bluuebunny/crossref_metadata_2025 huggingface dataset:
Mean growth rate when rare is not a reliable metric for persistence of species
Authors: Pande Jayant , Fung Tak , Chisholm Ryan , Shnerb Nadav M.
Published: November 2019

The coexistence of many species within ecological communities poses a long‐standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, , is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on and show that it fails to capture the effect of temporal random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in , since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as increases.
P‐glycoprotein: a role in the export of amyloid‐β in Alzheimer's disease?
Authors: Chai Amanda B. , Leung Gavin K. F. , Callaghan Richard , Gelissen Ingrid C.
Published: November 2019

The accumulation of amyloid‐β (Aβ) peptides is a key histopathological feature of the Alzheimer's brain. Defective clearance mechanisms result in toxic levels of soluble Aβ40 and Aβ42 oligomers, leading to impaired synaptic function, neurodegeneration and cognitive decline. Growing evidence points to the involvement of P‐glycoprotein (P‐gp or ABCB1), an ATP‐binding cassette transporter highly expressed on the luminal side of the blood–brain barrier, in facilitating the clearance of Aβ from the brain. In this review, we summarise evidence from human, animal and in vitro studies examining the contribution of P‐gp to Aβ clearance, and discuss the potential for P‐gp as a novel pharmacological target in Alzheimer's disease (AD). P‐gp expression and activity in the brain are inversely correlated with ageing, Aβ deposition and AD. Moreover, Aβ itself has been found to compromise the expression of P‐gp, thereby exacerbating Aβ deposition and disease. Despite decades of research, the pathophysiology of AD remains elusive. Understanding the normal versus impaired processing and clearance mechanisms affecting Aβ peptides will assist the development of more effective therapeutic agents to combat this progressive neurodegenerative condition that continues to devastate millions of patients globally.
Comparison between the Identification of Seniors at Risk and Triage Risk Screening Tool in predicting mortality of older adults visiting the emergency department: Results from Indonesia
Authors: Rizka Aulia , Harimurti Kuntjoro , Pitoyo Ceva W , Koesnoe Sukamto
Published: November 2019

Aim

Among others, the Identification of Seniors at Risk (ISAR) and Triage Risk Screening Tool (TRST) are widely used screening instruments for risk stratification of older adults visiting the emergency department (ED). In developing countries, such as Indonesia, older patients often present with acute and severe conditions, leading to a high mortality rate, in which the performance of these two instruments have not been studied. This study aimed to measure the performance of the ISAR and TRST to predict 1‐ and 3‐month mortality in older patients visiting the ED in Indonesia.

Methods

This was a prospective cohort study of older patients consecutively visiting the ED of Cipto Mangunkusumo Hospital, a national referral hospital in Jakarta, Indonesia, from January to July 2017. The area of under the curve (AUC) of the ISAR and TRST in predicting 1‐ and 3‐month mortality was measured.

Results

Of 771 participants, 400 (52.8%) were men. The 1 month‐mortality incidence was 22.8% (95% CI 21.3–24.8), and 3‐month mortality was 31.2% (95% CI 29.3–33.8). For 1‐month mortality, the ISAR showed AN AUC of 0.62 (95% CI 0.57–0.68), whereas the TRST showed an AUC of 0.58 (95% CI 0.52–0.64). For 3‐month mortality, the ISAR showed an AUC of 0.60 (95% CI 0.54–0.65), whereas the TRST showed an AUC of 0.57 (95% CI 0.51–0.62).

Conclusions

Both instruments showed moderate predictive ability, but the ISAR showed better performance in predicting 1‐ and 3‐month mortality of older patients visiting the ED in Indonesia. Geriatr Gerontol Int 2020; 20: 47–51.
Low‐temperature synthesis of tungsten diboride powders via a simple molten salt route
Authors: Ma Ke , Xue Xiangxin , Cao Xiaozhou
Published: November 2019

WB2 powders were successfully prepared at 1000°C using NaCl–KCl salts as molten salts. Compared to the conventional solid‐state reaction, the introduction of NaCl–KCl salts decreased the synthesis temperature of WB2 phase, which was related to the faster diffusion rate of particles in the liquid state than in the solid‐state. The effect of reaction temperature, time, and the amount of molten salts on the synthesis of WB2 were studied in detail. The template formation mechanism was considered to have played an essential part in the synthesis process. Transmission electron microscope analysis showed that the as‐synthesized WB2 powders exhibited a hexagonal crystal structure. Furthermore, the oxidation protective performance of as‐synthesized WB2 powders was investigated by TG‐DSC measurement.
TRIM21 controls Toll‐like receptor 2 responses in bone‐marrow‐derived macrophages
Authors: Sjöstrand Maria , Carow Berit , Nyberg William A. , Covacu Ruxandra , Rottenberg Martin E. , Espinosa Alexander
Published: November 2019

