bluuebunny/crossref_metadata_2025 huggingface dataset:
Scion Substitution: A New Strategy to Control Citrus Variegated Chlorosis Disease
Authors: Lopes Silvio A.
Published: July 2019

Citrus variegated chlorosis (CVC) disease, caused by the xylem-limited and insect-transmitted bacterium Xylella fastidiosa, has caused severe losses in orange production in Brazil. Disease control requires insecticide applications, tree removal, and pruning of symptomatic branches. Pruning success has been erratic, especially in areas of high disease incidence. In this work, in planta X. fastidiosa distribution and the effectiveness of severe pruning procedures for curing diseased adult trees were investigated. Most sampled upper parts of the trees contained X. fastidiosa, but at higher frequencies in symptomatic branches. Removal of all main branches (decapitation) was not effective and revealed a 20 to 30% incidence of latent infections. Trunk decapitation resulted in a higher number of healthy scions but killed 10 to 30% of the remaining trunks. Removal of all scion and grafting the newly sprouted shoots of ‘Rangpur’ lime (Citrus limonia Osbeck) or ‘Cleopatra’ (Citrus reshni Hort. ex Tan.) rootstocks with healthy buds allowed production of fast-growing and productive new scions that remained free from CVC for at least 2 years in four locations. With this method, highly affected trees do not need to be fully removed and the costs involved in this practice and in young tree acquisition and plantings are circumvented; therefore, it is a feasible option for less technically inclined small growers in Brazil.
Surveillance Mammography After Breast Conservation Therapy
Authors: Hasan Shaakir , Gresswell Steven , Colosimo Brittany , Weinberger Kevin , Anderson Sidney , Abel Stephen , Bigbee Matthew , Shindel Betty , Hilton Christie , Julian Thomas , Trombetta Mark
Published: July 2019

Introduction:

We investigated the downstream workup and costs associated with digital breast tomosynthesis (DBT) compared with 2-dimensional full field digital mammogram (FFDM) when employed as initial follow-up imaging in breast conservation therapy.

Methods:

Between the years 2015 and 2017, 450 consecutive breast conservation therapy patients, ages 32 to 89, with a follow-up DBT (n=162) or FFDM (n=288) were retrospectively reviewed. The primary endpoints were further workup after follow-up mammogram and associated health care costs at 1 year. A single DBT costs an estimated $149 compared with $111 for FFDM, based on Centers for Medicare claims data from the Oncology Care Model.

Results:

The first posttreatment mammogram was received within 3 (20%), 3 to 6 (32%), or after 6 months (48%) following radiation. Younger patients and those undergoing hypofractionated radiation were more likely to get DBT. There were no differences in stage, receptor status, or mammogram timing between those in the FFDM and DBT groups.

The following downstream workup ensued for DBT compared with FFDM imaging: 18% versus 29% short-interval (6-mo) mammogram (odds ratio=1.83, P=0.01), 6% versus 11% breast magnetic resonance imaging (odds ratio=1.90, P=0.08), 4% ultrasound for each, and 3% biopsy for each (1 positive in the FFDM group). Including downstream workup, the estimated cost per patient in the DBT group was $216.14 compared with $237.83 in the FFDM group. Independent predictors for reduced downstream workup per multivariable analysis were the use of DBT and first follow-up mammogram at least 6 months after radiation (P<0.05).

Discussion:

Excess workup was reduced with DBT compared with FFDM in the posttreatment setting, which translated to an improvement in cost efficiency in this study.
Cardiac Toxicity in Operable Esophageal Cancer Patients Treated With or Without Chemoradiation
Authors: Witt Jacob S. , Jagodinsky Justin C. , Liu Yifei , Yadav Poonam , Kuczmarska-Haas Aleksandra , Yu Menggang , Maloney James D. , Ritter Mark A. , Bassetti Michael F. , Baschnagel Andrew M.
Published: July 2019

Purpose:

The purpose of this study was to evaluate predictors of cardiac events in esophageal cancer patients treated with neoadjuvant chemoradiotherapy (NA CRT) followed by surgery compared with surgery alone.

Materials and Methods:

We retrospectively identified patients treated for esophageal cancer between 2006 and 2016. A total of 123 patients were identified; 70 were treated with surgery alone, and 53 were treated with NA CRT. Cardiac events were scored based on Common Terminology Criteria for Adverse Events (version 4.03), and dosimetric data was compiled for all patients who received radiation. Univariate analysis and multivariable analysis (MVA) were performed to identify predictors of cardiac events. Competing risk of death regression was performed to a model the cumulative incidence of cardiac events.

