bluuebunny/crossref_metadata_2025 huggingface dataset:
3. The geography of diversification
Authors: Lomolino Mark V.
Published: July 2020

“The geography of diversification” returns to a central theme of biogeography—that place matters, and that each region, down to an island or lake, can be an evolutionary arena, producing its own distinct plant and animal life. Case studies from the Hawaiian Islands, Madagascar, and the Rift Valley Lakes of East Africa illustrate the phenomenon of adaptive radiation, the process by which organisms diversify from an ancestral species into a multitude of new forms. This diversification is driven by the combined effects of biogeographic processes, geographic dimensions such as area and isolation, and ecological interactions among the species. Why are the adaptive radiations of some lineages so much greater than others?
sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies
Authors: Miller Thiago L A , Orpinelli Rego Fernanda , Buzzo José Leonel L , Galante Pedro A F
Published: July 2020

Motivation

Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need.

Results

Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity and genomic context and classifying them as somatic or polymorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them, in addition to finding polymorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of bona fide retroCNVs.

Availability and implementation

sideRETRO is available at https://github.com/galantelab/sideRETRO

Supplementary information

Supplementary data are available at Bioinformatics online.
Discovering a sparse set of pairwise discriminating features in high-dimensional data
Authors: Melton Samuel , Ramanathan Sharad
Published: July 2020

Motivation

Recent technological advances produce a wealth of high-dimensional descriptions of biological processes, yet extracting meaningful insight and mechanistic understanding from these data remains challenging. For example, in developmental biology, the dynamics of differentiation can now be mapped quantitatively using single-cell RNA sequencing, yet it is difficult to infer molecular regulators of developmental transitions. Here, we show that discovering informative features in the data is crucial for statistical analysis as well as making experimental predictions.

Results

We identify features based on their ability to discriminate between clusters of the data points. We define a class of problems in which linear separability of clusters is hidden in a low-dimensional space. We propose an unsupervised method to identify the subset of features that define a low-dimensional subspace in which clustering can be conducted. This is achieved by averaging over discriminators trained on an ensemble of proposed cluster configurations. We then apply our method to single-cell RNA-seq data from mouse gastrulation, and identify 27 key transcription factors (out of 409 total), 18 of which are known to define cell states through their expression levels. In this inferred subspace, we find clear signatures of known cell types that eluded classification prior to discovery of the correct low-dimensional subspace.

Availability and implementation

https://github.com/smelton/SMD.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Prospective Cohort Study in Nonhospitalized Household Contacts With Severe Acute Respiratory Syndrome Coronavirus 2 Infection: Symptom Profiles and Symptom Change Over Time
Authors: Yousaf Anna R , Duca Lindsey M , Chu Victoria , Reses Hannah E , Fajans Mark , Rabold Elizabeth M , Laws Rebecca L , Gharpure Radhika , Matanock Almea , Wadhwa Ashutosh , Pomeroy Mary , Njuguna Henry , Fox Garrett , Binder Alison M , Christiansen Ann , Freeman Brandi , Gregory Christopher , Tran Cuc H , Owusu Daniel , Ye Dongni , Dietrich Elizabeth , Pevzner Eric , Conners Erin E , Pray Ian , Rispens Jared , Vuong Jeni , Christensen Kim , Banks Michelle , O’Hegarty Michelle , Mills Lisa , Lester Sandra , Thornburg Natalie J , Lewis Nathaniel , Dawson Patrick , Marcenac Perrine , Salvatore Phillip , Chancey Rebecca J , Fields Victoria , Buono Sean , Yin Sherry , Gerber Susan , Kiphibane Tair , Dasu Trivikram , Bhattacharyya Sanjib , Westergaard Ryan , Dunn Angela , Hall Aron J , Fry Alicia M , Tate Jacqueline E , Kirking Hannah L , Nabity Scott
Published: July 2020

Background

Improved understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spectrum of disease is essential for clinical and public health interventions. There are limited data on mild or asymptomatic infections, but recognition of these individuals is key as they contribute to viral transmission. We describe the symptom profiles from individuals with mild or asymptomatic SARS-CoV-2 infection.

Methods

From 22 March to 22 April 2020 in Wisconsin and Utah, we enrolled and prospectively observed 198 household contacts exposed to SARS-CoV-2. We collected and tested nasopharyngeal specimens by real-time reverse-transcription polymerase chain reaction (rRT-PCR) 2 or more times during a 14-day period. Contacts completed daily symptom diaries. We characterized symptom profiles on the date of first positive rRT-PCR test and described progression of symptoms over time.

Results

We identified 47 contacts, median age 24 (3–75) years, with detectable SARS-CoV-2 by rRT-PCR. The most commonly reported symptoms on the day of first positive rRT-PCR test were upper respiratory (n = 32 [68%]) and neurologic (n = 30 [64%]); fever was not commonly reported (n = 9 [19%]). Eight (17%) individuals were asymptomatic at the date of first positive rRT-PCR collection; 2 (4%) had preceding symptoms that resolved and 6 (13%) subsequently developed symptoms. Children less frequently reported lower respiratory symptoms (21%, 60%, and 69% for <18, 18–49, and ≥50 years of age, respectively; P = .03).

