bluuebunny/crossref_metadata_2025 huggingface dataset:
E-learning for marine biotechnology: an example with a metagenomic approach
Authors: Liguori Ludovica , Citro Valentina , Hay-Mele Bruno , Andreotti Giuseppina , Cubellis Maria Vittoria
Published: November 2018

Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Hence the demand for graduates well-trained in bioinformatics has grown. Teaching bioinformatics has been incorporated in all traditional life science curricula. Better than teaching stand-alone bioinformatics, it would be useful to stress multidisciplinary and problem-solving aspects. Since bioinformatics relies heavily on the use of computers, e-learning is particularly convenient, but few examples have been produced so far. We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology with non-culturable microbes. We then lead the students through databases such as BRENDA, and programs such as BLAST and Clustal Omega. Lastly, we let the students querying these databases about molecules found in marine environments. At the end of the experience, students will have acquired practical knowledge of bioinformatics fundamentals.
A Bayesian Network Modeling for Departure Time Choice: A Case Study of Beijing Subway
Authors: Li Xian , Li Haiying , Xu Xinyue
Published: November 2018

Departure time choice is critical for subway passengers to avoid congestion during morning peak hours. In this study, we propose a Bayesian network (BN) model to capture departure time choice based on data learning. Factors such as travel time saving, crowding, subway fare, and departure time change are considered in this model. K2 algorithm is then employed to learn the BN structure, and maximum likelihood estimation (MLE) is adopted to estimate model parameters, according to the data obtained by a stated preference (SP) survey. A real-world case study of Beijing subway is illustrated, which proves that the proposed model has higher prediction accuracy than typical discrete choice models. Another key finding indicates that subway fare discount higher than 20% will motivate some passengers to depart 15 to 20 minutes earlier and release the pressure of crowding during morning peak hours.
Inhibition of mTORC1 by ER stress impairs neonatal β-cell expansion and predisposes to diabetes in the Akita mouse
Authors: Riahi Yael , Israeli Tal , Yeroslaviz Roni , Chimenez Shoshana , Avrahami Dana , Stolovich-Rain Miri , Alter Ido , Sebag Marina , Polin Nava , Bernal-Mizrachi Ernesto , Dor Yuval , Cerasi Erol , Leibowitz Gil
Published: November 2018

Unresolved ER stress followed by cell death is recognized as the main cause of a multitude of pathologies including neonatal diabetes. A systematic analysis of the mechanisms of β-cell loss and dysfunction in Akita mice, in which a mutation in the proinsulin gene causes a severe form of permanent neonatal diabetes, showed no increase in β-cell apoptosis throughout life. Surprisingly, we found that the main mechanism leading to β-cell dysfunction is marked impairment of β-cell growth during the early postnatal life due to transient inhibition of mTORC1, which governs postnatal β-cell growth and differentiation. Importantly, restoration of mTORC1 activity in neonate β-cells was sufficient to rescue postnatal β-cell growth, and to improve diabetes. We propose a scenario for the development of permanent neonatal diabetes, possibly also common forms of diabetes, where early-life events inducing ER stress affect β-cell mass expansion due to mTOR inhibition.
Human amnion‐derived mesenchymal stem cells promote osteogenesis of human bone marrow mesenchymal stem cells against glucolipotoxicity
Authors: Bian Yifeng , Ma Xiaojie , Wang Ruixia , Yuan Hua , Chen Ning , Du Yifei
Published: November 2018

Epidemiological evidence suggests that diabetes mellitus (DM) is an important factor in promoting periodontitis. It not only affects the attachment of connective tissue but also causes loss of alveolar bone. Hence, there is an urgent need to find an effective treatment for DM‐induced bone deficiency. This study aimed to investigate the effects of human amniotic mesenchymal stem cells (HAMSCs) on the proliferation and osteogenic differentiation of DM‐induced human bone marrow mesenchymal stem cells (HBMSCs). High glucose and palmitic acid (GP) were used to mimic DM‐induced glucolipotoxicity. The proliferation levels were measured using flow cytometry. Alkaline phosphatase activity substrate assays, Alizarin red S staining, and western blotting were used to investigate osteogenic differentiation. Oxidative stress was measured by assaying the levels of reactive oxygen species. This study found that glucolipotoxicity caused by GP remarkably inhibited cell proliferation and osteogenesis, and upregulated the oxidative stress level in HBMSCs. However, HAMSCs attenuated HBMSC dysfunction through antioxidant activity by influencing p38 mitogen‐activated protein kinase and vascular endothelial growth factor secretion. In conclusion, our findings indicate that HAMSCs might be suitable for treating DM‐mediated bone deficiency.
Social influence in investigative interviews: The effects of authority on informational elements produced in interviews and written statements
Authors: Matsumoto David , Hwang Hyisung C.
Published: November 2018

This study examined the effect of a principle of social influence—authority—on the informational elements in an investigative interview. Community participants told the truth or lied about a mock crime in a high or low authority context. Informational elements were coded from their oral responses in the interviews and written responses in a statement prior to the interviews. Rapport was rated by the interviewers and participants. The authority condition produced effects on the informational elements in both the interviews and written statements but mainly for truth tellers. Rapport also had direct effects on the informational elements but authority did not affect rapport and rapport did not mediate the effect of authority on the informational elements. These findings had theoretical, empirical, and practical implications.
Bioinspired Micro/Nanofluidic Ion Transport Channels for Organic Cathodes in High‐Rate and Ultrastable Lithium/Sodium‐Ion Batteries
Authors: Zhou Gangyong , Miao Yue‐E , Wei Zengxi , Mo LuLu , Lai Feili , Wu Yue , Ma Jianmin , Liu Tianxi
Published: November 2018