TRIM21 is an interferon‐stimulated E3 ligase that controls the activity of pattern‐recognition signaling via ubiquitination of interferon regulatory factors and DDX41. Previous studies on the role of TRIM21 in innate immune responses have yielded contradictory results, suggesting that the role of TRIM21 is cell specific. Here, we report that bone‐marrow‐derived macrophages (BMDMs) generated from Trim21−/− mice have reduced expression of mature macrophage markers. Reflecting their reduced differentiation in response to macrophage colony‐stimulating factor (M‐CSF), Trim21−/− BMDMs had decreased expression of M‐CSF signature genes. Although Trim21−/− BMDMs responded normally to Toll‐like receptor 9 (TLR9) activation, they produced lower levels of pro‐inflammatory cytokines in response to the TLR2 agonist PAM3CSK4. In line with this, the response to infection with the Bacillus Calmette–Guérin strain of Mycobacterium bovis was also diminished in Trim21−/− BMDMs. Our results indicate that TRIM21 controls responses to TLR2 agonists.
Understanding and measuring human B‐cell tolerance and its breakdown in autoimmune disease
Authors: Cashman Kevin S. , Jenks Scott A. , Woodruff Matthew C. , Tomar Deepak , Tipton Christopher M. , Scharer Christopher D. , Eun‐Hyung Lee F. , Boss Jeremy M. , Sanz Iñaki
Published: November 2019

The maintenance of immunological tolerance of B lymphocytes is a complex and critical process that must be implemented as to avoid the detrimental development of autoreactivity and possible autoimmunity. Murine models have been invaluable to elucidate many of the key components in B‐cell tolerance; however, translation to human homeostatic and pathogenic immune states can be difficult to assess. Functional autoreactive, flow cytometric, and single‐cell cloning assays have proven to be critical in deciphering breaks in B‐cell tolerance within autoimmunity; however, newer approaches to assess human B‐cell tolerance may prove to be vital in the further exploration of underlying tolerance defects. In this review, we supply a comprehensive overview of human immune tolerance checkpoints with associated mechanisms of enforcement, and highlight current and future methodologies which are likely to benefit future studies into the mechanisms that become defective in human autoimmune conditions.
German Commission Calls for Risk-Based Regulation of Algorithmic Systems
Authors: Tarran Brian
Published: November 2019

Data ethics body says control and oversight of automated systems should be based on severity and likelihood of harm
Measuring Society Who, What, When, Where, Why and How
Authors: Nagaraja Chaitra H.
Published: November 2019

Official statistics, such as the unemployment rate, can tell us much about the society we live in. But the public need a greater understanding of how these statistics are put together, what they count, and why, says Chaitra H. Nagaraja
An Uncertain State
Authors: Tarran Brian
Published: November 2019

The “what ifs?” of Brexit Britain. By Brian Tarran
A Severe Forecast
Authors: Fawcett Lee
Published: November 2019

Changes to the earth's climate brought on by global warming are leading to an increase in extreme weather events. Lee Fawcett explains how extreme value theory helps statisticians better anticipate the severity and likelihood of these events
Predictors of durable electrical isolation in the setting of second‐generation cryoballoon ablation: A comparison between left superior, left inferior, right superior, and right inferior pulmonary veins
Authors: Scala Oriana , Borio Gianluca , Paparella Gaetano , Varnavas Varnavas , Ströker Erwin , Guimaraes Osorio Thiago , Terasawa Muryo , Sieira Juan , Maj Riccardo , Rizzo Alessandro , Al‐Hosari Maysam M. , Galli Alessio , Brugada Pedro , de Asmundis Carlo , Chierchia Gian‐Battista
Published: November 2019

Aim

The aim of this study is to assess specific per‐vein procedural predictors of pulmonary vein (PV) late reconnection in cryoballoon ablation (CbA)

Methods and Results

We enrolled 148 consecutive patients undergoing a redo procedure after a previous index CbA in our center. A reconnection in at least one PV was found in 80 patients (54.1%) and the most frequently reconnected PV was the right inferior pulmonary vein (RIPV). Overall, pulmonary vein reconnection (PVr) was associated with longer time to −40°C (Tt−40°C) (54.4 ± 21.7 vs 67.6 ± 27.6 seconds; P < .001), warmer nadir temperature (NT) (−49.7°C ± 5.4°C vs −46.5°C ± 5.8°C; P < .001) and temperature at 60 seconds (−41.8°C ± 4.5°C vs −39.8°C ± 4.2°C; P < .001). The performance of these predictors differed between the veins. In particular, a comparable behavior was observed for left superior pulmonary vein (LSPV) and right superior pulmonary vein (RSPV), where NT ≤ −48°C showed a sensibility and a specificity, respectively, of 62% and 65% and 71% and 72% in predicting durable PV isolation. For RIPV, NT ≤ −48°C showed a sensitivity of 74% but low specificity (53%). Tt −40°C less than 60 seconds showed good negative predictive values, respectively, 83.9% for LSPV, 94.9% for left inferior pulmonary vein (LIPV), 90.2% for RSPV, and 82.7% for RIPV. Previous predictors cannot be used for LIPV.

