bluuebunny/crossref_metadata_2025 huggingface dataset:
The Acid Strength of the Lewis‐Brønsted Superacids – A QSPR Study
Authors: Sosnowska Anita , Brzeski Jakub , Skurski Piotr , Puzyn Tomasz
Published: February 2019

The acidity of Lewis‐Brønsted superacids can be derived from the theoretical calculations as the Gibbs free energy of the deprotonation reaction (ΔGacid), which describes the tendency of a studied compound to donate a proton. This paper presents the first Quantitative Structure – Property Relationship (QSPR) model that correlates the ΔGacid of superacid (HF/MeX3 formula (X=F, Cl, Br)) with their structure. Developed model is well fitted, roubustness, has good predictive abilities, fulfills all OECD recommendation for good model. Obtained results provide the insight into the relation of structural features of superacids, which are responsible for their acid strength – the structures characterized by strong F‐Me dative bond (with relatively large vibrational frequency), small positive partial atomic charge on Me central atom, possibly large polarity exhibit large acid strength. Such assumption can be used in the future as valuable information in the process of the designing new, stronger, more effective superacids.
Monitoring dendrimer conformational transition using 19F and 1H2O NMR
Authors: Taraban Marc B. , Deredge Daniel J. , Smith Margaret E. , Briggs Katharine T. , Li Yu , Jiang Zhong‐Xing , Wintrode Patrick L. , Yu Yihua Bruce
Published: February 2019

The conformational transition of a fluorinated amphiphilic dendrimer is monitored by the 1H signal from water, alongside the 19F signal from the dendrimer. High‐field NMR data (chemical shift δ, self‐diffusion coefficient D, longitudinal relaxation rate R1, and transverse relaxation rate R2) for both dendrimer (19F) and water (1H) match each other in detecting the conformational transition. Among all parameters for both nuclei, the water proton transverse‐relaxation rate R2(1H2O) displays the highest relative scale of change upon conformational transition of the dendrimer. Hydrogen/deuterium‐exchange mass spectrometry reveals that the compact form of the dendrimer has slower proton exchange with water than the extended form. This result suggests that the sensitivity of R2(1H2O) toward dendrimer conformation originates, at least partially, from the difference in proton exchange efficiency between different dendrimer conformations. Finally, we also demonstrated that this conformational transition could be conveniently monitored using a low‐field benchtop NMR spectrometer via R2(1H2O). The 1H2O signal thus offers a simple way to monitor structural changes of macromolecules using benchtop time‐domain NMR.
Signaling pathways involved in human sperm hyperactivated motility stimulated by Zn2+
Authors: Allouche‐Fitoussi Deborah , Bakhshi Danit , Breitbart Haim
Published: February 2019

To fertilize the egg, sperm cells must reside in the female reproductive tract for several hours during which they undergo chemical and motility changes collectively called capacitation. During capacitation, the sperm develop a unique type of motility known as hyperactivated motility (HAM). The semen contains Zn2+ in millimolar concentrations, whereas in the female reproductive tract the concentration is around 1 µM. In this study, we characterize the role of Zn
2+ in human sperm capacitation focusing on its effect on HAM. Western blot analysis revealed the presence of G protein‐coupled receptor 39 (GPR39) type Zn‐receptor localized mainly in the sperm tail. Zn
2+ at micromolar concentration stimulates HAM, which is mediated by a cascade involving GPR39‐AC‐cAMP‐PKA‐Src‐EGFR and phospholipase C. Both the transmembrane adenylyl cyclase (AC) and the soluble‐AC are involved in the stimulation of HAM by Zn
2+. The development of HAM is precisely regulated by cyclic adenosine monophosphate, in which relatively low concentration (5–10 µM) stimulated HAM, whereas at 30 µM no stimulation occurred. A similar response was seen when different concentrations of Zn
2+ were added to the cells; low Zn
2+ stimulated HAM, whereas at relatively high Zn
2+, no effect was seen. We further demonstrate that the Ca
2+‐channel CatSper involved in Zn
2+‐stimulated HAM. These data support a role for extracellular Zn
2+ acting via GPR39 to regulate signaling pathways in sperm capacitation, leading to HAM induction.
Intimate Consumption and New Sexual Subjects Among the Sambia of Papua New Guinea
Authors: Herdt Gilbert
Published: February 2019

