bluuebunny/crossref_metadata_2025 huggingface dataset:
Colour maps for fisheries acoustic echograms
Authors: Blackwell Robert E , Harvey Richard , Queste Bastien Y , Fielding Sophie
Published: November 2019

Echograms are used to visualize fisheries acoustic data, but choice of colour map has a significant effect on appearance. Quantitative echograms should use colour maps, which are colourful (have a perceived variety and intensity of colours), sequential (have monotonic lightness), and perceptually uniform (have consistency of perceived colour contrast over their range). We measure whether colour maps are colourful (M^(3)>0), sequential (rs=±1), and perceptually uniform (ρ = 1) using an approximately perceptually uniform colour space (CIELAB). Whilst all the fisheries acoustic colour maps tested are colourful, none is sequential or perceptually uniform. The widely used EK500 colour map is extremely colourful (M^(3)=186), not sequential (rs=0.06), and has highly uneven perceptual contrast over its range (ρ=0.26). Of the fisheries acoustic colour maps tested, the Large Scale Survey System default colour map is least colourful (M^(3)=79), but comes closest to being sequential (rs=−0.94), and perceptually uniform (ρ=0.95). Modern colour maps have been specifically designed for colour contrast consistency, accessibility for viewers with red-green colour-blindness, and legibility when printed in monochrome, and may be better suited to the presentation and interpretation of quantitative fisheries acoustic echograms.
In vitro study of trileaflet polytetrafluoroethylene conduit and its valve-in-valve transformation
Authors: Chang Te-I , Hsu Kang-Hong , Luo Chi-Wen , Yen Jen-Hong , Lu Po-Chien , Chang Chung-I
Published: November 2019

OBJECTIVES

Handmade trileaflet expanded polytetrafluoroethylene valved conduit developed using the flip-over method has been tailored for pulmonary valve reconstruction with satisfactory outcomes. We investigated the in vitro performance of the valve design in a mock circulatory system with various conduit sizes. In our study, the design was transformed into a transcatheter stent graft system which could fit in original valved conduits in a valve-in-valve fashion.

METHODS

Five different sizes of valved polytetrafluoroethylene vascular grafts (16, 18, 20, 22 and 24 mm) were mounted onto a mock circulatory system with a prism window for direct leaflets motion observation. Transvalvular pressure gradients were recorded using pressure transducers. Mean and instant flows were determined via a rotameter and a flowmeter. Similar flip-over trileaflet valve design was then carried out in 3 available stent graft sizes (23, 26 and 28.5 mm, Gore aortic extender), which were deployed inside the valved conduits.

RESULTS

Peak pressure gradient across 5 different sized graft valves, in their appropriate flow setting (2.0, 2.5 and 5.0 l/min), ranged from 4.7 to 13.2 mmHg. No significant valve regurgitation was noted (regurgitant fraction: 1.6–4.9%) in all valve sizes and combinations. Three sizes of the trileaflet-valved stent grafts were implanted in the 4 sizes of valved conduits except for the 16-mm conduit. Peak pressure gradient increase after valved-stent graft-in-valved-conduit setting was <10 mmHg in all 4 conduits.

CONCLUSIONS

The study showed excellent in vitro performance of trileaflet polytetrafluoroethylene valved conduits. Its valved stent graft transformation provided data which may serve as a reference for transcatheter valve-in-valve research in the future.
Generalized Logarithmic Hardy–Littlewood–Sobolev Inequality
Authors: Dolbeault Jean , Li Xingyu
Published: November 2019

This paper is devoted to logarithmic Hardy–Littlewood–Sobolev inequalities in the 2D Euclidean space, in the presence of an external potential with logarithmic growth. The coupling with the potential introduces a new parameter, with two regimes. The attractive regime reflects the standard logarithmic Hardy–Littlewood–Sobolev inequality. The 2nd regime corresponds to a reverse inequality, with the opposite sign in the convolution term, which allows us to bound the free energy of a drift–diffusion–Poisson system from below. Our method is based on an extension of an entropy method proposed by E. Carlen, J. Carrillo, and M. Loss, and on a nonlinear diffusion equation.
Measuring quality and impact of telehealth services in home dialysis patients
Authors: Lew Susie Q
Published: November 2019

US Medicare beneficiaries receiving home dialysis will have the opportunity to engage in telehealth beginning in 2019. This new paradigm, if successful, will be instituted internationally. Any changes in healthcare delivery, such as using telehealth, will affect the process and quality. Quality of care metrics is discussed, and they can be used to evaluate the three domains of structure, process, and outcome when applied to assess telehealth’s impact and quality on the dialysis population.
Long-term follow-up of HIV-infected patients on dolutegravir monotherapy
Authors: Tebano G , Soulié C , Schneider L , Blanc C , Agher R , Seang S , Valantin M A , Palich R , Tubiana R , Peytavin G , Marcelin A G , Assoumou L , Katlama C
Published: November 2019

Background

In recent years, dolutegravir monotherapy has been explored as a drug-reduced regimen for HIV patients.