Conjugated carbonyl compounds are considered as ideal substitutes for traditional inorganic electrodes in lithium/sodium ion batteries (LIBs/SIBs) due to their excellent redox reversibility and structural tunability. Here, a flexible sandwich‐structured 3,4,9,10‐perylenetetracarboxylic dianhydride (PTCDA)/reduced graphene oxide (RGO)/carbon nanotube (CNT) (PTCDA/RGO/CNT) composite film with bioinspired micro/nanofluidic ion transport channels and interconnected porous conductive frameworks is designed and obtained by vacuum‐filtration and heating methods for LIB/SIB applications. The PTCDA/RGO/CNT electrode with robust mechanical deformability exhibits high diffusion coefficients of Li+/Na+ and low Warburg coefficients. Thus, desirable electrochemical performances with high capacities of 131 and 126 mA h g−1 at 10 mA g−1, and ultralong cycling stability with over 99% capacity retention after 500 cycles at 200 mA g−1 are achieved for LIBs and SIBs, respectively. In particular, Li/Na‐ion full cells consisting of lithiated or sodiated electrospun carbon nanofiber anode and PTCDA/RGO/CNT‐based cathode are developed to exhibit high energy densities of 132.6 and 104.4 W h kg−1 at the power densities of 340 and 288 W kg−1 for LIBs and SIBs, respectively. The advantageous features demonstrated by constructing bioinspired micro/nanofluidic channels may provide a new pathway toward the design of next‐generation wearable energy storage devices.
Thin Film RuO2 Lithiation: Fast Lithium‐Ion Diffusion along the Interface
Authors: Kim Sungkyu , Evmenenko Guennadi , Xu Yaobin , Buchholz Donald Bruce , Bedzyk Michael , He Kai , Wu Jinsong , Dravid Vinayak P.
Published: November 2018

Although lithium‐ion batteries that run on the conversion reaction have high capacity, their cyclability remains problematic due to large volume changes and material pulverization. Dimensional confinement, such as 2D thin film or nanodots in a conductive matrix, is proposed as a way of improving the cyclic stability, but the lithiation mechanism of such dimensionally controlled materials remains largely unknown. Here, by in situ transmission electron microscopy, lithiation of thin RuO2 films with different thicknesses and directions of lithium‐ion diffusion are observed at atomic resolution to monitor the reactions. From the side‐wall diffusion in ≈4 nm RuO2 film, the ion‐diffusion and reaction are fast, called “interface‐dominant” mode. In contrast, in ≈12 nm film, the ion diffusion–reaction only occurs at the interface where there is a high density of defects due to misfits between the film and substrate, called the “interface‐to‐film” mode. Compared to the side‐wall diffusion, the reaction along the normal direction of the thin film are found to be sluggish (“layer‐to‐layer” mode). Once lithiation speed is higher, the volume expansion is larger and the intercalation stage becomes shorter. Such observation of preferential lithiation direction in 2D‐like RuO2 thin film provides useful insights to develop dimensionally confined electrodes for lithium‐ion batteries.
Liquid‐Alloy‐Assisted Growth of 2D Ternary Ga2In4S9 toward High‐Performance UV Photodetection
Authors: Wang Fakun , Gao Ting , Zhang Qi , Hu Zhi‐Yi , Jin Bao , Li Liang , Zhou Xing , Li Huiqiao , Van Tendeloo Gustaaf , Zhai Tianyou
Published: November 2018

2D ternary systems provide another degree of freedom of tuning physical properties through stoichiometry variation. However, the controllable growth of 2D ternary materials remains a huge challenge that hinders their practical applications. Here, for the first time, by using a gallium/indium liquid alloy as the precursor, the synthesis of high‐quality 2D ternary Ga2In4S9 flakes of only a few atomic layers thick (≈2.4 nm for the thinnest samples) through chemical vapor deposition is realized. Their UV‐light‐sensing applications are explored systematically. Photodetectors based on the Ga2In4S9 flakes display outstanding UV detection ability (R
λ = 111.9 A W−1, external quantum efficiency = 3.85 × 104%, and D* = 2.25 × 1011 Jones@360 nm) with a fast response speed (τring ≈ 40 ms and τdecay ≈ 50 ms). In addition, Ga2In4S9‐based phototransistors exhibit a responsivity of ≈104 A W−1@360 nm above the critical back‐gate bias of ≈0 V. The use of the liquid alloy for synthesizing ultrathin 2D Ga2In4S9 nanostructures may offer great opportunities for designing novel 2D optoelectronic materials to achieve optimal device performance.
1D Fibers and 2D Patterns Made of Quantum Dot‐Embedded DNA via Electrospinning and Electrohydrodynamic Jet Printing
Authors: Arasu Velu , Hwang Sangyeon , Zhang Bin , Byun Doyoung , Park Sung Ha
Published: November 2018