Conclusions

Household contacts with laboratory-confirmed SARS-CoV-2 infection reported mild symptoms. When assessed at a single timepoint, several contacts appeared to have asymptomatic infection; however, over time all developed symptoms. These findings are important to inform infection control, contact tracing, and community mitigation strategies.
Quantified coronary total plaque volume from computed tomography angiography provides superior 10-year risk stratification
Authors: Deseive Simon , Kupke Maximilian , Straub Ramona , Stocker Thomas J , Broersen Alexander , Kitslaar Pieter , Martinoff Stefan , Massberg Steffen , Hadamitzky Martin , Hausleiter Jörg
Published: July 2020

Aims 

Automated coronary total plaque volume (TPV) quantification derived from coronary computed tomographic angiography (CTA) datasets provide exact and reliable assessment of calcified and non-calcified coronary atherosclerosis burden. The aim of this analysis was to investigate the long-term predictive value of TPV.

Methods and results 

TPV was quantified in 1577 patients undergoing coronary CTA and cardiovascular events were collected during 10.5 years (interquartile range 6.0–11.4) of follow-up. The study endpoint comprised cardiac death and acute coronary syndrome and occurred in 59 (3.7%) patients. Coronary TPV provided additive prognostic value over clinical risk assessed with the Morise Score and coronary artery disease severity (rise in C-index from 0.744 to 0.769, P = 0.03). A category-based reclassification approach combining the Morise Score and TPV revealed superior risk stratification (categorical net reclassification improvement: 0.48 with 95% CI 0.13–0.68, P < 0.001) and resulted in reclassification of 800 (51%) patients compared with the Morise Score alone. The 10-year risk for the study endpoint was 0.6% (95% CI 0–1.3) for patients classified as low risk (n = 807), 4.8% (95% CI 2.4–7.2) for patients at intermediate risk (n = 400), and 10.3% (95% CI 6.6–13.9) for patients at high risk (n = 370) using the combined reclassification approach.

Conclusion 

Quantification of TPV from coronary CTA permits an improved 10-year cardiovascular risk stratification.
Patient response, treatments, and mortality for acute myocardial infarction during the COVID-19 pandemic
Authors: Wu Jianhua , Mamas Mamas , Rashid Muhammad , Weston Clive , Hains Julian , Luescher Tom , de Belder Mark A , Deanfield John E , Gale Chris P
Published: July 2020

Aims

COVID-19 might have affected the care and outcomes of hospitalized acute myocardial infarction (AMI). We aimed to determine whether the COVID-19 pandemic changed patient response, hospital treatment, and mortality from AMI.

Methods and results

Admission was classified as non-ST-elevation myocardial infarction (NSTEMI) or STEMI at 99 hospitals in England through live feeding from the Myocardial Ischaemia National Audit Project between 1 January 2019 and 22 May 2020. Time series plots were estimated using a 7-day simple moving average, adjusted for seasonality. From 23 March 2020 (UK lockdown), median daily hospitalizations decreased more for NSTEMI [69 to 35; incidence risk ratios (IRR) 0.51, 95% confidence interval (CI) 0.47–0.54] than STEMI (35 to 25; IRR 0.74, 95% CI 0.69–0.80) to a nadir on 19 April 2020. During lockdown, patients were younger (mean age 68.7 vs. 66.9 years), less frequently diabetic (24.6% vs. 28.1%), or had cerebrovascular disease (7.0% vs. 8.6%). ST-elevation myocardial infarction more frequently received primary percutaneous coronary intervention (81.8% vs. 78.8%), thrombolysis was negligible (0.5% vs. 0.3%), median admission-to-coronary angiography duration for NSTEMI decreased (26.2 vs. 64.0 h), median duration of hospitalization decreased (4 to 2 days), secondary prevention pharmacotherapy prescription remained unchanged (each > 94.7%). Mortality at 30 days increased for NSTEMI [from 5.4% to 7.5%; odds ratio (OR) 1.41, 95% CI 1.08–1.80], but decreased for STEMI (from 10.2% to 7.7%; OR 0.73, 95% CI 0.54–0.97).

Conclusion

During COVID-19, there was a substantial decline in admissions with AMI. Those who presented to hospital were younger, less comorbid and, for NSTEMI, had higher 30-day mortality.
Surgical treatment for a pulmonary artery aneurysm with stenosis of the quadricuspid pulmonary valve
Authors: Hara Hiroyuki , Kanemitsu Naoki , Hori Yuki , Hirao Shingo
Published: July 2020

We report a case of pulmonary artery aneurysm and pulmonary stenosis with a quadricuspid pulmonary valve in a 64-year-old woman. While pulmonary artery disease had been found as a child, she needed no treatment because of the absence of symptoms and her normal physical development. She began experiencing dyspnoea on exertion 3 years ago. Echocardiography showed pulmonary artery aneurysm and severe pulmonary stenosis with a quadricuspid valve. Computed tomography showed a pulmonary artery aneurysm extending from its main trunk to the bilateral branches. The pulmonary valve was replaced, and the pulmonary trunk and its bilateral branch were reconstructed. The patient’s postoperative course was uneventful.
Beyond the second-order magnetic anisotropy tensor: higher-order components due to oriented magnetite exsolutions in pyroxenes, and implications for palaeomagnetic and structural interpretations
Authors: Biedermann Andrea R , Jackson Mike , Chadima Martin , Hirt Ann M , Feinberg Joshua M
Published: July 2020

