0.06 and SRMR=0.03) and E excellent fit (CFI=1.0, TLI=1.0, RMSEA=0.00 and SRMR=0.01).

The AASD was internally consistent (Cronbach’s alpha=0.84), without difference in mean student scores by institution. Mean AASD score was positive for medical students outside New South Wales (73.2/114).

Mean I score for all Australian students was negative, with female respondents’ mean E score significantly higher than their counterparts. A positive correlation between student age and I score was noted.

Conclusions

The AASD is internally consistent and generalisable within Australia, with acceptable structural validity for measuring medical student attitudes towards older people within a four-factor model. Student attitudes were positive globally and within all factors except I. Female students rated older persons E more positively. Older students recorded more positive attitudes towards I of older people.
Low-density lipoprotein cholesterol and all-cause mortality: findings from the China health and retirement longitudinal study
Authors: Zhou Liang , Wu Ying , Yu Shaobo , Shen Yueping , Ke Chaofu
Published: August 2020

Objectives

To investigate the relationship between low-density lipoprotein cholesterol (LDL-C) and all-cause mortality among middle-aged and elderly Chinese population.

Design

Prospective cohort study.

Setting

This study used data from the China Health and Retirement Longitudinal Study.

Participants

Middle-aged and elderly participants with complete data were enrolled for a 4-year follow-up of total mortality and plasma levels of LDL-C, including 4981 male respondents and 5529 female respondents.

Results

During a 4-year follow-up, there were 305 and 219 deaths in men and women, respectively. Compared with the first quintile (Q1) of LDL-C, the adjusted HRs (95% CIs) were 0.818 (0.531 to 1.260) for Q2, 0.782 (0.507 to 1.208) for Q3, 0.605 (0.381 to 0.962) for Q4 and 0.803 (0.506 to 1.274) for Q5 in men. The results from restricted cubic spine (RCS) showed that when the 20th percentile of LDL-C levels (84 mg/dL) was used as the reference, a lower LDL-C concentration (<84 mg/dL) was associated with a higher 4-year all-cause mortality risk. By contrast, both quintile analysis and RCS analysis did not show a statistically significant association in women.

Conclusions

Compared with moderately elevated LDL-C (eg, 117–137 mg/dL), a lower plasma level of LDL-C (eg, ≤84 mg/dL) was associated with an increased risk of 4-year all-cause mortality in middle-aged and elderly Chinese men. The results suggest the potential harmful effect of a quite low level of LDL-C on total mortality.
Is untargeted iron supplementation harmful when iron deficiency is not the major cause of anaemia? Study protocol for a double-blind, randomised controlled trial among non-pregnant Cambodian women
Authors: Fischer Jordie AJ , Pei Lulu X , Goldfarb David M , Albert Arianne , Elango Rajavel , Kroeun Hou , Karakochuk Crystal D
Published: August 2020

Introduction

The WHO recommends daily oral iron supplementation for 12 weeks in women and adolescents where anaemia prevalence is greater than 40%. However, if iron deficiency is not a major cause of anaemia, then, at best, untargeted iron supplementation is a waste of resources; at worst, it could cause harm. Further, different forms of iron with varying bioavailability may present greater risks of harm.

Methods and analysis

A 12-week three-arm, double-blind, randomised controlled supplementation trial was conducted in Cambodia to determine if there is potential harm associated with untargeted iron supplementation. We will recruit and randomise 480 non-pregnant women (ages 18–45 years) to receive one of three interventions: 60 mg elemental iron as ferrous sulfate (the standard, commonly used form), 18 mg ferrous bisglycinate (a highly bioavailable iron amino acid chelate) or placebo. We will measure ferritin concentrations (to evaluate non-inferiority between the two forms of iron), as well as markers of potential harm in blood and stool (faecal calprotectin, gut pathogen abundance and DNA damage) at baseline and 12 weeks. Mixed-effects generalised linear models will be used to assess the effect of iron on ferritin concentration and markers of potential harm at 12 weeks.

Ethics and dissemination

Ethical approval was obtained from the University of British Columbia Clinical Research Ethics Board (H18-02610), the Children's and Women's Health Centre of British Columbia Research Ethics Board (H18-02610) and the National Ethics Committee for Health Research in Cambodia (273-NECHR). Findings will be published in peer-reviewed journals, presented to stakeholders and policymakers globally and shared within participants’ communities.