Methods

This was a retrospective observational study, including patients virologically suppressed for ≥6 months, without previous virological failure (VF) under integrase inhibitors (INIs), who had been switched to dolutegravir monotherapy (50 mg/day). The primary aim was to report the proportion of VF at week 48 (W48) and week 96 (W96) of dolutegravir monotherapy. The evolution from baseline to W48 of residual viraemia on ultra-deep sequencing and HIV DNA was also evaluated.

Results

Sixty-one patients were included. Prior to switching to dolutegravir monotherapy, they had a median (IQR) of 15.4 (6.5–19.9) years of antiretroviral exposure, 5.8 (3.2–10.3) years of viral suppression and 687 (461–848) CD4+ cells/mm3. They remained on dolutegravir monotherapy for a median (IQR) of 100 (29–148) weeks. Forty-two out of 61 patients (68.9%) reached W48 and 32 out of 61 patients (52.5%) reached W96. VF occurred in three patients, with the emergence of INI resistance. VF occurred before W24 and in patients pre-exposed to INIs. At W48, the probability of VF (Kaplan–Meier analysis) was 5.6% (95% CI = 1.8%–16.4%). The same result was obtained at W96. Detectable residual viraemia did not increase and median HIV DNA did not change significantly (2.4 log/106 cells at baseline and 2.3 log/106 cells at W48). Dolutegravir plasma concentration was above the IC90 in 41/41 samples, from 22 patients.

Conclusions

Long-term follow-up showed a low risk of VF under dolutegravir monotherapy, in a selected population of patients with previous long-term virological suppression and low HIV reservoir.
Understanding the nature and scope of clinical research commentaries in PubMed
Authors: Rogers James R , Mills Hollis , Grossman Lisa V , Goldstein Andrew , Weng Chunhua
Published: November 2019

Scientific commentaries are expected to play an important role in evidence appraisal, but it is unknown whether this expectation has been fulfilled. This study aims to better understand the role of scientific commentary in evidence appraisal. We queried PubMed for all clinical research articles with accompanying comments and extracted corresponding metadata. Five percent of clinical research studies (N = 130 629) received postpublication comments (N = 171 556), resulting in 178 882 comment–article pairings, with 90% published in the same journal. We obtained 5197 full-text comments for topic modeling and exploratory sentiment analysis. Topics were generally disease specific with only a few topics relevant to the appraisal of studies, which were highly prevalent in letters. Of a random sample of 518 full-text comments, 67% had a supportive tone. Based on our results, published commentary, with the exception of letters, most often highlight or endorse previous publications rather than serve as a prominent mechanism for critical appraisal.
Effect of dietary medium-chain fatty acids on nursery pig growth performance, fecal microbial composition, and mitigation properties against porcine epidemic diarrhea virus following storage
Authors: Gebhardt Jordan T , Thomson Katelyn A , Woodworth Jason C , Dritz Steve S , Tokach Michael D , DeRouchey Joel M , Goodband Robert D , Jones Cassandra K , Cochrane Roger A , Niederwerder Megan C , Fernando Samodha , Abbas Waseem , Burkey Thomas E
Published: November 2019

An experiment was conducted to evaluate the effect of dietary medium-chain fatty acid (MCFA) addition on nursery pig growth performance, fecal microbial composition, and mitigation of porcine epidemic diarrhea virus (PEDV) following storage. A total of 360 pigs (DNA 400 × 200, Columbus, NE; initially 6.7 ± 0.07 kg) were randomized to pens (5 pigs per pen) on the day of weaning (approximately 20 d of age), allowed a 6-d acclimation, blocked by BW, and randomized to dietary treatment (9 pens per treatment). All MCFA (Sigma–Aldrich, St. Louis, MO) were guaranteed ≥98% purity, including hexanoic (C6:0), octanoic (C8:0), and decanoic (C10:0) acids. Treatment diets were formulated in 2 phases (7 to 11 and 11 to 23 kg BW) and formulated to meet or exceed NRC requirement estimates. Treatments (n = 8) were a dose response including 0%, 0.25%, 0.5%, 1.0%, and 1.5% added MCFA blend (1:1:1 ratio C6:0, C8:0, and C10:0), as well as treatments with individual additions of 0.5% C6:0, C8:0, or C10:0. Fecal samples were collected from pigs fed control and 1.5% MCFA blend diets on days 0 and 14 and analyzed using 16s rDNA sequencing. Following feed manufacture, feed was stored in bags at barn temperature and humidity for 40 d before laboratory inoculation with PEDV. Subsamples of retained feed were inoculated with PEDV to achieve a titer of 104 TCID50/g and separate sample bottles were analyzed on 0 and 3 d post-inoculation (dpi). Overall, ADG and ADFI were increased (linear, P ≤ 0.010) and feed efficiency (G:F) improved (linear, P = 0.004) with increasing MCFA blend. Pigs fed 0.5% C8:0 had greater (P = 0.038) ADG compared with pigs fed the control diet, and G:F was improved (P ≤ 0.024) when pigs were fed 0.5% C6:0, 0.5% C8:0, or 0.5% C10:0 compared with control. An inclusion level × day interaction was observed (quadratic, P = 0.023), where PEDV Ct values increased (quadratic, P = 0.001) on 0 dpi with increasing levels of MCFA blend inclusion and also increased on 3 dpi (linear, P < 0.001). Fecal microbial diversity and composition were similar between control and 1.5% MCFA blend. In summary, the use of MCFA in nursery pig diets improves growth performance, provides residual mitigation activity against PEDV, and does not significantly alter fecal microbial composition.
The Price of Inattention: Evidence from the Swedish Housing Market
Authors: Repetto Luca , Solís Alex
Published: November 2019