Exsolved iron oxides in silicate minerals can be nearly ideal palaeomagnetic recorders, due to their single-domain-like behaviour and the protection from chemical alteration by their surrounding silicate host. Because their geometry is crystallographically controlled by the host silicate, these exsolutions possess a shape preferred orientation that is ultimately controlled by the mineral fabric of the silicates. This leads to potentially significant anisotropic acquisition of remanence, which necessitates correction to make accurate interpretations in palaeodirectional and palaeointensity studies. Here, we investigate the magnetic shape anisotropy carried by magnetite exsolutions in pyroxene single crystals, and in pyroxene-bearing rocks based on torque measurements and rotational hysteresis data. Image analysis is used to characterize the orientation distribution of oxides, from which the observed anisotropy can be modelled. Both the high-field torque signal and corresponding models contain components of higher order, which cannot be accurately described by second-order tensors usually used to describe magnetic fabrics. Conversely, low-field anisotropy data do not show this complexity and can be adequately described with second-order tensors. Hence, magnetic anisotropy of silicate-hosted exsolutions is field-dependent and this should be taken into account when interpreting isolated ferromagnetic fabrics, and in anisotropy corrections.
Acute kidney injury in patients operated on for type A acute aortic dissection: incidence, risk factors and short-term outcomes
Authors: Wang Zhigang , Ge Min , Chen Tao , Chen Cheng , Zong Qiuyan , Lu Lichong , Wang Dongjin
Published: July 2020

OBJECTIVES

Acute kidney injury (AKI) is a relatively common complication after an operation for type A acute aortic dissection and is indicative of a poor prognosis. We examined the risk factors for and the outcomes of developing AKI in patients being operated on for thoracic aortic diseases.

METHODS

We retrospectively analysed 712 patients with acute type A dissection who had deep hypothermic circulatory operations from January 2014 to December 2018, emphasizing those who developed AKI. Logistic regression models were used to identify predisposing factors for the postoperative development of AKI.

RESULTS

Among all enrolled patients, 359 (50.4%) had AKI; of these, 133 were diagnosed as stage 1 (18.7%), 126 were stage 2 (17.7%) and 100 were stage 3 (14.0%). Postoperative haemodialysis was required in 111 patients (15.9%). The development of AKI after aortic surgery contributed to the higher mortality rate within 30 days after surgery (P < 0.001), longer stay in the intensive care unit (P = 0.01) and longer hospital stay (P < 0.001). Binary logistic regression analysis showed that preoperative cystatin C levels [odds ratio (OR) 2.615, 95% confidence interval (CI) 1.139–6.002; P = 0.023] and postoperative ventilation time (OR 1.019, 95% CI 1.005–1.034; P = 0.009) were independent risk factors for developing AKI. Multiple ordinal logistic regression analyses showed that the preoperative cystatin C level (OR 2.921, 95% CI 1.542–5.540; P = 0.001) was an independent risk factor associated with the severity of AKI.

CONCLUSIONS

Our data suggested that the development of AKI after surgery for type A acute aortic dissection was common and associated with an increased short-term mortality rate. The preoperative cystatin C level was identified as an indicator for the occurrence and severity of AKI postoperatively. Furthermore, we discovered that longer postoperative ventilation time was also associated with the development of AKI.
A triple-drug treatment regimen to accelerate elimination of lymphatic filariasis: From conception to delivery
Authors: Weil Gary J , Jacobson Julie A , King Jonathan D
Published: July 2020

The Global Programme to Eliminate Lymphatic Filariasis (LF) is using mass drug administration (MDA) of antifilarial medications to treat filarial infections, prevent disease and interrupt transmission. Almost 500 million people receive these medications each year. Clinical trials have recently shown that a single dose of a triple-drug combination comprised of ivermectin, diethylcarbamazine and albendazole (IDA) is dramatically superior to widely used two-drug combinations for clearing larval filarial parasites from the blood of infected persons. A large multicenter community study showed that IDA was well-tolerated when it was provided as MDA. IDA was rapidly advanced from clinical trial to policy and implementation; it has the potential to accelerate LF elimination in many endemic countries.
Temocillin dosage adjustment in a preterm infant with severe renal disease: a case report
Authors: Dumangin Guillaume , Brenkman Matthieu , Pape Elise , Kolodziej Allan , Gambier Nicolas , Vrillon Isabelle , Charmillon Alexandre , Scala-Bertola Julien
Published: July 2020

Background

Temocillin is a carboxypenicillin antibiotic indicated in complicated urinary tract infections due to susceptible ESBL-producing Enterobacteriaceae. While temocillin therapeutic schemes for adult patients with normal or impaired renal function are evidence based, little is known in paediatric populations.

Objectives

We report herein the management of temocillin treatment in a preterm infant with end-stage renal disease.

Patients and methods

The patient was a 7-month-old preterm infant born at 35 weeks gestation and treated by temocillin for 10 days for a bacteraemic urinary tract infection due to a susceptible ESBL-producing Enterobacter cloacae complex strain. Temocillin was administered by continuous infusion using a loading dose of 25 mg followed by a maintenance dose of 70 mg daily. Determination of MIC and temocillin plasma and urinary concentration was performed.

