bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of transverse reinforcement to avoid premature buckling of main bars
Authors: Dhakal Rajesh Prasad , Su Junsheng
Published: August 2017

This paper proposes an enhancement to the current strength and confinement‐based design of transverse reinforcement in rectangular and circular reinforced concrete members to ensure that the flexural strength of reinforced concrete sections does not degrade excessively due to buckling of longitudinal bars until the desired level of plastic deformation is achieved. Antibuckling design criteria are developed based on a popular bar buckling model that uses a bar buckling parameter (combining the bar diameter, yield strength, and buckling length) to solely describe the bar buckling behavior. The value of buckling parameter that limits the buckling‐induced stress loss to 15% in compression bars at the strain corresponding to the design ductility is determined. For a bar of known diameter and yield strength, the maximum allowable buckling length can then be determined, which serves as the maximum limit for the tie/stirrup/hoop spacing. Lateral stiffness required to restrain the buckling tendency of main bars at the locations of the ties/stirrups/hoops depends on the flexural rigidity of the main bars and the buckling length (equal to or multiple of tie/hoop/stirrup spacing), whereas the antibuckling stiffness (ie, resistance) provided by the ties/stirrups/hoops depends on their size, number, and arrangement. Using the above concept, design recommendations for the amount, arrangement, and spacing of rectangular and circular ties/stirrups/hoops are then established to ensure that the antibuckling stiffness of the provided transverse reinforcement is greater than the stiffness required to restrain the buckling‐prone main bars. Key aspects of the developed method are verified using experimental tests from literature.
Current and potential pharmacological and psychosocial interventions for anxiety symptoms and disorders in patients with schizophrenia: structured review
Authors: Howells Fleur M. , Kingdon David G. , Baldwin David S.
Published: August 2017

Objective

Between 30% and 62% of patients with schizophrenia present with co‐morbid anxiety disorders that are associated with increased overall burden. Our aim was to summarize current and potential interventions for anxiety in schizophrenia.

Design

Structured review, summarizing pharmacological and psychosocial interventions used to reduce anxiety in schizophrenia and psychosis.

Results

Antipsychotics have been shown to reduce anxiety, increase anxiety, or have no effect. These may be augmented with another antipsychotic, anxiolytic, or antidepressant. Novel agents, such as L‐theanine, pregabalin, and cycloserine, show promise in attenuating anxiety in schizophrenia. Psychosocial therapies have been developed to reduce the distress of schizophrenia. Cognitive behavioural therapy (CBT) has shown that benefit and refinements in the therapy have been successful, for example, for managing worry in schizophrenia. CBT usually involves more than 16 sessions, as short courses of CBT do not attenuate the presentation of anxiety in schizophrenia. To address time and cost, the development of manualized CBT to address anxiety in schizophrenia is being developed.

Conclusions

The presence of coexisting anxiety symptoms and co‐morbid anxiety disorders should be ascertained when assessing patients with schizophrenia or other psychoses as a range of pharmacological and psychosocial treatments are available.
Inherited SHQ1 mutations impair interaction with NAP57/dyskerin, a major target in dyskeratosis congenita
Authors: Bizarro Jonathan , Meier U. Thomas
Published: August 2017

Background

The inherited bone marrow failure syndrome dyskeratosis congenita (DC) is most frequently caused by mutations in DKC1 (MIM# 300126), the gene encoding NAP57 (aka dyskerin). The typically missense mutations modulate the interaction of NAP57 with its chaperone SHQ1, but no DC mutations have been identified in SHQ1 (MIM# 613663). Here, we report on two compound heterozygous mutations in SHQ1 in a patient with a severe neurological disorder including cerebellar degeneration.

Methods

The SHQ1 mutations were identified by patient exome sequencing. The impact of the mutations was assessed in pulldown assays with recombinant NAP57.

Results

The SHQ1 mutations were the only set of mutations consistent with an autosomal recessive mode of inheritance. The mutations map to the SHQ1‐NAP57 interface and impair the interaction of the recombinant SHQ1 variants with NAP57.

Conclusion

Intrauterine growth retardation and the neurological phenotype of the patient are reminiscent of the severe clinical variant of DC, the Hoyeraal‐Hreidarsson syndrome (HH). Hence, SHQ1 screening may be warranted in patients with inherited bone marrow failure syndromes.
A comparison of methods for estimating the temporal change in a continuous variable: Example of HbA1c in patients with diabetes
Authors: Sheppard Therese , Tamblyn Robyn , Abrahamowicz Michal , Lunt Mark , Sperrin Matthew , Dixon William G.
Published: August 2017

Purpose

To compare the more complex technique, functional principal component analysis (FPCA), to simpler methods of estimating values of sparse and irregularly spaced continuous variables at given time points in longitudinal data using a diabetic patient cohort from UK primary care.

