bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association Between Parental Age and Autism‐Related Outcomes in Children at High Familial Risk for Autism
Authors: Lyall Kristen , Song Lanxin , Botteron Kelly , Croen Lisa A. , Dager Stephen R. , Fallin M. Daniele , Hazlett Heather C. , Kauffman Elizabeth , Landa Rebecca , Ladd‐Acosta Christine , Messinger Daniel S. , Ozonoff Sally , Pandey Juhi , Piven Joseph , Schmidt Rebecca J. , Schultz Robert T. , Stone Wendy L. , Newschaffer Craig J. , Volk Heather E.
Published: April 2020

Advanced parental age is a well‐replicated risk factor for autism spectrum disorder (ASD), a neurodevelopmental condition with a complex and not well‐defined etiology. We sought to determine parental age associations with ASD‐related outcomes in subjects at high familial risk for ASD. A total of 397 younger siblings of a child with ASD, drawn from existing prospective high familial risk cohorts, were included in these analyses. Overall, we did not observe significant associations of advanced parental age with clinical ASD diagnosis, Social Responsiveness Scale, or Vineland Adaptive Behavior Scales scores. Instead, increased odds of ASD were found with paternal age < 30 years (adjusted odds ratio [AOR] = 2.83 and 95% confidence intervals [CI] = 1.14–7.02). Likewise, younger age (<30 years) for both parents was associated with decreases in Mullen Scales of Early Learning early learning composite (MSEL‐ELC) scores (adjusted β = −9.62, 95% CI = −17.1 to −2.15). We also found significant increases in cognitive functioning based on MSEL‐ELC scores with increasing paternal age (adjusted β associated with a 10‐year increase in paternal age = 5.51, 95% CI = 0.70–10.3). Results suggest the potential for a different relationship between parental age and ASD‐related outcomes in families with elevated ASD risk than has been observed in general population samples. Autism Res 2020, 13: 998‐1010. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.

Lay Summary

Previous work suggests that older parents have a greater likelihood of having a child with autism. We investigated this relationship in the younger siblings of families who already had a child with autism. In this setting, we found a higher likelihood of autism, as well as poorer cognitive scores, in the siblings with younger fathers, and higher cognitive scores in the siblings with older parents. These results suggest that parental age associations may differ based on children's familial risk for autism.
Judicial gatekeeping on scientific validity with risk assessment tools
Authors: Hamilton Melissa
Published: April 2020

Risk assessment tools driven by algorithms offer promising advantages in predicting the recidivism risk of defendants. Jurisdictions are increasingly relying upon risk tool outcomes to help judges at sentencing with their decisions on whether to incarcerate or whether to use community‐based sanctions. Yet as sentencing has significant consequences for public safety and individual rights, care must be taken that the tools relied upon are appropriate for the task. Judges are encouraged to act as gatekeepers to evaluate whether the forensic risk assessment tool offered has a sufficient level of validity in that it is fit for the purposes of sentencing, provides an acceptable level of accuracy in its predictions, and achieves an adequate standard of reliability with regard to its outcomes.
Development and validation of a nomogram to predict survival after curative resection of nonmetastatic colorectal cancer
Authors: Hong Tingting , Cai Dongyan , Jin Linfang , Zhang Ying , Lu Tingxun , Hua Dong , Wu Xiaohong
Published: April 2020

Background

We aimed to develop a clinical applicable nomogram to predict overall survival (OS) for patients with curatively resected nonmetastatic colorectal cancer.

Methods

Records from a retrospective cohort of 846 patients with complete information were used to construct the nomogram. The nomogram was validated in a prospective cohort of 379 patients. The performance of the nomogram was evaluated with concordance index (c‐index), time‐dependent receiver operating characteristic (ROC) curves, calibration plots, and decision curve analyses for discrimination, accuracy, calibration ability, and clinical net benefits respectively, and further compared with AJCC 8th TNM staging and the MSKCC nomogram. Risk stratification based on nomogram scores was performed with recursive partitioning analysis.

Results

The nomogram incorporated age, Glasgow prognostic score, pretreatment carcinoembryonic antigen levels, T staging, N staging, number of harvested lymph nodes, and histological grade. Compared with the 8th AJCC staging and MSKCC model, the nomogram had a statistically higher c‐index (0.77, 95% CI: 0.73‐0.80), bigger areas under the time‐dependent ROC curves (AUC at 3 years: 79; at 5 years: 79), and improved clinical net benefits. Calibration plots revealed no deviations from reference lines. All results were reproducible in the validation cohort. Nomogram‐based risk stratification successfully discriminated patients within each AJCC stage (all log‐rank P < .05).

Conclusion

We established an accurate, reliable, and easy‐to‐use nomogram to predict OS after curative resection for nonmetastatic colorectal cancer (CRC). The nomogram outperformed the 8th AJCC staging and the MSKCC model and could aid in personalized treatment and follow‐up strategy for CRC patients.
Evaluating overall survival and competing risks of survival in patients with early‐stage breast cancer using a comprehensive nomogram
Authors: Xu Yan‐Bo , Liu Hong , Cao Qi‐Hua , Ji Jia‐Li , Dong Rong‐Rong , Xu Dong
Published: April 2020

Background

Patients with early‐stage breast cancer (BC) live long but have competing comorbidities. This study aimed to estimate the effect of cancer and other causes of death in patients with early‐stage BC and further quantify the survival differences.