Results:

The overall rates of grade ≥3 cardiac events were 24.5% in the NA CRT group versus 10% in the surgery group (P=0.04). On MVA, use of NA CRT (P<0.01, hazard ratio [HR]: 3.45, 95% confidence interval [CI]: 1.35-9.09) predicted for grade ≥3 cardiac events, though no dosimetric variable predicted for grade ≥3 cardiac events or overall survival. On MVA, NA CRT predicted for pericardial effusions of any grade (P<0.01, HR: 3.70, 95% CI: 1.67-8.33). The V45 Gy was the most significant predictor of pericardial effusions (P=0.012, HR: 1.03, 95% CI: 1.01-1.06)

Conclusions:

NA CRT significantly increased the rate of grade ≥3 cardiac events compared with patients treated with surgery alone. Although no dosimetric parameter predicted for grade ≥3 cardiac events or survival, the V45 Gy predicted for pericardial effusions.
Opinions and main sources of information about menopause among middle-aged Brazilian women
Authors: de Arruda Amaral Isabel Cristina Gardenal , Baccaro Luiz Francisco , Lui-Filho Jeffrey Frederico , Osis Maria José Duarte , Pedro Adriana Orcesi , Costa-Paiva Lúcia
Published: July 2019

Objectives:

The aim of this study was to evaluate women's opinions about menopause and the sources of information they use to deepen their understanding of the topic.

Methods:

Population-based study with 749 Brazilian women aged 45 to 60 years. The answers to the question “What is menopause?” were typed and coded, and categories that emerged from the interviewees’ own speech were created. The answers to the question: “Where or from whom did you get information about menopause?” were also analyzed.

Results:

The mean age of women was 52.5 (± 4.4) years. Of them, 68% were postmenopausal. According to 67.5% of the interviewees, the concept of menopause encompassed changes in the menstrual cycle and hormones. For 48%, menopause meant physical changes such as “hot flushes and vaginal dryness.” For 22.7%, menopause represented psychological changes. The concept of menopause was associated with some change in sexuality for 7.6% of the interviewees. Approximately 18% could not explain what menopause meant. Regarding the sources of information, 44.5% of the women attributed this knowledge to friends and relatives. Doctors or health services were mentioned by 44.3% of women. Television or radio was cited by 22.0%; magazines, newspapers, or books were cited by 14.0%; and the Internet was cited by 6.8% of women. Fifty-two women (6.9%) reported having no source of information about menopause.

Conclusions:

Most of the interviewees relate the term “menopause” to physiological events. There seems to be a suppressed demand for information on the various aspects of the menopausal transition among middle-aged Brazilian women.
HOMOZYGOSITY FOR A NOVEL DOUBLE MUTANT ALLELE (G1961E/L857P) UNDERLIES CHILDHOOD-ONSET ABCA4-RELATED RETINOPATHY IN THE UNITED ARAB EMIRATES
Authors: Khan Arif O.
Published: July 2019

Purpose:

Stargardt disease (On-Line Mendelian Inheritance In Man 242000, STGD1) is the most common inherited macular dystrophy. STGD1 is typically a young-adult-onset disease that is recurrently associated with the ABCA4 mutant allele G1961E in homozygosity or compound heterozygosity. The genetics of ABCA4-related retinopathy in the Arabian Gulf region have not been well-studied. This report reviews the experience of the Ocular Genetics Service at Cleveland Clinic Abu Dhabi with clinically diagnosed ABCA4-related retinopathy in Emirati patients who underwent genetic testing.

Methods:

Retrospective case series (2016–2018, inclusive).

Results:

All 22 identified patients (19 families; 11 males, 11 females; first visual symptoms 5–33 years old) were found to harbor biallelic ABCA4 pathologic variants. There were 14 childhood-onset cases (onset before 18 years of age; 12 families; 7 males, 7 females; first visual symptoms from 5 to 12 years old, median 8)—all were homozygous, 11 for the same novel double mutant allele G1961E/L857P. Those who underwent electroretinography (8) had cone-rod rather than isolated macular dystrophy. There were 8 adult-onset cases (onset at or after 18 years of age; 7 families; 4 males, 4 females; first visual symptoms from 18 to 33 years old, median 22)—all were compound heterozygous, seven harboring the common G1961E mutant allele.

Conclusion:

The molecular yield for biallelic ABCA4 pathogenic variants is high for clinically diagnosed ABCA4-related retinopathy in Emiratis (100% in this case series). Homozygosity for a novel complex allele G1961E/L857P causes a childhood-onset cone-rod dystrophy rather than the young-adult-onset macular dystrophy that is associated with G1961E alone. This G1961/L857P complex allele likely represents a founder effect for the region.
RESOLUTION OF A SUBFOVEAL CHOROIDAL CAVERN AFTER HALF-DOSE PHOTODYNAMIC THERAPY FOR CENTRAL SEROUS CHORIORETINOPATHY
Authors: Sakurada Yoichi , Parikh Ravi , Freund K. Bailey
Published: July 2019

Purpose:

To describe resolution of a subfoveal choroidal cavern after half-dose verteporfin photodynamic therapy for persistent central serous chorioretinopathy.

Methods:

Case report.

Results:

A 43-year-old man was referred for treatment of chorioretinopathy in his left eye. On presentation, swept-source optical coherence tomography demonstrated a serous retinal detachment and a 161-μm-thick subfoveal choroidal cavern showing a characteristic tail of hypertransmission extending posteriorly. Subfoveal choroidal thickness measured 456 μm in the affected eye. Complete resolution of subretinal fluid and the subfoveal choroidal cavern were observed 3 months after half-dose verteporfin photodynamic therapy. Twelve months after treatment, subfoveal choroidal thickness had decreased further to 276 μm, and visual acuity had improved to 20/15.