Methods

The setting for this study is the Clinical Practice Research Datalink (CPRD), a UK general practice research database. For 16,034 diabetic patients identified in CPRD, with at least 2 measures in a 30‐month period, HbA1c was estimated after temporarily omitting (i) the final and (ii) middle known values using linear interpolation, simple linear regression, arithmetic mean, random effects, and FPCA. Performance of each method was assessed using mean prediction error. The influence on predictive accuracy of (1) more homogeneous populations and (2) number and range of known HbA1c values was explored.

Results

When estimating the last observation, the predictive accuracy of FPCA was highest with over half of predicted values within 0.4 units, equivalent to laboratory measurement error. Predictive accuracy improved when estimating the middle observation with almost 60% predicted values within 0.4 units for FPCA. These results were marginally better than that achieved by simpler approaches, such as last‐occurrence‐carried‐forward linear interpolation. This pattern persisted with more homogeneous populations as well as when variability in HbA1c measures coupled with frequency of data points were considered.

Conclusions

When estimating change from baseline to prespecified time points in electronic medical records data, a marginal benefit to using the more complex modelling approach of FPCA exists over more traditional methods.
Self‐assembled chiral nanostructures of amphiphilic peptide: from single molecule to aggregate
Authors: Zhou Ting , Zhang Zhiqing , Zhang Xuemei , Wang Chen , Xu Guiying , Yang Yanlian
Published: August 2017

We report interesting hierarchical self‐assembled architectures from a designed amphiphilic peptide. The bisignate cotton effects in circular dichroism spectra show typical peptide aggregation‐induced. The observation of peptide assembly structures from initial particles and fibrils to ribbon structures is supported by microscopy (atomic force microscopy and transmission electron microscopy). The visualization of individual peptide at the single molecular level offered insights of the intermolecular interactions responsible for the formation of aggregates, which is investigated by scanning tunneling microscopy. The orientation of intermolecular bonds between carboxylic and amine group and the hydrophobic interactions between alanine residues could be the dominant driving force for the assembly chirality at near‐neutral pH. The single molecular and aggregate level evidence in this manuscript will shed light on the understanding of hierarchical chiral self‐assembly pathway and the underlying mechanism. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
The importance of assessing parameter sensitivity when using biophysical models: a case study using plethodontid salamanders
Authors: Peterman William E. , Gade Meaghan
Published: August 2017

Landscapes are continually changing due to numerous assaults, including habitat alteration, anthropogenic disturbances, and climate change. Understanding how species will respond to these changes is of critical importance for conservation and management. Mechanistic models, such as biophysical models (BPMs), are an increasingly popular tool to predict how local population dynamics or species’ distributions may be altered in response to environmental and climate changes. By mechanistically modeling relationships between environmental conditions, physiology and behavior, it is possible to make accurate predictions about how species may respond. However, BPMs are often difficult to implement due to lack of appropriate, species‐specific data that is biologically realistic or relevant. In this study, we present a BPM for the salamander Plethodon jordani and assess how adding more biological realism has potential to alter model predictions about annual energy budgets. Additionally, we conducted local and global sensitivity analyses to evaluate the importance of accurately specifying model parameter values and functional relationships. We found that the addition of biological realism resulted in greater model complexity as well as substantially different estimates of energy balance. Correct parameterization of biophysical models is also critical, as small changes in parameter values can result in disproportionately large changes in downstream model estimates. Our model highlights the overall importance of using ecologically relevant and specific data for input parameters, as well as careful assessment of parameter sensitivity. We encourage researchers to be aware of the data they are using to parameterize BPMs, and urge the collection of system‐specific data that is relevant in spatial and temporal scale. We also recommend greater and more transparent use of sensitivity analyses to provide a better understanding of the model, as well as greater confidence in model predictions.
Medical students’ perceptions of a novel institutional incident reporting system
Authors: Gordon Morris , Parakh Dillan
Published: August 2017

Background Errors in healthcare are a major patient safety issue, with incident reporting a key solution. The incident reporting system has been integrated within a new medical curriculum, encouraging medical students to take part in this key safety process. The aim of this study was to describe the system and assess how students perceived the reporting system with regards to its role in enhancing safety.

Methods Employing a thematic analysis, this study used interviews with medical students at the end of the first year. Thematic indices were developed according to the information emerging from the data. Through open, axial and then selective stages of coding, an understanding of how the system was perceived was established.

Results Analysis of the interview specified five core themes: (1) Aims of the incident reporting system; (2) internalized cognition of the system; (3) the impact of the reporting system; (4) threshold for reporting; (5) feedback on the systems operation. Selective analysis revealed three overriding findings: lack of error awareness and error wisdom as underpinned by key theoretical constructs, student support of the principle of safety, and perceptions of a blame culture.