Materials and methods

Data of patients diagnosed with BC between 2010 and 2016 were collected from the Surveillance, Epidemiology, and End Results database. The cumulative incidence function for breast cancer–specific mortality (BCSM) and other cause‐specific mortality (OCSM) was estimated, and the differences were tested using the Gray test. The nomogram for estimating 3‐, 4‐, and 5‐year overall survival (OS), breast cancer–specific survival, and other cause‐specific survival was established based on Cox regression analysis and Fine and Gray competing risk analysis. The discriminative ability, calibration, and precision of the nomogram were evaluated and compared using C statistics, calibration plots, and area under the receiver operating characteristic curve.

Results

A total of 196 304 eligible patients with early‐stage BC were identified in this study. Of these, 12 417 (6.3%) patients died: 5628 (45.3%) due to BC and 6789 (54.7%) due to other causes. Five validated variables were incorporated to develop the prognostic nomogram: age, grade, tumor size, subtype, and surgery of primary site (Figure 3). Age was a strong predictive factor, which was more obvious in OCSM. The effect of surgery was more prominent in BCSM. Increased tumor size was correlated with OS and BCSM and slightly correlated with OCSM. Grade and subtype differences were more predominant in BCSM than in OCSM. The established nomogram was well calibrated and displayed good discrimination.

Conclusions

We evaluate OS and competing risks of death in patients with early‐stage BC, establishing the first comprehensive prognostic nomogram.
Modified percutaneous suture‐mediated patent fossa ovalis closure for prevention of cerebral ischemic events
Authors: Gaspardone Achille , De Santis Antonella , Giannico Maria B. , Sgueglia Gregory A.
Published: April 2020

Percutaneous suture‐mediated transcatheter patent fossa ovalis (PFO) closure has been shown to be an effective and safe technique with self‐evident advantages due to the lack of a permanent device heart implant. The success of this novel technique relies on an optimal catch of the interatrial septa, especially the septum primum which is floppier than the bulkier muscular septum secundum. We hypothesized that double suture of septum primum would further improve the efficacy of the procedure by increasing the surface contact between the septa when the septum primum is bent into the right atrium. We have provided proof of this concept by implementing a modified technique in two patients with PFO and cerebral ischemic events.
Thermodynamic Models and Central Composite Design for Calcium Sulfate Dihydrate Solubility
Authors: Kiran-Yildirim Bercem , Gencaslan Aybala , Titiz-Sargut Sibel
Published: April 2020

The solubility of calcium sulfate dihydrate (gypsum) was measured in HCl solutions in the presence of Cr3+ and Fe3+ ions at various temperatures. The results indicate that the solubility of gypsum is fairly dependent on the concentrations of HCl and impurities, i.e., Cr3+ and Fe3+ ions. The experimental data were analyzed by applying the Buchowski‐Kiazczak (λh) model and the modified Apelblat model. Some thermodynamic parameters, such as the standard molar dissolution enthalpy, the standard molar Gibbs energy, and the entropy of solutions, were calculated by Van't Hoff analysis and Gibbs equation. The influences of the concentrations of both HCl and impurities, i.e., Cr3+ and Fe3+ ions, and temperature on the gypsum solubility were examined by applying the central composite design.
Control over Kinetic and Thermodynamically Driven Pathways of Crystallization to Yield Cofacial and Slipped‐Stack Dimers in Single Crystals
Authors: Ghosh Tapan , Birudula Srikanth , Kalita Kalyan Jyoti , Vijayaraghavan Ratheesh K.
Published: April 2020

Control over the molecular packing in the solid state is of utmost importance in regulating the bulk optical properties of organic semiconductors. The electronic coupling between the molecules makes it possible to improve the properties of the bulk materials. This work reports an example of control over the selective formation of polymorphic single crystals of donor–acceptor‐type small‐molecule compound 25TR by 1) kinetic or 2) thermodynamic course of crystallisation to yield slipped stack (S) and cofacial (C) dimers in the single crystals. The distinct optical characteristics of the C‐dimer and S‐dimer are summarised. Both forms show significant excitonic interactions in the solid state, and the S‐dimeric form has strong yellowish orange fluorescence, whereas the C‐dimeric form is non‐fluorescent in the crystalline state. DFT calculations and differential scanning calorimetric experiments revealed that the C‐dimer polymorph is the thermodynamically stable form with a free energy offset of 0.43 eV in comparison with the S‐dimer. Interestingly, the thermodynamically driven non‐fluorescent single crystal was found to be convertible to its fluorescent form irreversibly by thermal trigger. The charge‐carrier‐transport characteristics of these two polymorphs were computed by using the Marcus–Hush formalism. The computations of the charge‐carrier‐transport behaviour revealed that the S‐dimer (25TR(R)) is ambipolar, whereas the C‐dimer (25TR(Y)) is predominantly n‐type.
Structural Transformation of SnS2 to SnS by Mo Doping Produces Electro/Photocatalyst for Hydrogen Production
Authors: Kadam Sunil R. , Ghosh Sirshendu , Bar‐Ziv Ronen , Bar‐Sadan Maya
Published: April 2020