Conclusion:

After half-dose verteporfin photodynamic therapy for chorioretinopathy, resolution of subretinal fluid was accompanied by resolution of a subfoveal choroidal cavern at 3 months and a 39.5% reduction in subfoveal choroidal thickness at 1 year.
Identifying Pigment Enclosure in Cosmetic Contact Lenses
Authors: Korde Vrushali , McDow Kimberly , Rollins Dominique , Stinchcomb Rowena , Esposito Heather
Published: July 2019

Objective:

The presence of surface pigment in cosmetic contact lenses may influence possible ocular health issues and contact lens discomfort. Two in vitro test methods were developed to investigate whether a variety of cosmetic contact lenses are manufactured with a visible clear layer, indicating that the pigment bulk is enclosed within the lens matrix.

Methods:

Two in vitro test methods using bright field microscopy and optical coherence tomography (OCT) were developed to assess whether a clear layer in a cosmetic contact lens could be identified. The OCT instrument in this study provided a limit of detection (LOD) of 2.4 μm in the identification of a clear layer. The cross-sectioning microscopy method described in this article requires a trained technician to execute; however, the LOD is smaller at 0.4 μm.

Results:

Both test methods described were used to assess whether a clear layer could be identified on 19 commercially available cosmetic contact lens products across six manufacturers. Only one of the six manufacturers (5 of 19 products) produced lens images in which a clear layer was identified using either method.

Conclusions:

Most of cosmetic contact lenses analyzed in this study contain the bulk of the pigment within 0.4 μm of the surface (beyond the limit of detection of the instruments used in this study) or on the surface itself.
Changing Indications for Corneal Transplantations in Southern Taiwan From 2008 to 2018
Authors: Wang Tso-Wen , Chi Ying-Chen , Hsu Pying-Sing , Kuo Ni-Wen , Chen Jiunn-Liang
Published: July 2019

Objectives:

To investigate the changing indications for corneal transplantations in southern Taiwan from 2008 to 2018 and compare the results with those of other previous studies.

Methods:

We retrospectively reviewed the records of patients who underwent corneal transplantations from January 2008 to December 2018 at Kaohsiung Veterans General Hospital. The patients' age, sex, indication for corneal transplantation, and the surgical technique were recorded and analyzed.

Results:

In total, 336 patients (421 eyes) were included in our study from January 1, 2008, to December 31, 2018. The mean age was 63.6±15.3 years; 371 penetrating keratoplasty (88.1%), 35 deep anterior lamellar keratoplasty (8.3%), and 15 Descemet-stripping automated endothelial keratoplasty (3.6%) were performed. The leading indication for corneal transplantation was regraft (n=103, 24.5%), followed by bullous keratopathy (n=82, 19.5%), corneal scar and opacity (n=79, 18.8%), keratitis (n=59, 14.0%), corneal dystrophy (n=58, 13.8%), other indications (n=26, 6.2%), and keratoconus (n=14, 3.3%).

Conclusion:

The indications for corneal transplantations changed with time in Taiwan. Regraft was the leading indication, but there was a decreasing trend over time. The proportion of bullous keratopathy increased significantly over the past decade and is the second most common indication, similar to the most developed countries. Both corneal scar and opacity, and keratitis showed a decreasing trend of occurrence compared with a previous study in Taiwan. The proportion of keratoconus remained low, making it the least common indication for corneal transplantation.
Evaluation of the Cancer Control P.L.A.N.E.T. Web Portal
Authors: Percy-Laurry Antoinette , Heurtin-Roberts Suzanne , Norton Wynne E. , McDonnell Cheryl , Uy Annabelle , Chambers David A.
Published: July 2019

Context:

The Cancer Control P.L.A.N.E.T. (P.L.A.N.E.T.) Web portal was designed to ease access to data and evidence-based resources for cancer control practitioners and researchers focused on developing, implementing, and evaluating cancer control programs.

Objectives:

To determine usability, applicability, and opportunities to improve the P.L.A.N.E.T. Web portal after significant changes to the portal over time.

Design:

The National Cancer Institute surveyed and interviewed cancer control professionals to assess factors influencing utilization of P.L.A.N.E.T. Data were collected from May 2017 to June 2018 via partner agencies, electronic publications, and online links.

Outcome Measures:

Descriptive statistics with χ2 test were used to analyze the quantitative data and examine the relationship among variables. Qualitative interviews further informed the quantitative analysis.

Results:

Of the 724 participants surveyed, 51% were users of P.L.A.N.E.T., with the majority accessing P.L.A.N.E.T. within the last 6 months. Most users felt that P.L.A.N.E.T. effectively met their needs for accessing specific cancer data, identifying evidenced-based programs, and ascertaining details on various cancer topics. There were statistically significant differences in demographic characteristics between users and nonusers of P.L.A.N.E.T., where users were more likely to have more experience in the cancer field, were older in age, and located in southern states.