Do behavioral biases affect prices in a high-stakes market? We study the role of left-digit bias in the purchase of an apartment. Left-digit bias is the failure to fully process digits after the first, perceiving prices just below a round number (such as $3.99) as cheaper than their round counterpart ($4). Apartments with asking prices just below round millions are sold at a 3%–5% higher final price after an auction. This effect appears not to be driven by differences in observables or in real estate agents’ behavior. Auctions for apartments listed just below round numbers are more competitive and attract more bidders and bids.
Reinforcement and the Proliferation of Species
Authors: Calabrese Gina M , Pfennig Karin S
Published: November 2019

Adaptive radiations are characterized by the rapid proliferation of species. Explaining how adaptive radiations occur therefore depends, in part, on identifying how populations become reproductively isolated—and ultimately become different species. Such reproductive isolation could arise when populations adapting to novel niches experience selection to avoid interbreeding and, consequently, evolve mating traits that minimize such hybridization via the process of reinforcement. Here, we highlight that a downstream consequence of reinforcement is divergence of conspecific populations, and this further divergence can instigate species proliferation. Moreover, we evaluate when reinforcement will—and will not—promote species proliferation. Finally, we discuss empirical approaches to test what role, if any, reinforcement plays in species proliferation and, consequently, in adaptive radiation. To date, reinforcement’s downstream effects on species proliferation remain largely unknown and speculative. Because the ecological and evolutionary contexts in which adaptive radiations occur are conducive to reinforcement and its downstream consequences, adaptive radiations provide an ideal framework in which to evaluate reinforcement’s role in diversification.
Early Marriage in Iran: A Pragmatic Approach
Authors: Asghari Shamin
Published: November 2019

The international human rights system has identified any marriage before the age of 18 as forced marriage or a harmful traditional practice which should be eradicated mainly through legal reform. In many legal systems, the minimum age of marriage is still below 18. In Iran, girls can marry at the age of 13 and boys at the age of 15. Thus, the issue of early marriage has been a point of struggle between the international human rights system and Iran. What is lost in these mainly legal debates is the reality of early marriage. Those who advocate for the eradication of early marriage present a singular perception of such marriage as forced and harmful, while those who oppose the international approach in Iran merely focus on the Islamic roots of the current legislation. In practice, marriage is a complicated social construct. To address early marriage, one should analyse different causes and contexts that influence this institution and determine whether the negative consequences apply in all cases of early marriage. This article argues that the international human rights system should provide a context-sensitive response to early marriage. The human rights discourse is not the only setting for addressing early marriage. The general categorization of early marriage as a violation of human rights fails to recognize various factors that influence the timing of marriage, in particular girls’ agency. To effectively address early marriage in Iran, a multidisciplinary approach is necessary.
Negotiating Space for Queer-Identifying Young People in a Refugee Organization: Viability, Complexities and Tensions
Authors: Mahn Churnjeet , Milne Ej , Guzman Mayra , Ahmed Farhio
Published: November 2019

There is relative invisibility and silence around the presence, management and support of queer people in mainstream refugee organizations in the United Kingdom. Institutional silencing exists, particularly where visibility or acknowledgement has the potential to disrupt existing structures. At the same time, queer refugees face the risk of exclusion, and may also undertake self-censoring. Drawing on empirical data from an innovative, cross-disciplinary, community-based participatory research project between a United Kingdom-based refugee organization and two universities, this article explores the viability, complexities and tensions inherent in making queer identities visible. While highlighting the potential of arts-based methods to explore inclusive approaches to sexuality, we discuss the limits of this work and the resistance it created. This article is co-authored by members of RX—a collective of young people with refugee backgrounds; two community researchers; a humanities researcher; and a peace-studies researcher.
Integrative analysis of the nuclear proteome in Pinus radiata reveals thermopriming coupled to epigenetic regulation
Authors: Lamelas Laura , Valledor Luis , Escandón Mónica , Pinto Gloria , Cañal María Jesús , Meijón Mónica
Published: November 2019

