bluuebunny/crossref_metadata_2025 huggingface dataset:
Jasmonic acid‐responsive AabHLH1 positively regulates artemisinin biosynthesis in Artemisia annua
Authors: Li Ling , Hao Xiaolong , Liu Hang , Wang Wei , Fu Xueqing , Ma Yanan , Shen Qian , Chen Minghui , Tang Kexuan
Published: February 2019

Artemisia annua is the only natural source of the sesquiterpenoid artemisinin, which is widely used to treat malaria. The phytohormone jasmonic acid (JA) can significantly promote artemisinin biosynthesis in A. annua. AabHLH1 can bind and activate artemisinin biosynthetic genes, such as AaADS and AaCYP71AV1. In this study, we proved that AabHLH1 was responsive to MeJA treatment and highly expressed in glandular trichome‐enriched tissues, and that its expression profile was similar to that of AaADS. Yeast two‐hybrid assays showed that AabHLH1 interacted with all nine AaJAZ proteins in A. annua. Functional analysis with transgenic plants showed that several artemisinin biosynthetic genes were upregulated in AabHLH1‐OE transgenic A. annua lines and downregulated in AabHLH1‐EAR lines; furthermore, the artemisinin content was increased in the AabHLH1‐OE lines and decreased in the AabHLH1‐EAR lines. These results demonstrate that the JA‐induced AabHLH1 positively regulates artemisinin biosynthesis by regulating the biosynthetic genes, and thus provide new insight into the regulatory mechanism of JA‐induced artemisinin biosynthesis in A. annua.
Quantification of proteomic and metabolic burdens predicts growth retardation and overflow metabolism in recombinant Escherichia coli
Authors: Zeng Hong , Yang Aidong
Published: February 2019

Escherichia coli has been the host organism most frequently investigated for efficient recombinant protein production. However, the production of a foreign protein in recombinant
E. coli often leads to growth deterioration and elevated secretion of acetic acid. Such observed phenomena have been widely linked with cell stress responses and metabolic burdens originated particularly from the increased energy demand. In this study, flux balance analysis and dynamic flux balance analysis were applied to investigate the observed growth physiology of recombinant
E. coli, incorporating the proteome allocation theory and an adjustable maintenance energy level (ATPM) to capture the proteomic and energetic burdens introduced by recombinant protein synthesis. Model predictions of biomass growth, substrate consumption, acetate excretion, and protein production with two different strains were in good agreement with the experimental data, indicating that the constraint on the available proteomic resource and the change in ATPM might be important contributors governing the growth physiology of recombinant strains. The modeling framework developed in this work, currently with several limitations to overcome, offers a starting point for the development of a practical, model‐based tool to guide metabolic engineering decisions for boosting recombinant protein production.
Streptomycin‐induced ribosome engineering complemented with fermentation optimization for enhanced production of 10‐membered enediynes tiancimycin‐A and tiancimycin‐D
Authors: Zhuang Zhoukang , Jiang Chengzhou , Zhang Fan , Huang Rong , Yi Liwei , Huang Yong , Yan Xiaohui , Duan Yanwen , Zhu Xiangcheng
Published: February 2019

Tiancimycins (TNMs) are a group of 10‐membered anthraquinone‐fused enediynes, newly discovered from Streptomyces sp. CB03234. Among them, TNM‐A and TNM‐D have exhibited excellent antitumor performances and could be exploited as very promising warheads for the development of anticancer antibody‐drug conjugates (ADCs). However, their low titers, especially TNM‐D, have severely limited following progress. Therefore, the streptomycin‐induced ribosome engineering was adopted in this work for strain improvement of CB03234, and a TNMs high producer S. sp. CB03234‐S with the K43N mutation at 30S ribosomal protein S12 was successfully screened out. Subsequent media optimization revealed the essential effects of iodide and copper ion on the production of TNMs, while the substitution of nitrogen source could evidently promote the accumulation of TNM‐D, and the ratio of produced TNM‐A and TNM‐D was responsive to the change of carbon and nitrogen ratio in the medium. Further amelioration of the pH control in scaled up 25 L fermentation increased the average titers of TNM‐A and TNM‐D up to 13.7 ± 0.3 and 19.2 ± 0.4 mg/L, respectively. The achieved over 45‐fold titer improvement of TNM‐A, and 109‐fold total titer improvement of TNM‐A and TNM‐D enabled the efficient purification of over 200 mg of each target molecule from 25 L fermentation. Our efforts have demonstrated a practical strategy for titer improvement of anthraquinone‐fused enediynes and set up a solid base for the pilot scale production and preclinical studies of TNMs to expedite the future development of anticancer ADC drugs.
Electron‐acceptor loadings affect chloroform dechlorination in a hydrogen‐based membrane biofilm reactor
Authors: Lai YenJung Sean , Ontiveros‐Valencia Aura , Coskun Tamer , Zhou Chen , Rittmann Bruce E.
Published: February 2019