Although DNA‐based 2D thin films are easily constructed, 1D fibers and 2D patterns made of DNA are seldom produced due to fabrication complexity. Here, the feasibility of constructing 1D fibers with various diameters and 2D patterns of any shape made of cetyltrimethylammonium chloride (CTMA)‐modified DNA (CDNA, which serves as an ink) via electrospinning and electrohydrodynamic (EHD) jet printing, respectively is demonstrated. The tunable parameters in electrospinning and EHD jet printing systems (e.g., applied bias voltage (V), printing speed (S), and flowrate (F)) are evaluated and the photoluminescence characteristics, UV luminescence photographs, and confocal laser scanning microscope images of the 1D and 2D structures are analyzed. Based on the observations, the fiber diameter decreases as V increases for electrospinning. For EHD, the 1D line widths are inversely proportional to S and V and directly proportional to F. 2D free‐standing mats are also constructed by peeling the mats from the collector after completion of electrospinning. Finally, the QD‐embedded letters of “SKKU” are written on given substrates by an EHD system for verification of pattern drawing. The research gives perspective to construction of CDNA‐based functional scaffolds for bioengineering, stretchable fiber mats for flexible electronics, and direct printing of patterns for microchannel applications.
Biallelic COLGALT1 variants are associated with cerebral small vessel disease
Authors: Miyatake Satoko , Schneeberger Sacha , Koyama Norihisa , Yokochi Kenji , Ohmura Kayo , Shiina Masaaki , Mori Harushi , Koshimizu Eriko , Imagawa Eri , Uchiyama Yuri , Mitsuhashi Satomi , Frith Martin C. , Fujita Atsushi , Satoh Mai , Taguri Masataka , Tomono Yasuko , Takahashi Keita , Doi Hiroshi , Takeuchi Hideyuki , Nakashima Mitsuko , Mizuguchi Takeshi , Takata Atsushi , Miyake Noriko , Saitsu Hirotomo , Tanaka Fumiaki , Ogata Kazuhiro , Hennet Thierry , Matsumoto Naomichi
Published: November 2018

Objective

Approximately 5% of cerebral small vessel diseases are hereditary, which include COL4A1/COL4A2‐related disorders. COL4A1/COL4A2 encode type IV collagen α1/2 chains in the basement membranes of cerebral vessels. COL4A1/COL4A2 mutations impair the secretion of collagen to the extracellular matrix, thereby resulting in vessel fragility. The diagnostic yield for COL4A1/COL4A2 variants is around 20 to 30%, suggesting other mutated genes might be associated with this disease. This study aimed to identify novel genes that cause COL4A1/COL4A2‐related disorders.

Methods

Whole exome sequencing was performed in 2 families with suspected COL4A1/COL4A2‐related disorders. We validated the role of COLGALT1 variants by constructing a 3‐dimensional structural model, evaluating collagen β (1‐O) galactosyltransferase 1 (ColGalT1) protein expression and ColGalT activity by Western blotting and collagen galactosyltransferase assays, and performing in vitro RNA interference and rescue experiments.

Results

Exome sequencing demonstrated biallelic variants in COLGALT1 encoding ColGalT1, which was involved in the post‐translational modification of type IV collagen in 2 unrelated patients: c.452 T > G (p.Leu151Arg) and c.1096delG (p.Glu366Argfs*15) in Patient 1, and c.460G > C (p.Ala154Pro) and c.1129G > C (p.Gly377Arg) in Patient 2. Three‐dimensional model analysis suggested that p.Leu151Arg and p.Ala154Pro destabilized protein folding, which impaired enzymatic activity. ColGalT1 protein expression and ColGalT activity in Patient 1 were undetectable. RNA interference studies demonstrated that reduced ColGalT1 altered COL4A1 secretion, and rescue experiments showed that mutant COLGALT1 insufficiently restored COL4A1 production in cells compared with wild type.

Interpretation

Biallelic COLGALT1 variants cause cerebral small vessel abnormalities through a common molecular pathogenesis with COL4A1/COL4A2‐related disorders. Ann Neurol 2018;84:843–853
Dynamic Expression Profiles of Sox9 in Embryonic, Post Natal, and Adult Heart Valve Cell Populations
Authors: Gallina Donika , Lincoln Joy
Published: November 2018

Heart valves are dynamic structures and abnormalities during embryonic development can lead to premature lethality or congenital malformations present at birth. The transcription factor Sox9 has been shown to be critical for early and late stages of valve formation, but its defined expression pattern throughout embryonic, post natal, and adult growth and maturation is incomplete. Here we use an antibody to detect 1‐100 amino acids of Sox9 and show that in the developing embryo, Sox9 is not detected in valve endothelial cells (VECs) lining the primitive valve structures, but is highly expressed in the endothelial‐derived valve interstitial cell population following endothelial‐to‐mesenchymal transformation. Expression is maintained in this cell population after birth, but is additionally detected in VECs from post natal day 1. Using a specific antibody to detect a phosphorylated form of Sox9 at Serine 181 (pSox9), we note enrichment of pSox9 in VECs at post natal days 1 and 10 and this pattern correlates with the known upstream kinase RockI, and downstream target, Aggrecan. The contribution of Sox9 to post natal growth and maturation of the valve is not known, but this study provides insights for future work examining the differential functions of Sox9 protein in valve cell populations. Anat Rec, 302:108–116, 2019. © 2018 Wiley Periodicals, Inc.
Risk factors for brain metastases in patients with non–small‐cell lung cancer
Authors: An Ning , Jing Wang , Wang Haoyi , Li Ji , Liu Yang , Yu Jinming , Zhu Hui
Published: November 2018