Conclusion:

Results indicate that P.L.A.N.E.T. is seen as a viable and credible source for cancer control program planning and delivery. A reassessment of P.L.A.N.E.T.'s goals is warranted, which may support reaching out to new audiences, amplifying or removing underutilized resources, and adding additional resources and topics. Consideration for training and tutorials on P.L.A.N.E.T. would benefit partner agencies and build capacity for evidence-based program development.
Right Ventricular Function and Long-Term Outcome in Sepsis: A Retrospective Cohort Study
Authors: Winkelhorst Jurgen C. , Bootsma Inge T. , Koetsier Peter M. , de Lange Fellery , Boerma Evert C.
Published: July 2019

Background:

Sepsis-related myocardial dysfunction is associated with impaired outcome. Traditionally, in this setting the main focus has been on left ventricular performance. Currently, specific knowledge on the prognostic importance of right ventricular dysfunction is scarce. The aim of this study was to determine whether right ventricular ejection fraction (RVEF) is predictive of long-term mortality in sepsis.

Methods:

Single-centre retrospective cohort study in adult patients admitted to the ICU with severe sepsis and septic shock, and equipped with a pulmonary artery catheter within the first day after admission. RVEF was recorded as an average over the first 24 h (sample rate of 1 per min). Patients were separated a priori into subgroups according to their RVEF: RVEF less than 20% (A), RVEF 20% to 30% (B), and RVEF more than 30% (C). The primary endpoint was 1-year all-cause mortality.

Results:

In a 7-year period, 101 patients fulfilled all entry criteria and 98 were included in the study. One-year all-cause mortality was significantly different between groups: 57% in group A (n = 21), 18% in group B (n = 55), and 23% in group C (n = 22); P = 0.003. Kaplan–Meier survival analysis revealed a clear separation between groups A and B/C (X
2 = 14.00, P = 0.001). In a multivariate logistic regression analysis RVEF, both as a categorical variable (RVEF <20%) and as a continuous variable remained independently associated with the primary endpoint (odds ratio [OR] 4.1; 95% confidence interval [CI], 1.3–13.4; P = 0.018 and OR 0.92; 95% CI, 0.85–0.99; P = 0.018, respectively).

Conclusions:

RVEF was independently associated with 1-year all-cause mortality in a highly selected group of patients with severe sepsis and septic shock.
How smooth is a dolphin? The ridged skin of odontocetes
Authors: Wainwright Dylan K. , Fish Frank E. , Ingersoll Sam , Williams Terrie M. , St Leger Judy , Smits Alexander J. , Lauder George V.
Published: July 2019

Dolphin skin has long been an inspiration for research on drag reduction mechanisms due to the presence of skin ridges that could reduce fluid resistance. We gatheredin vivothree-dimensional surface data on the skin from five species of odontocetes to quantitatively examine skin texture, including the presence and size of ridges. We used these data to calculatek+values, which relate surface geometry to changes in boundary layer flow. Our results showed that while ridge size differs among species, odontocete skin was surprisingly smooth compared to the skin of other swimmers (average roughness = 5.3 µm). In addition, the presence of ridges was variable among individuals of the same species. We predict that odontocete skin ridges do not alter boundary layer flows at cruising swimming speeds. By combiningk+values and morphological data, our work provides evidence that skin ridges are unlikely to be an adaptation for drag reduction and that odontocete skin is exceptionally smooth compared to other pelagic swimmers.
The loud scratch: a newly identified gesture of Sumatran orangutan mothers in the wild
Authors: Fröhlich Marlen , Lee Kevin , Mitra Setia Tatang , Schuppli Caroline , van Schaik Carel P.
Published: July 2019

The communicative function of primates' self-directed behaviours like scratching has gained increasing attention in recent years, but their intentional use is still debated. Here, we addressed this issue by exploring the communicative function of ‘loud scratches’ in wild Sumatran orangutans. Building on previous studies in chimpanzees, we examined the prediction that audio-visual loud scratches are used communicatively in mother–infant travel coordination. Specifically, we examined whether individual, social and scratch features affected the use of pre-move scratches, markers of intentional signal use and approach responses. We analysed a total of 1457 scratching bouts, produced by 17 individuals (including four mothers and their dependent offspring) observed during 305 h of focal follows. Overall, we found that scratching bouts preceded departure mainly when these were produced by mothers and showed features of exaggeration. If the scratching individual was a mother, associates were more likely to be visually attentive during pre-move scratches than in other contexts. Approach or follow responses to scratches by individuals in association were predicted by context, the relationship with the scratcher (i.e. offspring) and the associate's attentional state. We conclude that orangutan mothers use loud scratches as communicative strategies to coordinate joint travel with their infants.
Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans
Authors: King Benedict
Published: July 2019