Results

Clinical improvement was observed 24 h after the initiation of temocillin treatment. Temocillin concentrations ranged between 21.6 and 35.5 mg/L in urine between the first and the sixth day of treatment and between 47.0 and 61.8 mg/L in plasma after 6 and 10 days of treatment, respectively. Temocillin concentrations were found to be above the determined MIC of 6 mg/L. From the measured concentrations, we can postulate that 100%fT>MIC was achieved in urine and at least equal to 40% in plasma.

Conclusions

Temocillin dosing adjustment performed in the present reported case allowed safe and effective treatment. The strategy described herein could be used as a basis for further clinical studies relative to temocillin use in a paediatric population with renal impairment.
Awakening the Serpent King: Ritual and Textual Ontologies in Garhwal, Uttarakhand
Authors: Jassal Aftab S
Published: July 2020

In the north Indian state of Uttarakhand, the god Nagaraja, associated with the pan--Indian god Krishna, is an extremely popular deity. However, there exist key disjunctures in how Nagaraja is known, experienced and worshiped in the north Indian state of Uttarakhand by jāgar performers—low--caste ritual specialists, storytellers, and musicians—on the one hand, and high--caste temple priests, on the other. Temple priests were generally dismissive of the practices of the jāgar performers, often re--directing my interest in regional narratives of Nagaraja to the Sanskrit--language Bhagavadgita and Bhagavata Purana (the Gita--Bhagavat), which they saw as authoritative and ‘original' sources of oral and vernacular traditions. This interpretation, however, was highly contested by jāgar performers who articulated a non--essentialist, ritually efficacious, rhetorical, oral and vernacular ‘textual ontology.' Jāgar performers not only critiqued Brahminical notions of textual purity and essentialism but also assumptions within the academic study of Hinduism about the relationship between vernacular religious practices and textual Hinduism, or the so--called Great and Little traditions of Hinduism. By ‘textual ontology,' I describe how different relations to textual authority and knowledge in turn reveal distinctive ways of creating, knowing, and interacting with deities and the world. In challenging priestly and western scholarly notions of text, this article offers a radically different view of textual production, transmission, and authority.
The current clinical use of adjuvant analgesics for refractory cancer pain in Japan: a nationwide cross-sectional survey
Authors: Tagami Keita , Matsuoka Hiromichi , Ariyoshi Keisuke , Oyamada Shunsuke , Hiratsuka Yusuke , Kizawa Yoshiyuki , Koyama Atsuko , Inoue Akira
Published: July 2020

Background

Although adjuvant analgesics are used to treat opioid-refractory cancer pain, there is insufficient evidence to support this practice and limited data to guide the choice depending on cancer pain pathophysiology, dose titration and starting dose. This survey aimed to clarify the current use of adjuvant analgesics for treating opioid-refractory cancer pain.

Methods

In this cross-sectional study, we sent an online survey questionnaire to 208 certified palliative care specialists. Primary outcomes were (i) effective pathophysiological mechanism of cancer pain and (ii) initiating doses and time period to the first response to each adjuvant analgesic therapy.

Results

In total, 87 (42%) palliative care specialists responded. Of all patients with cancer pain, 40% of patients (median) with refractory cancer pain were prescribed adjuvant analgesics. Additionally, 94.3, 93.1 and 86.2% of palliative care specialists found dexamethasone/betamethasone effective for neuropathic pain caused by tumor-related spinal cord compression, pregabalin effective for malignant painful radiculopathy and dexamethasone/betamethasone effective for brain tumor or leptomeningeal metastases-related headache, respectively. The median starting dose of pregabalin, dexamethasone/betamethasone, lidocaine and ketamine were 75, 4, 200, and 50 mg/day, respectively, and the median time to the first response of those medications were 5, 3, 2 and 3 days, respectively.

Conclusions

Many palliative care specialists select adjuvant analgesics depending on the pathophysiological mechanism of cancer pain in each case. They used such adjuvant analgesics in low doses for cancer pain with short first-response periods.
Is ‘viability’ viable? Abortion, conceptual confusion and the law in England and Wales and the United States
Authors: Romanis Elizabeth Chloe
Published: July 2020

In this paper, I explore how viability, meaning the ability of the fetus to survive post-delivery, features in the law regulating abortion provision in England and Wales and the USA. I demonstrate that viability is formalized differently in the criminal law in England and Wales and the USA, such that it is quantified and defined differently. I consider how the law might be applied to the examples of artificial womb technology and anencephalic fetuses. I conclude that there is incoherence in the meaning of viability and argue that it is thus a conceptually illegitimate basis on which to ground abortion regulation. This is both because of the fluidity of the concept and because how it has been thus far understood in the law is unsupported by medical realities. Furthermore, it has the effect of heavily diluting pregnant people’s rights with overly moralistic limitations on access to healthcare.
Child and Family Factors Associated With Posttraumatic Stress Responses Following a Traumatic Medical Event: The Role of Medical Team Support
Authors: Sadeh Yaara , Dekel Rachel , Brezner Amichai , Landa Jana , Silberg Tamar
Published: July 2020

Objectives

This study examined the contribution of pretrauma psychosocial factors (child emotional functioning, family resources, family functioning, and social support) and environmental factors (mother’s posttraumatic stress symptoms [PTSSs], medical team support [MTS]) to PTSSs of injured or seriously ill children within a pediatric rehabilitation setting. It was hypothesized that psychosocial variables would be strongly associated with child’s PTSS; that mother’s PTSS and MTS would mediate the association between psychosocial factors and child’s PTSS; that mother’s report on child’s PTSS would mediate the association between mother’s PTSS and child’s PTSS.