Brain metastases (BM) are severe incidents in patients with non–small‐cell lung cancer (NSCLC). The controversial value of prophylactic cranial irradiation (PCI) in NSCLC in terms of survival benefit prompted us to explore the possible risk factors for BM in NSCLC and identify the potential population most likely to benefit from PCI. Risk factors for brain metastases in NSCLC are reviewed in this article. Identifying patients with a higher risk of BM could possibly increase the benefit of PCI while reducing the discomfort and risks caused by unnecessary invasive procedures in the NSCLC patient population. Future studies might focus on finding a solid basis for the prediction of the occurrence of brain metastases and for the therapeutic decision on the use of PCI.
Revascularization of coronary chronic total occlusions with subintimal tracking and reentry followed by deferred stenting: Experience from a high‐volume referral center
Authors: Goleski Patrick J. , Nakamura Kenta , Liebeskind Emily , Salisbury Adam C. , Grantham J. Aaron , McCabe James M. , Lombardi William L.
Published: November 2018

Objectives

To determine whether a variation of an abandoned antegrade percutaneous coronary intervention (PCI) technique, termed subintimal tracking and reentry (STAR), could be a safe and effective strategy to contend with complex coronary chronic total occlusions (CTO) when other strategies fail.

Background

Complex CTOs require advanced techniques such as the retrograde approach, which is associated with higher complication rates than antegrade strategies.

Methods

The medical records of 32 consecutive patients who underwent deferred stenting following STAR (DSS) between January 2015 and May 2017 at a high‐volume referral center were retrospectively reviewed. The primary endpoint was technical success at the time of a second procedure following STAR‐based balloon angioplasty, defined as successful stenting or the presence of Thrombolysis in Myocardial Infarction Study Group (TIMI) 3 flow with <50% residual stenosis if the vessel caliber was inappropriate for stenting.

Results

Of 781 CTO PCI procedures, STAR was performed in 45 (5.8%) and DSS in 32 (4.1%), constituting the analysis cohort. The median Japanese‐CTO score was 2.5 [interquartile range (IQR) 1.0–3.0]. Median inter‐procedure time was 2.4 months [1.7–3.3 months]. Technical success was achieved in 28 (88%) patients; 23 (72%) patients were treated with stents and 5 (16%) with balloon angioplasty alone. Combined complications included one clinical perforation, one MI, and one stent thrombosis.

Conclusions

Deferred stenting after subintimal plaque modification via the STAR technique is a safe and effective strategy to contend with complex CTO lesions when other techniques are prohibitively high risk or have failed.
A Peptide Backbone Stapling Strategy Enabled by the Multicomponent Incorporation of Amide N‐Substituents
Authors: Ricardo Manuel G. , Marrrero Javiel F. , Valdés Oscar , Rivera Daniel G. , Wessjohann Ludger A.
Published: November 2018

The multicomponent backbone N‐modification of peptides on solid‐phase is presented as a powerful and general method to enable peptide stapling at the backbone instead of the side chains. This work shows that a variety of functionalized N‐substituents suitable for backbone stapling can be readily introduced by means of on‐resin Ugi multicomponent reactions conducted during solid‐phase peptide synthesis. Diverse macrocyclization chemistries were implemented with such backbone N‐substituents, including the ring‐closing metathesis, lactamization, and thiol alkylation. The backbone N‐modification method was also applied to the synthesis of α‐helical peptides by linking N‐substituents to the peptide N‐terminus, thus featuring hydrogen‐bond surrogate structures. Overall, the strategy proves useful for peptide backbone macrocyclization approaches that show promise in peptide drug discovery.
The association between Medicare accountable care organization enrollment and breast, colorectal, and prostate cancer screening
Authors: Resnick Matthew J. , Graves Amy J. , Gambrel Robert J. , Thapa Sunita , Buntin Melinda B. , Penson David F.
Published: November 2018

Background

Despite the rapid diffusion of accountable care organizations (ACOs), the effect of ACO enrollment on cancer diagnosis, treatment, and survivorship remains unknown. The objective of this study was to determine whether Medicare Shared Savings Program (MSSP) ACO enrollment was associated with changes in screening for breast, colorectal, and prostate cancers.

Methods

The authors built a cohort of Medicare beneficiaries from 2006 through 2014 comprising 39,218,652 person‐years of observation before and 17,252,345 person‐years of observation after MSSP enrollment. The Centers for Medicare & Medicaid Services attribution methodology was recapitulated; and screening services were identified for breast, colorectal, and prostate cancer, implementing both sensitive and specific definitions of cancer screening. Adjusted difference‐in‐differences analyses were performed using linear regression to characterize changes in annual screening rates after ACO enrollment relative to contemporaneous changes in a non‐ACO control group of Medicare beneficiaries.

Results

Medicare beneficiaries attributed to ACO‐enrolled providers had higher rates of breast, colorectal, and prostate cancer screening before enrollment. A 1.8% relative reduction in breast cancer screening was observed among women attributed to ACO providers (P < .0001), a 2.4% relative increase was observed in colorectal cancer screening (P = .0259), and a 3.4% relative reduction was observed in prostate cancer screening among men attributed to ACO providers (P = .0025) compared with contemporaneous changes in non‐ACO controls.