Conclusions Students did not interpret reporting as a manner to support institutional learning and safety, rather many perceived it as a tool for a blame culture. The impact reporting had on students was unexpected and may give insight into how other undergraduates and early graduates interpret such a system. Future studies should aim to produce interventions that can support a reporting culture.
Ruxolitinib for secondary hemophagocytic lymphohistiocytosis
Authors: Sin Jonathan H. , Zangardi Mark L.
Published: August 2017

Hemophagocytic lymphohistiocytosis (HLH) is an immune-mediated disorder resulting in hyperactivation of inflammatory cytokines. If left untreated, the uncontrolled inflammatory response can lead to significant tissue injury and potentially life-threatening multi-organ dysfunction. Conventional immunosuppressive agents are available for the management of HLH, including dexamethasone, cyclosporine, and etoposide; however, patients may not respond to these therapies. Clinicians may turn toward alternative pharmacologic agents that likely have less clinical evidence. We describe a case of secondary HLH that did not respond favorably to conventional treatments. Serum inflammatory markers continued to rise significantly with clinical deterioration and worsening pancytopenia. The severe thrombocytopenia and neutropenia were deemed to have contributed to a spontaneous subdural hematoma and candidemia, respectively. Ruxolitinib, a Janus kinase (JAK) 1/2 inhibitor, was then utilized as a novel salvage therapy based on available in vivo murine data at the time. Following initiation, there was improvement seen in several disease markers, including serum ferritin, lactate dehydrogenase, fibrinogen, and liver function tests. However, the pancytopenia did not show signs of recovery. The patient ultimately expired after 7 days of ruxolitinib treatment. It is unclear if the improvement in disease markers was attributed to JAK inhibition alone. However, this experience combined with the positive in vivo murine data suggests that ruxolitinib may serve as a potential treatment option for HLH, pending the release of more robust data. To our knowledge, this is the first human case report describing the use of ruxolitinib for HLH. Future studies are warranted to determine the role of ruxolitinib in this setting.
Memory and Justice in Post-Genocide Rwanda
Authors: Longman Timothy
Published: August 2017

Following times of great conflict and tragedy, many countries implement programs and policies of transitional justice, none more extensive than in post-genocide Rwanda. Placing Rwanda's transitional justice initiatives in their historical and political context, this book examines the project undertaken by the post-genocide government to shape the collective memory of the Rwandan population, both through political and judicial reforms but also in public commemorations and memorials. Drawing on over two decades of field research in Rwanda, Longman uses surveys and comparative local case studies to explore Rwanda's response both at a governmental and local level. He argues that despite good intentions and important innovations, Rwanda's authoritarian political context has hindered the ability of transnational justice to bring the radical social and political transformations that its advocates hoped. Moreover, it continues to heighten the political and economic inequalities that underline ethnic divisions and are an important ongoing barrier to reconciliation.
The Psychoses of Menstruation and Childbearing
Authors: Brockington Ian
Published: August 2017

Childbearing, from the standpoint of psychological medicine, is the most complex event in human experience. Of the dozens of disorders that affect the generative process, or are unleashed as complications, many fall under the heading of 'psychoses' - profound disturbances of thought, perception, cognition and behaviour. These psychoses disrupt personal and family life at a critical time. Reviewing the wide range of psychoses that complicate the reproductive process, Ian Brockington proposes radical changes to the concepts of postpartum and menstrual psychoses, with suggestions for fresh research initiatives. Armed with this comprehensive knowledge and wielding a raft of interventions, many women can be restored to health and their vital roles in the family and community. When the risk factors are known, multidisciplinary preventive strategies can transform the lives of vulnerable women. This is essential reading for psychiatrists, obstetricians and gynaecologists, midwives, general practitioners, neuroscientists and related professions worldwide.
Toward a science of translational science
Authors: Smith Caleb , Baveja Roohi , Grieb Teri , Mashour George A.
Published: August 2017

Translational research as a discipline has experienced explosive growth over the last decade as evidenced by significant federal investment and the exponential increase in related publications. However, narrow project-focused or process-based measurement approaches have resulted in insufficient techniques to measure the translational progress of institutions or large-scale networks. A shift from traditional industrial engineering approaches to systematic investigation using the techniques of scientometrics and network science will be required to assess the impact of investments in translational research.
Contemporary evolutionary psychology and the evolution of intelligence
Authors: Lewis David M. G. , Al-Shawaf Laith , Anderson Mike
Published: August 2017

Burkart et al.'s impressive synthesis will serve as a valuable resource for intelligence research. Despite its strengths, the target article falls short of offering compelling explanations for the evolution of intelligence. Here, we outline its shortcomings, illustrate how these can lead to misguided conclusions about the evolution of intelligence, and suggest ways to address the article's key questions.
Hierarchy, multidomain modules, and the evolution of intelligence
Authors: de Jesus Dias Martins Mauricio , Di Paolo Laura Desirèe
Published: August 2017