Methods

Participants were 196 children hospitalized following an injury/illness and assessed M = 47.7 days postevent. Children completed measures of PTSS, mothers completed measures of their own PTSS, child’s PTSS, and pretrauma psychosocial factors. Family’s therapist completed a MTS measure. Structural equation modeling was employed to evaluate the study hypotheses.

Results

Pretrauma family structure and resources were associated with child’s self-reported PTSS; each pretrauma variable and mother’s report of child’s PTSS was significantly associated. Although mother’s PTSS was not directly associated with child’s PTSS, this relationship was mediated by mother’s report of child’s PTSS. MTS mediated the relationship between pretrauma social support and mother’s PTSS.

Conclusion

This study further explicates the utility of a biopsychosocial framework in predicting childhood PTSS. Findings confirm the role of pretrauma factors and environmental factors at the peritrauma period in the development of PTSS following a pediatric injury/illness. Mother’s PTSS and MTS may be appropriate targets for prevention and early intervention.
Notes from the Field: Conducting Research with Resettled Refugee Women
Authors: Agha Erum , Cuddeback Gary S
Published: July 2020

Understanding the unique health and behavioral health needs of refugees is critical to developing culturally sensitive interventions and services for this vulnerable population. This paper highlights the process of recruiting participants for a study exploring these needs for resettled refugee women from their own perspectives and the perspectives of resettlement service providers. We recruited 14 resettled refugee women and seven service providers to participate in a semi-structured interview, which included open-ended questions and culturally-relevant vignettes designed to stimulate discussion about health and behavioral health issues. Participating women were receptive to the vignettes and were highly engaged in the study. With respect to methods, we found that it is feasible and practical to collect qualitative data using vignettes coupled with semi-structured interview questions. With respect to recruiting strategies, participants were more responsive to personal connections rather than to advertisements for recruitment. This paper reports the methodology; study results are reported separately.
Origin and functional differentiation of (E)-β-ocimene synthases reflect the expansion of monoterpenes in angiosperms
Authors: Ding Guangyu , Zhang Shaoyu , Ma Bi , Liang Jiubo , Li Han , Luo Yiwei , He Ningjia
Published: July 2020

The acquisition of new metabolic activities is a major force driving evolution. We explored, from the perspectives of gene family expansion and the evolutionary adaptability of proteins, how new functions have arisen in which terpene synthases diverged. Monoterpenoids are diverse natural compounds that can be divided into cyclic and acyclic skeleton forms according to their chemical structure. We demonstrate, through phylogenetic reconstructions and genome synteny analyses, that the (E)-β-ocimene synthases, which are acyclic monoterpene synthases (mTPSs), appear to have arisen several times in independent lineages during plant evolution. Bioinformatics analyses and classical mutation experiments identified four sites (I388, F420, S446, and F485) playing important roles in the neofunctionalization of mTPSs. Incubation of neryl diphosphate with Salvia officinalis 1,8-cineole synthase (SCS) and mutated proteins show that these four sites obstruct the isomerization of geranyl diphosphate. Quantum mechanical/molecular mechanical molecular dynamics simulations of models of SCS, SCSY420F/I446S, and SCSN338I/Y420F/I446S/L485F with (3R)-linalyl diphosphate suggest that mutations changed the configuration of the intermediate to obtain new activities. These results provide new perspectives on the evolution of mTPSs, explain the convergent evolution of (E)-β-ocimene synthases at the molecular level, and identify key residues to control the specificity of engineered mTPSs.
When did Population III star formation end?
Authors: Liu Boyuan , Bromm Volker
Published: July 2020

We construct a theoretical framework to study Population III (Pop III) star formation in the post-reionization epoch (z ≲ 6) by combining cosmological simulation data with semi-analytical models. We find that due to radiative feedback (i.e. Lyman–Werner and ionizing radiation) massive haloes ($M_{\rm halo}\gtrsim 10^{9}\ \rm M_{\odot }$) are the major (≳90 per cent) hosts for potential Pop III star formation at z ≲ 6, where dense pockets of metal-poor gas may survive to form Pop III stars, under inefficient mixing of metals released by supernovae. Metal mixing is the key process that determines not only when Pop III star formation ends, but also the total mass, MPopIII, of active Pop III stars per host halo, which is a crucial parameter for direct detection and identification of Pop III hosts. Both aspects are still uncertain due to our limited knowledge of metal mixing during structure formation. Current predictions range from early termination at the end of reionization (z ∼ 5) to continuous Pop III star formation extended to z = 0 at a non-negligible rate $\sim \!10^{-7}\ \rm M_{\odot }\ yr^{-1}\ Mpc^{-3}$, with $M_{\rm PopIII}\sim 10^{3}-10^{6}\ \rm M_{\odot }$. This leads to a broad range of redshift limits for direct detection of Pop III hosts, zPopIII ∼ 0.5–12.5, with detection rates $\lesssim 0.1-20\ \rm arcmin^{-2}$, for current and future space telescopes (e.g. HST, WFIRST, and JWST). Our model also predicts that the majority (≳90 per cent) of the cosmic volume is occupied by metal-free gas. Measuring the volume-filling fractions of this metal-free phase can constrain metal-mixing parameters and Pop III star formation.
Bipolar planetary nebulae from outflow collimation by common envelope evolution
Authors: Zou Yangyuxin , Frank Adam , Chen Zhuo , Reichardt Thomas , De Marco Orsola , Blackman Eric G , Nordhaus Jason , Balick Bruce , Carroll-Nellenback Jonathan , Chamandy Luke , Liu Baowei
Published: July 2020