Conclusions

Small‐magnitude reductions were observed in breast and prostate cancer screening rates, and a small increase was observed in colorectal cancer screening associated with ACO enrollment. Although ACO enrollment does not appear to drive wholesale changes in cancer screening, small differences may map to meaningful changes in the epidemiology of screen‐detected cancers among Medicare beneficiaries.
A MnCo2O4@NiMoO4 Core‐Shell Composite Supported on Nickel Foam as a Supercapacitor Electrode for Energy Storage
Authors: Chen Tao , Shi Rui , Zhang Yuanyuan , Wang Zhenghua
Published: November 2018

A MnCo2O4@NiMoO4 composite was synthesized on nickel foam by a two‐step method. The composite has a core‐shell structure in which MnCo2O4 nanoneedles are wrapped by NiMoO4 nanoflakes. The MnCo2O4@NiMoO4/Ni foam is applied as a binder‐free electrode for supercapacitors and it achieves a specific capacitance of up to 1718 F g−1 at a current density of 1 A g−1, and 84 % capacitance retention after 6000 charge‐discharge cycles. The capacitance of the MnCo2O4@NiMoO4 composite is much higher than MnCo2O4 nanoneedles and NiMoO4 nanoflakes alone. Moreover, a hybrid supercapacitor is assembled by applying the MnCo2O4@NiMoO4/Ni foam as the positive electrode, activated carbon/Ni foam as the negative electrode. The hybrid supercapacitor reaches an energy density of up to 42.3 W h kg−1 at a power density of 797 W kg−1, a power density of 6256 W kg−1 at an energy density of 17.4 W h kg−1, and 86 % capacitance retention after 2000 charge‐discharge cycles. The results suggest that the rational design of electrode materials with such structure and composition is an effective strategy to improve electrochemical performance.
Hemodynamic Effects of Intravenous, High‐Dose Lipid Emulsion With and Without Metoprolol Infusion in Healthy Volunteers: A Randomized Clinical Trial
Authors: Petersen Kasper Meidahl , Bøgevig Søren , Petersen Tonny Studsgaard , Jensen Thomas Bo , Dalhoff Kim Peder , Henriksen Trine , Poulsen Henrik Enghusen , Christensen Mikkel Bring
Published: November 2018

In a double‐blinded, randomized, crossover trial, we investigated the hemodynamic effects of high‐dose intravenous lipid emulsion (ILE) with/without metoprolol. Ten healthy volunteers each completed 4 trial days (placebo + ILE; metoprolol + placebo; metoprolol + ILE; placebo + placebo) in random order. Metoprolol was administered as an initial bolus (10 mg), followed by an infusion (50 mg) from 5 to 30 minutes. ILE was administered as a bolus at 12.5 minutes (2.5 mL/kg), followed by a 15‐minute infusion (0.25 mL/kg per minute). On metoprolol + ILE days (compared with metoprolol + placebo) after 120 minutes, mean heart rates were significantly higher (difference, 5.5 beats per minute (bpm); 95% confidence interval (CI), 3.0–8.1 bpm; P < 0.001), and average relative cardiac output was higher (difference, 10 percentage points; 95% CI, 5–15 percentage points; P < 0.001). The hemodynamic effect of ILE developed gradually. ILE had no effect on plasma metoprolol or major adverse events. In conclusion, high‐dose ILE has relatively marginal and delayed hemodynamic effects that may have limited clinical relevance in the short‐term clinical toxicological setting.
Functional coordination between leaf traits and biomass allocation and growth of four herbaceous species in a newly established reservoir riparian ecosystem in China
Authors: Xiong Gaoming , Zhang Aiying , Fan Dayong , Ge Jielin , Yang Dan , Xie Zongqiang , Zhang Wangfeng
Published: November 2018

The flood‐dry‐flood cycle in the reservoir riparian zone (RRZ) of the Three Gorges Dam has dramatically altered the riparian ecosystem structure and composition. Previous field studies have shown that leaf traits varied greatly and were restricted to the lower‐investment and faster‐return end of the global leaf spectrum, which are typical characteristics of fast‐growing species. However, it is unclear as to the mechanism underpinning the growth potential of these species and how it will respond to soil nutrient availability and temperature. Here, we linked the plant functional traits of four representative dominant C4 herbaceous species (Setaria viridis, Echinochloa crusgalli, Cynodon dactylon and Hemarthria altissima) to their relative growth rates (RGR) under ambient and elevated temperatures, with different nitrogen and phosphorus levels, to explore the potential mechanism of species growth in the newly established reservoir riparian ecosystem in the Three Gorges Reservoir Area, China. We grew seedlings of these species in four open‐top chambers, with three levels of nutrient supplies under two temperature gradients (ambient temperature and an elevated temperature of 4°C). We found that the responses of the RGR and plant traits to soil N and P supply levels and temperature varied considerably among studied species. E. crusgalli displayed the lowest RGR associated with relatively low specific leaf area (SLA), leaf nitrogen content (LN), stem mass ratio (SMR), and high leaf mass ratio (LMR) and was less affected by soil N and P supply levels and temperature. C. dactylon and H. altissima showed the highest RGR compared to the other two species grown at the substrate of N = 0.4 mg/g, P = 0.2 mg/g at ambient air temperature, associated with a relatively high SMR, low LMR and low plant carbon content (PCC). However, the RGR advantage of the two species was diminished at elevated temperatures, while S. viridis showed the highest RGR compared to the other species. Across all datasets, the RGR had no association with the leaf area ratio (LAR) and SLA. The RGR also showed no significant relationships with the LN and leaf phosphorus content (LP). On the other hand, the RGR was captured adequately by the SMR, which can therefore be considered as a powerful functional marker of species’ functioning in this newly established reservoir riparian ecosystem. Our study provides some insight into the underlying mechanisms of species growth in reservoir riparian ecosystems.
Patterns of authorship in ecology and evolution: First, last, and corresponding authorship vary with gender and geography
Authors: Fox Charles W. , Ritchey Josiah P. , Paine C. E. Timothy
Published: November 2018