In this commentary, we support a complex, mosaic, and multimodal approach to the evolution of intelligence. Using the arcuate fasciculus as an example of discontinuity in the evolution of neurobiological architectures, we argue that the strict dichotomy of modules versus G, adopted by Burkart et al. in the target article, is insufficient to interpret the available statistical and experimental evidence.
Evolution, brain size, and variations in intelligence
Authors: Matzel Louis D. , Sauce Bruno
Published: August 2017

Across taxonomic subfamilies, variations in intelligence (G) are sometimes related to brain size. However, within species, brain size plays a smaller role in explaining variations in general intelligence (g), and the cause-and-effect relationship may be opposite to what appears intuitive. Instead, individual differences in intelligence may reflect variations in domain-general processes that are only superficially related to brain size.
It's time to move beyond the “Great Chain of Being”
Authors: Sternberg Robert J.
Published: August 2017

The target article provides an anthropocentric model of understanding intelligence in nonhuman animals. Such an idea dates back to Plato and, more recently, Lovejoy: On Earth, humans are at the top and other animals at successively lower levels. We then evaluate these other animals by our anthropocentric folk theories of their intelligence rather than by their own adaptive requirements.
Disentangling learning from knowing: Does associative learning ability underlie performances on cognitive test batteries?
Authors: van Horik Jayden O. , Lea Stephen E. G.
Published: August 2017

Are the mechanisms underlying variations in the performance of animals on cognitive test batteries analogous to those of humans? Differences might result from procedural inconsistencies in test battery design, but also from differences in how animals and humans solve cognitive problems. We suggest differentiating associative-based (learning) from rule-based (knowing) tasks to further our understanding of cognitive evolution across species.
When does cultural transmission favour or instead substitute for general intelligence?
Authors: Whiten Andrew
Published: August 2017

The cultural intelligence hypothesis is an exciting new development. The hypothesis that it encourages general intelligence is intriguing, but it presents a paradox insofar as social learning is often suggested to instead reduce reliance on individual cognition and exploration. There is thus a need to specify more clearly the contexts in which cultural transmission may select for general intelligence.
An all-positive correlation matrix is not evidence of domain-general intelligence
Authors: Arden Rosalind , Zietsch Brendan P.
Published: August 2017

We welcome the cross-disciplinary approach taken by Burkart et al. to probe the evolution of intelligence. We note several concerns: the uses of g and G, rank-ordering species on cognitive ability, and the meaning of general intelligence. This subject demands insights from several fields, and we look forward to cross-disciplinary collaborations.
Genomic data can illuminate the architecture and evolution of cognitive abilities
Authors: Lee James J. , Chabris Christopher F.
Published: August 2017

Does general intelligence exist across species, and has it been a target of natural selection? These questions can be addressed with genomic data, which can rule out artifacts by demonstrating that distinct cognitive abilities are genetically correlated and thus share a biological substrate. This work has begun with data from humans and can be extended to other species; it should focus not only on general intelligence but also specific capacities like language and spatial ability.
Trump Administration Moving Closer to Picking Science Director
Authors: Showstack Randy
Published: August 2017

The White House is considering separating the usually merged roles of director of the Office of Science and Technology Policy and assistant to the president for science and technology.
Are Studies That Evaluate Ecosystem Services Useful?
Authors: Witman Sarah
Published: August 2017

Ecologists find flaws in the approach to research that focuses on services ecosystems provide to humans. These flaws limit certain studies’ utility.
Could a Newfound Molecule on Titan Be a Building Block for Life?
Authors: Wendel JoAnna
Published: August 2017

The discovery of vinyl cyanide in the atmosphere of Saturn’s moon Titan has huge implications for life—but not as we know it.
A Promising New Tool for Forecasting Volcanic Hazards
Authors: Cook Terri
Published: August 2017

A new model that simulates the behavior of surging ash clouds may help scientists to better predict the hazards associated with the deadliest type of volcanic flows.
Artificial Snow Could Make Alpine Glacier Grow Again
Authors: den Hond Bas
Published: August 2017

A retired professor devises a plan and evaluates the cost of saving one town’s signature glacier from climate change.
Indonesian Cave Reveals Nearly 5,000 Years of Tsunamis
Authors: Kornei Katherine
Published: August 2017

Researchers explore a coastal cave containing layers of sand deposited by 11 prehistoric tsunamis and demonstrate that the time period between massive waves is highly variable.
Improving Water Resources Management from the Ground Up
Authors: Witman Sarah
Published: August 2017

The key to sustainable water resources management isn’t satellite technology yet—it’s a new spin on time-tested rain and stream gauges.
Small Towns Brace for Historic Eclipse Crowds
Authors: Wendel JoAnna , O'Hanlon Larry
Published: August 2017