The morphology of bipolar planetary nebulae (PNe) can be attributed to interactions between a fast wind from the central engine and the dense toroidal-shaped ejecta left over from common envelope (CE) evolution. Here we use the 3D hydrodynamic adaptive mesh refinement (AMR) code AstroBEAR to study the possibility that bipolar PN outflows can emerge collimated even from an uncollimated spherical wind in the aftermath of a CE event. The output of a single CE simulation via the smoothed particle hydrodynamics (SPH) code phantom serves as the initial conditions. Four cases of winds, all with high enough momenta to account for observed high momenta pre-PN outflows, are injected spherically from the region of the CE binary remnant into the ejecta. We compare cases with two different momenta and cases with no radiative cooling versus application of optically thin emission via a cooling curve to the outflow. Our simulations show that in all cases highly collimated bipolar outflows result from deflection of the spherical wind via the interaction with the CE ejecta. Significant asymmetries between the top and bottom lobes are seen in all cases. The asymmetry is strongest for the lower momentum case with radiative cooling. While real post-CE winds may be aspherical, our models show that collimation via ‘inertial confinement’ will be strong enough to create jet-like outflows even beginning with maximally uncollimated drivers. Our simulations reveal detailed shock structures in the shock-focused inertial confinement (SFIC) model and develop a lens-shaped inner shock that is a new feature of SFIC-driven bipolar lobes.
Properties of the post in-spiral common envelope ejecta II: dust formation
Authors: Iaconi Roberto , Maeda Keiichi , Nozawa Takaya , De Marco Orsola , Reichardt Thomas
Published: July 2020

We study the formation of dust in the expanding gas ejected as a result of a common envelope binary interaction. In our novel approach, we apply the dust formation model of Nozawa et al. to the outputs of the 3D hydrodynamic SPH simulation performed by Iaconi et al. that involves a giant of 0.88 M⊙ and 83 R⊙, with a companion of 0.6 M⊙ placed on the surface of the giant in circular orbit. After simulating the dynamic in-spiral phase, we follow the expansion of the ejecta for $\simeq 18\, 000$ d. During this period, the gas is able to cool down enough to reach dust formation temperatures. Our results show that dust forms efficiently in the window between ≃ 300 d (the end of the dynamic in-spiral) and ≃ 5000 d. The dust forms in two separate populations; an outer one in the material ejected during the first few orbits of the companion inside the primary’s envelope and an inner one in the rest of the ejected material. We are able to fit the grain-size distribution at the end of the simulation with a double power law. The slope of the power law for smaller grains is flatter than that for larger grains, creating a knee-shaped distribution. The power-law indexes are, however, different from the classical values determined for the interstellar medium. We also estimate that the contribution to cosmic dust by common envelope events is not negligible and comparable to that of novae and supernovae.
Acute kidney injury e-alerts in pregnancy: rates, recognition and recovery
Authors: Gama Rouvick M , Clark Katherine , Bhaduri Mahua , Clery Amanda , Wright Kelly , Smith Priscilla , Martin Hayley , Vincent Royce P , Jayawardene Satish , Bramham Kate
Published: July 2020

Background

Acute kidney injury (AKI) in pregnancy (Pr-AKI) is associated with substantial maternal morbidity and mortality. E-alerts are routinely used for detection of AKI in non-pregnant patients but their role in maternity care has not been explored.

Methods

All pregnant or postpartum women with AKI e-alerts for AKI Stages 1–3 (Kidney Disease Improving Global Outcomes (KDIGO) criteria) were identified at a tertiary centre >2 years. Two women matched by delivery date for each case were selected as controls. AKI stage, recognition of AKI, pregnancy outcomes, renal recovery, AKI aetiology and risk factors were extracted from electronic patient records.

Results

288 of 11 922 (2.4%) women had AKI e-alerts, of which only 118 (41%) were recognized by the obstetric team. Common Pr-AKI causes included infection (48%), pre-eclampsia (26%) and haemorrhage (25%), but no cause was identified in 15% of women. Renal function recovered in 213 (74%) women, but in 47 (17%) repeat testing was not undertaken and 28 (10%) did not recover function. Hypertensive disorders of pregnancy and Caesarean section were associated with increased incidence of Pr-AKI compared with controls.

Conclusions

Pr-AKI e-alerts were identified in ∼1 in 40 pregnancies. However, a cause for Pr-AKI was not identified in many cases and e-alerts may have been triggered by gestational change in serum creatinine. Pregnancy-specific e-alert algorithms may be required. However, 1 in 10 women with Pr-AKI had not recovered kidney function on repeat testing. Better understanding of long-term impacts of Pr-AKI on pregnancy and renal outcomes is needed to inform relevant Pr-AKI e-alert thresholds.
Networking retinomorphic sensor with memristive crossbar for brain-inspired visual perception
Authors: Wang Shuang , Wang Chen-Yu , Wang Pengfei , Wang Cong , Li Zhu-An , Pan Chen , Dai Yitong , Gao Anyuan , Liu Chuan , Liu Jian , Yang Huafeng , Liu Xiaowei , Cheng Bin , Chen Kunji , Wang Zhenlin , Watanabe Kenji , Taniguchi Takashi , Liang Shi-Jun , Miao Feng
Published: July 2020