The position of an author on the byline of a paper affects the inferences readers make about their contributions to the research. We examine gender differences in authorship in the ecology literature using two datasets: submissions to six journals between 2010 and 2015 (regardless of whether they were accepted), and manuscripts published by 151 journals between 2009 and 2015. Women were less likely to be last (i.e., “senior”) authors (averaging ~23% across journals, years, and datasets) and sole authors (~24%), but more likely to be first author (~38%), relative to their overall frequency of authorship (~31%). However, the proportion of women in all authorship roles, except sole authorship, has increased year‐on‐year. Women were less likely to be authors on papers with male last authors, and all‐male papers were more abundant than expected given the overall gender ratio. Women were equally well represented on papers published in higher versus lower impact factor journals at all authorship positions. Female first authors were less likely to serve as corresponding author of their papers; this difference increased with the degree of gender inequality in the author's home country, but did not depend on the gender of the last author. First authors from non‐English‐speaking countries were less likely to serve as corresponding author of their papers, especially if the last author was from an English‐speaking country. That women more often delegate corresponding authorship to one of their coauthors may increase the likelihood that readers undervalue their role in the research by shifting credit for their contributions to coauthors. We suggest that author contribution statements be more universally adopted and that these statements declare how and/or why the corresponding author was selected for this role.
Testes mass in the livebearing fish Brachyrhaphis rhabdophora (Poeciliidae) varies hypoallometrically with body size but not between predation environments
Authors: Brown Haley N. , Gale Brittany Herrod , Johnson Jerald B. , Belk Mark C.
Published: November 2018

In this study, we considered potential causes of variation in testis size in the livebearing fish Brachyrhaphis rhabdophora. We evaluated variation in testes mass among individual males and among populations that occupy different selective environments. First, we predicted that small males should allocate more to testes mass than large males (i.e., hypoallometric pattern) based on a sperm competition argument. Second, based on life history theory and associated differences in mortality rates between populations that coexist with many fish predators and those with few predators, we predicted that males in high‐predation environments should allocate more to testes mass than males in habitats with few predators. Our results showed that small males allocated proportionally more to testes mass than larger males (slope of testes mass to body mass was hypoallometric). However, there was no effect of predator environment on testes mass independent of body size differences. In this system, size‐specific patterns of reproductive allocation in males (hypoallometry) differ from that seen in females (hyperallometry). Allocation to testes mass may respond to differences in mortality rate through selection on body size.
Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens
Authors: Lonsinger Robert C. , Adams Jennifer R. , Waits Lisette P.
Published: November 2018

Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long‐term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (Ne). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) Ne for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The Ne of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for Ne (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining Ne. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short‐term negative consequences of low Ne. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.
Methuselah’s daughters: Paternal age has little effect on offspring number and quality in Cardiocondyla ants
Authors: Heinze Jürgen , Hanoeffner Michaela , Delabie Jacques H. C. , Schrempf Alexandra
Published: November 2018

Male age may directly or indirectly affect the fitness of their female mating partners and their joint progeny. While in some taxa of insects, old males make better mates and fathers, young males excel in others. Males of most social Hymenoptera are relatively short lived and because of testis degeneration have only a limited sperm supply. In contrast, the wingless fighter males of the ant Cardiocondyla obscurior live for several weeks and produce sperm throughout their lives. Wingless males engage in lethal combat with rival males and the winner of such fights can monopolize mating with all female sexuals that emerge in their nests over a prolonged timespan. Here, we investigate if male age has an influence on sperm quality, the queen's lifespan and productivity, and the size and weight of their offspring. Queens mated to one‐week or six‐week‐old males did not differ in life expectancy and offspring production, but the daughters of young males were slightly heavier than those of old males. Our data suggest negligible reproductive senescence of C. obscurior males even at an age, which only few of them reach. This matches the reproductive strategy of Cardiocondyla ants, in which freshly emerging female sexuals rarely have the option to mate with males other than the one present in their natal nest.
Weather fluctuations affect the impact of consumers on vegetation recovery following a catastrophic die‐off
Authors: He Qiang , Silliman Brian R. , van de Koppel Johan , Cui Baoshan
Published: November 2018

Prolonged droughts exacerbated by climate change have been widely documented to interact with consumers to decimate vegetation in many ecosystems. Although climate change is increasing within‐year variation in precipitation and temperature, how weather fluctuations affect the impact of consumers on vegetation processes remains poorly understood. In a salt marsh that has recently experienced drought‐associated vegetation die‐off, we investigated how top‐down control of plant recovery by a prominent salt marsh grazer varies with weather. Our results showed that grazing‐driven plant mortality varied strongly with weather in spring, with intense grazing occurring during cool, wet days immediately following rain. Intense grazing on cool, wet days across the generally dry spring season had a strong impact that eliminated plant seedlings that could otherwise have become tolerant of grazing in the following summer, thereby restricting vegetation recovery and contributing to the persistence of an unvegetated salt barren state. Thus, weather fluctuations can modulate the impact of consumers on vegetation recovery, a fundamental process underlying the fate of ecosystems after disturbances. A multi‐timescale perspective on top‐down control that combines the impact of short‐term fluctuations in weather and that of long‐term variation in mean climate can not only help understand ecosystem dynamics in an increasingly variable climate, but may also inform conservation strategies or recovery plans for ecosystems that are already lost to climate change.
Comprehensive Study of Mononuclear Osmium Complexes with Various Pyrene Ligands
Authors: Zych Dawid , Slodek Aneta , Matuszczyk Daniel , Golba Sylwia
Published: November 2018