Some towns have known for a decade to prepare; others learned as little as a year ago about the event and what it might bring to their locale.
A versatile platform for precise synthesis of asymmetric molecular brush in one shot
Authors: Xu Binbin , Feng Chun , Huang Xiaoyu
Published: August 2017

Asymmetric molecular brushes emerge as a unique class of nanostructured polymers, while their versatile synthesis keeps a challenge for chemists. Here we show the synthesis of well-defined asymmetric molecular double-brushes comprising two different side chains linked to the same repeat unit along the backbone by one-pot concurrent atom transfer radical polymerization (ATRP) and Cu-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The double-brushes are based on a poly(Br-acrylate-alkyne) homopolymer possessing an alkynyl for CuAAC reaction and a 2-bromopropionate initiating group for ATRP in each repeat unit. The versatility of this one-shot approach is demonstrated by CuAAC reaction of alkynyl/poly(ethylene oxide)-N3 and ATRP of various monomers. We also show the quantitative conversion of pentafluorophenyl ester groups to amide groups in side chains, allowing for the further fabrication of diverse building blocks. This work provides a versatile platform for facile synthesis of Janus-type double-brushes with structural and functional control, in a minimum number of reactions.
RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes
Authors: Abatemarco Joseph , Sarhan Maen F. , Wagner James M. , Lin Jyun-Liang , Liu Leqian , Hassouneh Wafa , Yuan Shuo-Fu , Alper Hal S. , Abate Adam R.
Published: August 2017

Synthetic biology and metabolic engineering seek to re-engineer microbes into “living foundries” for the production of high value chemicals. Through a “design-build-test” cycle paradigm, massive libraries of genetically engineered microbes can be constructed and tested for metabolite overproduction and secretion. However, library generation capacity outpaces the rate of high-throughput testing and screening. Well plate assays are flexible but with limited throughput, whereas droplet microfluidic techniques are ultrahigh-throughput but require a custom assay for each target. Here we present RNA-aptamers-in-droplets (RAPID), a method that greatly expands the generality of ultrahigh-throughput microfluidic screening. Using aptamers, we transduce extracellular product titer into fluorescence, allowing ultrahigh-throughput screening of millions of variants. We demonstrate the RAPID approach by enhancing production of tyrosine and secretion of a recombinant protein in Saccharomyces cerevisiae by up to 28- and 3-fold, respectively. Aptamers-in-droplets affords a general approach for evolving microbes to synthesize and secrete value-added chemicals.
Glycoprotein 2 is a specific cell surface marker of human pancreatic progenitors
Authors: Cogger Kathryn F. , Sinha Ankit , Sarangi Farida , McGaugh Emily C. , Saunders Diane , Dorrell Craig , Mejia-Guerrero Salvador , Aghazadeh Yasaman , Rourke Jillian L. , Screaton Robert A. , Grompe Markus , Streeter Philip R. , Powers Alvin C. , Brissova Marcela , Kislinger Thomas , Nostro M. Cristina
Published: August 2017

PDX1+/NKX6-1+ pancreatic progenitors (PPs) give rise to endocrine cells both in vitro and in vivo. This cell population can be successfully differentiated from human pluripotent stem cells (hPSCs) and hold the potential to generate an unlimited supply of β cells for diabetes treatment. However, the efficiency of PP generation in vitro is highly variable, negatively impacting reproducibility and validation of in vitro and in vivo studies, and consequently, translation to the clinic. Here, we report the use of a proteomics approach to phenotypically characterize hPSC-derived PPs and distinguish these cells from non-PP populations during differentiation. Our analysis identifies the pancreatic secretory granule membrane major glycoprotein 2 (GP2) as a PP-specific cell surface marker. Remarkably, GP2 is co-expressed with NKX6-1 and PTF1A in human developing pancreata, indicating that it marks the multipotent pancreatic progenitors in vivo. Finally, we show that isolated hPSC-derived GP2+ cells generate β-like cells (C-PEPTIDE+/NKX6-1+) more efficiently compared to GP2− and unsorted populations, underlining the potential therapeutic applications of GP2.
Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development
Authors: Phillips Tom J. , Scott Hannah , Menassa David A. , Bignell Ashleigh L. , Sood Aman , Morton Jude S. , Akagi Takami , Azuma Koki , Rogers Mark F. , Gilmore Catherine E. , Inman Gareth J. , Grant Simon , Chung Yealin , Aljunaidy Mais M. , Cooke Christy-Lynn , Steinkraus Bruno R. , Pocklington Andrew , Logan Angela , Collett Gavin P. , Kemp Helena , Holmans Peter A. , Murphy Michael P. , Fulga Tudor A. , Coney Andrew M. , Akashi Mitsuru , Davidge Sandra T. , Case C. Patrick
Published: August 2017