This article examines the transformation of sexual meanings, attitudes, norms, and practices surrounding depletion and pollution across decades (1974–2010) among the Sambia of Papua New Guinea. In the premodern village, all sexual intercourse, whether with boy‐initiates or women, was ritualized and ultimately controlled by the men's secret society. Intimate consumption refers traditionally to a symbolic complex of beliefs, concepts, emotions, and ritual experiences involving sexuality, bodily health, social relationships, and gendered politics. But it also covers sexual anxieties corresponding to the transfer and loss of bodily fluids via the perceived depletion and pollution of self and body. For adult men, the sense of intimate consumption requires repeated substance replenishment and purification. Intimate consumption made oral and vaginal sex highly rule‐bound, taboo laden, and intensely regulated in terms of the meaning, scope, duration, and intended goals of sexual exchange. Pacification, colonization, out‐migration, Seventh Day Adventist (SDA) Christianity, and primary schooling in the Sambia Valley over a period of decades instigated social transformations that challenged and wore down this system of sexual regulation. Thus, the transition from ritual to non‐ritual practices, i.e., more individualistic sexual relationships, highlight narratives of change in the Sambia sexuality. With the demise of ritual initiation in the 1980s and 1990s, and the appearance of HIV and SikAids in the Sambia Valley, explicit ritual sexual techniques were no longer socialized. Modernity (in the sense of a set of policies, attitudes, and rules introduced through institutions such as the government community school) and SDA church sociality influenced both the pace and form of this sexual transformation. Among the greatest changes was the expansion of female agency and sexual autonomy, and personal decision‐making vis‐à‐vis especially marriage and also romance, courtship, and sex. Notably, oral sex, once universal and mandatory, largely disappeared from Sambia intimate relations. Today, spousal intimacy reveals a different set of more ‘modern’ meanings and behaviors compared to two generations ago, e.g., more mutualistic and companionate. Intimate consumption remains a worry for certain Sambia young men and women today however, influenced in part by the rise of the HIV pandemic, mobility, and the absence of normative narratives of sexuality in villages and town settlements. This creates public spaces wherein new sexual subjects have emerged in the villages and urban settlements within the Sambia Valley and in settlements throughout PNG.
Ulcer‐associated cell lineage expresses genes involved in regeneration and is hallmarked by high neutrophil gelatinase‐associated lipocalin (NGAL) levels
Authors: Thorsvik Silje , van Beelen Granlund Atle , Svendsen Tarjei D , Bakke Ingunn , Røyset Elin S , Flo Trude H , Damås Jan K , Østvik Ann E , Bruland Torunn , Sandvik Arne K
Published: February 2019

Neutrophil gelatinase‐associated lipocalin (NGAL), also known as Lipocalin 2, is an antimicrobial protein, encoded by the gene LCN2, strongly upregulated in inflammatory bowel disease (IBD) and a promising biomarker for IBD. Here we demonstrate that NGAL is highly expressed in all parts of pyloric metaplasia, also known as the ulcer‐associated cell lineage (UACL), a metaplastic cell lineage suggested to play a role in wound healing in Crohn's disease (CD). We further show NGAL expression in regenerative intestinal crypts and in undifferentiated patient‐derived colonoids. This indicates that NGAL is important in the tissue regeneration process. The remarkable overexpression of NGAL in UACL led us to explore the pathobiology of these cells by transcriptome‐wide RNA sequencing. This study is, to our knowledge, the first to characterize the UACL at this level. Biopsies with UACL and inflamed non‐UACL epithelium from the terminal ileum of CD patients and epithelium from healthy controls were laser capture microdissected for RNA sequencing. Among the 180 genes differentially expressed between UACL and control epithelium, the ten most‐upregulated genes specific for UACL were MUC5AC, PGC, MUC6, MUC5B, LCN2, POU2AF1, MUC1, SDC3, IGFBP5, and SLC7A5. PDX1 was among the most upregulated in both UACL and inflamed non‐UACL epithelium. Immunohistochemistry and iDisco 3D visualization was used to characterize UACL histo‐morphologically, and to validate protein expression of 11 selected differentially expressed genes. Among these genes, LCN2, NOTCH2, PHLDA1, IGFBP5, SDC3, BPIFB1, and RCN1 have previously not been linked to UACL. Gene expression results were analyzed for functional implications using MetaCore, showing that differentially expressed genes are enriched for genes involved in cell migration and motility, and for biomarkers of gastrointestinal neoplasia. These results support a role for UACL as part of the reepithelialization process during and after destructive intestinal inflammation. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Indications and results of diagnostic biopsy in pediatric renal tumors: A retrospective analysis of 317 patients with critical review of SIOP guidelines
Authors: de la Monneraye Yvan , Michon J. , Pacquement H. , Aerts I. , Orbach Daniel. , Doz F. , Bourdeaut F. , Sarnacki S. , Philippe‐Chomette P. , Audry G. , Coulomb A. , Fréneaux P. , Klijanienko J. , Berrebi D. , Zucker J.‐M. , Schleiermacher G. , Brisse H.J.
Published: February 2019

Objectives

According to the Renal Tumor Study Group (RTSG) of the International Society of Paediatric Oncology (SIOP), diagnostic biopsy of renal tumors prior to neoadjuvant chemotherapy is not mandatory unless the presentation is atypical for a Wilms tumor (WT). This study addresses the relevance of this strategy as well as the accuracy and safety of image‐guided needle biopsy.

Methods

Clinical, radiological, and pathological data from 317 children (141 males/176 females, mean age: 4 years, range, 0–17.6) consecutively treated in one SIOP‐affiliated institution were retrospectively analyzed.

Results

Presumptive chemotherapy for WT was decided for 182 patients (57% of the cohort), 24 (8%) were operated upfront, and 111 (35%) were biopsied at diagnosis. A non‐WT was confirmed after surgery in 5/182 (3%), 11/24 (46%), and 28/111 (25%), respectively. Age at diagnosis was the most commonly (46%) used criterion to go for biopsy but a nine‐year threshold should be retrospectively considered more relevant. Tumor volumes of clear cell sarcoma of the kidney and WT were significantly higher than those of other tumors (P = 0.002). The agreement between core‐needle biopsy (CNB) and final histology was 99%. No significant morbidity was associated with CNB.