Despite it being an important issue in the context of climate change, for most plant species it is not currently known how abiotic stresses affect nuclear proteomes and mediate memory effects. This study examines how Pinus radiata nuclei respond, adapt, ‘remember’, and ‘learn’ from heat stress. Seedlings were heat-stressed at 45 °C for 10 d and then allowed to recover. Nuclear proteins were isolated and quantified by nLC-MS/MS, the dynamics of tissue DNA methylation were examined, and the potential acquired memory was analysed in recovered plants. In an additional experiment, the expression of key gene genes was also quantified. Specific nuclear heat-responsive proteins were identified, and their biological roles were evaluated using a systems biology approach. In addition to heat-shock proteins, several clusters involved in regulation processes were discovered, such as epigenomic-driven gene regulation, some transcription factors, and a variety of RNA-associated functions. Nuclei exhibited differential proteome profiles across the phases of the experiment, with histone H2A and methyl cycle enzymes in particular being accumulated in the recovery step. A thermopriming effect was possibly linked to H2A abundance and over-accumulation of spliceosome elements in recovered P. radiata plants. The results suggest that epigenetic mechanisms play a key role in heat-stress tolerance and priming mechanisms.
Sacramental Vision in Annie Dillard’s Holy the Firm
Authors: Matheson Rachel
Published: November 2019

In this article I explore the central motif of vision in Annie Dillard’s short poetic narrative, Holy the Firm. Attention to the book’s tripartite structure reveals a movement through an aesthetic appreciation of creation, to an intellectual contemplation of the Fall, finally culminating in a mystical vision of wholeness in the redemptive descent of Christ. I turn to Julian of Norwich’s parable of the Lord and Servant in order to illuminate their shared attunement to the workings of divine love in the face of human suffering. For Dillard, Christ’s kenotic love is continually revealed in the Christian sacraments of baptism and communion. Finally, I suggest that through the artist, the thinker, and the nun, Dillard leads her reader toward a sacramental vision of the world, which locates the holy in the everyday.
Cool white dwarfs as standards for infrared observations
Authors: Gentile Fusillo Nicola Pietro , Tremblay Pier-Emmanuel , Bohlin Ralph C , Deustua Susana E , Kalirai Jason S
Published: November 2019

In the era of modern digital sky surveys, uncertainties in the flux of stellar standards are commonly the dominant systematic error in photometric calibration and can often affect the results of higher level experiments. The Hubble Space Telescope (HST) spectrophotometry, which is based on computed model atmospheres for three hot (Teff$\gt 30\, 000$ K) pure hydrogen (DA) white dwarfs, is currently considered the most reliable and internally consistent flux calibration. However, many next-generation facilities (e.g. Harmoni on E-ELT, Euclid, and JWST) will focus on IR observations, a regime in which white dwarf calibration has not yet been robustly tested. Cool DA white dwarfs have energy distributions that peak close to the optical or near-infrared, do not have shortcomings from UV metal line blanketing, and have a reasonably large sky density (≃4 deg−2 at G < 20), making them, potentially, excellent calibrators. Here, we present a pilot study based on STIS + WFC3 observations of two bright DA white dwarfs to test whether targets cooler than current hot primary standards (Teff$\lt 20\, 000$ K) are consistent with the HST flux scale. We also test the robustness of white dwarf models in the IR regime from an X-shooter analysis of Paschen lines and by cross-matching our previously derived Gaia white dwarf catalogue with observations obtained with 2MASS, UKIDSS, VHS, and WISE.
Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation
Authors: Rao Vinay Kumar , Swarnaseetha Adusumalli , Tham Guo-Hong , Lin Wei-Qi , Han Bin-Bin , Benoukraf Touati , Xu Guo-Liang , Ong Chin-Tong
Published: November 2019

Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.
Nuptiality to regulate the commons? The case of the Don Cossacks (South Russia), 1867–1916
Authors: Bonneuil Noël , Fursa Elena
Published: November 2019

Sustainability in the commons has been associated with the optimal net present value controlled by the harvest rate under stationary population. Population growth however disrupts this scheme. In traditional societies, fertility was regulated by age at marriage. In times of population growth and limited resources, economic sustainability then requires that age of marriage should be raised. In the case study of the Don Cossacks, 1867–1916, early marriage, which was an important marker of social cohesion, was too slow to increase when mortality declined, fuelling a population growth that threatened the agrarian economy: age at marriage then appears to be essential to the theory of the commons in traditional societies.
Orbitozygomatic Craniotomy for Giant Anterior Communicating Artery Aneurysm: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: November 2019