There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the ‘psarolepid’ osteichthyans. The ‘psarolepids’, which include the earliest known osteichthyans, are weakly supported as stem osteichthyans under parsimony but strongly supported as sarcopterygians in Bayesian analysis. The Bayesian result is driven by just two characters, both of which relate to the intracranial joint of sarcopterygians. Important characters that support a stem osteichthyan affinity for ‘psarolepids’, such as the absence of tooth enamel, have virtually no effect in a Bayesian framework. This is because of a bias towards characters with relatively complete sampling, a bias that has previously been reported for molecular data. This has important implications for Bayesian analysis of morphological datasets in general, as characters from different body parts commonly have different levels of coding completeness. Methods to critically appraise character support for conflicting phylogenetic hypotheses, such as that used here, should form an important part of phylogenetic analyses.
Feeding in murky waters: acclimatization and landmarks improve foraging efficiency of zebrafish (
Danio rerio
) in turbid waters
Authors: Sekhar M. A. , Singh Richa , Bhat Anuradha , Jain Manjari
Published: July 2019

Fish inhabiting human-dominated ecosystems are prone to altered sensory environments in which they must live and function. Increased turbidity is one such change that they must deal with. We tested whether an increase in water turbidity and the presence of visual landmarks (coloured stones) affect the foraging efficiency of wild zebrafish. We also tested the influence of extended exposure to differing turbidity levels on the subsequent foraging efficiency of acclimatized individuals. Feeding latency (time taken to find food) increased significantly with increase in turbidity levels from a minimum of 4 s to
ca
300 s. However, extended exposure of fish to varying levels of turbidity decreased feeding latencies in acclimatized conditions, indicating that acclimatization to the immediate visual environment plays an important role in determining foraging success. Most significantly, we found that feeding latencies in turbid conditions decreased significantly if visual landmarks were present. This demonstrates that zebrafish use visual landmark cues to navigate to foraging sites when visibility is impaired. This study has important implications on the role of behavioural plasticity and spatial learning in animals that allow them to cope with altered sensory environments such as episodes of enhanced turbidity that could be natural or anthropogenic.
Superregular grammars do not provide additional explanatory power but allow for a compact analysis of animal song
Authors: Morita T. , Koda H.
Published: July 2019

A pervasive belief with regard to the differences between human language and animal vocal sequences (song) is that they belong to different classes of computational complexity, with animal song belonging to regular languages, whereas human language is superregular. This argument, however, lacks empirical evidence since superregular analyses of animal song are understudied. The goal of this paper is to perform a superregular analysis of animal song, using data from gibbons as a case study, and demonstrate that a superregular analysis can be effectively used with non-human data. A key finding is that a superregular analysis does not increase explanatory power but rather provides for compact analysis: fewer grammatical rules are necessary once superregularity is allowed. This pattern is analogous to a previous computational analysis of human language, and accordingly, the null hypothesis, that human language and animal song are governed by the same type of grammatical systems, cannot be rejected.
Disease classification via gene network integrating modules and pathways
Authors: Mi Zhilong , Guo Binghui , Yin Ziqiao , Li Jiahui , Zheng Zhiming
Published: July 2019

Disease classification based on gene information has been of significance as the foundation for achieving precision medicine. Previous works focus on classifying diseases according to the gene expression data of patient samples, and constructing disease network based on the overlap of disease genes, as many genes have been confirmed to be associated with diseases. In this work, the effects of diseases on human biological functions are assessed from the perspective of gene network modules and pathways, and the distances between diseases are defined to carry out the classification models. In total, 1728 diseases are divided into 12 and 14 categories by the intensity and scope of effects on pathways, respectively. Each category is a mix of several types of diseases identified based on congenital and acquired factors as well as diseased tissues and organs. The disease classification models on the basis of gene network are parallel with traditional pathology classification based on anatomic and clinical manifestations, and enable us to look at diseases in the viewpoint of commonalities in etiology and pathology. Our models provide a foundation for exploring combination therapy of diseases, which in turn may inform strategies for future gene-targeted therapy.
Congruence, fossils and the evolutionary tree of rodents and lagomorphs
Authors: Asher Robert J. , Smith Martin R. , Rankin Aime , Emry Robert J.
Published: July 2019

Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and
Ischyromys
rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support
Ischyromys
in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and
Aplodontia
from extinct, ‘protrogomorph’-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.
Diversity and its decomposition into variety, balance and disparity
Authors: van Dam Alje
Published: July 2019

Diversity is a central concept in many fields. Despite its importance, there is no unified methodological framework to measure diversity and its three components of variety, balance and disparity. Current approaches take into account disparity of the types by considering their pairwise similarities. Pairwise similarities between types may not adequately capture total disparity, since they do not take into account in which way pairs are similar. Hence, pairwise similarities do not discriminate between similarities of types in terms of the same feature and similarities in which all pairs share different features. This paper presents an alternative approach which is based on the overlap of features over the whole set of types. This results in a measure of diversity that takes into account the aspects of variety, balance and disparity. Based on this measure, the ‘ABCdecomposition’ is introduced, which provides separate measures for the variety, balance and disparity, allowing them to enter analysis separately. The method is illustrated by analysing the industrial diversity from 1850 to present while taking into account the overlap in occupations they employ. Finally, the framework is extended to take into account disparity considering multiple features, providing a helpful tool in analysis of high-dimensional data.
Soy protein isolate-carboxymethyl cellulose conjugates with pH sensitivity for sustained avermectin release
Authors: Chen Long , Zhou Hongjun , Hao Li , Chen Huayao , Zhou Xinhua
Published: July 2019