Conclusion

The use of SIOP criteria to identify patients eligible for presumptive WT neoadjuvant chemotherapy or upfront surgery avoided biopsy in 65% of children and led to a 97% rate of appropriate preoperative chemotherapy. Image‐guided CNB is a safe and accurate diagnostic procedure. The relevance of SIOP biopsy criteria might be improved by using an older age threshold (9 years instead of 6 years) and by adding initial tumor volume.
Effects of polyimide/silica and polyimide/pores fillers on the morphology, thermal, mechanical, and tribological properties of polytetrafluoroethylene composites
Authors: Zhao Yuanliang , Qi Xiaowen , Ma Jian , Dong Yu , Yang Yulin
Published: February 2019

The effects of polyimide with silica (SiO2‐PI) and pores (porous PI) on the morphology, thermal, mechanical, and tribological properties of polytetrafluoroethylene (PTFE) composites were investigated. SiO2‐PI and porous PI fillers decrease the compactness of PTFE matrices within PTFE/SiO2‐PI composites and PTFE/porous‐PI composites. In addition, SiO2‐PI fillers improve the interfacial bonding between PI fillers and PTFE matrices, which is opposite to the detrimental effect of porous PI fillers. Thermal and mechanical properties of PTFE composites were deteriorated apparently. The friction coefficients of PTFE/SiO2‐PI and PTFE/porous‐PI composites are 9.5% and 8.5% lower than that of PTFE/PI, respectively. The wear resistance of PTFE/SiO2‐PI and PTFE/porous‐PI composites is enhanced by 77.8% and 70.1%, respectively. Scanning electron microscopy (SEM) of worn surface indicates that SiO2‐PI and porous PI fillers protect PTFE matrices from counterpart ball, which inhibits the plastic flow of PTFE matrices effectively. In addition, the uneven worn surface decreases the contact area between PTFE composites and counterpart ball. Compared with SiO2‐PI fillers, the extension of porous PI fillers in friction process increases the contact area between PTFE composites and counterpart, which induces the relatively poor tribological performance of PTFE/porous‐PI. Furthermore, SiO2‐PI and porous PI fillers contribute to the formation of smooth and uniform transfer films, which improve the tribological performance of PTFE composites effectively. In addition, compared with adding SiO2‐PI into PTFE, the addition of SiO2 nanoparticles into PTFE/PI induces the rough and uniform transfer films, which is bad for tribological performance of PTFE/PI/SiO2 composites. POLYM. COMPOS., 40:3438–3452, 2019. © 2019 Society of Plastics Engineers
A new analytic tool developed to assess safe use recommendations
Authors: Cocoros Noelle M. , Wagner Anita , Haynes Kevin , Petrone Andrew B. , Fazio‐Eynullayeva Elnara , Ding Yulan , Izem Rima , Lee Joo‐Yeon , Major Jacqueline M. , Nguyen Michael , Ju Jing
Published: February 2019

Purpose

Develop a flexible analytic tool for the Food and Drug Administration's (FDA's) Sentinel System to assess adherence to safe use recommendations with two capabilities: characterize adherence to patient monitoring recommendations for a drug, and characterize concomitant medication use before, during, and/or after drug therapy.

Methods

We applied the tool in the Sentinel Distributed Database to assess adherence to the labeled recommendation that patients treated with dronedarone undergo electrocardiogram (ECG) testing no less often than every 3 months. Measures of length of treatment, time to first ECG, number of ECGs, and time between ECGs were assessed. We also assessed concomitant use of contraception among female users of mycophenolate per label recommendations (concomitancy 4 weeks before through 6 weeks after discontinuation of mycophenolate). Unadjusted results were stratified by age, month‐year, and sex.

Results

We identified 21 457 new episodes of dronedarone use of greater than or equal to 90 days (July 2009 to September 2015); 86% had greater than or equal to one ECG, and 22% met the recommendation of an ECG no less often than every 3 months. We identified 21 942 new episodes of mycophenolate use among females 12 to 55 years (January 2016 to September 2015); 16% had greater than or equal to 1 day of concomitant contraception dispensed, 12% had concomitant contraception use for greater than or equal to 50% of the 4 weeks before initiation through 6 weeks after mycophenolate; younger females had more concomitancy. These results may be underestimates as the analyses are limited to claims data.