Compared to human vision, conventional machine vision composed of an image sensor and processor suffers from high latency and large power consumption due to physically separated image sensing and processing. A neuromorphic vision system with brain-inspired visual perception provides a promising solution to the problem. Here we propose and demonstrate a prototype neuromorphic vision system by networking a retinomorphic sensor with a memristive crossbar. We fabricate the retinomorphic sensor by using WSe2/h-BN/Al2O3 van der Waals heterostructures with gate-tunable photoresponses, to closely mimic the human retinal capabilities in simultaneously sensing and processing images. We then network the sensor with a large-scale Pt/Ta/HfO2/Ta one-transistor-one-resistor (1T1R) memristive crossbar, which plays a similar role to the visual cortex in the human brain. The realized neuromorphic vision system allows for fast letter recognition and object tracking, indicating the capabilities of image sensing, processing and recognition in the full analog regime. Our work suggests that such a neuromorphic vision system may open up unprecedented opportunities in future visual perception applications.
Outpatient Parenteral Antimicrobial Therapy in the Time of COVID-19: The Urgent Need for Better Insurance Coverage
Authors: Mansour Omar , Keller Sara , Katz Morgan , Townsend Jennifer L
Published: July 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease it causes, coronavirus disease 2019 (COVID-19), are placing unprecedented pressure on every health care system. Patients who require weeks of intravenous antibiotic therapy after hospital discharge due to severe bacterial infections, generally referred to as outpatient parenteral antibiotic therapy (OPAT), are at increased risk for contracting and/or transmitting COVID-19 due to extensive contact with the health care system. To reduce the risk of COVID-19 among this vulnerable patient population, providers overseeing OPAT care need to consider the relative safety of the different OPAT sites of care. Home-based OPAT should be emphasized to minimize hospital stays and prevent skilled nursing facility admissions. Medicare reimbursement policies need to urgently change to provide comprehensive coverage of home infusion services.
Atypical hemolytic uremic syndrome with peripheral gangrene and homocysteinemia in a child
Authors: Al-Ahmad Molham , Kharita Lubna , Wannous Hala
Published: July 2020

Atypical hemolytic uremic syndrome (aHUS) is a rare, progressive, life-threating disease that frequently has a genetic component; it is usually caused by familial, sporadic or idiopathic reasons. We report a case of aHUS in a 21-month-old girl with coexisting of methylenetetrahydrofolate reductase mutations, homocysteinemia and thalassemia minor complicated by peripheral gangrene as extrarenal manifestation.
Congenital erythropoietic porphyria (Gunther disease): a case report
Authors: Kahila Ali , Zamlout Ali , Mazloum Abdaljawad , Laila Omar , Badran Ayham
Published: July 2020

Congenital erythropoietic porphyria (CEP or Gunther disease) is a very rare subtype of porphyria with a prevalence of <0.9 per 1 000 000. A 13-year-old female patient came to our hospital complaining of a severe cutaneous ulceration and scarring. The symptoms began in her first year of life as urine discoloration and skin blistering in sun-exposed areas. The family had been trapped in a high-risk conflict zone in Syria for many years, which precipitated the aggravation of symptoms. Based on clinical examination and laboratory tests, we diagnosed the patient with CEP and treated her with vitamin D supplementation alongside chronic blood transfusions, strict photoprotection and psychotherapy. After 7 months, there were no longer active ulcers or novel complications. Psychotherapy and patient education were important for her psychological development at this age. This treatment limited the deterioration of the symptoms and made the patient more committed to the periodic examinations.
Cerebral paradoxical embolism associated with patent foramen ovale and idiopathic venous thromboembolism in a 31-year-old patient
Authors: Timnou Bekouti Jean , Ravakiniaina Ranaivosoa Mialy , Adossou Akuvi Claude , Diawara Alpha , Camara Ansoumane , Rambolarimanana Manitrahasina , Lawani Pierre , Ranjatson Alain , Houeze Richard , Roynard Jean Louis
Published: July 2020

Paradoxical embolism is the passage of venous thrombi into the arterial circulation through a pulmonary or intracardiac shunt. We report the management of a 31-year-old patient who initially presented with chest pain and right brachiofacial paresis. A diagnosis of paradoxical cerebral embolism associated with a spontaneous venous thromboembolism and a patent foramen ovale was made. The patient benefited from thrombolytic therapy and lifelong anticoagulation with good recovery. This case showed that percutaneous closure of a patent foramen ovale needs to be discussed individually.
Introducing Psychology
Authors: Raeff Catherine
Published: July 2020

This chapter sets the stage for a new way of thinking about human functioning by identifying some complexities of human functioning—that is, holism, dynamics, variability, multicausality, and individuality. It also introduces a questioning stance that can lead psychology in new theoretical and empirical directions. The chapter traces some of the history of psychology and how it came to be defined largely in terms of research methods that are rooted in the natural sciences. It also describes contemporary conventional psychology in terms of fragmenting, objectifying, and aggregating practices, as well as deterministic conceptions of causality.
Questioning Convention
Authors: Raeff Catherine
Published: July 2020