Conclusions

Freezing behavior and reconnection rates differ significantly among the four PVs. Freezing temperature parameters strongly predict late PVr in superior PVs and are slightly different in RIPV but can be applied as well. LIPV freezing behavior is the most different. Its reconnection is uncommon even in the subset of worse freezing temperatures and specific CB predictors cannot be identified.
An hypoxia‐tolerant flatfish: consequences of sustained stress on the slender sole Lyopsetta exilis (Pleuronectidae) in the context of a changing ocean
Authors: Tunnicliffe Verena , Gasbarro Ryan , Juanes Francis , Qualley Jessica , Soderberg Nicole , Chu Jackson W. F.
Published: November 2019

Slender sole Lyopsetta exilis is an abundant groundfish on the continental shelf and inner waters of British Columbia, Canada, where it reaches a maximum standard length of 44 cm. Benthic image surveys coupled with oxygen measurements in Saanich Inlet document a dense population in bottom conditions near anoxia (0.03 ml l−1 oxygen) where diel migrating zooplankton intersect the bottom; we confirm this species is a planktivore, which limits its depth range to the base of the migration layer. In a comparison with slender sole from a nearby well‐oxygenated habitat, several probable effects of living in severe hypoxia emerge: both sexes are significantly smaller in Saanich and the sex ratio is male‐skewed. Otoliths from the Saanich fish were difficult to read due to many checks, but both sexes were smaller at age with the largest female (20 cm) from the hypoxia zone registering 17 years. Hypoxia appears to have a direct consequence on growth despite good food supply in this productive basin. Hyperventilation, a low metabolic rate and a very low critical oxygen tension help this fish regulate oxygen uptake in severely hypoxic conditions; it will be particularly resilient as the incidence of hypoxia increases on the continental shelf. Data from small‐mesh bottom‐trawl surveys over four decades reveal an increase in mean annual catch per unit effort in southern regions of the province, including the outer shelf and the Strait of Georgia. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) ichthyoplankton database records a general decline in fish larvae on the Oregon–California shelf since 1990, but slender sole larvae are increasing there, as they are in the Strait of Georgia. We project that the slender sole will gain relative benefits in the future warming, deoxygenated northeast Pacific Ocean.
Oral health status of children with epilepsy in Hong Kong
Authors: Yeung Patricia M. , Wong Virginia C. N. , McGrath Colman P. , Yiu Cynthia K. Y. , Lee Gillian H. M.
Published: November 2019

Aim

This study assessed and compared the oral health status, dental trauma experience and oral health habits of children with and without epilepsy.

Methods

Thirty‐five children with epilepsy aged 3‐18 years old were recruited from the pediatric neurology clinics of 2 university‐affiliated district hospitals. A sample of 35 age‐ and gender‐matched healthy children was recruited as controls. Clinical data on caries, gingival health, oral hygiene level and dental trauma were collected and compared between the groups. Information about children’s oral health habits and reported dental trauma experience were obtained by structured questionnaire.

Results

Children with epilepsy had significantly poorer gingival health than healthy controls. No significant differences in dental caries experience, oral hygiene level, dental trauma experience, oral health habits and dental care service utilization were observed between the children with and without epilepsy. Among the children with epilepsy, those taking more than 1 antiepileptic drug had a greater prevalence of dental caries when compared with those receiving mono‐antiepileptic drug therapy. The presence of gingival hyperplasia indicated poorer gingival health in epileptic children.

Conclusion

The study shows that children with epilepsy had poorer oral health status in terms of gingival health than those without epilepsy.
MRI‐Based Manual versus Automated Corpus Callosum Volumetric Measurements in Multiple Sclerosis
Authors: Platten Michael , Martola Juha , Fink Katharina , Ouellette Russell , Piehl Fredrik , Granberg Tobias
Published: November 2019

BACKGROUND AND PURPOSE

Corpus callosum atrophy is a neurodegenerative biomarker in multiple sclerosis (MS). Manual delineations are gold standard but subjective and labor intensive. Novel automated methods are promising but require validation. We aimed to compare the robustness of manual versus automatic corpus callosum segmentations based on FreeSurfer.

METHODS

Nine MS patients (6 females, age 38 ± 13 years, disease duration 7.3 ± 5.2 years) were scanned twice with repositioning using 3‐dimensional T1‐weighted magnetic resonance imaging on three scanners (two 1.5 T and one 3.0 T), that is, six scans/patient, on the same day. Normalized corpus callosum areas were measured independently by a junior doctor and neuroradiologist. The cross‐sectional and longitudinal streams of FreeSurfer were used to segment the corpus callosum volume.

RESULTS

Manual measurements had high intrarater (junior doctor .96 and neuroradiologist .96) and interrater agreement (.94), by intraclass correlation coefficient (P < .001). The coefficient of variation was lowest for longitudinal FreeSurfer (.96% within scanners; 2.0% between scanners) compared to cross‐sectional FreeSurfer (3.7%, P = .001; 3.8%, P = .058) and the neuroradiologist (2.3%, P = .005; 2.4%, P = .33). Longitudinal FreeSurfer was also more accurate than cross‐sectional (Dice scores 83.9 ± 7.5% vs. 78.9 ± 8.4%, P < .01 relative to manual segmentations). The corpus callosum measures correlated with physical disability (longitudinal FreeSurfer r = –.36, P < .01; neuroradiologist r = –.32, P < .01) and cognitive disability (longitudinal FreeSurfer r = .68, P < .001; neuroradiologist r = .64, P < .001).

CONCLUSIONS

FreeSurfer's longitudinal stream provides corpus callosum measures with better repeatability than current manual methods and with similar clinical correlations. However, due to some limitations in accuracy, caution is warranted when using FreeSurfer with clinical data.
Persistent Microembolic Signals in the Cerebral Circulation on Transcranial Doppler after Intravenous Sulfur Hexafluoride Microbubble Infusion
Authors: Aarli Sander Johan , Novotny Vojtech , Thomassen Lars , Kvistad Christopher Elnan , Logallo Nicola , Fromm Annette
Published: November 2019

BACKGROUND AND PURPOSE

Microembolic signals (MES) are detectable by transcranial Doppler monitoring and associated with increased risk of first or recurrent ischemic stroke. MES detection can also illuminate stroke etiology and the effect of prophylactic treatment. MES detection cannot accurately distinguish between stroke‐related microemboli and ultrasound contrast agents. These agents contain microbubbles and are frequently used in neuro‐ and cardiovascular diagnostics. We aimed to assess how long after contrast infusion microbubbles are detectable by transcranial Doppler monitoring.