Conclusions

We developed a tool for use in databases formatted to the Sentinel Common Data Model that can assess adherence to safe use recommendations involving patient monitoring and concomitant drug use over time.
Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis
Authors: Temple Henry , Mortimer Jenny C. , Tryfona Theodora , Yu Xiaolan , Lopez‐Hernandez Federico , Sorieul Mathias , Anders Nadine , Dupree Paul
Published: February 2019

All members of the DUF579 family characterized so far have been described to affect the integrity of the hemicellulosic cell wall component xylan: GXMs are glucuronoxylan methyltransferases catalyzing 4‐O–methylation of glucuronic acid on xylan; IRX15 and IRX15L, although their enzymatic activity is unknown, are required for xylan biosynthesis and/or xylan deposition. Here we show that the DUF579 family members, AGM1 and AGM2, are required for 4‐O–methylation of glucuronic acid of a different plant cell wall component, the highly glycosylated arabinogalactan proteins (AGPs).
Musculoskeletal Women's Health Education in Physiatry: A Mismatch in Residency Education and Clinical Practice
Authors: Bennis Stacey , Rho Monica
Published: February 2019

Background

Musculoskeletal Women's Health (MSK WH) is a niche subspecialty within physical medicine & rehabilitation (PM&R). Women make up 50.7% of the population of the United States but are burdened with higher rates of musculoskeletal disease compared to men. MSK WH topics are not included in PM&R or Primary Care Accreditation Council for Graduate Medical Education (ACGME) program requirements. Given the comprehensive training provided in PM&R, physiatrists are ideal candidates to diagnose, treat, and provide education on MSK WH conditions.

Objective

To identify the prevalence of formalized MSK WH education and of WH physiatrists at ACGME‐accredited PM&R residency programs.

Design

Cross‐sectional survey design.

Setting

Computer‐based survey.

Participants

ACGME‐accredited residency programs (N = 86; as of February 2017).

Methods

A single, multiple choice, computer‐generated Research Electronic Data Capture (REDCap) survey with branching logic was sent to all ACGME‐accredited PM&R residency programs (N = 86).

Outcomes

The primary outcome was to assess the prevalence of women's health curricula at ACGME‐accredited PM&R residency programs in the United States. The secondary outcome was to assess the prevalence of WH physiatrists at these programs.

Results

Eighty‐six ACGME‐accredited PM&R residency programs were contacted with 55 completed responses (64% response rate). Only six programs (11%) reported the presence of a formal WH curriculum at their residency program. In contrast, 25 programs (45%) reported having WH physiatrists at their institutions, and 36 programs (65%) reported that general physiatrists were providing WH‐related care.

Conclusions

The study findings identify a mismatch between the prevalence of MSK WH residency education (11% of programs) and the prevalence of physiatrists providing MSK WH care (66% of programs). Physiatrists are ideally suited to manage MSK WH care. Based on the findings of this cross‐sectional study, residency programs and governing bodies should evaluate these trends and consider the addition of topics pertinent to women's musculoskeletal health into PM&R graduate medical education.

Level of Evidence

III.
Micromechanical modeling of anisotropic behavior of oriented semicrystalline polymers
Authors: Mirkhalaf Mohsen , van Dommelen Johannes A. W. , Govaert Leon E. , Furmanski Jevan , Geers Marc G. D.
Published: February 2019

Some manufacturing processes of polymeric materials, such as injection molding or film blowing, cause the final product to be highly anisotropic. In this study, the mechanical behavior of drawn polyethylene (PE) tapes is investigated via micromechanical modeling. An elasto‐viscoplastic micromechanical model, developed within the framework of the so‐called composite inclusion model, is presented to capture the anisotropic behavior of oriented semicrystalline PE. Two different phases, namely amorphous and crystalline (both described by elasto‐viscoplastic constitutive models), are considered at the microstructural level. The initial oriented crystallographic structure of the drawn tapes is taken into account. It was previously shown by Sedighiamiri et al. (Comp. Mater. Sci. 2014, 82, 415) that by only considering the oriented crystallographic structure, it is not possible to capture the macroscopic anisotropic behavior of drawn tapes. The main contribution of this study is the development of an anisotropic model for the amorphous phase within the micromechanical framework. An Eindhoven glassy polymer (EGP)‐based model including different sources of anisotropy, namely anisotropic elasticity, internal stress in the elastic network and anisotropic viscoplasticity, is developed for the amorphous phase and incorporated into the micromechanical model. Comparisons against experimental results reveal remarkable improvements of the model predictions (compared to micromechanical model predictions including isotropic amorphous domains) and thus the significance of the amorphous phase anisotropy on the overall behavior of drawn PE tapes. © 2019 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 378–391
Phase I study of PF‐04895162, a Kv7 channel opener, reveals unexpected hepatotoxicity in healthy subjects, but not rats or monkeys: clinical evidence of disrupted bile acid homeostasis
Authors: Aleo Michael D. , Aubrecht Jiri , D. Bonin Paul , Burt Deborah A. , Colangelo Jennifer , Luo Lina , Schomaker Shelli , Swiss Rachel , Kirby Simon , C. Rigdon Greg , Dua Pinky
Published: February 2019