SnS and SnS2 are layered semiconductors, with potential promising properties for electro‐ and photocatalytic hydrogen (H2) production. The vast knowledge in preparation and modification of layered structures was still not employed successfully in this system to fully maximize its potential. Here, the first report of structural transformation of SnS2 into SnS with Mo‐doping as a bifunctional catalyst for the hydrogen evolution reaction (HER) is reported. The structural phase transition optimized the properties of the material, providing a more delicate morphology with additional catalytic sites. The electrochemical studies showed overpotential of 377 mV at 10 mA cm−2 for HER with Tafel slopes of 100 mV dec−1 in 0.5 m H2SO4 for 10 % Mo‐SnS. The same structure acts as an efficient photocatalyst in the generation of H2 from water under visible illumination with rate of 0.136 mmol g−1 h−1 of H2, which is 20 times higher than pristine SnS2 under visible light.
On‐Chip Neo‐Glycopeptide Synthesis for Multivalent Glycan Presentation
Authors: Mende Marco , Tsouka Alexandra , Heidepriem Jasmin , Paris Grigori , Mattes Daniela S. , Eickelmann Stephan , Bordoni Vittorio , Wawrzinek Robert , Fuchsberger Felix F. , Seeberger Peter H. , Rademacher Christoph , Delbianco Martina , Mallagaray Alvaro , Loeffler Felix F.
Published: April 2020

Single glycan–protein interactions are often weak, such that glycan binding partners commonly utilize multiple, spatially defined binding sites to enhance binding avidity and specificity. Current array technologies usually neglect defined multivalent display. Laser‐based array synthesis technology allows for flexible and rapid on‐surface synthesis of different peptides. By combining this technique with click chemistry, neo‐glycopeptides were produced directly on a functionalized glass slide in the microarray format. Density and spatial distribution of carbohydrates can be tuned, resulting in well‐defined glycan structures for multivalent display. The two lectins concanavalin A and langerin were probed with different glycans on multivalent scaffolds, revealing strong spacing‐, density‐, and ligand‐dependent binding. In addition, we could also measure the surface dissociation constant. This approach allows for a rapid generation, screening, and optimization of a multitude of multivalent scaffolds for glycan binding.
A HF Loaded Lewis‐Acidic Aluminium Chlorofluoride for Hydrofluorination Reactions
Authors: Kervarec Maëva‐Charlotte , Kemnitz Erhard , Scholz Gudrun , Rudić Svemir , Braun Thomas , Jäger Christian , Michalchuk Adam A. L. , Emmerling Franziska
Published: April 2020

The very strong Lewis acid aluminium chlorofluoride (ACF) was loaded with anhydrous HF. The interaction between the surface of the catalyst and HF was investigated using a variety of characterization methods, which revealed the formation of polyfluorides. Moreover, the reactivity of the HF‐loaded ACF towards the hydrofluorination of alkynes was studied.
Cu‐Catalyzed Reductive gem‐Difunctionalization of Terminal Alkynes via Hydrosilylation/Hydroamination Cascade: Concise Synthesis of α‐Aminosilanes
Authors: Nishino Soshi , Hirano Koji , Miura Masahiro
Published: April 2020

A copper‐catalyzed reductive gem‐difunctionalization of terminal alkynes with hydrosilanes and hydroxylamines has been developed. The reaction proceeds via hydrosilylation/hydroamination cascade, and the readily available and simple terminal alkynes can be transformed into the corresponding α‐aminosilanes of medicinal interest in a single operation. Additionally, the use of chiral bisphosphine ligand successfully makes the reaction enantioselective to deliver the optically active α‐aminosilanes with good enantiomeric ratios.
Germline and somatic DNA repair gene alterations in prostate cancer
Authors: Dall’Era Marc A. , McPherson John D. , Gao Allen C. , DeVere White Ralph W. , Gregg Jeffrey P. , Lara Primo N.
Published: April 2020

Background

Emerging evidence has suggested that DNA repair gene alterations may be important in prostate cancer pathogenesis. In the current study, the authors sought to characterize alterations in DNA repair pathway genes in both primary and metastatic prostate tumors with attention to tissue distribution as well as specific genomic alterations.

Methods

The authors studied the distribution and type of alterations in 24 genes that are considered important for DNA repair in 944 prostate cancers harvested from localized and metastatic tumors. Tumor DNA underwent hybrid capture for all coding exons of 287 or 395 cancer‐related genes plus select introns from 19 or 31 genes frequently rearranged in cancer. Captured libraries were sequenced to a median exon coverage depth of >×500. Specific genomic alterations were characterized and the frequencies of mutations by tissue site (prostate vs metastases) were compared using logistic regression.

Results

A total of 152 patients from the cohort of 944 men (16%) harbored a germline or somatic mutation in ≥1 DNA repair genes. The most frequently mutated genes were BRCA2 (11.4%) and ATM (5.8%), followed by MSH6 (2.5%) and MSH2 (2.1%). Mutations were identified in approximately 20.1% of primary prostate tumors compared with 18.8% of bone metastases. When stratified by tissue site, the highest rates of DNA repair mutations were found in solid organ metastases, including brain and visceral metastases, compared with prostate.