METHODS

Ten healthy volunteers received an intravenous infusion of stabilized sulfur hexafluoride microbubbles (SonoVue®) for 30 minutes. The infusion was followed by continuous unilateral Doppler monitoring (TCD‐X, Atys Medical, Soucieu‐en‐Jarrest, France) for 3.5 hours.

RESULTS

MES persisted for 12 to 77 minutes (median 40.5 minutes), and the frequency tended to decrease gradually until cessation.

CONCLUSIONS

None of the subjects had detectable MES for more than 77 minutes after ultrasound contrast infusion. MES detection with the intent to detect stroke‐related microemboli should wait for at least this long after completed infusion.
The traditional uses, phytochemistry, pharmacology and toxicology of Cinnamomi ramulus: a review
Authors: Liu Jia , Zhang Qing , Li Ruo-Lan , Wei Shu-Jun , Huang Chun-Yan , Gao Yong-Xiang , Pu Xu-Feng
Published: November 2019

Objectives

Cinnamomi ramulus (called Guizhi in Chinese) is a traditional medicine used to treat gastrointestinal dysfunction, cancer, arthritis, osteoporosis, spleen deficiency, Alzheimer’s disease and obesity. This review aimed to provide a systematic summary on the geographical distribution, botany, traditional application, phytochemistry, pharmacology, pharmacokinetics, toxicology and other aspects of Cinnamomi ramulus.

Key finding

So far, more than 121 chemical compounds have been isolated from Cinnamomi ramulus, including volatile oil, organic acids, triterpenoid saponins, coumarins, tannins, flavonoids and flavonoid glycosides, steroids and polysaccharides. This paper reviews the pharmacological effects of Cinnamomi ramulus on antibacterial, anti-inflammatory, antiviral, antitumour, antipyretic and analgesic, antidiabetic and antiplatelet aggregation effects. Furthermore, the present review also indicates that Cinnamomi ramulus has the potential to develop into drugs for treating various diseases with high efficacy and low toxicity.

The convictive evidence from modern pharmacology research supports the traditional application of Cinnamomi ramulus. However, further studies on the structure–activity relationship of some of the isolated compounds may improve their biological potency. More toxicological studies will also contribute to the progress of clinical trial studies.
Melatonin duration gates photoperiodic vocal state change in a songbird
Authors: Harpole Clifford E. , Miles Meredith D. , Cassone Vincent M.
Published: November 2019

Seasonally breeding animals concentrate courtship to a particular time of year such that their offspring will be reared in a favorable environment. In house sparrows, Passer domesticus, primary (gonads) and secondary (song, plumage, beak color, etc) sexual characteristics are expressed differentially depending on the photoperiod. Removal of the pineal gland (PINX) has no effect on seasonal rhythms in gonad size but alters the photostimulated increase in vocal rate and complexity. Administration of long durations of melatonin, indicative of short days of winter, prevents seasonal recrudescence of song control nuclei in photostimulated house sparrows. In this study, male PINX house sparrows were exposed to three durations of melatonin, while vocalization and locomotor behavior were recorded as they were transitioned from short photoperiod to equinoctial photoperiods of spring. Birds receiving short duration melatonin or vehicle control increased dawn and dusk choruses as well as call complexity. Long durations of melatonin prevented this expansion to a spring‐like vocal state observed in birds receiving the short duration of melatonin or vehicle control. The daily distribution of locomotor activity, beak color, and testis size was unaffected by treatment. Vocal state change was defined by our measures in two capacities: (i) increased dawn and dusk choruses, and (ii) an increase in calls associated with territory and mate attraction compared to the winter‐like “social song.” We conclude that house sparrows use the calendar information provided by melatonin duration to control seasonal vocalization behavior, independent of effects on and of the gonads.
Being in a Seclusion Room: The Forensic Psychiatric Inpatients’ Perspective
Authors: Askew Louise , Fisher Paul , Beazley Peter
Published: November 2019

Accessible Summary

What is known on the subject

Existing qualitative research has found inpatient service users to experience seclusion as highly distressing, with feelings of vulnerability, abuse and neglect often featuring in participants’ accounts.

The physical environment of the seclusion room and the interaction with clinical staff shape service users’ personal seclusion experience.

What the paper adds to existing knowledge

The majority of research on this topic focuses on seclusion within other restrictive practices. This paper provides new knowledge on one specific component of seclusion, the experience of being in the room, and draws attention to the specific psychological needs of service users during that aspect of their experience.

This research provides new knowledge by exclusively exploring forensic inpatients’ experience of the seclusion room, an under researched and often stigmatized population.

What are the implications to practice

The findings support the need for a caring and non‐threatening therapeutic interaction with a secluded service user for the duration of time they are in the seclusion room.

The findings suggest that necessary nursing procedures, such as observations, should be carried out discretely and sensitively to avoid service users feeling abused and frightened.