During a randomized Phase 1 clinical trial the drug candidate, PF‐04895162 (ICA‐105665), caused transaminase elevations (≥grade 1) in six of eight healthy subjects treated at 300 mg twice daily for 2‐weeks (NCT01691274). This was unexpected since studies in rats (<6 months) and cynomolgus monkeys (<9 months) treated up to 100 mg/kg/day did not identify the liver as a target organ. Mechanistic studies showed PF‐04895162 had low cytotoxic potential in human hepatocytes, but inhibited liver mitochondrial function and bile salt export protein (BSEP) transport. Clinical relevance of these postulated mechanisms of liver injury was explored in three treated subjects that consented to analysis of residual pharmacokinetic plasma samples. Compared to a nonresponder, two subjects with transaminase elevations displayed higher levels of miRNA122 and total/conjugated bile acid species, whereas one demonstrated impaired postprandial clearance of systemic bile acids. Elevated taurine and glycine conjugated to unconjugated bile acid ratios were observed in two subjects, one before the onset of elevated transaminases. Based on the affinity of conjugated bile acid species for transport by BSEP, the profile of plasma conjugated/unconjugated bile acid species was consistent with inhibition of BSEP. These data collectively suggest that the human liver injury by PF‐04895162 was due to alterations in bile acid handling driven by dual BSEP/mitochondrial inhibition, two important risk factors associated with drug‐induced liver injury in humans. Alterations in systemic bile acid composition were more important than total bile acids in the manifestation of clinical liver injury and may be a very early biomarker of BSEP inhibition.
Magnesium Nanocomposite Coatings for Protection of a Lightweight Al Alloy: Modes of Corrosion Protection, Mechanisms of Failure
Authors: Davidson Rachel D. , Cubides Yenny , Andrews Justin L. , McLain Chelsea M. , Castaneda Homero , Banerjee Sarbajit
Published: February 2019

In light of the increased emphasis on lightweighting of vehicular components and continued use of high‐performance aluminum alloys in the aerospace industry, designing alternatives to carcinogenic chromium‐based corrosion control systems has emerged as an urgent imperative. The high activity of aluminum and the heterogeneous surface structure of Al alloys renders effective corrosion inhibition a formidable challenge. Here, the effective corrosion protection of AA7075 alloys by Mg/polyetherimide nanocomposite coatings prepared by dispersing solution‐grown Mg nanocrystals within a polyamic acid matrix followed by imidization on the substrate are demonstrated. The active nanocrystal filler and nanocomposite are characterized using powder X‐ray diffraction (XRD), Fourier transform infrared spectroscopy, and cross‐sectional electron microscopy. Electrochemical impedance spectroscopy (EIS) and open circuit potential (OCP) responses of coatings are evaluated over the course of 100 days of exposure to a 3.5 wt% aqueous solution of NaCl. These results suggest that the nanocomposite coatings endow efficacious cathodic and barrier protection to the underlying alloy substrate. The Mg/PEI nanocomposite coatings endow immediate cathodic protection to AA7075 substrates upon salt water immersion with rapid mobilization of the active filler. The nanocomposites represent a vital addition to the sparse set of chrome‐free options for corrosion protection of lightweight alloys.
Numerical investigation of Rossby waves for nonlinear shallow‐water equations on the sphere
Authors: Bénard Pierre
Published: February 2019

Although Rossby modes of the nonlinear shallow‐water system on the rotating sphere are suspected to be close to their counterpart for the non‐divergent barotropic vorticity equation, little is known about their properties. A numerical procedure is employed to approximate some of these modes for which an analytical expression is known in the non‐divergent case. For stationary modes, the procedure simply consists in iteratively applying a time filter in a forecast initialised with the non‐divergent mode. For zonally propagating modes, a change of frame allows a similar method to be used with only very minor changes to the forecast model. For stable modes, the structure may be approached with high precision by extending the length of the time filter used in the numerical procedure. The structure of the wind divergence field of Rossby modes is then revealed. The modes identified by this mean undergo instabilities of a similar nature to those for the barotropic vorticity equation system. The stability domain and growth rates are explored. Some avenues for improving test cases based on Rossby modes for shallow‐water systems are finally discussed.
Variational Quantum Circuit Model for Knowledge Graph Embedding
Authors: Ma Yunpu , Tresp Volker , Zhao Liming , Wang Yuyi
Published: February 2019

In this work, the first quantum Ansätze for the statistical relational learning on knowledge graphs using parametric quantum circuits are proposed. Two types of variational quantum circuits for knowledge graph embedding are introduced. Inspired by the classical representation learning, latent features for entities are first considered as coefficients of quantum states, while predicates are characterized by parametric gates acting on the quantum states. For the first model, the quantum advantages disappear when it comes to the optimization of this model. Therefore, a second quantum circuit model is introduced where embeddings of entities are generated from parameterized quantum gates acting on the pure quantum state. The benefit of the second method is that the quantum embeddings can be trained efficiently meanwhile preserving the quantum advantages. It is shown that the proposed methods can achieve comparable results to the state‐of‐the‐art classical models, for example, RESCAL, DistMult. Furthermore, after optimizing the models, the complexity of inductive inference on the knowledge graphs might be reduced with respect to the number of entities.
Literacy and Phonological Skills in Oral Deaf Children and Hearing Children With a History of Dyslexia
Authors: Herman Rosalind , E. Kyle Fiona , Roy Penny
Published: February 2019