New mononuclear osmium complexes M1–M4 with various NCN‐cyclometalating pyrene ligands were synthesized and thoroughly characterized with particular emphasis on the nature of NCN‐cyclometalating pyrene ligands on the properties of target compounds. Structural properties were achieved by using the theoretical studies (DFT). Moreover, spectroscopic and theoretical studies (TD‐DFT) show the character of transitions and allow to understand the behavior of molecules during the stepwise oxidative titrations by using the cerium ammonium nitrate (CAN) solutions what resulted in M1+–M4+. The obtained experimental and theoretical data show the significant differences between the mononuclear osmium complexes M1–M4 in reference to used pyrene ligands.
The analysis of formation of polymer‐containing oily sludge produced during the wastewater treatment in offshore oilfield
Authors: Chen Bin , Zhao Lin , Wang Chengsheng , Chen Shijia , Wu Xiaoyan , Li Qi , Zuo Qingquan
Published: November 2018

In this paper, a study on formation of polymer‐containing oily sludge (PCOS) produced during polymer‐containing oily wastewater (PCOW) treatment was carried out. First, the composition of PCOW and PCOS was compared. The results showed that not all the oil in PCOW transferred into the PCOS and the water‐insoluble polymer in PCOS was the mixture of residual polymer (HMPAM) after the polymer flooding and cationic flocculant (CPAM) using for treating wastewater. Then, flocculation and zeta potential tests presented that hydrophobic water‐insoluble polymer was formed by electrostatic neutralization between HMPAM and CPAM. At last, dual‐polarization interferometry (DPI) tests were innovatively used to investigate the interaction between the water‐insoluble polymer and oil components. The results revealed that the order of interaction between water‐insoluble polymer and oil components was saturate < aromatic < resin < asphaltene. In one word, the PCOS was formed by interactions among HMPAM, CPAM and some oil components, especially the asphaltene, resin, and aromatic.
Human CD96 Correlates to Natural Killer Cell Exhaustion and Predicts the Prognosis of Human Hepatocellular Carcinoma
Authors: Sun Haoyu , Huang Qiang , Huang Mei , Wen Hao , Lin Renyong , Zheng Meijuan , Qu Kun , Li Kun , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: November 2018

Immune checkpoint blockade has become a promising therapeutic approach to reverse immune cell exhaustion. Coinhibitory CD96 and T‐cell immunoglobulin and ITIM domain (TIGIT), together with costimulatory CD226, bind to common ligand CD155. The balancing between three receptors fine‐tunes immune responses against tumors. In this study, we investigated the expression of CD96, TIGIT, and CD226 in 55 fresh human hepatocellular carcinoma (HCC) samples, 236 paraffin‐embedded HCC samples, and 20 normal human livers. The cumulative percentage, absolute count, and mean fluorescence intensity (MFI) of CD96+ NK cells are significantly increased in the intratumoral tissues of HCC and break the balance between three receptors. Human CD96+ NK cells are functionally exhausted with impaired interferon‐gamma (IFN‐γ) and tumor necrosis factor‐alpha (TNF‐α) production, high gene expression of interleukin (IL)‐10 and transforming growth factor‐beta 1 (TGF‐β1), and low gene expression of T‐bet, IL‐15, perforin, and granzyme B. In addition, blocking CD96‐CD155 interaction specifically increases lysis of HepG2 cells by NK cells. HCC patients with a high level of CD96 or CD155 expression within tumor are strongly associated with deteriorating disease condition and shorter disease‐free survival (DFS) and overall survival times. Patients with a higher cumulative percentage of CD96+ NK cells within tumor also exhibit shorter DFS. High plasma level of TGF‐β1 in HCC patients up‐regulates CD96 expression and dynamically shifts the balance between CD96, TIGIT, and CD226 in NK cells. Blocking TGF‐β1 specifically restores normal CD96 expression and reverses the dysfunction of NK cells. Conclusion: These findings indicate that human intratumoral CD96+ NK cells are functionally exhausted and patients with higher intratumoral CD96 expression exhibit poorer clinical outcomes. Blocking CD96‐CD155 interaction or TGF‐β1 restores NK cell immunity against tumors by reversing NK cell exhaustion, suggesting a possible therapeutic role of CD96 in fighting liver cancer.
Vesicle‐bound EBV‐BART13‐3p miRNA in circulation distinguishes nasopharyngeal from other head and neck cancer and asymptomatic EBV‐infections
Authors: Ramayanti Octavia , Verkuijlen Sandra A.W.M. , Novianti Putri , Scheepbouwer Chantal , Misovic Branislav , Koppers‐Lalic Danijela , van Weering Jan , Beckers Lisa , Adham Marlinda , Martorelli Debora , Middeldorp Jaap M. , Pegtel Dirk Michiel
Published: November 2018