Giant intracranial aneurysms pose a significant surgical challenge because of the associated difficulty in achieving adequate visualization of the parent artery and aneurysm neck. This patient had an incidentally identified giant anterior communicating artery aneurysm. An orbitozygomatic craniotomy was performed for aneurysm exposure and aneurysmal neck dissection. Aneurysm dome opening and thrombectomy was performed to debulk the aneurysmal mass, which facilitated subsequent aneurysmal neck visualization. Sequential utilization of temporary clips of the bilateral A1 and bilateral A2 vessels reduced hemorrhage during thrombectomy. Multiple permanent clips were applied along the dissected aneurysm neck to permit occlusion. A small fracture of the aneurysm neck was identified, and cotton was applied with subsequent tamponade utilizing a fenestrated clip to maintain hemostasis. Indocyanine green fluoroscopy was used to verify parent and distant vessel patency. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Lenticulostriate Artery Aneurysm: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: November 2019

Saccular aneurysms that arise from the origin of or along a lenticulostriate artery are rarely observed. In general, occlusion of the lenticulostriate artery is discouraged because of the risk of a capsular infarction. This patient was a woman with moyamoya disease who demonstrated a fusiform aneurysm of a lenticulostriate artery. Image guidance was critical to correctly identify the location of the aneurysm. The lenticulostriate artery was occluded by a surgical clip to obliterate the aneurysm and consequently the flow through the artery. However, the patient tolerated the procedure well and did not experience an ischemic stroke from the vessel occlusion. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Microsurgical Resection of Brainstem Arteriovenous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: November 2019

Brainstem arteriovenous malformations (AVMs) are rare lesions (2%-6% of all intracranial AVMs) that are surgically challenging because of the high eloquence of the brainstem, including dense fiber tracts, cranial nerves, and multiple vital cerebrovascular structures. All these lesions possess eloquence and deep venous drainage, making them innately Spetlzer–Martin grade III or above. This patient had a large midbrain AVM with a complex clinical course beginning with ventriculoperitoneal shunting due to mass effect; the patient experienced 4 hemorrhages, underwent radiation treatment, and finally underwent surgical resection. The surgical approach involved a large torcular craniotomy exposing all posterior sinuses at the confluence. The vein of Galen was exposed and carried deeply to permit ambient cistern opening and relaxation of the cerebellum. Because of earlier radiation therapy, the vessels had undergone hyalinosis, which resulted in difficult manipulation of the nidus but did permit excellent coagulation of the vessels. The complete nidus was removed, as confirmed on postoperative angiography. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Opioid Prescribing to Medicare Part D Enrollees, 2013–2017: Shifting Responsibility to Pain Management Providers
Authors: Romman Adam N , Hsu Connie M , Chou Lin-Na , Kuo Yong-Fang , Przkora Rene , Gupta Rajnish K , Lozada M James
Published: November 2019

Objective

To examine opioid prescribing frequency and trends to Medicare Part D enrollees from 2013 to 2017 by medical specialty and provider type.

Methods

We conducted a retrospective, cross-sectional, specialty- and provider-level analysis of Medicare Part D prescriber data for opioid claims from 2013 to 2017. We analyzed opioid claims and prescribing trends for specialties accounting for ≥1% of all opioid claims.

Results

From 2013 to 2017, pain management providers increased Medicare Part D opioid claims by 27.3% to 1,140 mean claims per provider in 2017; physical medicine and rehabilitation providers increased opioid claims 16.9% to 511 mean claims per provider in 2017. Every other medical specialty decreased opioid claims over this period, with emergency medicine (–19.9%) and orthopedic surgery (–16.0%) dropping opioid claims more than any specialty. Physicians overall decreased opioid claims per provider by –5.2%. Meanwhile, opioid claims among both dentists (+5.6%) and nonphysician providers (+10.2%) increased during this period.

Conclusions

From 2013 to 2017, pain management and PMR increased opioid claims to Medicare Part D enrollees, whereas physicians in every other specialty decreased opioid prescribing. Dentists and nonphysician providers also increased opioid prescribing. Overall, opioid claims to Medicare Part D enrollees decreased and continue to drop at faster rates.
Biologic therapy in supra-aortic Takayasu arteritis can improve symptoms of cerebral ischaemia without surgical intervention
Authors: Porter Andrew , Youngstein Taryn , Tombetti Enrico , Mason Justin C
Published: November 2019

Objectives

Takayasu arteritis commonly results in severe arterial injury with stenoses, occlusions and occasionally aneurysms. Arterial disease may compromise organ blood flow and result in significant cardiovascular morbidity and premature mortality. Involvement of the supra-aortic arteries is common, and in its most severe form may compromise cerebral blood supply, resulting in signs of cerebral ischaemia including visual impairment, dysphasia, transient hemiparesis, loss of consciousness and stroke. In addition to combination immunosuppression, the management paradigm for symptomatic cerebral ischaemia includes revascularization. The invasive nature of this surgery, the risk of complications and the relatively high rate of re-stenosis is of concern to patients and their physicians alike. The aim of this study was to determine whether combined immunosuppression with early escalation to biologic therapy improved outcomes and reduced the need for high risk surgical intervention.