Introduction

Contemporary qualitative research has explored service users’ experience of seclusion and has found it to be a highly distressing and potentially traumatizing experience for service users. The majority of the existing literature has researched seclusion within the context of other restrictive practices, resulting in findings that can only be considered an overview of the experience. The studies also rarely access participants with histories of considerable violence and imprisonment.

Question

What is forensic psychiatric inpatients’ experience of being in a seclusion room?

Method

Seven inpatients in a medium secure hospital were interviewed, and interpretative phenomenological analysis (IPA) was used to analyse the data.

Results

Four superordinate themes were identified: “intense fear,” ‘not getting the care I needed,” ‘I am being abused” and “power struggle.”

Discussion

While participants were in the seclusion room, they experienced extreme fear. Staff interaction played a considerable role in shaping the participants’ experience. Staff actions were interpreted as neglectful and abusive. Participants experienced struggling for power with staff, seeking out power when left in a powerless position.

Implications for practice

These findings suggested that a carefully tailored therapeutic interaction is required during seclusion in order to safeguard the mental health of forensic inpatients.
High rate of hepatitis C reinfection following antiviral treatment in the North East England Prisons
Authors: Bhandari Rajan , Morey Sarah , Hamoodi Abi , Thompson Craig , Jones Dee , Hewett Margaret , Hunter Ewan , Taha Yusri , McPherson Stuart
Published: November 2019

To achieve elimination of hepatitis C (HCV), a critical group to prioritise for diagnosis and treatment is the prison population, where HCV prevalence is high. A universal offer of blood‐borne virus testing (UOBBVT) programme and a new treatment pathway were introduced to seven North East England (NEE) Prisons. Our aim was to assess: (a) the proportion of individuals with active HCV commencing direct‐acting antivirals (DAAs); (b) the outcomes following DAA treatment; (3) the reinfection rate following sustained virological response (SVR).

Data were collected prospectively on BBVT uptake, HCV positivity, HCV treatment outcomes and reinfection from March 2016 onwards. 8538 individuals had BBV testing. In total, 612 (7.2%) and 374 (4.4%) were HCV antibody positive and HCV RNA positive, respectively. Ultimately, 266 (71%) individuals commenced DAAs. Overall 111 achieved a documented SVR (42%), 17 (6%) failed treatment, 30 (11%) were still on treatment or had not reached 12 weeks post‐treatment at time of analysis, and 108 (41%) were lost to follow‐up. In those with a known outcome (n = 128), 87% achieved SVR. Worryingly, of those who achieved SVR, 21 (19%) were subsequently identified as having been reinfected (median time from SVR to documented reinfection 13 (range 7‐25) months). The reinfection rate was 0.406 cases per person‐year follow‐up. In conclusion, Implementation of a UOBBVT programme and new treatment pathway resulted in increased diagnosis and treatment of HCV in the NEE prison population. However, the high HCV reinfection rate suggests a need to improve harm reduction approaches.
Signature of sexual conflict is actually conflict resolved
Authors: Mank Judith E. , Shu Jacelyn J. , Wright Alison E.
Published: November 2019

There has been substantial interest of late in using population genetic methods to study sexual conflict, where an allele increases the fitness of one sex at some cost to the other (Mank, 2017). Population genomic scans for sexual conflict offer an important advance given the difficulties of identifying antagonistic alleles from more traditional methods, and could greatly increase our understanding of the extent and loci of sexual conflict. This is particularly true for studies in natural populations, for which obtaining accurate fitness measurements for each sex can be challenging. In this issue of Molecular Ecology, Bissegger, Laurentino, Roesti, and Berner (2019) present a cautionary tale about how to interpret these population genomic data.
Automated classification of indoor environmental quality control using stacked ensembles based on electroencephalograms
Authors: Kim Jimin , Kim Hakpyeong , Hong Taehoon
Published: November 2019

This study aims to develop an automated classification of indoor air quality control using the machine learning based on an electroencephalogram (EEG) signal. Two experiments were conducted: The first aimed to select an EEG channel based on the brain wave indices when the indoor environmental quality (IEQ) changes. We then extract the brain wave indices’ feature when the subjects conduct adaptive behaviors and predict the IEQ condition control using machine learning including the stacked ensembles. The extracted features were classified using base estimators such as distributed random forest, gradient boosting machine (GBM), generalized linear models (GLMs), deep neural network, and new predicted data were retrained and predicted by metalearner (i.e., GLM). In Dimension 1, the air conditioning system and the air ventilation system, and the area under curve (AUC) of the proposed stacked ensembles trained by base estimators was the highest, 0.9038. In Dimension 2, turning on and turning off, the AUC of the GBM is the highest, 0.8384. Based on these results, the EEG signal can be used to suggest an automatic IEQ control model that can then reduce the drowsiness, and increase attention.
An in vitro DNA phosphorothioate modification reaction
Authors: Pu Tianning , Mei Zhiling , Zhang Wei , Liang Wei‐Jun , Zhou Xiufen , Liang Jingdan , Deng Zixin , Wang Zhijun
Published: November 2019