Conclusions

DNA repair gene mutations are more common in metastatic than localized prostate tumors. Visceral and other solid organ metastases appear enriched for these mutations compared with localized tumors or bone and lymph node metastases.
Extra‐Terrestrial Gas‐Phase Stereoinversion in Amino Acid Leucine: Thermal and Photochemical Channels
Authors: Rani Namrata , Vikas
Published: April 2020

Enantiomeric‐excess of the left‐handed enantiomer of proteinogenic amino acids has been reported in the meteoritic samples of carbonaceous chondrites. Such chiral‐bias is recently being believed due to the removal of right‐handed enantiomer through its selective destruction by circularly polarized ultraviolet (UV) radiations in interstellar space. The present work through quantum mechanical computations explores various thermal and photochemical channels for stereoinversion in proteinogenic amino acid Leucine, under the gas‐phase conditions akin to different temperature zones of interstellar medium (ISM). A thermochemical and kinetic analysis for the feasibility of the proposed channels is also carried out in different regions of ISM. The initiation of stereoinversion along all the ground‐state thermal channels is found to be restricted by a very high energy barrier which, however, is proposed to be substantially reduced if the initial step proceeds via an excited‐state. This work reveals that the stereoinversion in Leucine is quite feasible in ISM, provided it is initiated photochemically by UV radiations, which are abundant in ISM.
Valorization of Plastic Wastes for the Synthesis of Imidazolium‐Based Self‐Supported Elastomeric Ionenes
Authors: Demarteau Jeremy , O'Harra Kathryn E. , Bara Jason E. , Sardon Haritz
Published: April 2020

Imidazolium‐based ionenes are known to be high‐performance materials for a great variety of applications. The preparation of these polymers requires the use of bis‐imidazole starting monomers, which are commonly prepared by using toxic chloride reagents. In this study, bis‐imidazole monomers are synthesized by organocatalytic chemical recycling of discarded plastics through chemical depolymerization. By using poly(ethylene terephthalate) and bisphenol A polycarbonate as starting materials, different monomers containing amide or urea functionalities are prepared to produce high‐molecular‐weight ionic polymers. These novel ionenes show excellent elastomeric and self‐healing behavior, serving as a promising means to expand the exploration of plastic wastes as a source of new materials.
Application Settings versus Fixed Photomultiplier Tube Voltages for Optimal Cytometer Stability over Time, and Effect on Reusing a Compensation Matrix
Authors: Andersen Morten Nørgaard , Skovbo Anni , Petersen Charlotte Christie , Hokland Marianne
Published: April 2020

In flow cytometry, a compensation matrix is commonly reused over time, especially in clinical laboratories, to save time and reagents. However, generating a same‐day compensation matrix is considered the best practice by many experts. BD Biosciences developed Cytometer Setup and Tracking software to deliver proper instrument characterization, performance tracking, and stability. BD's “Application Settings” enable daily cytometer adjustments of photomultiplier tube (PMT) settings to correct for day‐to‐day variations in instrument performance. Here, we investigated if using Application Settings would improve data stability over time, including the impact on data stability when reusing a compensation matrix. We consecutively analyzed peripheral blood mononuclear cell (PBMC) aliquots from a single healthy donor together with 8‐peak Rainbow beads and daily compensation controls (22 runs in total over 6.5 months). We found larger variation within both PBMC subset quantifications and median fluorescence intensity (MFI) levels when using Application Settings (i.e., daily adjusted PMTs) compared to fixed PMT voltages (both with the same Day 0 compensation matrix applied). This larger variation was partly due to errors in compensation, but was also seen for Rainbow beads MFI data (not impacted by compensation), and thus likely produced by imprecise adjustments of PMTs by Applications Settings. Notably, the larger variation observed with Application Settings was most pronounced on a few days of the experiment with very large deviations, whereas on most days Application Settings and Fixed PMTs performed similar. The present results call for caution in using Application Settings in longitudinal studies, especially if also reusing a compensation matrix. In contrast, reusing a compensation matrix over time with fixed PMT voltages yielded stable results comparable with running same‐day compensation controls. © 2020 International Society for Advancement of Cytometry
A new combination of adaptive channel estimation methods and TORC equalizer in MC‐CDMA systems
Authors: Zidane Mohammed , Dinis Rui
Published: April 2020

Adaptive systems identification has been widely studied, but most studies have focused on the convergence of these methods. Applications of equalization systems have also received much attention. This paper presents a new combination of adaptive Broadband Radio Access Networks (BRAN) channel identification algorithms for multicarrier code division multiple access (MC‐CDMA) systems downlink equalization. In fifth‐generation (5G) wireless communications, MC‐CDMA is expected to support the associated networks. The BRAN E channel parameters, representing an outdoor scenario normalized for MC‐CDMA systems, are identified using a recursive least mean pth power algorithm with logarithmic transformation (RlogLMP). For validity and test aim, this algorithm is compared with the existing recursive least square (RLS) and least mean square (LMS) algorithms. Moreover, we use the estimated coefficients in the adaptive equalization problem. We give a review of the threshold orthogonality restoring combining (TORC) equalizer, which is coupled with the presented algorithms to counteract channel fading, as evaluated by the bit error rate (BER). Our performance results show that the RlogLMP algorithm can estimate the measured BRAN E channel with good efficiency for various values of the signal‐to‐noise ratio (SNR), as compared with the classical algorithms RLS and LMS. In adaptive equalization problems, the achieved results demonstrate that two thresholds ρTH in the TORC equalizer minimize the performance degradation, in terms of the BER, of the MC‐CDMA system under multipath channel fading with very good accuracy, especially if the coefficients are estimated with the specific case of the power p in the RlogLMP algorithm.
A comprehensive review of computational techniques for the prediction of drug side effects
Authors: Sachdev Kanica , Gupta Manoj K.
Published: April 2020