Some neuropsychiatric disease, including schizophrenia, may originate during prenatal development, following periods of gestational hypoxia and placental oxidative stress. Here we investigated if gestational hypoxia promotes damaging secretions from the placenta that affect fetal development and whether a mitochondria-targeted antioxidant MitoQ might prevent this. Gestational hypoxia caused low birth-weight and changes in young adult offspring brain, mimicking those in human neuropsychiatric disease. Exposure of cultured neurons to fetal plasma or to secretions from the placenta or from model trophoblast barriers that had been exposed to altered oxygenation caused similar morphological changes. The secretions and plasma contained altered microRNAs whose targets were linked with changes in gene expression in the fetal brain and with human schizophrenia loci. Molecular and morphological changes in vivo and in vitro were prevented by a single dose of MitoQ bound to nanoparticles, which were shown to localise and prevent oxidative stress in the placenta but not in the fetus. We suggest the possibility of developing preventative treatments that target the placenta and not the fetus to reduce risk of psychiatric disease in later life.
RETRACTED ARTICLE: Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda)
Authors: Khodami Sahar , McArthur J. Vaun , Blanco-Bercial Leocadio , Martinez Arbizu Pedro
Published: August 2017

For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoidas. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloidaordo. nov., Smirnovipinidaefam. nov. and Cyclopicinidaefam. novare proposed as new taxa.
Joining smallholder farmers’ traditional knowledge with metric traits to select better varieties of Ethiopian wheat
Authors: Mancini Chiara , Kidane Yosef G. , Mengistu Dejene K. ,   Melfa and Workaye Farmer Community, Amit  , Letegabriel  , Tsedal  , Tinasu B. , Letekiros  , Hadash  , Letemedhin  , Tinasu A. , Kiros  , Leteberhan  , Letekidan  , Hareya  , Letecheal  , Hiritu  , Ametezigu  , Amlak Yohannes G. , Slassie Priest Gebre G. , Girmay Priest G. Selamma , Gebre G. Micheal , Mesfin G. Slassie , Desta Kahsay , Teklay Solomon , Kidan Haftu G. , Egziabher Tesfay G. , Desalegn Priest Weldeslassie , Gebre Hailemariam , Micheal Hiluf G. , Mebrahtu Girmay , Hailemichael  , Teklay Amare , Tesfay Esit , Gitehun Asrebeb , Tadesse Endale , Asfaw Mariye , Aragaw Kassaye , Brku Tegaye , Tadasse Yeshi , Hailu Mariye , Kassun Adisse , Gel aw Guzguz , Emagn Melkam , Mitku Fenta , Mengste Asres , Yigzaw Bzunesh , Tesfaw Eset , Belay Tesfaw , Yirga Wodaje , Sisay Priest Agaju , Hailu Bewuketu , Wale Priest Tefera , Setegn Mulugeta , Tesfie Tilaye , Meretie Biset , Kassie Libay , Biset Tegaye , Hailu Yemataw , Agazu Libay , Yigzaw Mulatie , Yigzaw Adimasu , Abate Getachew , Pè Mario Enrico , Fadda Carlo , Dell’Acqua Matteo
Published: August 2017

Smallholder farming communities face highly variable climatic conditions that threaten locally adapted, low-input agriculture. The benefits of modern crop breeding may fail to reach their fields when broadly adapted genetic materials do not address local requirements. To date, participatory methods only scratched the surface of the exploitability of farmers’ traditional knowledge in breeding. In this study, 30 smallholder farmers in each of two locations in Ethiopia provided quantitative evaluations of earliness, spike morphology, tillering capacity and overall quality on 400 wheat genotypes, mostly traditional varieties, yielding altogether 192,000 data points. Metric measurements of ten agronomic traits were simultaneously collected, allowing to systematically break down farmers’ preferences on quantitative phenotypes. Results showed that the relative importance of wheat traits differed by gender and location. Farmer traits were variously contributed by metric traits, and could only partially be explained by them. Eventually, farmer trait values were used to produce a ranking of the 400 wheat varieties identifying the trait combinations most desired by farmers. The study scale and methods lead to a better understanding of the quantitative basis of Ethiopian smallholder farmer preference in wheat, broadening the discussion for the future of local, sustainable breeding efforts accommodating farmers’ knowledge.
One-domain CD4 Fused to Human Anti-CD16 Antibody Domain Mediates Effective Killing of HIV-1-Infected Cells
Authors: Li Wei , Wu Yanling , Kong Desheng , Yang Hongjia , Wang Yanping , Shao Jiping , Feng Yang , Chen Weizao , Ma Liying , Ying Tianlei , Dimitrov Dimiter S.
Published: August 2017