Oral deaf children and hearing children with dyslexia both experience literacy challenges, although their reasons differ. The authors explored the problems underlying poor literacy in each group and drew implications for reading interventions. Data were collected using standardized literacy and phonological measures from 69 severe‐to‐profoundly prelingually deaf children ages 10 and 11 years, all communicating with spoken language, and compared with equivalent data from 20 hearing children with a history of dyslexia matched on reading ability. Children were given a large battery of tasks assessing word and nonword reading, spelling, vocabulary, and reading‐related skills, including letter sound knowledge, phonological awareness, rapid automated naming, and verbal short‐term memory. Striking similarities were observed for word reading, nonword reading, and spelling across groups, and associations between the measures and reading‐related skills were similar. However, differences between the two groups emerged in the strength of association between literacy and vocabulary. Regression analyses confirmed vocabulary as a key predictor of literacy in the oral deaf group. These results suggest that not only children with a history of dyslexia but also oral deaf children who struggle with reading should receive specialist literacy support. Reading interventions for oral deaf children should target phonological and language skills within a fully integrated approach.
Inclusive sustainability withinfavelaupgrading and incremental housing: The case of Rocinha in Rio de Janeiro
Authors: Martins A. Nuno , Saavedra Farias Jacira
Published: February 2019

This paper addresses two different urban phenomena that currently take place in Rocinha, the most prominentfavela(slum) of Rio de Janeiro, with more than 100 000 inhabitants. On the one hand, that of the houses' expansion typically accomplished through constructions on the rooftop (the upper slab), operations locally known as theconstrução de laje(upper slab construction). On the other hand, new urban spaces as a result of public resettlement operations consisting of the clearing of tangled webs of narrow, dark and unhealthy alleys that crisscross up and down thefavela. As an example, we will take the case of the 4th Street operation, a multidimensional process of de‐densification that involved heavy demolition, the removal of many houses and relocation of the dwellers. This urban renewal was carried out with resources from a federal programme and conducted by the state government, but with the involvement of different local actors, including local associations and community activists. The study focuses on the social sustainability issues underlying the private and public process, analysing the roles played by the different stakeholders and their interactions. The collection of data and subsequent analysis comprises diverse methods including literature review, examination of architectural and urban projects, surveys, interviews with architects and other municipal and private technicians, as well as inquiries to the householders. These interviews and inquiries revealed thefavela's dwellers' perception regarding the two‐year process and, in particular, the role played by the different actors involved. The conclusions highlight the social networks that arose and consolidated during the slum upgrading process and analyse the interactions among the members of those networks.
Natural‐resource dependence and life expectancy: A nonlinear relationship
Authors: Madreimov Timur , Li Leiming
Published: February 2019

In this paper, we revisit the link between natural resources and quality of life, measured by life expectancy over the period 1990–2011. Using fixed effect and panel‐corrected standard‐errors regression estimators we document that there is inverted U‐shaped relationship between natural‐resource dependence and longevity. This implies that in the long run, natural‐resource dependence hampers human development. This effect remains robust after a set of robustness checks.
The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers
Authors: Denk Thomas , Grimm Guido W.
Published: February 2019

Phylogenetic relationships among species of Quercus (oaks) from western Eurasia including the western part of the Himalayas are examined for the first time. Based on ITS and 5S–IGS data three major infrageneric groups are recognized for western Eurasia: the cerroid, iliciod, and roburoid oaks. While individuals of the cerroid and ilicoid groups cluster according to their species, particularly in the 5S–IGS analyses, individuals of species of roburoid oaks do not cluster with exception of Quercus pontica. The Cypriot endemic Quercus alnifolia belongs to the ilicoid oaks, in contrast to traditional views placing it within the cerroid oaks. Based on all ITS data available, the groups identified for western Eurasia can be integrated into a global infrageneric framework for Quercus. The Ilex group is resurrected as a well–defined group that comprises taxa traditionally placed into six subsections of Q. sects. Cerris and Lepidobalanus (white oaks) sensu Camus. Phylogenetic reconstructions suggest two major lineages within Quercus, each consisting of three infrageneric groups. Within the first lineage, the Quercus group (roburoid oaks in western Eurasia) and the Lobatae group evolved by “budding” as is reflected by incomplete lineage sorting, high variability within groups, and low differentiation among groups. The groups of the second lineage, including the Cyclobalanopsis, Cerris (cerroid oaks in western Eurasia), and Ilex (ilicoid oaks in western Eurasia) groups, evolved in a more tree–like fashion.
A molecular phylogeny reveals frequent changes of growth form in Carlina (Asteraceae)
Authors: Wahrmund Ute , Heklau Heike , Röser Martin , Kästner Arndt , Vitek Ernst , Ehrendorfer Friedrich , von Hagen K. Bernhard
Published: February 2019