Trial registration number

ClinicalTrials.gov Registry (NCT04017598).
What clinical challenges are associated with diagnosing and managing work-related mental health conditions? A qualitative study in general practice
Authors: Chakraborty Samantha Paubrey , Dermentzis Jacinta , Brijnath Bianca , Ivey Eli , Mazza Danielle
Published: August 2020

Objective

When providing care for patients with work-related mental health conditions (MHCs), the general practitioner’s (GP) role includes clinical care, patient advocacy and assessment of a patient’s ability to work. GPs can experience difficulty representing these competing roles. As clinical guidelines were being developed to assist GPs in providing this care, our aim was to identify the clinical challenges GPs experience when diagnosing and managing patients with work-related MHCs.

Design

Qualitative research.

Setting

This study was conducted in general practice and workers’ compensation settings across Australia.

Participants

Twenty-five GPs, seven psychiatrists and nine compensation scheme workers. GPs were eligible to participate if they were actively treating (or treated within the previous three years) patient(s) who had submitted a workers’ compensation claim for a MHC. Psychiatrists and compensation scheme workers were eligible to participate if they were active in these roles, as they are best placed to identify additional clinical challenges GPs themselves did not raise.

Method

Participants were invited by letter to participate in qualitative semi-structured telephone interviews. Prior to each interview, participants were asked to reflect on two case vignettes, each depicting a patient’s illness trajectory over 12 months. Data were thematically analysed using inductive and deductive techniques and then categorised by stages of clinical reasoning.

Results

Participants reported clinical challenges across four key areas: (1) Diagnosis (identifying appropriate diagnostic tools, determining the severity and work-relatedness of a MHC, and managing the implications of labelling the patient with MHC). (2) Management (determining optimal treatment, recommending work participation). (3) Referral (ambiguity of communication pathways within compensation schemes). (4) Procedure (difficulties navigating compensation systems).

Conclusion

We found that GPs experienced clinical challenges at all stages of care for people with work-related MHCs. We were also able to identify systemic and procedural issues that influence a GP’s ability to provide care for patients with work-related MHCs.
Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research
Authors: McAloon Conor , Collins Áine , Hunt Kevin , Barber Ann , Byrne Andrew W , Butler Francis , Casey Miriam , Griffin John , Lane Elizabeth , McEvoy David , Wall Patrick , Green Martin , O'Grady Luke , More Simon J
Published: August 2020

Objectives

The aim of this study was to conduct a rapid systematic review and meta-analysis of estimates of the incubation period of COVID-19.

Design

Rapid systematic review and meta-analysis of observational research.

Setting

International studies on incubation period of COVID-19.

Participants

Searches were carried out in PubMed, Google Scholar, Embase, Cochrane Library as well as the preprint servers MedRxiv and BioRxiv. Studies were selected for meta-analysis if they reported either the parameters and CIs of the distributions fit to the data, or sufficient information to facilitate calculation of those values. After initial eligibility screening, 24 studies were selected for initial review, nine of these were shortlisted for meta-analysis. Final estimates are from meta-analysis of eight studies.

Primary outcome measures

Parameters of a lognormal distribution of incubation periods.

Results

The incubation period distribution may be modelled with a lognormal distribution with pooled mu and sigma parameters (95% CIs) of 1.63 (95% CI 1.51 to 1.75) and 0.50 (95% CI 0.46 to 0.55), respectively. The corresponding mean (95% CIs) was 5.8 (95% CI 5.0 to 6.7) days. It should be noted that uncertainty increases towards the tail of the distribution: the pooled parameter estimates (95% CIs) resulted in a median incubation period of 5.1 (95% CI 4.5 to 5.8) days, whereas the 95th percentile was 11.7 (95% CI 9.7 to 14.2) days.

Conclusions

The choice of which parameter values are adopted will depend on how the information is used, the associated risks and the perceived consequences of decisions to be taken. These recommendations will need to be revisited once further relevant information becomes available. Accordingly, we present an R Shiny app that facilitates updating these estimates as new data become available.