To set the stage for a new way of thinking about human functioning, the goal of this chapter is to constructively question some of psychology’s conventional practices and assumptions. This chapter questions psychology’s practices of fragmenting, objectifying, quantifying, and aggregating. It also raises issues regarding the dominant deterministic approach to causality in conventional psychology. The chapter includes a consideration of qualitative research, which provides alternatives to traditional research methods in psychology. The chapter ends by identifying some issues and questions that will be addressed with the new theoretical framework for understanding human functioning that will be presented in subsequent chapters. Criteria for evaluating theorizing are also identified.
Developmental Processes
Authors: Raeff Catherine
Published: July 2020

Based on the conceptual claim that action develops and that the psychological processes that comprise action develop, the goal of this chapter is to conceptualize what happens during the development of action and how action develops. Organismic-developmental theory is used to explain what happens during action development in terms of differentiation and integration, and in terms of progress toward cultural goals of development. Sociocultural theory is used to explain how action develops as individuals participate with others in cultural practices. The chapter further considers how action develops through individual, social, cultural, bodily, and environmental processes. The chapter ends with a discussion of how development is relevant to all of psychology and need not be treated as a fragmented subfield or area of specialization.
Implications for Thinking about Individuality and Variability
Authors: Raeff Catherine
Published: July 2020

This chapter presents some implications and applications of the theoretical framework that is presented in Chapters 5, 6, and 7. It promotes thinking about action non-dichotomously by addressing how action is simultaneously general and individualized, as well as simultaneously stable and variable. It is argued that general or universal human processes can be played out in individualized ways of acting and in how individuals subjectively construct experience. The chapter then focuses on how the theoretical framework provides a basis for thinking about how action is both stable and variable. This chapter also considers issues pertaining to personality and what it means to know someone. It ends by using the theoretical framework to think non-dichotomously about how varied aspects of human action occur simultaneously.
Casting a Wide Net
Authors: Raeff Catherine
Published: July 2020

The goal of this chapter is to further consider how the theoretical framework presented in the book is applicable to so much of what people do, as well as to so many complex human issues and concerns. In this chapter, a wide net is cast to consider how the theoretical framework is applicable to eating, freedom, attitudes, extreme action, and art. By thinking about these topics in terms of action, readers can see how the book’s theoretical framework provides a common language for thinking systematically about a wide range of complex issues. The chapter shows how the book’s action perspective provides ways of thinking systematically about the complexities of action as people go about their lives in all corners of the world.
Complex and Empathic Understanding
Authors: Raeff Catherine
Published: July 2020

This chapter ties varied strands of the book together by first considering how the theoretical framework can be used to address the complexities of human action identified in Chapter 1 (i.e., holism, dynamics, variability, multicausality, and individuality). The chapter also offers guidelines for using the theoretical framework to think systematically about what people do in varied circumstances. The book ends by considering the complex and empathic image of and vision for humanity that the theoretical framework reflects and hopefully promotes and promulgates. In doing so, the chapter raises varied issues regarding diversity and commonality, as well as openness to change.
Pitch
Authors: Malawey Victoria
Published: July 2020

The domain of pitch refers to listeners’ perceptions of frequency. Pitch’s most transparent and absolute aspects—range, tessitura, and intonation—interrelate with registration, a nuanced multidimensional aspect engaging both pitch and quality. Leonard Cohen’s iconic “Hallelujah” (1984) and cover versions by Jeff Buckley (1994), Rufus Wainwright (2001), k. d. lang (2004), Imogen Heap (2006), Alexandra Burke (2008) and Kate McKinnon (2016) serve as exemplars for investigating aspects of pitch. Drawing upon disparate fields ranging from vocal science to feminist linguistics, this chapter also examines how aspects of pitch and registration relate to broader issues of identity formation, particularly as they serve as signifiers of gender and age.
Synthesis, or Why Covers of Elliott Smith Songs Don’t Work
Authors: Malawey Victoria
Published: July 2020

As a means of synthesis, this chapter applies elements from the conceptual model (engaging elements of pitch, prosody, quality, and technological mediation) in analyses of three recordings by Elliott Smith—“Between the Bars” (1997), “Twilight” (2004), and “Roman Candle” (1994)—and their respective cover versions by Seth Avett and Jessica Lea Mayfield (2015). For some songs recorded by artists whose voices connote a particular brand of longing or desperation, the same quality of emotion becomes impossible to convey through other singing voices, suggesting that the quality of emotion is inextricably linked to the alterity of the singing voice. Furthermore, the connection between quality of singing voices and quality of emotion informs listeners’ constructions of authenticity in popular music.
The Watershed
Authors: Ochoa Espejo Paulina
Published: July 2020

Borders stability is desirable, but if borders had to be redrawn, what principle should be used to do so? Existing principles conflict: Uti possidetis favors the status quo, while the principle of self-determination is revisionist and favors unified peoples, and political cosmopolitanism seeks to undo borders altogether. This chapter offers an alternative: the Watershed Model of territorial politics, which draws borders around places. The model uses place-specific duties to identify non-state and nonmarket local cooperative institutions of resource use (specifically water) as a template to draw local political borders. The local institutions used for border drawing are intrinsically connected to geographic features, which means that border plebiscites do not fall into the same circularity as under the principle of self-determination. The Watershed Model, moreover, uses water conservation as a principle that those inside and outside the border could accept, because water conservation is both a universal and a local (and context-sensitive) value.