Drugs refer to the chemical compounds that are consumed by the human body and induce a change by interacting with the protein targets. The drugs may induce favorable or unfavorable changes in the human body. The unfavorable changes that are elicited by the drugs in the human body are known as drug side effects. These side effects range from minor reactions like headache to serious reactions such as cardiac arrest, cancer, or even death. The drugs are tested for their side effects based on laboratory experiments. However, these experiments are costly as well as prolonged. An alternative to the laboratory experiments is provided through the computational methods. Many computational techniques for identifying the drug side effects have been developed in the recent past. This review aims to summarize the important studies and contributions in the field of drug side effect prediction by computational techniques. A description of the data sets related to drug side effects and the metrics used for the evaluation of drug side effect prediction methods have also been explained. This article also highlights the future research that can be undertaken in this field. To the best of our knowledge, this is the first extensive review of the computational methods that have been developed for drug side effect prediction.
Antiurolithiatic effects of pentacyclic triterpenes: The distance traveled from therapeutic aspects
Authors: Lobine Devina , Ahmed Salman , Aschner Michael , Khan Haroon , Mirzaei Hamed , Mahomoodally Mohamad F.
Published: April 2020

Globally, approximately 12% of the population is inflicted by various types of urolithiasis. Standard treatments are available both to avert and treat urolithiasis, but with significant adverse side effects. Pentacyclic triterpenes represent a group of naturally occurring compounds which holds immense potential as therapeutic for treating kidney stone. This review aims to provide an integrative description on how pentacyclic triterpenes can effectively treat calcium oxalate urolithiasis through various mechanisms such as antioxidant, anti‐inflammatory, diuretic, and angiotensin‐converting enzyme inhibition. Some of the pentacylic triterpenes which shows promising activities include lupeol, oleanolic acid, betulin, and taraxasterol. Moreover, future perspectives in the development of pentacyclic triterpenes in formulations/drugs for urinary stone prevention are highlighted. It is anticipated that compiled information would serve as a scientific baseline to advocate further investigations on the potential of pentacyclic triterpenes in urolithiasis remediation.
The salmeterol anomaly and the need for a urine threshold
Authors: Jacobson Glenn A. , Hostrup Morten
Published: April 2020

Salmeterol is a long acting beta2‐agonist (LABA) used widely for the treatment of airways disease. There is evidence that beta2‐agonists, including salmeterol, have the potential for performance enhancing effects when delivered at supratherapeutic doses. For this reason, all beta2‐agonists are currently on the Prohibited List issued by the World Anti‐Doping Agency (WADA), regardless of dosing route with some exemptions for inhaled salbutamol, formoterol, and salmeterol when used at therapeutic inhaled doses. For 2020, salmeterol use is permitted up to a therapeutic dosing threshold of 200 μg daily, but unlike salbutamol and formoterol, there is an anomaly; currently there is no urine threshold to control for supratherapeutic dosing beyond this dosing threshold. Salmeterol, however, is reportable as an adverse analytical finding (AAF) at levels above 10 ng/mL. Complicating matters is that following inhalation, salmeterol parent drug is present at relatively low levels compared with other beta2‐agonists due to rapid metabolism to the metabolite, alpha‐hydroxysalmeterol, which is typically present at higher levels than the parent drug. Moreover, peak parent drug levels following permitted therapeutic dosing are below the minimum required performance level (MRPL) of 10 ng/mL for salmeterol (50% of the MRPL that analytical laboratories are required to meet for non‐threshold beta2‐agonists), hence the presence of salmeterol may be unreported. For consistency, a urine threshold should be introduced for salmeterol as a matter of priority, to balance the needs of athletes who use salmeterol therapeutically up to the agreed dosing threshold, with the need to control supratherapeutic dosing for doping intentions and athlete harm minimization.
Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly
Authors: Forister Matthew L. , Yoon Su'ad A. , Philbin Casey S. , Dodson Craig D. , Hart Bret , Harrison Joshua G. , Shelef Oren , Fordyce James A. , Marion Zachary H. , Nice Chris C. , Richards Lora A. , Buerkle C. Alex , Gompert Zach
Published: April 2020

Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant‐animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to investigate the effects of indivdiual compounds and suites of covarying phytochemicals on caterpillar performance. We find that survival, development time, and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti‐herbivore action. The plant‐insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides, and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes.
Facilitation cascades create a predation refuge for biodiversity in a novel connected habitat
Authors: Lanham Brendan S. , Poore Alistair G. B. , Gribben Paul E.
Published: April 2020