Carboxymethyl cellulose (CMC) was grafted onto the surface of soy protein isolate (SPI) to obtain soy protein isolate-carboxymethyl cellulose conjugate (SPC). Avermectin (AVM) was hydrophobically encapsulated as a model drug to obtain SPC@AVM. The reaction between SPI and CMC was confirmed by infrared spectroscopy, thermal analysis and SDS-PAGE electrophoresis. The results of scanning electron microscopy showed that the average particle size of the drug-loaded microspheres was 129 nm and the shape of microspheres changed from block to spherical after the addition of AVM. After encapsulation of AVM, the absolute value of zeta potential was greater than 15 mV, which indicated better stability. Compared to AVM solution, SPC@AVM showed more wettability on the leaf surface and the contact angle on the leaves decreased from 71.64° to 57.33°. The maximum liquid holding capacity increased by 41.41%, from 8.85 to 12.52 mg cm
−2
, which effectively reduced leaf loss. SPC@AVM also prevented UV photolysis, wherein the half-life was extended from 18 to 68 min when exposed to UV light. Moreover, toxicity tests showed that the encapsulation of AVM was beneficial to retain the insecticidal effect of AVM in the presence of ultraviolet light. The release rate of AVM showed pH responsiveness and the release rate under neutral conditions was faster than acidic and alkaline conditions. Moreover, the process conformed to the Weibull model.
A simple model for learning in volatile environments
Authors: Piray Payam , Daw Nathaniel D.
Published: July 2019

Sound principles of statistical inference dictate that uncertainty shapes learning. In this work, we revisit the question of learning in volatile environments, in which both the first and second-order statistics of observations dynamically evolve over time. We propose a new model, the volatile Kalman filter (VKF), which is based on a tractable state-space model of uncertainty and extends the Kalman filter algorithm to volatile environments. The proposed model is algorithmically simple and encompasses the Kalman filter as a special case. Specifically, in addition to the error-correcting rule of Kalman filter for learning observations, the VKF learns volatility according to a second error-correcting rule. These dual updates echo and contextualize classical psychological models of learning, in particular hybrid accounts of Pearce-Hall and Rescorla-Wagner. At the computational level, compared with existing models, the VKF gives up some flexibility in the generative model to enable a more faithful approximation to exact inference. When fit to empirical data, the VKF is better behaved than alternatives and better captures human choice data in two independent datasets of probabilistic learning tasks. The proposed model provides a coherent account of learning in stable or volatile environments and has implications for decision neuroscience research.
An epigenetic predictor of death captures multi-modal measures of brain health
Authors: Hillary Robert F. , Stevenson Anna J. , Cox Simon R. , McCartney Daniel L. , Harris Sarah E. , Seeboth Anne , Higham Jon , Sproul Duncan , Taylor Adele M. , Redmond Paul , Corley Janie , Pattie Alison , Valdés Hernández Maria del. C , Muñoz-Maniega Susana , Bastin Mark E. , Wardlaw Joanna M. , Horvath Steve , Ritchie Craig W. , Spires-Jones Tara L. , McIntosh Andrew M. , Evans Kathryn L. , Deary Ian J. , Marioni Riccardo E.
Published: July 2019

Individuals of the same chronological age exhibit disparate rates of biological ageing. Consequently, a number of methodologies have been proposed to determine biological age and primarily exploit variation at the level of DNA methylation (DNAm) – a commonly studied epigenetic mechanism. A novel epigenetic clock, termed ‘DNAm GrimAge’ has outperformed its predecessors in predicting the risk of mortality as well as a number of age-related morbidities. However, the association between DNAm GrimAge and cognitive or neuroimaging phenotypes remains unknown. We explore these associations in the Lothian Birth Cohort 1936 (n=709, mean age 73 years). Higher DNAm GrimAge was strongly associated with all-cause mortality over twelve years of follow-up (Hazard Ratio per standard deviation increase in GrimAge: 1.81, P < 2.0 × 10-16). Higher DNAm GrimAge was associated with lower age 11 IQ (β=-0.11), lower age 73 general cognitive ability (β=-0.18), decreased brain volume (β=-0.25) and increased brain white matter hyperintensities (β=0.17). Sixty-eight of 137 health- and brain-related phenotypes tested were significantly associated with DNAm GrimAge. Adjusting all models for childhood cognitive ability attenuated to non-significance a small number of associations (12/68 associations; 6 of which were cognitive traits), but not the association with general cognitive ability (33.9% attenuation). Higher DNAm GrimAge cross-sectionally associates with lower cognitive ability and brain vascular lesions in older age, independently of early life cognitive ability. Thus, this epigenetic predictor of mortality is also associated with multiple different measures of brain health and may aid in the prediction of age-related cognitive decline.
An integrated brain-machine interface platform with thousands of channels
Authors: Musk Elon ,   Neuralink
Published: July 2019