The genus Carlina, with its 28 currently accepted species, ranks among the most thoroughly studied plant genera in Europe. Previous evolutionary hypotheses rested on a priori assumptions of character change, but for this study, DNA sequence data from nuclear ETS and three chloroplast regions obtained from all but one species of Carlina were used to produce a phylogenetic hypothesis. The results reveal that early branching lineages were morphologically divergent and that growth form shifts occurred more often and in different directions than previously thought, rendering a reconstruction of character states for the common ancestor of Carlina difficult to achieve. Nonetheless, results indicate that treelets were not plesiomorphic and that they most likely evolved in parallel in two island lineages growing in Macaronesia and in the Aegean. In addition, an independent evolution of two annual species in Carlina was revealed and most of the 50 morphological, biochemical, and karyological characters plotted on the tree proved to be homoplasic. Twenty–three anatomical characters from the stem–base/hypocotyl region provided no clear evidence for secondary woodiness and only the length of libriform fibers was clearly associated with plant height, but not without exceptions.
Molecular phylogeny of the genus Arum (Araceae) inferred from multi–locus sequence data and AFLPs
Authors: Linz Jeanine , Stökl Johannes , Urru Isabella , Krügel Tamara , Stensmyr Marcus C. , Hansson Bill S.
Published: February 2019

For centuries the wonderful looking, but foul smelling, Arum lilies have fascinated botanists. The floral odour of many species is believed to mimic faeces—the oviposition substrate of their pollinators, mainly coprophilous flies and beetles. But not all of the 29 Arum species produce a bad floral smell. The genus has evolved a variety of pollination mechanisms, including sweet and wine–like odours, and maybe even pheromone mimicry. In order to study the evolution of the pollination syndromes in Arum, a detailed and reliable phylogeny is a crucial basis. Here we present the first detailed molecular phylogeny of the genus Arum. By combining three chloroplast and one nuclear loci, as well as AFLPs, a highly resolved tree with good statistical support was obtained. The phylogeny is in most parts in congruence with the traditional classification of the genus. By comparing the phylogeny with the data on the pollination biology of the genus we could show that the mimicry of faeces is the oldest and most basal pollination mechanism, but is also present in the youngest and most derived species. The phylogeny presented here will help to study the evolution of deceptive pollination mechanisms in Arum.
Evolutionary dynamics across discontinuous freshwater systems: Rapid expansions and repeated allopolyploid origins in the Palearctic white water–lilies (Nymphaea)
Authors: Volkova Polina A. , Trávníček Pavel , Brochmann Christian
Published: February 2019

White water–lilies (Nymphaea) provide an excellent model for studying evolutionary diversification in a discontinuous habitat system, which has experienced dramatic differences in connectivity during different climatic periods. Here we explore cytogenetic and molecular variation and phylogenetic relationships in the Eurasian clade of this genus based on relative nuclear DNA contents, AFLP fingerprints, and nuclear (ITS) and cpDNA sequences. In line with some recent taxonomic treatments, our results support that the Eurasian clade consists of three species. We show that the Eurosiberian N. candida is an allopolyploid that originated at least twice by hybridization in the wide overlap zone between the mainly European N. alba lineage and the mainly Asian N. tetragona lineage. The N. alba lineage served as the chloroplast donor except for the Karelian N. candida, but the ITS region of the allopolyploid was homogenized in the direction of N. alba in all cases. The southern, widespread lineage of N. candida probably originated first, whereas the northwestern lineage, restricted to a small, previously glaciated area in Karelia, may have originated as late as in the current interglacial. We observed only low levels of DNA sequence variation within N. alba and N. tetragona, indicating rapid range expansions possibly preceeded by strong bottlenecks in glacial refugia. Our results suggest that populations of freshwater organisms found now in disjunct aquatic habitats across Eurasia were connected during previous climatic periods. These connections promoted rapid expansions of divergent lineages and repeated formation of evolutionary novelty via hybridization and polyploidization.
Chromosomal evolution in Mediterranean species ofOphryssect.Pseudophrys(Orchidaceae): An analysis of karyotypes and polyploidy
Authors: García-Barriuso Mónica , Bernardos Sonia , Amich Francisco
Published: February 2019

In an effort to clarify the patterns of chromosome evolution inOphryssect.Pseudophrys(Orchidaceae), chromosome counts were made of 18 O. sect.Pseudophrystaxa from the central–western Mediterranean Basin (Iberian Peninsula and North Africa). The present results provide, for the first time, the chromosome numbers of O.algarvensis, O. arnoldii, O. bilunulataandO. dianica; four other taxa (O. atlantica, O. lupercalis, O. fusca, O. sicula) yielded chromosome numbers not previously reported for the Iberian Peninsula. The results support the idea that the basic plesiomorphic number ofOphrysisx= 18, with 2n = 36 in most species. About 40% of the specimens were polyploids. Karyomorphological data do not support classification of the investigated species into groups. However, the data reveal some geographical differentiation and suggest a possible direction of chromosomal evolution inOphryssect.Pseudophrys.
The Madeiran plants collected by Sir Hans Sloane in 1687, and his descriptions
Authors: de Sequeira Miguel Menezes , Santos-Guerra Arnoldo , Jarvis Charles E. , Oberli Andreas , Carine Mark A. , Maunder Michael , Francisco-Ortega Javier
Published: February 2019