Phosphorothioation (PT) involves the replacement of a nonbridging phosphate oxygen on the DNA backbone with sulfur. In bacteria, the procedure is both sequence‐ and stereo‐specific. We reconstituted the PT reaction using purified DndCDE from Salmonella enterica and IscS from Escherichia coli. We determined that the in vitro process of PT was oxygen sensitive. Only one strand on a double‐stranded (ds) DNA substrate was modified in the reaction. The modification was dominant between G and A in the GAAC/GTTC conserved sequence. The modification between G and T required the presence of PT between G and A on the opposite strand. Cysteine, S‐adenosyl methionine (SAM) and the formation of an iron‐sulfur cluster in DndCDE (DndCDE‐FeS) were essential for the process. Results from SAM cleavage reactions support the supposition that PT is a radical SAM reaction. Adenosine triphosphate (ATP) promoted the reaction but was not essential. The data and conclusions presented suggest that the PT reaction in bacteria involves three steps. The first step is the binding of DndCDE‐FeS to DNA and searching for the modification sequence, possibly with the help of ATP. Cysteine locks DndCDE‐FeS to the modification site with an appropriate protein conformation. SAM triggers the radical SAM reaction to complete the oxygen‐sulfur swapping.
Ty‐1, a universal resistance gene against geminiviruses that is compromised by co‐replication of a betasatellite
Authors: Voorburg Corien M. , Yan Zhe , Bergua‐Vidal Maria , Wolters Anne‐Marie A. , Bai Yuling , Kormelink Richard
Published: November 2019

Tomato yellow leaf curl virus (TYLCV), a begomovirus, causes large yield losses and breeding for resistance is an effective way to combat this viral disease. The resistance gene Ty‐1 codes for an RNA‐dependent RNA polymerase and has recently been shown to enhance transcriptional gene silencing of TYLCV. Whereas Ty‐1 was earlier shown to also confer resistance to a bipartite begomovirus, here it is shown that Ty‐1 is probably generic to all geminiviruses. A tomato Ty‐1 introgression line, but also stable transformants of susceptible tomato cv. Moneymaker and Nicotiana benthamiana (N. benthamiana) expressing the Ty‐1 gene, exhibited resistance to begomoviruses as well as to the distinct, leafhopper‐transmitted beet curly top virus, a curtovirus. Stable Ty‐1 transformants of N. benthamiana and tomato showed fewer symptoms and reduced viral titres on infection compared to wild‐type plants. TYLCV infections in wild‐type N. benthamiana plants in the additional presence of a betasatellite led to increased symptom severity and a consistent, slightly lowered virus titre relative to the high averaged levels seen in the absence of the betasatellite. On the contrary, in Ty‐1 transformed N. benthamiana viral titres increased in the presence of the betasatellite. The same was observed when these Ty‐1‐encoding plants were challenged with TYLCV and a potato virus X construct expressing the RNA interference suppressor protein βC1 encoded by the betasatellite. The resistance spectrum of Ty‐1 and the durability of the resistance are discussed in light of antiviral RNA interference and viral counter defence strategies.
Carnap and Quine on analyticity: The nature of the disagreement
Authors: Hylton Peter
Published: November 2019

The difference between Carnap and Quine over analyticity is usually thought to turn on a disagreement as to whether there is a notion of meaning, or rules of language, which enable us to define that idea. This paper argues that the more important disagreement is epistemological. Quine came to accept a notion of analyticity. That leaves him in a position somewhat like Putnam's in ‘The Analytic and the Synthetic’: that there is a notion of analyticity, but that it is of no philosophical importance. But their reasons for thinking analyticity unimportant are quite different: for Putnam it is because all analytic truths are trivial; for Quine, the notion of analyticity itself is unimportant. I contrast Putnam's position with that of Carnap, and also contrast Carnap and Quine. Analyticity only has the force that it has for Carnap because he accepts the Principle of Tolerance, the idea that changes within a language and changes of language are subject to justification in different senses. Quine rejects that idea. That is why he does not take analyticity to be philosophically important or useful.
Reactive oxygen species dosage in Arabidopsis chloroplasts can improve resistance towards Colletotrichum higginsianum by the induction of WRKY33
Authors: Schmidt Andree , Mächtel Rebecca , Ammon Alexandra , Engelsdorf Timo , Schmitz Jessica , Maurino Veronica G. , Voll Lars M.
Published: November 2019

Arabidopsis plants overexpressing glycolate oxidase in chloroplasts (GO5) and loss‐of‐function mutants of the major peroxisomal catalase isoform, cat2‐2, produce increased hydrogen peroxide (H2O2) amounts from the respective organelles when subjected to photorespiratory conditions like increased light intensity.

Here, we have investigated if and how the signaling processes triggered by H2O2 production in response to shifts in environmental conditions and the concomitant induction of indole phytoalexin biosynthesis in GO5 affect susceptibility towards the hemibiotrophic fungus Colletotrichum higginsianum.

Combining histological, biochemical, and molecular assays, we found that the accumulation of the phytoalexin camalexin was comparable between GO genotypes and cat2‐2 in the absence of pathogen. Compared with wild‐type, GO5 showed improved resistance after light‐shift‐mediated production of H2O2, whereas cat2‐2 became more susceptible and allowed significantly more pathogen entry. Unlike GO5, cat2‐2 suffered from severe oxidative stress after light shifts, as indicated by glutathione pool size and oxidation state.