Brain-machine interfaces (BMIs) hold promise for the restoration of sensory and motor function and the treatment of neurological disorders, but clinical BMIs have not yet been widely adopted, in part because modest channel counts have limited their potential. In this white paper, we describe Neuralink’s first steps toward a scalable high-bandwidth BMI system. We have built arrays of small and flexible electrode “threads”, with as many as 3,072 electrodes per array distributed across 96 threads. We have also built a neurosurgical robot capable of inserting six threads (192 electrodes) per minute. Each thread can be individually inserted into the brain with micron precision for avoidance of surface vasculature and targeting specific brain regions. The electrode array is packaged into a small implantable device that contains custom chips for low-power on-board amplification and digitization: the package for 3,072 channels occupies less than (23 × 18.5 × 2) mm3. A single USB-C cable provides full-bandwidth data streaming from the device, recording from all channels simultaneously. This system has achieved a spiking yield of up to 70% in chronically implanted electrodes. Neuralink’s approach to BMI has unprecedented packaging density and scalability in a clinically relevant package.
Antifungal potency and modes of action of a novel olive tree defensin against closely related ascomycete fungal pathogens
Authors: Li Hui , Velivelli Siva L. S. , Shah Dilip M.
Published: July 2019

Antimicrobial peptides play a pivotal role in the innate immunity of plants. Defensins are cysteine-rich antifungal peptides with multiple mechanisms of action (MOA). A novel Oleaceae-specific defensin gene family was discovered in the genome sequences of the wild and cultivated species of a perennial olive tree, Olea europaea. Antifungal properties of an olive tree defensin OefDef1.1 were investigated against a necrotrophic ascomycete fungal pathogen Botrytis cinerea in vitro and in planta. OefDef1.1 displayed potent antifungal activity against this pathogen by rapidly permeabilizing the plasma membrane of the conidial and germling cells. Interestingly, it was translocated to the cytoplasm and induced reactive oxygen species in the germlings, but not in the conidia. In medium containing high concentrations of Na1+, antifungal activity of OefDef1.1 against B. cinerea was significantly reduced. In contrast, OefDef1.1_V1 variant in which the γ-core motif of OefDef1.1 was replaced by that of a Medicago truncatula defensin MtDef4 displayed Na1+-tolerant antifungal activity and was more potent in reducing the virulence of B. cinerea in planta. OefDef1.1 also exhibited potent antifungal activity against three hemibiotrophic ascomycete pathogens Fusarium graminearum, F. oxysporum and F. virguliforme. Significant differences were observed among the four pathogens in their responses to OefDef1.1 in growth medium with or without the high concentrations of Na1+. The varied responses of closely related ascomycete pathogens to this defensin have implications for engineering disease resistance in plants.
C6orf203 controls OXPHOS function through modulation of mitochondrial protein biosynthesis
Authors: Palacios-Zambrano Sara , Vázquez-Fonseca Luis , González-Páramos Cristina , Mamblona Laura , Sánchez-Caballero Laura , Nijtmans Leo , Garesse Rafael , Fernández-Moreno Miguel Angel
Published: July 2019

Mitochondria are essential organelles present in the vast majority of eukaryotic cells. Their central function is to produce cellular energy through the OXPHOS system, and functional alterations provoke so-called mitochondrial OXPHOS diseases. It is estimated that several hundred mitochondrial proteins have unknown functions. Very recently, C6orf203 was described to participate in mitochondrial transcription under induced mitochondrial DNA depletion stress conditions. Here, we describe another role for C6orf203, specifically in OXPHOS biogenesis under regular culture conditions. HEK293T C6orf203-Knockout (KO) cells generated by CRISPR/Cas9 genome editing showed both reduced grow in galactose, as a carbon source, and in their oxygen consumption capability, strongly suggesting an OXPHOS dysfunction. C6orf203-KO also provoked a depletion of OXPHOS proteins and decreased the activity of the mitochondrial respiratory chain complexes. C6orf203 was present in high molecular weight complexes compatible with mitoribosomes, and in vivo labelling of de novo mitochondrial proteins synthesis revealed that C6orf203-KO severely but not completely affected the translation of mitochondrial mRNAs. Taken together, we describe herein a new function for C6orf203, making it a potential OXPHOS disease-related candidate.
An Evolutionarily Conserved Receptor-like Kinases Signaling Module Controls Cell Wall Integrity During Tip-Growth
Authors: Westermann Jens , Streubel Susanna , Franck Christina Maria , Lentz Roswitha , Dolan Liam , Boisson-Dernier Aurélien
Published: July 2019