Methods

A retrospective review of 145 Takayasu arteritis patients attending Imperial College Healthcare between 2010–2018 was conducted to identify those with cerebral ischaemia secondary to supra-aortic disease and to analyse their treatment and outcomes.

Results

Eight patients (5.5%) were identified. Seven patients received long-term combined immunosuppressive therapy and six were prescribed biologics. The data revealed a higher than expected comprehensive response to therapy, with significant falls in disease activity, the cerebral ischaemia score and the prednisolone dose required, over a median follow-up of 37 months. Serial imaging analysis detected no arterial disease progression after the initiation of optimal therapy. Only one patient required surgical intervention for persistent neurological symptoms.

Conclusion

Early use of biologic therapy in those with supra-aortic Takayasu arteritis presenting with cerebral ischaemia may reduce the numbers of patients requiring surgical intervention and improve outcomes.
Lowest-Low Fertility in South Korea: Policy and Domestic Labor Supports and the Transition to Second Birth
Authors: Kim Joeun , Luke Nancy
Published: November 2019

Scholars and policymakers contend that severe work-family constraints for women are a key contributor to lowest-low fertility in industrialized countries. Two separate areas of research have examined supports that could alleviate these constraints and potentially increase fertility: institutional support in the form of public policies and domestic labor support from male partners. There are few studies considering the influence of both policy and domestic labor supports and no investigations of the interplay between these two support mechanisms. We develop and test a theoretical framework that considers how the combination of these supports could alleviate women’s work-family constraints and increase fertility. Using the case of South Korea, a country with one of the most sustained lowest-low fertility rates in history, we examined the relationship between women’s eligibility for parental leave and husbands’ share of domestic labor and the transition to a second birth. Our analyses revealed that both supports, independently, had positive effects on the likelihood of a second birth. More importantly, we found that husbands’ domestic labor had a positive influence on fertility only when women’s access to parental leave was limited, suggesting that policy and domestic labor supports are substitutes and alleviate the same underlying work-family constraint in the Korean context. Our study underscores the importance of understanding the nature of work-family conflict across countries and how various supports―alone or in combination―could relieve women’s constraints on childbearing and upturn lowest-low fertility.
When morphometry meets taxonomy: morphological variation and species boundaries in Proboscoida (Cnidaria: Hydrozoa)
Authors: Cunha Amanda F , Collins Allen G , Marques Antonio C
Published: November 2019

Species delimitation in marine taxa is often problematic given large intraspecific variation. Based on extensive, recently published genetic sampling from specimens of the hydrozoan families Campanulariidae, Clytiidae and Obeliidae, we evaluate morphological variation in this group, correlating morphometric and phylogenetic patterns for species delimitation. Several species of Campanulariidae are confidently delimited based on differences in size (e.g. Bonneviella species, Tulpa tulipifera and Rhizocaulus verticillatus), while others are re-identified and corroborated based on differences in perisarc thickness (e.g. Silicularia rosea, Orthopyxis and Campanularia species). In Clytiidae, the length and diameter of hydrothecae, height of hydrothecal cusps and perisarc thickness delimit the species Clytia linearis, C. elsaeoswaldae and C. noliformis from others. However, few characters reliably differentiate the clades associated with the nominal species C. gracilis and C. hemisphaerica. In Obeliidae, Obelia geniculata is distinctive in its higher perisarc thickness, and corroborated as a widely distributed species. Obelia longissima and clades refered to O. dichotoma are subtly distinguished, showing a few differences in size and branching of colonies. The taxonomic implications of these results are discussed. With a few exceptions, species can be delimited based on morphometric patterns, once morphological variation is compared.
Molecular detection of H. pylori antibiotic‐resistant genes and molecular docking analysis
Authors: Chu Aining , Wang Dan , Guo Qianqian , Lv Zhi , Yuan Yuan , Gong Yuehua
Published: November 2019