Bispecific killer cells engagers (BiKEs) which can bind to natural killer (NK) cells through the activating receptor CD16A and guide them to cells expressing the HIV-1 envelope glycoprotein (Env) are a promising new weapon for elimination of infected cells and eradication of the virus. Here we report the design, generation and characterization of BiKEs which consist of CD16A binding human antibody domains fused through a flexible linker to an engineered one-domain soluble human CD4. In presence of cells expressing HIV-1 envelope glycoproteins (Envs), these BiKEs activated specifically CD16A-expressing Jurkat T cells, degranulated NK cells, induced cytokine production and killed Env-expressing cells. They also effectively mediated killing of chronically and acutely HIV-1 infected T cells by human peripheral blood mononuclear cells. The presumed ability of these CD4-based BiKEs to bind all HIV-1 isolates, their small size and fully human origin, combined with high efficacy suggest their potential for HIV-1 eradication.
Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax
Authors: Lee Junki , Waminal Nomar Espinosa , Choi Hong-Il , Perumal Sampath , Lee Sang-Choon , Nguyen Van Binh , Jang Woojong , Kim Nam-Hoon , Gao Li-zhi , Yang Tae-Jin
Published: August 2017

Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species
Authors: Bernardes Samuel C. , Pepato Almir R. , von Rintelen Thomas , von Rintelen Kristina , Page Timothy J. , Freitag Hendrik , de Bruyn Mark
Published: August 2017

The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.
Recovery of hippocampal functions and modulation of muscarinic response by electroacupuncture in young diabetic rats
Authors: Soligo Marzia , Piccinin Sonia , Protto Virginia , Gelfo Francesca , De Stefano Maria Egle , Florenzano Fulvio , Berretta Erica , Petrosini Laura , Nisticò Robert , Manni Luigi
Published: August 2017

The muscarinic receptor response to acetylcholine regulates the hippocampal-related learning, memory, neural plasticity and the production and processing of the pro-nerve growth factor (proNGF) by hippocampal cells. The development and progression of diabetes generate a mild cognitive impairment reducing the functions of the septo-hippocampal cholinergic circuitry, depressing neural plasticity and inducing proNGF accumulation in the brain. Here we demonstrate, in a rat model of early type-1 diabetes, that a physical therapy, the electroacupuncture, counteracts the diabetes-induced deleterious effects on hippocampal physiology by ameliorating hippocampal-related memory functions; recovering the impaired long-term potentiation at the dentate gyrus (DG-LTP) and the lowered expression of the vesicular glutamate transporter 1; normalizing the activity-dependent release of proNGF in diabetic rat hippocampus. Electroacupuncture exerted its therapeutic effects by regulating the expression and activity of M1- and M2-acetylcholine muscarinic receptors subtypes in the dentate gyrus of hippocampus. Our results suggest that a physical therapy based on repetitive sensory stimulation could promote hippocampal neural activity, neuronal metabolism and functions, and conceivably improve the diabetes-induced cognitive impairment. Our data can support the setup of therapeutic protocols based on a better integration between physical therapies and pharmacology for the cure of diabetes-associated neurodegeneration and possibly for Alzheimer’s disease.
Working memory accuracy for multiple targets is driven by reward expectation and stimulus contrast with different time-courses
Authors: Klink P. Christiaan , Jeurissen Danique , Theeuwes Jan , Denys Damiaan , Roelfsema Pieter R.
Published: August 2017

The richness of sensory input dictates that the brain must prioritize and select information for further processing and storage in working memory. Stimulus salience and reward expectations influence this prioritization but their relative contributions and underlying mechanisms are poorly understood. Here we investigate how the quality of working memory for multiple stimuli is determined by priority during encoding and later memory phases. Selective attention could, for instance, act as the primary gating mechanism when stimuli are still visible. Alternatively, observers might still be able to shift priorities across memories during maintenance or retrieval. To distinguish between these possibilities, we investigated how and when reward cues determine working memory accuracy and found that they were only effective during memory encoding. Previously learned, but currently non-predictive, color-reward associations had a similar influence, which gradually weakened without reinforcement. Finally, we show that bottom-up salience, manipulated through varying stimulus contrast, influences memory accuracy during encoding with a fundamentally different time-course than top-down reward cues. While reward-based effects required long stimulus presentation, the influence of contrast was strongest with brief presentations. Our results demonstrate how memory resources are distributed over memory targets and implicates selective attention as a main gating mechanism between sensory and memory systems.
Modal beam splitter: determination of the transversal components of an electromagnetic light field
Authors: Mazilu Michael , Vettenburg Tom , Ploschner Martin , Wright Ewan M. , Dholakia Kishan
Published: August 2017

The transversal profile of beams can always be defined as a superposition of orthogonal fields, such as optical eigenmodes. Here, we describe a generic method to separate the individual components in a laser beam and map each mode onto its designated detector with low crosstalk. We demonstrate this with the decomposition into Laguerre-Gaussian beams and introduce a distribution over the integer numbers corresponding to the discrete orbital and radial momentum components of the light field. The method is based on determining an eigenmask filter transforming the incident optical eigenmodes to position eigenmodes enabling the detection of the state of the light field using single detectors while minimizing cross talk with respect to the set of filter masks considered.
Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis
Authors: He Si Mei , Song Wan Ling , Cong Kun , Wang Xiao , Dong Yang , Cai Jing , Zhang Jia Jin , Zhang Guang Hui , Yang Jian Li , Yang Sheng Chao , Fan Wei
Published: August 2017