Cell‐free microRNA (miRNA) in biofluids released by tumors in either protein or vesicle‐bound form, represent promising minimally‐invasive cancer biomarkers. However, a highly abundant non‐tumor background in human plasma and serum complicates the discovery and detection of tumor‐selective circulating miRNAs. We performed small RNA sequencing on serum and plasma RNA from Nasopharyngeal Carcinoma (NPC) patients. Collectively, Epstein Barr virus‐encoded miRNAs, more so than endogenous miRNAs, signify presence of NPC. However, RNAseq‐based EBV miRNA profiles differ between NPC patients, suggesting inter‐tumor heterogeneity or divergent secretory characteristics. We determined with sensitive qRT‐PCR assays that EBV miRNAs BART7‐3p, BART9‐3p and BART13‐3p are actively secreted by C666.1 NPC cells bound to extracellular vesicles (EVs) and soluble ribonucleoprotein complexes. Importantly, these miRNAs are expressed in all primary NPC tumor biopsies and readily detected in nasopharyngeal brushings from both early and late‐stage NPC patients. Increased levels of BART7‐3p, BART9‐3p and particularly BART13‐3p, distinguish NPC patient sera from healthy controls. Receiver operating characteristic curve analysis using sera from endemic NPC patients, other head and neck cancers and individuals with asymptomatic EBV‐infections reveals a superior diagnostic performance of EBV miRNAs over anti‐EBNA1 IgA serology and EBV‐DNA load (AUC 0.87–0.96 vs 0.86 and 0.66 respectively). The high specificity of circulating EBV‐BART13‐3p (97%) for NPC detection is in agreement with active secretion from NPC tumor cells. We conclude EV‐bound BART13‐3p in circulation is a promising, NPC‐selective, biomarker that should be considered as part of a screening strategy to identify NPC in endemic regions.
Basal biomarkers nestin and INPP4B predict gemcitabine benefit in metastatic breast cancer: Samples from the phase III SBG0102 clinical trial
Authors: Asleh Karama , Lyck Carstensen Stina , Tykjær Jørgensen Charlotte L. , Burugu Samantha , Gao Dongxia , Won Jennifer R. , Jensen Maj‐Britt , Balslev Eva , Lænkholm Anne‐Vibeke , Nielsen Dorte L. , Ejlertsen Bent , Nielsen Torsten O.
Published: November 2018

In a formal prospective‐retrospective analysis of the phase III SBG0102 clinical trial randomizing metastatic breast cancer patients to gemcitabine‐docetaxel or to single agent docetaxel, patients with basal‐like tumors by PAM50 gene expression had significantly better overall survival in the gemcitabine arm. By immunohistochemistry (IHC), triple negative status was not predictive, but more specific biomarkers have since become available defining basal‐like by nestin positivity or loss of inositol‐polyphosphate‐4‐phosphate (INPP4B). Here, we evaluate their capacity to identify which patients benefit from gemcitabine in the metastatic setting. Nestin and INPP4B staining and interpretation followed published methods. A prespecified statistical plan evaluated the primary hypothesis that patients with basal‐like breast cancer, defined as “nestin+ or INPP4B−”, would have superior overall survival on gemcitabine‐docetaxel when compared to docetaxel. Interaction tests, Kaplan–Meier curves and forest plots were used to assess prognostic and predictive capacities of biomarkers relative to treatment. Among 239 cases evaluable for our study, 36 (15%) had been classified as basal‐like by PAM50. “Nestin+ or INPP4B−” was observed in 41 (17%) of the total cases and was significantly associated with PAM50 basal‐like subtype. Within an estimated median follow‐up of 13 years, patients assigned as IHC basal “nestin+ or INPP4B‐” had significantly better overall survival on gemcitabine‐docetaxel versus docetaxel monotherapy (HR = 0.31, 95%CI: 0.16–0.60), whereas no differences were observed for other patients (HR = 0.99), p‐interaction < 0.01. In the metastatic setting, women with IHC basal breast cancers defined as “nestin+ or INPP4B‐” have superior overall survival when randomized to gemcitabine‐containing chemotherapy compared to docetaxel alone. These findings need to be validated using larger prospective‐retrospective phase III clinical trials series.
Clinicopathological, microenvironmental and genetic determinants of molecular subtypes in KEAP1/NRF2‐mutant lung cancer
Authors: Cai Mei‐Chun , Chen Minjiang , Ma Pengfei , Wu Jie , Lu Haijiao , Zhang Shengzhe , Liu Jin , Zhao Xiaojing , Zhuang Guanglei , Yu Zhuang , Fu Yujie
Published: November 2018

Somatic KEAP1‐NRF2 pathway alterations are frequently detected in both lung adenocarcinomas and squamous cell carcinomas. However, the biological characteristics and molecular subtypes of KEAP1/NRF2‐mutant lung cancer remain largely undefined. Here, we performed a stepwise, integrative analytic and experimental interrogation of primary tumors and cancer cell lines harboring KEAP1 or NFE2L2 (encoding NRF2) gene mutations. First, we discovered that KEAP1/NRF2‐mutant lung cancer presented APOBEC‐mediated mutational signatures, impaired tumor angiogenesis, elevated hypoxic stress and deficient immune‐cell infiltrates. Second, gene expression‐based subtyping revealed three molecular subsets of KEAP1/NRF2‐mutant lung adenocarcinomas and two molecular subsets of KEAP1/NRF2‐mutant lung squamous cell carcinomas, each associated with distinguishing genetic, differentiation, immunological and clinicopathological properties. Third, single‐sample prediction allowed for de novo identification of KEAP1/NRF2‐active tumors within KEAP1/NRF2‐wild‐type samples. Our data demonstrate that KEAP1/NRF2‐mutant lung cancer is a microenvironmentally distinct, biologically heterogeneous, and clinically underestimated disease. These new pathological and molecular insights may accelerate the development of efficacious therapeutic strategies against human malignancies featured by KEAP1‐NRF2 pathway activation.