We discuss a connection between elevated oxidative stress and dampened induction of salicylic acid mediated defense in cat2‐2. Genetic analyses demonstrated that induced resistance of GO5 is dependent on WRKY33, but not on camalexin production. We propose that indole carbonyl nitriles might play a role in defense against C. higginsianum.
Core outcome set for behavioural weight management interventions for adults with overweight and obesity: Standardised reporting of lifestyle weight management interventions to aid evaluation (STAR‐LITE)
Authors: Mackenzie Ruth M. , Ells Louisa J. , Simpson Sharon Anne , Logue Jennifer
Published: November 2019

Behavioural weight management interventions in research studies and clinical practice differ in length, advice, frequency of meetings, staff, and cost. Few real‐world programmes have published patient outcomes and those that have used different ways of reporting information, making it impossible to compare interventions and develop the evidence base. To address this issue, we have developed a core outcome set for behavioural weight management intervention programmes for adults with overweight and obesity. Outcomes were identified via systematic review of the literature. A representative expert group was formed comprising people with experience of adult weight management services. An online Delphi process was employed to reach consensus as to which outcomes should be measured and reported and which definitions/instruments should be utilised. The expert group identified eight core outcomes and 12 core processes for reporting by weight management services. Eleven outcomes and five processes were identified as optional. The most appropriate definitions/instruments for measuring each outcome/process were also agreed. Our core outcome set will ensure consistency of reporting. This will allow behavioural weight management interventions to be compared, revealing which interventions work best for which members of the population and helping inform development of adult behavioural weight management interventions.
An integrative review of exercise interventions among community‐dwelling adults with Alzheimer's disease
Authors: Li Bei , Liu Congying , Wan Qiaoqin , Yu Fang
Published: November 2019

Aims

To synthesise the current research on exercise interventions and health‐related outcomes among community‐dwelling adults with Alzheimer's disease (AD).

Methods

Integrative review of the literature reporting exercise interventions among people with AD living in the communities.

Results

Seventeen studies presented in 24 quantitative papers with 1,068 participants diagnosed with Alzheimer's disease were reviewed. The interventions varied in intervention programme characteristics (e.g. baseline assessments, type of exercise, exercise dose, outcome measurements). Among them, (a) 13 studies appeared beneficial to physical fitness in different areas; (b) 9 studies reported the effects on cognitive ability and two studies showed the positive effects; (c) 12 studies reported the participants' adherence, but only 2 studies reported the participants' adherence using attendance and training intensity.

Conclusion

Exercise is proven to be effective in physical fitness among community‐dwelling patients with AD. Future studies should verify the effects on cognitive function and possible mechanisms of different exercise types using more sensitive and objective outcome measurements. Additionally, treatment fidelity, cost‐effectiveness and long‐term effects should be explored.

Implication for practice

Exercise may be effective and feasible for community‐dwelling people with AD, but its effects on cognition need to be verified in the future. This review provided recommendations for assisting nurses and other clinicians in developing, implementing, and/or evaluating exercise interventions for patients with AD.
Philosophy of science and the replicability crisis
Authors: Romero Felipe
Published: November 2019

Replicability is widely taken to ground the epistemic authority of science. However, in recent years, important published findings in the social, behavioral, and biomedical sciences have failed to replicate, suggesting that these fields are facing a “replicability crisis.” For philosophers, the crisis should not be taken as bad news but as an opportunity to do work on several fronts, including conceptual analysis, history and philosophy of science, research ethics, and social epistemology. This article introduces philosophers to these discussions. First, I discuss precedents and evidence for the crisis. Second, I discuss methodological, statistical, and social‐structural factors that have contributed to the crisis. Third, I focus on the philosophical issues raised by the crisis. Finally, I discuss several proposals for solutions and highlight the gaps that philosophers could focus on.
Soil management in a mountain agroecosystem and clubroot disease
Authors: Bhering A. S. , Carmo M. G. F. , Coelho I. S. , Lima E. S. A. , de Carvalho C. F. , Saraiva A. L. R. F. , Passos S. R. , Amaral Sobrinho N. M. B.
Published: November 2019

Clubroot, caused by Plasmodiophora brassicae, is a disease limiting the production of Brassica species. Its severity varies according to the density of the pathogen's resting spores and environmental conditions. Although the soil environment (including its physical, chemical and biological characteristics) is determinant in the development of the disease, little is known regarding these characteristics in tropical regions, such as Brazil. The objective of this study was to investigate the relationships between soil attributes, bacterial population composition and clubroot intensity in a tropical mountain agroecosystem. Soil and plant samples were collected from 17 cauliflower‐producing localities in Nova Friburgo, Brazil. The physical and chemical attributes, the bacterial population composition, the number of pathogen resting spores in the soil samples, and the clubroot severity were evaluated. Based on bacterial population composition, two distinct groups of soils were identified, which varied in attributes such as organic matter, potential acidity, pH and disease severity. The organic matter level was associated with differences in soil acidity, bacterial population composition and disease intensity, but there was not a cause and effect relationship between bacterial population composition and clubroot severity. Under the conditions of this agroecosystem, soils with increased organic matter presented higher acidity potential (H + Al), which was strongly correlated to clubroot severity. Thus, high acidity potential could be a key factor leading to clubroot development in mountain regions of Brazil.
Do soil inoculants accelerate dryland restoration? A simultaneous assessment of biocrusts and mycorrhizal fungi
Authors: Chaudhary V. Bala , Akland Kristine , Johnson Nancy C. , Bowker Matthew A.
Published: November 2019