Dactylicapnos scandens (D. Don) Hutch (Papaveraceae) is a well-known traditional Chinese herb used for treatment of hypertension, inflammation, bleeding and pain for centuries. Although the major bioactive components in this herb are considered as isoquinoline alkaloids (IQAs), little is known about molecular basis of their biosynthesis. Here, we carried out transcriptomic analysis of roots, leaves and stems of D. scandens, and obtained a total of 96,741 unigenes. Based on gene expression and phylogenetic relationship, we proposed the biosynthetic pathways of isocorydine, corydine, glaucine and sinomenine, and identified 67 unigenes encoding enzymes potentially involved in biosynthesis of IQAs in D. scandens. High performance liquid chromatography analysis demonstrated that while isocorydine is the most abundant IQA in D. scandens, the last O-methylation biosynthesis step remains unclear. Further enzyme activity assay, for the first time, characterized a gene encoding O- methyltransferase (DsOMT), which catalyzes O-methylation at C7 of (S)-corytuberine to form isocorydine. We also identified candidate transcription factor genes belonging to WRKY and bHLH families that may be involved in the regulation of IQAs biosynthesis. Taken together, we first provided valuable genetic information for D. scandens, shedding light on candidate genes involved in IQA biosynthesis, which will be critical for further gene functional characterization.
Expression of CXCR4 on T-cell subsets and Plasma IL-17 Concentrations in Patients with Aplastic Anaemia
Authors: Niu Qian , Zhou Qiang , Liu Yumei , Jiang Hong
Published: August 2017

Acquired aplastic anaemia (AA) is caused by T-cells migrating to and attacking bone marrow (BM) in response to chemokines (e.g., CXCR4). We investigated CXCR4 expressions on circulating T-cell subsets, plasma IL-17A concentrations, and their correlations with AA manifestations. We enrolled 71 patients with acquired AA (36 severe AA cases [SAA] and 35 non-severe AA cases [NSAA]) and 42 healthy volunteers. We used flow cytometry and ELISA to measure circulating CD4+ and CD8+ T-cells, their CXCR4 expressions, and plasma IL-17A concentrations. Compared to the healthy controls, SAA patients had fewer peripheral CD4+ T-cells, more CD8+ T-cells, and a significantly decreased CD4+/CD8+ ratio which was positively correlated with AA manifestations. Patients with SAA or NSAA had higher proportions of CD4+CXCR4+ and CD8+CXCR4+ T-cells, which were negatively correlated with haemoglobin concentrations and absolute neutrophil counts. Patients with SAA or NSAA had higher plasma IL-17A concentrations, which were negatively correlated with AA manifestations and the CD4+/CD8+ ratio. IL-17A concentrations showed a very week correlation with CD4+CXCR4+ T-cells frequencies, and no correlation with CD8+CXCR4+ T-cells frequencies. Aberrant CXCR4 expression may allow circulating T-cells, especially CD8+ T-cells, to infiltrate BM during AA progression. Elevated IL-17A concentrations may contribute to AA progression outside of the CXCR4-SDF-1α axis.
Theoretical Studies of Intracellular Concentration of Micro-organisms’ Metabolites
Authors: Yang Hai-Feng , Zhang Xiao-Nan , Li Yan , Zhang Yong-Hong , Xu Qin , Wei Dong-Qing
Published: August 2017

With the rapid growth of micro-organism metabolic networks, acquiring the intracellular concentration of microorganisms’ metabolites accurately in large-batch is critical to the development of metabolic engineering and synthetic biology. Complementary to the experimental methods, computational methods were used as effective assessing tools for the studies of intracellular concentrations of metabolites. In this study, the dataset of 130 metabolites from E. coli and S. cerevisiae with available experimental concentrations were utilized to develop a SVM model of the negative logarithm of the concentration (-logC). In this statistic model, in addition to common descriptors of molecular properties, two special types of descriptors including metabolic network topologic descriptors and metabolic pathway descriptors were included. All 1997 descriptors were finally reduced into 14 by variable selections including genetic algorithm (GA). The model was evaluated through internal validations by 10-fold and leave-one-out (LOO) cross-validation, as well as external validations by predicting -logC values of the test set. The developed SVM model is robust and has a strong predictive potential (n = 91, m = 14, R2 = 0.744, RMSE = 0.730, Q2 = 0.57; R2p = 0.59, RMSEp = 0.702, Q2p = 0.58). An effective tool could be provided by this analysis for the large-batch prediction of the intracellular concentrations of the micro-organisms’ metabolites.