To explore the mutation characteristics of H. pylori resistance‐related genes to antibiotics of clarithromycin (CAM), levofloxacin (LVX) and metronidazole, 23SrRNA, gyrA, gyrB, rdxA, and frxA genes were amplified and sequenced, respectively. Molecular docking study was performed to explore molecular interactions between chemotherapeutic agents and target proteins. In the CAM‐resistant strains, the mutation rate in site A2143G was 74.2% (n = 23). The interactions in sites of G1949A, C1953T, and G2211T with CAM were weaker after mutation. In the LVX‐resistant strains, the mutation rates in 87 (N to K/I) and 91 (D to N/Y/G) of gyrA were 28.6% (n = 16) and 12.5% (n = 7), respectively. We could infer by docking studies that N87 K/I, D91Y/G/N, D99N, and D143E mutations in GyrA protein all had weakened interaction with LVX. The mutation types of RdxA protein consisted of protein truncation caused by premature stop codons (n = 26, 33.3%), frameshift mutations (n = 8, 10.3%), FMN‐binding sites (n = 16, 20.5%), and the others (n = 11, 14.1%). Docking analysis showed that some mutations in those four types of RdxA protein could reduce interaction with MNZ, and play a significant role in antibiotic resistance. What's more, we performed natural transformation with some of these mutated DNA fragments to see if they really impact susceptibility to antibiotics. Our study suggested that in addition to the reported mutation sites, H. pylori antibiotic resistance in this region may also be associated with changes in some new sites. Our study provides novel ideas and methods for the identification of H. pylori resistance‐related mutations, and also clues and basis for further investigation on specific molecular mechanism.
The impact of public health interventions on the future prevalence of ESBL-producingKlebsiella pneumoniae: a population based mathematical modelling study
Authors: Salazar-Vizcaya Luisa , Atkinson Andrew , Kronenberg Andreas , Plüss-Suard Catherine , Kouyos Roger , Kachalov Viacheslav , Troillet Nicolas , Marschall Jonas , Sommerstein Rami
Published: November 2019

Background

Extended-spectrum betalactamase (ESBL-) producingK. pneumoniaeis one of the most common causes of infections with antimicrobial resistant bacteria worldwide. The spread of colonization of humans with this pathogen is on the rise. The future prevalence of colonization with ESBL-producingK. pneumoniae, and the potential of public health interventions to lower it, remain uncertain.

Methods

Based on detailed data on antimicrobial consumption and susceptibility systematically recorded for over 13 years in a Swiss region, we developed a mathematical model toi)reconstruct the observed course of colonization with ESBL-producingK. pneumoniae;andii)to assess the potential impact of public health interventions on future trends in colonization.

Results

Simulated prevalence of colonization with ESBL-producingK. pneumoniaestabilized in the near future when rates of antimicrobial consumption and in-hospital transmission remained stable in the main analyses (simulated prevalence in 2025 was 5.3% (5.0%-9.1%) in hospitals and 2.7% (2.1%-4.6%) in the communityversus5.6% (5.1%-9.5%) and 2.8% (2.2%-5.0%) in 2019). The largest changes in future prevalence were observed in simulations that assumed changes in overall antimicrobial consumption. When overall antimicrobial consumption was set to decrease by 50%, prevalence in 2025 declined by 89% in hospitals and by 84% in the community. A 50% decline in transmission rate within hospitals led to a reduction in prevalence of 43% in hospitals and of 13% in the community by 2025. Prevalence changed much less (≤9%) across scenarios with reduced carbapenem consumption. Assuming higher rates for the contribution from external sources of colonization, led to decreasing estimations of future prevalence in hospitals. While high uncertainty remains on the magnitude of these contribution, the best model fit suggested that as much as 46% (95% CI: 12%-96 %) of observed colonizations could be attributable to sources other than human-to-human transmission within the geographical setting (i.e., non-local transmission).

Conclusions

This study suggests that overall antimicrobial consumption will be, by far, the most powerful driver of future prevalence and that a large fraction of colonizations could be attributed to non-local transmission.
A novel feature fusion based on the evolutionary features for protein fold recognition using support vector machines
Authors: Refahi Mohammad Saleh , Mir A. , Nasiri Jalal A.
Published: November 2019

Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting features from protein sequences and using a strong classifier. Feature extraction techniques generally utilize syntactical-based information, evolutionary-based information and physiochemical-based information to extract features. In recent years, Finding an efficient technique for integrating discriminate features have been received advancing attention. In this study, we integrate Auto-Cross-Covariance (ACC) and Separated dimer (SD) evolutionary feature extraction methods. The results features are scored by Information gain (IG) to define and select several discriminated features. According to three benchmark datasets, DD, RDD and EDD, the results of the support vector machine (SVM) show more than 6% improvement in accuracy on these benchmark datasets.
Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism
Authors: Jin Yang , Olsen Rolf Erik , Harvey Thomas Nelson , Østensen Mari-Ann , Li Keshuai , Santi Nina , Vadstein Olav , Vik Jon Olav , Sandve Simen Rød , Olsen Yngvar
Published: November 2019