Biological soil crusts (biocrusts) and arbuscular mycorrhizal (AM) fungi are communities of soil organisms often targeted to assist in the achievement of multiple ecological restoration goals. In drylands, benefits conferred from biocrust and AM fungal inoculation, such as improved native plant establishment and soil stabilization, have primarily been studied separately. However, comparisons between these two types of soil inoculants and investigations into potential synergies between them, particularly at the plant community scale, are needed to inform on‐the‐ground management practices in drylands. We conducted two full‐factorial experiments—one in greenhouse mesocosms and one in field plots—to test the effects of AM fungal inoculation, biocrust inoculation, and their interaction on multiple measures of dryland restoration success. Biocrust inoculation promoted soil stabilization and plant drought tolerance, but had mixed effects on native plant diversity (positive in greenhouse, neutral in field) and productivity (negative in greenhouse, neutral in field). In greenhouse mesocosms, biocrust inoculation reduced plant biomass, which was antagonistic to % root length colonized by AM fungi. Inoculation with native or commercial AM fungi did not influence plant establishment, drought tolerance, or soil stabilization in either study, and few synergistic effects of simultaneous inoculation of AM fungi and biocrusts were observed. These results suggest that, depending on the condition of existing soil communities, inoculation with AM fungi may not be necessary to promote dryland restoration goals, while inoculation with salvaged biocrust inoculation may be beneficial in some contexts.
Overexpression of BUNDLE SHEATH DEFECTIVE 2 improves the efficiency of photosynthesis and growth in Arabidopsis
Authors: Busch Florian A. , Tominaga Jun , Muroya Masato , Shirakami Norihiko , Takahashi Shunichi , Yamori Wataru , Kitaoka Takuya , Milward Sara E. , Nishimura Kohji , Matsunami Erika , Toda Yosuke , Higuchi Chikako , Muranaka Atsuko , Takami Tsuneaki , Watanabe Shunsuke , Kinoshita Toshinori , Sakamoto Wataru , Sakamoto Atsushi , Shimada Hiroshi
Published: November 2019

Bundle Sheath Defective 2, BSD2, is a stroma‐targeted protein initially identified as a factor required for the biogenesis of ribulose 1,5‐bisphosphate carboxylase/oxygenase (RuBisCO) in maize. Plants and algae universally have a homologous gene for BSD2 and its deficiency causes a RuBisCO‐less phenotype. As RuBisCO can be the rate‐limiting step in CO2 assimilation, the overexpression of BSD2 might improve photosynthesis and productivity through the accumulation of RuBisCO. To examine this hypothesis, we produced BSD2 overexpression lines in Arabidopsis. Compared with wild type, the BSD2 overexpression lines BSD2ox‐2 and BSD2ox‐3 expressed 4.8‐fold and 8.8‐fold higher BSD2 mRNA, respectively, whereas the empty‐vector (EV) harbouring plants had a comparable expression level. The overexpression lines showed a significantly higher CO2 assimilation rate per available CO2 and productivity than EV plants. The maximum carboxylation rate per total catalytic site was accelerated in the overexpression lines, while the number of total catalytic sites and RuBisCO content were unaffected. We then isolated recombinant BSD2 (rBSD2) from E. coli and found that rBSD2 reduces disulfide bonds using reductants present in vivo, for example glutathione, and that rBSD2 has the ability to reactivate RuBisCO that has been inactivated by oxidants. Furthermore, 15% of RuBisCO freshly isolated from leaves of EV was oxidatively inactivated, as compared with 0% in BSD2‐overexpression lines, suggesting that the overexpression of BSD2 maintains RuBisCO to be in the reduced active form in vivo. Our results demonstrated that the overexpression of BSD2 improves photosynthetic efficiency in Arabidopsis and we conclude that it is involved in mediating RuBisCO activation.
DO/ART4gene sequencing in sub‐Saharan cohorts and African migrants: useful data describing the diversity and spreading of rare variants
Authors: Chapel‐Fernandes Sylvie , Movia Catherine , Jordier François , Durousseau de Coulgeans Cécile , Chiaroni Jacques , Bailly Pascal
Published: November 2019

BACKGROUND

Due to the unavailability of immunological reagents, the Dombrock blood group is insufficiently explored in African populations and can be a source of alloimmunization. A large study including pygmoid and nonpygmoid ethnic groups from East, Central, and West continental Africa, together with African migrants like Comorians, Afro‐Caribbean from Martinique, and Maroons from French Guiana would be helpful to increase transfusion safety.

STUDY DESIGN AND METHODS

Using genomic DNA extracted from blood samples collected from 336 nonpygmoid and 51 pygmoid Africans as well as 268 samples of African descent,DOcoding regions were PCR‐amplified and sequenced.

RESULTS

DO*AandDO*Balleles were detected in almost all groups, with a clear predominance ofDO*Bin every cohort tested.DO*JOandDO*HYallele frequencies reached 10% or more in several ethnic groups.DO*B‐SH‐Gln149Lys,DO*B‐Ile5Thr, andDO*DODEvariants were identified both in African ethnic groups and outside Africa. Twelve novel variants were characterized on aDO*Aor aDO*Bbackground. Five of them were found in both African and migrant cohorts, the others were restricted to either within or outside Africa. NoDO*DOYA,DO*DOLG,DO*DOLC, norDO*DOMRvariants were observed. A first phylogenetic tree was proposed including all variant alleles.

CONCLUSION

This study across continental Africa and countries with African migrants provides a useful overview ofDombrockallele diversity and distribution. The identification of 12 new alleles underlines the importance of genotyping forDombrockalleles, particularly to improve transfusion safety in countries hosting migrant populations of African descent.