Communities structured via facilitation cascades whereby one habitat‐forming species promotes a secondary habitat‐forming species with synergistic effects on biodiversity are increasingly documented. Habitat‐formers can also extend the realized niche of other habitat‐forming species by facilitating their recruitment into novel environments across heterogeneous landscapes. However, further understanding of whether secondary habitat‐formers in these novel environments differ in their structure or support different communities from those settled in their natal habitat is required. Here, we investigated whether abiotic and biotic conditions in a novel connected habitat influence biodiversity within a secondary habitat‐former facilitated outside its natal habitat. We contrasted the morphology of the habitat‐forming alga, Sirophysalis trinodis, and its associated fish and epifaunal community occurring on rocky reef (natal habitat) and on nearby a biogenic hard substrate, live clam shells (novel habitat) in soft sediments. The algae on clams had a different morphology to those on the rocky shore and supported increased abundance of some epifaunal species. A reciprocal transplant experiment of S. trinodis individuals among habitats found that differences in the abundance of epifauna were explained by the increased abundance and consumption rates of predatory fish on the reef habitat compared to soft‐sediment habitats, and not by differences in algal morphology between habitats. We demonstrate that facilitation promotes a secondary habitat‐former into a novel habitat, which then enhances the abundance of associated epifauna by providing a predation refuge. This study contributes to a small but growing body of research demonstrating landscape‐scale effects of facilitation cascades, and that basal habitat‐formers can extend the realized niche of secondary habitat‐formers and their associated communities.
Estimating arthropod survival probability from field counts: a case study with monarch butterflies
Authors: Grant Tyler J. , Flockhart D. T. Tyler , Blader Teresa R. , Hellmich Richard L. , Pitman Grace M. , Tyner Sam , Norris D. Ryan , Bradbury Steven P.
Published: April 2020

Survival probability is fundamental for understanding population dynamics. Methods for estimating survival probability from field data typically require marking individuals, but marking methods are not possible for arthropod species that molt their exoskeleton between life stages. We developed a novel Bayesian state‐space model to estimate arthropod larval survival probability from stage‐structured count data. We performed simulation studies to evaluate estimation bias due to detection probability, individual variation in stage duration, and study design (sampling frequency and sample size). Estimation of cumulative survival probability from oviposition to pupation was robust to potential sources of bias. Our simulations also provide guidance for designing field studies with minimal bias. We applied the model to the monarch butterfly (Danaus plexippus), a declining species in North America for which conservation programs are being implemented. We estimated cumulative survival from egg to pupation from monarch counts conducted at 18 field sites in three landcover types in Iowa, USA, and Ontario, Canada: road right‐of‐ways, natural habitats (gardens and restored meadows), and agricultural field borders. Mean predicted survival probability across all landcover types was 0.014 (95% CI: 0.004–0.024), four times lower than previously published estimates using an ad hoc estimator. Estimated survival probability ranged from 0.002 (95% CI: 7.0E−7 to 0.034) to 0.058 (95% CI: 0.013–0.113) at individual sites. Among landcover types, agricultural field borders in Ontario had the highest estimated survival probability (0.025 with 95% CI: 0.008–0.043) and natural areas had the lowest estimated survival probability (0.008 with 95% CI: 0.009–0.024). Monarch production was estimated as adults produced per milkweed stem by multiplying survival probabilities by eggs per milkweed at these sites. Monarch production ranged from 1.0 (standard deviation [SD] = 0.68) adult in Ontario natural areas in 2016 to 29.0 (SD = 10.42) adults in Ontario agricultural borders in 2015 per 6809 milkweed stems. Survival estimates are critical to monarch population modeling and habitat restoration efforts. Our model is a significant advance in estimating survival probability for monarch butterflies and can be readily adapted to other arthropod species with stage‐structured life histories.
Loss of consumers constrains phenotypic evolution in the resulting food web
Authors: Barbour Matthew A. , Greyson-Gaito Christopher J. , Sotoodeh Arezoo , Locke Brendan , Bascompte Jordi
Published: April 2020

The loss of biodiversity is altering the structure of ecological networks; however, we are currently in a poor position to predict how these altered communities will affect the evolution of remaining populations. Theory on fitness landscapes provides a framework for predicting how selection alters the evolutionary trajectory and adaptive potential of populations, but often treats the network of interacting populations as a “black box.” Here, we integrate ecological networks and fitness landscapes to examine how changes in food-web structure shape phenotypic evolution. We conducted a field experiment that removed a guild of larval parasitoids that imposed direct and indirect selection pressures on an insect herbivore. We then measured herbivore survival as a function of three key phenotypic traits to estimate directional, quadratic, and correlational selection gradients in each treatment. We used these selection gradients to characterize the slope and curvature of the fitness landscape to understand the direct and indirect effects of consumer loss on phenotypic evolution. We found that the number of traits under directional selection increased with the removal of larval parasitoids, indicating evolution was more constrained toward a specific combination of traits. Similarly, we found that the removal of larval parasitoids altered the curvature of the fitness landscape in such a way that tended to decrease the evolvability of the traits we measured in the next generation. Our results suggest that the loss of trophic interactions can impose greater constraints on phenotypic evolution. This indicates that the simplification of ecological communities may constrain the adaptive potential of remaining populations to future environmental change.
Dye extract of calyces of Hibiscus sabdariffa has photodynamic antibacterial activity: A prospect for sunlight‐driven fresh produce sanitation
Authors: Majiya Hussaini , Galstyan Anzhela
Published: April 2020