Rooting cells and pollen tubes – key adaptative innovations that evolved during the colonization and subsequent radiation of plants on land – expand by tip-growth. Tip-growth relies on a tight coordination between the protoplast growth and the synthesis/remodeling of the external cell wall. In root hairs and pollen tubes of the seed plant Arabidopsis thaliana, cell wall integrity (CWI) mechanisms monitor this coordination through the Malectin-like receptor kinases (MLRs) such as AtANXUR1 and AtFERONIA that act upstream of the AtMARIS PTI1-like kinase. Here, we show that rhizoid growth in the early diverging plant, Marchantia polymorpha, is also controlled by an MLR and PTI1-like signaling module. Rhizoids, root hairs and pollen tubes respond similarly to disruption of MLR and PTI1-like encoding genes. Thus, the MLR/PTI1-like signaling module that controls CWI during tip-growth is conserved between M. polymorpha and A. thaliana suggesting it was active in the common ancestor of land plants.
SEQUIN multiscale imaging of mammalian central synapses reveals loss of synaptic microconnectivity resulting from diffuse traumatic brain injury
Authors: Sauerbeck Andrew D. , Gangolli Mihika , Reitz Sydney J. , Salyards Maverick H. , Kim Samuel H. , Hemingway Christopher , Makkapati Tejaswi , Kerschensteiner Martin , Brody David L. , Kummer Terrance T.
Published: July 2019

The complex microconnectivity of the mammalian brain underlies its computational abilities, and its vulnerability to injury and disease. It has been challenging to illuminate the features of this synaptic network due in part to the small size and exceptionally dense packing of its elements. Here we describe a rapid and accessible super-resolution imaging and image analysis workflow—SEQUIN—that identifies, quantifies, and characterizes central synapses in animal models and in humans, enabling automated volumetric imaging of mesoscale synaptic networks without the laborious production of large histological arrays. Using SEQUIN, we identify delayed cortical synapse loss resulting from diffuse traumatic brain injury. Similar synapse loss is observed in an Alzheimer disease model, where SEQUIN mesoscale mapping of excitatory synapses across the hippocampus identifies region-specific synaptic vulnerability to neurodegeneration. These results establish a novel, easily implemented and robust nano-to-mesoscale synapse quantification and molecular characterization method. They furthermore identify a mechanistic link—synaptopathy—between Alzheimer neurodegeneration and its best-established epigenetic risk factor, brain trauma.
Unlinked rRNA genes are widespread among Bacteria and Archaea
Authors: Brewer Tess E. , Albertsen Mads , Edwards Arwyn , Kirkegaard Rasmus H. , Rocha Eduardo P. C. , Fierer Noah
Published: July 2019

Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in Bacteria and Archaea. These ribosomal rRNA genes are typically organized into a single operon, an arrangement that is thought to facilitate gene regulation. In reality, some Bacteria and Archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are not co-located, but are instead separated across the genome and referred to as “unlinked”. This rearrangement has previously been treated as a rare exception or a byproduct of genome degradation in obligate intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are much more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, Planctomycetes, and Euryarchaeota, and occur in differential frequencies across natural environments. We found that up to 41% of the taxa in soil, including dominant taxa, had unlinked rRNA genes, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and obligatory intracellular species. Unlinked rRNA genes are also associated with changes in RNA metabolism, notably the loss of RNaseIII. We propose that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation.
The Noise-Resilient Brain: Resting-State Oscillatory Activity Predicts Words-In-Noise Recognition
Authors: Houweling Thomas , Becker Robert , Hervais-Adelman Alexis
Published: July 2019

The role of neuronal oscillations in the processing of speech has recently come to prominence. Since resting-state (RS) brain activity has been shown to predict both task-related brain activation and behavioural performance, we set out to establish whether inter-individual differences in spectrally-resolved RS-MEG power are associated with variations in words-in-noise recognition in a sample of 88 participants made available by the Human Connectome Project. Positive associations with resilience to noise were observed with power in the range 21 and 29Hz in a number of areas along the left temporal gyrus and temporo-parietal association areas peaking in left posterior superior temporal gyrus (pSTG). Significant associations were also found in the right posterior superior temporal gyrus in the frequency range 30 to 40Hz. We propose that individual differences in words-in-noise performance are related to baseline excitability levels of the neural substrates of phonological processing.

Highlights

Power of resting MEG activity predicts Words-In-Noise recognition performance

Significant associations in higher beta and lower gamma frequency band

Strongest in left-lateralised perisylvian cluster peaking in posterior STG

Effects are spectrally and spatially consistent with phoneme-level processing
Stabilization of cultural innovations depends on population density: testing an epidemiological model of cultural evolution against a global dataset of rock art sites and climate-based estimates of ancient population densities
Authors: Walker Richard , Eriksson Anders , Ruiz Camille , Newton Taylor Howard , Casalegno Francesco
Published: July 2019

Demographic models of human cultural evolution have high explanatory potential but weak empirical support. Here we use a global dataset of rock art sites and climate and genetics-based estimates of ancient population densities to test a new model based on epidemiological principles. The model focuses on the process whereby a cultural innovation becomes endemic in a population. It predicts that this cannot occur unless population density exceeds a critical value. Analysis of the data, using a Bayesian statistical framework, shows that the model has stronger empirical support than a null model, where rock art detection rates and population density are independent, or a proportional model where detection is directly proportional to population density. Comparisons between results for different geographical areas and periods yield qualitatively similar results, supporting the robustness of the model. Re-analysis of the rock art data, using a second set of independent population estimates, yields similar results. We conclude that population density above a critical threshold is a necessary condition for the maintenance of rock art as a stable part of a population’s cultural repertoire. Methods similar to those described can be used to test the model for other classes of archaeological artifact and to compare it against other models.