The Macaronesian Islands comprise the Atlantic archipelagos of Azores, Madeira, Selvagens, Canaries and Cape Verde. These islands were a major focus for plant exploration during the 17th and 18th centuries. Sir Hans Sloane (1660–1753), one of the most important patrons and sponsors of natural sciences and botanical research, visited Madeira on his way to Jamaica in 1687. Although he stayed in Madeira for only three days, he collected plant specimens of 38 taxa (including one brown alga) and made important observations concerning the flora and fauna of Madeira from near Funchal. Sixty–six polynomial names of plants from the island are recorded in Sloane's published work along with 18 copperplate engravings, ostensibly from Madeira, although our study shows that only thirteen of them are of taxa occurring on the island. Fourteen of the sixty–six polynomials reported by Sloane relate to Macaronesian endemic taxa, six of them restricted to Madeira. Our study shows that nine of the fifteen polynomials that he putatively recorded for Madeira and/or the Antilles or for which he was unsure of their origin are from the West Indies and do not occur on this Macaronesian island. Two of the taxa that are listed for Madeira and the Caribbean Islands were likely to be present in both insular systems. Although there is evidence of earlier botanical explorations in Macaronesia, the herbarium collections made by Sloane in Madeira represent the earliest documented plant hunting expedition to Macaronesia, and Sir Hans Sloane can be considered as one of the pioneers of botanical exploration in these Atlantic Islands. Sloane's records provide an early floristic study of a diverse island flora.
Making a case for the original spelling of an epithet: 'Correction' of the original spelling of Agaricus rachodes to Agaricus rhacodes (Basidiomycota) is unjustified
Authors: Vellinga Else C. , Pennycook Shaun R.
Published: February 2019

We present the rather unusual case of the spelling of the epithet 'rachodes'. In 1833 Vittadini described a new agaric species with the name Agaricus rachodes, but supplied no etymology. A variant spelling 'rhacodes' was first printed in 1849, apparently as a random mistranscription, but gained increasing currency from about the mid 1870s, and both names have been in use ever since. Two possible roots for the name are the Greek words 'ρακος' (rag) and 'ραχος' (bush, quickset hedge), for which transliterated derivations may vary from 'racodes' to 'rhachodes'. Since Vittadini's consistent spelling cannot be considered an orthographic error, the original spelling has to be retained (ICBN Art. 60.1). A proposal to conserve the alternative spelling 'rhacodes' could be based only on its preponderant use, a situation that has never existed during the 175 year history of the name, and certainly does not exist now. In order to resolve this impasse, a proposal is published separately to conserve Agaricus rachodes with the original spelling 'rachodes' under ICBN Art. 14.11, as a means of enforcing Art. 60.1.
The typification of Zamia erosa and the priority of that name over Z. amblyphyllidia
Authors: Calonje Michael , Meerow Alan W. , Stevenson Dennis W.
Published: February 2019

The lectotype designation of Zamia erosa O.F. Cook & G.N. Collins by Eckenwalder (1980) is corrected to a neotype as it does not constitute original material on which Cook & Collins based their description. The neotype designation is itself superseded, as the specimen selected by Eckenwalder is in serious conflict with the protologue, a conclusion based on over–looked descriptive and geographic information in the protologue, and new collections recently made near the type locality. A new neotype is designated. We have further determined that Z. erosa is an earlier validly published name for the species currently known as Zamia amblyphyllidia D.W. Stev.
Ribosomal RNA genes evolution in Tragopogon: A story of New and Old World allotetraploids and the synthetic lines
Authors: Malinska Hana , Tate Jennifer A. , Mavrodiev Evgeny , Matyasek Roman , Lim K. Yoong , Leitch Andrew R. , Soltis Douglas E. , Soltis Pamela S. , Kovarik Ales
Published: February 2019

Tragopogon mirus Ownbey and Tragopogon miscellus Ownbey are recent allotetraploids that have formed recurrently within the last 80 years, following the introduction of the diploids T. dubius Scop., T. pratensis L. and T. porrifolius L. from Europe to North America. In some areas, the progenitor diploids still occur along with expanding populations of the allotetraploids, and the polyploids at those locations likely represent descendents of the nearby diploids. In most natural populations of T. mirus and T. miscellus, there are far fewer rDNA units of the common parent (T. dubius) than there are of the other diploid parent and in some rarely occurring individuals, one parental locus was >90% deleted. Nevertheless, in contrast to several ancient Old World allotetraploids, gene copies from both parents are readily detected by molecular methods in both T. mirus and T. miscellus. In one population of T. mirus and herbarium specimens collected at the time of species origin the gene ratios were balanced. Several lineages of T. mirus and T. miscellus were recently successfully resynthesized from diploid species. Among 181 synthetic individuals analyzed, we observed frequent deviations from copy‐number additivity; that is in most cases, the T. dubius homeologs were reduced in copy number. At the epigenetic level, the genes of T. dubius origin dominate expression in most natural and synthetic allopolyploids. The fact that some rDNA genotypes seen in 80‐year‐old allopolyploids are already evident in the first generation of synthetic lines supports the hypothesis that the extent and tempo of rDNA homogenization in older allopolyploids is largely influenced by genetic and epigenetic changes in the early generations. Thus, T. mirus and T. miscellus that formed repeatedly in the wild within the last century represent a unique system to study the early stages of genome evolution following interspecific hybridization and genome duplication. This review summarizes recent works on the rDNA chromosomal organization, repeat and loci inheritance and gene expression.