Photodynamic sanitation of fresh produce could help reduce spoilage and disease transmissions where conventional methods of sanitation are not available, and sunlight is available for free. In this study, we evaluated the photostability and photodynamic antibacterial activity of the dye extracts of calyces of Hibiscus sabdariffa. The dye extracts were very photostable in water but bleached in acetate‐HCl buffer (pH 4.6), phosphate buffer saline (pH 7.2), and tris base‐HCl buffer (pH 8.6). The photostability correlated with the photodynamic antibacterial activity of the dye extracts. Both the methanol and water dye extracts at the concentration of 0.0625 mg/ml caused complete inactivation of Bacillus subtilis (reductions of 8.5 log CFU/ml) within 2 min either with the visible light exposure at 10 mW/cm2 or in the dark without the light exposure. Reductions of 4.8 log CFU/ml and 2.2 log CFU/ml of Escherichia coli were observed when 1 mg/ml of methanol and water dye extracts were used, respectively, in water with the light exposure at 10 mW/cm2 for 20 min. Discussions are included about the ease of the dye extractions of the calyces of H. sabdariffa even in water without the need of energy for heating and the suitability of the dye extracts for the fresh produce sanitation. Dye extract of calyces of H. sabdariffa has photodynamic and nonphotodynamic antibacterial activity which could be exploited for the development of a low‐tech sunlight‐driven fresh produce sanitation system that is cheap, sustainable, and environmentally friendly.
Cellular Location of HNF4α is Linked With Terminal Liver Failure in Humans
Authors: Florentino Rodrigo M. , Fraunhoffer Nicolas A. , Morita Kazutoyo , Takeishi Kazuki , Ostrowska Alina , Achreja Abhinav , Animasahun Olamide , Haep Nils , Arazov Shohrat , Agarwal Nandini , Collin de l'Hortet Alexandra , Guzman‐Lepe Jorge , Tafaleng Edgar N. , Mukherjee Amitava , Troy Kris , Banerjee Swati , Paranjpe Shirish , Michalopoulos George K. , Bell Aaron , Nagrath Deepak , Hainer Sarah J. , Fox Ira J. , Soto‐Gutierrez Alejandro
Published: April 2020

Hepatocyte nuclear factor 4 alpha (HNF4α) is a transcription factor that plays a critical role in hepatocyte function, and HNF4α‐based reprogramming corrects terminal liver failure in rats with chronic liver disease. In the livers of patients with advanced cirrhosis, HNF4α RNA expression levels decrease as hepatic function deteriorates, and protein expression is found in the cytoplasm. These findings could explain impaired hepatic function in patients with degenerative liver disease. In this study, we analyzed HNF4α localization and the pathways involved in post‐translational modification of HNF4α in human hepatocytes from patients with decompensated liver function. RNA‐sequencing analysis revealed that AKT‐related pathways, specifically phospho‐AKT, is down‐regulated in cirrhotic hepatocytes from patients with terminal failure, in whom nuclear levels of HNF4α were significantly reduced, and cytoplasmic expression of HNF4α was increased. cMET was also significantly reduced in failing hepatocytes. Moreover, metabolic profiling showed a glycolytic phenotype in failing human hepatocytes. The contribution of cMET and phospho‐AKT to nuclear localization of HNF4α was confirmed using Spearman's rank correlation test and pathway analysis, and further correlated with hepatic dysfunction by principal component analysis. HNF4α acetylation, a posttranslational modification important for nuclear retention, was also significantly reduced in failing human hepatocytes when compared with normal controls. Conclusion: These results suggest that the alterations in the cMET‐AKT pathway directly correlate with HNF4α localization and level of hepatocyte dysfunction. This study suggests that manipulation of HNF4α and pathways involved in HNF4α posttranslational modification may restore hepatocyte function in patients with terminal liver failure.
Triple solutions of micropolar nanofluid in the presence of radiation over an exponentially preamble shrinking surface: Convective boundary condition
Authors: Lund Liaquat Ali , Omar Zurni , Raza Jawad , Khan Ilyas
Published: April 2020

In this study, we attempt to obtain all probable multiple solutions of the magnetohydrodynamic (MHD) steady flow of micropolar nanofluid on an exponentially shrinking surface by the consideration of concentration slip, thermal radiation, and convective boundary condition with help of the revised model of Buongiorno. The significance of the mass suction on the existence of multiple solutions is integrated. The suitable pseudo‐exponential similarity variables have been adopted to transfer the system of nonlinear partial differential equations into a system of nonlinear quasi‐ordinary ordinary differential equations. The resultant system has been solved by employing the Runge–Kutta fourth‐order method along with the shooting method. Three different ranges of solutions are noticed, namely triple solutions and single solution. When ranges of the suction parameter are and , then there exist triple solutions otherwise there exists only single solution. The effect of the numerous emerging parameters on the velocity profile, angular velocity profile, temperature profile, concentration profile, coefficient of skin friction, and local Nusselt and Sherwood numbers are demonstrated graphically. Results reveal that the velocity of the rotating fluid particles near the rigid surface declines regularly by the rise of the micropolar parameter in the second and first solutions.
Analysis of exergetic performance for a solar air heater with metal foam fins
Authors: Farhan Ammar A. , Obaid Zain Alabdeen H. , Hussien Sally Q.
Published: April 2020