Domestication of Salmo salar has imposed strong selection for production traits since the 1970s. The domestication has also imposed a radical shift in diet. Whereas wild salmon eats invertebrates, crustaceans and fish, the dietary lipids in domestic feed has since 1990 gradually shifted from fish oil (FO) to vegetable oil (VO), causing a decrease intake of long-chain polyunsaturated fatty acids (LC-PUFA). We tested the hypothesis that this shift has induced domestication-specific features of lipid metabolism in a 96-day feeding trial of domesticated and wild salmon fed diets based on FO, VO or phospholipids (PL). We addressed this by sampling tissues central in fat uptake (pyloric caeca) and processing (liver) and quantifying RNA expression and fatty acid composition. Domesticated salmon grew faster than wild salmon, with higher gene expression in glucose and lipid metabolism pathways. The promoters of differentially expressed genes were enriched for transcription factors involved in circadian clock regulation. Domesticated salmon had lower expression of cry2 and nr1d1, genes involved in negative regulation of circadian rhythm, with possible implications for the diurnal cycle of feed ingestion and basal metabolic rate. Only wild salmon showed a significant impact on growth of VO versus PL or FO feed, whereas domesticated but not wild salmon upregulated key LC-PUFA synthesis genes fads2d5 and fads2d6a in response to VO diet. Domesticated salmon had higher LC-PUFA but lower 18:3n-3 and 18:2n-6 in liver when fed VO, suggesting that domesticated salmon can better compensate for dietary shortage of LC-PUFA compared to wild salmon.
Quantifying the prevalence of assortative mating in a human population
Authors: Jaffe Klaus
Published: November 2019

For the first time, empirical evidence allowed to construct the frequency distribution of a genetic relatedness index between the parents of about half a million individuals living in the UK. The results suggest that over 30% of the population is the product of parents mating assortatively. The rest is probably the offspring of parents matching the genetic composition of their partners randomly. High degrees of genetic relatedness between parents, i.e. extreme inbreeding, was rare. This result shows that assortative mating is likely to be highly prevalent in human populations. Thus, assuming only random mating among humans, as widely done in ecology and population genetic studies, is not an appropriate approximation to reality. The existence of assortative mating has to be accounted for. The results suggest the conclusion that both, assortative and random mating, are evolutionary stable strategies. This improved insight allows to better understand complex evolutionary phenomena, such as the emergence and maintenance of sex, the speed of adaptation, runaway adaptation, maintenance of cooperation, and many others in human and animal populations.
Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective
Authors: Chehida Yacine Ben , Thumloup Julie , Schumacher Cassie , Harkins Timothy , Aguilar Alex , Borrell Asunción , Ferreira Marisa , Rojas-Bracho Lorenzo , Roberston Kelly M. , Taylor Barbara L. , Víkingsson Gísli A. , Weyna Arthur , Romiguier Jonathan , Morin Phillip A. , Fontaine Michael C.
Published: November 2019

Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastalversusoceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.
Different principles govern different scales of brain folding
Authors: Mallela Arka N. , Deng Hansen , Bush Alan , Goldschmidt Ezequiel
Published: November 2019

The signature folds of the human brain are formed through a complex and developmentally regulated process. In vitro and in silico models of this process demonstrate a random pattern of sulci and gyri, unlike the highly ordered and conserved structure seen in the human cortex. Here, we account for the large-scale pattern of cortical folding by combining advanced fetal MRI with nonlinear diffeomorphic registration and volumetric analysis. Our analysis demonstrates that in utero brain growth follows a logistic curve, in the absence of an external volume constraint. The Sylvian fissure forms from interlobar folding, where separate lobes overgrow and close an existing subarachnoid space. In contrast, other large sulci, which are the ones represented in existing models, fold through an invagination of a flat surface, a mechanistically different process. Cortical folding is driven by multiple spatially and temporally different mechanisms, therefore regionally distinct biological process may be responsible for the global geometry of the adult brain.
Global analysis of non-animal peroxidases provides insights into the evolutionary basis of this gene family in green lineage
Authors: Mbadinga Duchesse Lacour Mbadinga , Li Qiang , Ranocha Philippe , Martinez Yves , Cooper Endymion D. , Dunand Christophe
Published: November 2019

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolutionary history of this family of proteins. Here, we report for the first time an exhaustive evolutionary analysis of non-animal peroxidases using integratedin silicoand biochemical strategies. Thanks to the availability of numerous genomic sequences from many species belonging to different kingdoms together with expert and exhaustive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organismsin silico. First, we show that the presence or absence of non-animal peroxidases can be correlated with the presence or absence of certain organelles or with specific biological processes. Examining a wide range of organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class III peroxidases (CIII Prx) were only detected in plants and Class II peroxidases (CII Prx) in fungi related to wood decay and plant degradation.

Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed in protein extracts obtained from 30 different eukaryotic organisms strongly support the distribution of the sequences resulting from ourin silicoanalysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.