In this experimental study, an exergetic analysis is presented for solar air heaters (SAHs) that have absorber plates equipped with different fin arrangements. The following two types of fins were used: solid fins (conventional) and metal foam fins. Longitudinal, staggered, and corrugated fin arrangements in SAHs were investigated under the weather conditions experienced in Baghdad, Iraq in February to April 2018. The exergy efficiency and exergy loss of the SAHs were evaluated for five air mass flow rates ranging from 0.011 to 0.059 kg/s. Based on the exergy analysis, SAHs with metal foam fins are more efficient than those with solid fins. In addition, corrugated metal foam fins introduce more turbulent flow than the other fin configurations. It was found that the exergy loss and the exergy efficiency were directly proportional to the values of solar irradiance and air mass flow rates. At solar noon, the maximum values for exergy change were 127 and 89 W/m2 for air mass flow rates of 0.011 and 0.059 kg/s, respectively.
Evaluation of automated computed tomography segmentation to assess body composition and mortality associations in cancer patients
Authors: Cespedes Feliciano Elizabeth M. , Popuri Karteek , Cobzas Dana , Baracos Vickie E. , Beg Mirza Faisal , Khan Arafat Dad , Ma Cydney , Chow Vincent , Prado Carla M. , Xiao Jingjie , Liu Vincent , Chen Wendy Y. , Meyerhardt Jeffrey , Albers Kathleen B. , Caan Bette J.
Published: April 2020

Background

Body composition from computed tomography (CT) scans is associated with cancer outcomes including surgical complications, chemotoxicity, and survival. Most studies manually segment CT scans, but Automatic Body composition Analyser using Computed tomography image Segmentation (ABACS) software automatically segments muscle and adipose tissues to speed analysis. Here, we externally evaluate ABACS in an independent dataset.

Methods

Among patients with non‐metastatic colorectal (n = 3102) and breast (n = 2888) cancer diagnosed from 2005 to 2013 at Kaiser Permanente, expert raters annotated tissue areas at the third lumbar vertebra (L3). To compare ABACS segmentation results to manual analysis, we quantified the proportion of pixel‐level image overlap using Jaccard scores and agreement between methods using intra‐class correlation coefficients for continuous tissue areas. We examined performance overall and among subgroups defined by patient and imaging characteristics. To compare the strength of the mortality associations obtained from ABACS's segmentations to manual analysis, we computed Cox proportional hazards ratios (HRs) and 95% confidence intervals (95% CI) by tertile of tissue area.

Results

Mean ± SD age was 63 ± 11 years for colorectal cancer patients and 56 ± 12 for breast cancer patients. There was strong agreement between manual and automatic segmentations overall and within subgroups of age, sex, body mass index, and cancer stage: average Jaccard scores and intra‐class correlation coefficients exceeded 90% for all tissues. ABACS underestimated muscle and visceral and subcutaneous adipose tissue areas by 1–2% versus manual analysis: mean differences were small at −2.35, −1.97 and −2.38 cm2, respectively. ABACS's performance was lowest for the <2% of patients who were underweight or had anatomic abnormalities. ABACS and manual analysis produced similar associations with mortality; comparing the lowest to highest tertile of skeletal muscle from ABACS versus manual analysis, the HRs were 1.23 (95% CI: 1.00–1.52) versus 1.38 (95% CI: 1.11–1.70) for colorectal cancer patients and 1.30 (95% CI: 1.01–1.66) versus 1.29 (95% CI: 1.00–1.65) for breast cancer patients.

Conclusions

In the first study to externally evaluate a commercially available software to assess body composition, automated segmentation of muscle and adipose tissues using ABACS was similar to manual analysis and associated with mortality after non‐metastatic cancer. Automated methods will accelerate body composition research and, eventually, facilitate integration of body composition measures into clinical care.
Understanding evolution of SARS‐CoV‐2: A perspective from analysis of genetic diversity of RdRp gene
Authors: Kasibhatla Sunitha M. , Kinikar Meenal , Limaye Sanket , Kale Mohan M. , Kulkarni‐Kale Urmila
Published: April 2020

Coronavirus disease 2019 emerged as the first example of “Disease X”, a hypothetical disease of humans caused by an unknown infectious agent that was named as novel coronavirus and subsequently designated as severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The origin of the outbreak at the animal market in Wuhan, China implies it as a case of zoonotic spillover. The study was designed to understand evolution of Betacoronaviruses and in particular diversification of SARS‐CoV‐2 using RNA dependent RNA polymerase (RdRp) gene, a stable genetic marker. Phylogenetic and population stratification analyses were carried out using maximum likelihood and Bayesian methods, respectively. Molecular phylogeny using RdRp showed that SARS‐CoV‐2 isolates cluster together. Bat‐CoV isolate RaTG13 and Pangolin‐CoVs are observed to branch off prior to SARS‐CoV‐2 cluster. While SARS‐CoV form a single cluster, Bat‐CoVs form multiple clusters. Population‐based analyses revealed that both SARS‐CoV‐2 and SARS‐CoV form separate clusters with no admixture. Bat‐CoVs were found to have single and mixed ancestry and clustered as four sub‐populations. Population‐based analyses of Betacoronaviruses using RdRp revealed that SARS‐CoV‐2 is a homogeneous population. SARS‐CoV‐2 appears to have evolved from Bat‐CoV isolate RaTG13, which diversified from a common ancestor from which Pangolin‐CoVs have also evolved. The admixed Bat‐CoV sub‐populations indicate that bats serve as reservoirs harboring virus ensembles that are responsible for zoonotic spillovers such as SARS‐CoV and SARS‐CoV‐2. The extent of admixed isolates of Bat‐CoVs observed in population diversification studies underline the need for periodic surveillance of bats and other animal reservoirs for potential spillovers as a measure towards preparedness for emergence of zoonosis.