Chloroform (CF) can undergo reductive dechlorination to dichloromethane, chloromethane, and methane. However, competition for hydrogen (H2), the electron‐donor substrate, may cause poor dechlorination when multiple electron acceptors are present. Common acceptors in anaerobic environments are nitrate (NO3−), sulfate (SO42−), and bicarbonate (HCO3−). We evaluated CF dechlorination in the presence of HCO3− at 1.56 e− Eq/m2‐day, then NO3− at 0.04–0.15 e− Eq/m2‐day, and finally NO3− (0.04 e− Eq/m2‐day) along with SO42− at 0.33 e− Eq/m2‐day in an H2‐based membrane biofilm reactor (MBfR). When the biofilm was initiated with CF‐dechlorination conditions (no NO3− or SO42−), it yielded a CF flux of 0.14 e− Eq/m2‐day and acetate production via homoacetogenesis up to 0.26 e− eq/m2‐day. Subsequent addition of NO3− at 0.05 e− Eq/m2‐day maintained full CF dechlorination and homoacetogenesis, but NO3− input at 0.15 e− Eq/m2‐day caused CF to remain in the reactor's effluent and led to negligible acetate production. The addition of SO42− did not affect CF reduction, but SO42− reduction significantly altered the microbial community by introducing sulfate‐reducing Desulfovibrio and more sulfur‐oxidizing Arcobacter. Dechloromonas appeared to carry out CF dechlorination and denitrification, whereas Acetobacterium (homoacetogen) may have been involved with hydrolytic dechlorination. Modifications to the electron acceptors fed to the MBfR caused the microbial community to undergo changes in structure that reflected changes in the removal fluxes.
Enhancing the functionality of a microscale bioreactor system as an industrial process development tool for mammalian perfusion culture
Authors: Sewell David J , Turner Richard , Field Ray , Holmes William , Pradhan Rahul , Spencer Christopher , Oliver Stephen G , Slater Nigel KH , Dikicioglu Duygu
Published: February 2019

Without a scale‐down model for perfusion, high resource demand makes cell line screening or process development challenging, therefore, potentially successful cell lines or perfusion processes are unrealized and their ability untapped. We present here the refunctioning of a high‐capacity microscale system that is typically used in fed‐batch process development to allow perfusion operation utilizing in situ gravity settling and automated sampling. In this low resource setting, which involved routine perturbations in mixing, pH and dissolved oxygen concentrations, the specific productivity and the maximum cell concentration were higher than 3.0 × 106 mg/cell/day and 7 × 10
7 cells/ml, respectively, across replicate microscale perfusion runs conducted at one vessel volume exchange per day. A comparative analysis was conducted at bench scale with vessels operated in perfusion mode utilizing a cell retention device. Neither specific productivity nor product quality indicated by product aggregation (6%) was significantly different across scales 19 days after inoculation, thus demonstrating this setup to be a suitable and reliable platform for evaluating the performance of cell lines and the effect of process parameters, relevant to perfusion mode of culturing.
Deregulation of methanol metabolism reverts transcriptional limitations of recombinant Pichia pastoris (Komagataella spp) with multiple expression cassettes under control of the AOX1 promoter
Authors: Cámara Elena , Monforte Sergi , Albiol Joan , Ferrer Pau
Published: February 2019

The methanol‐regulated alcohol oxidase promoter (PAOX1) of Pichia pastoris (syn. Komagataella spp. ) is one of the strongest promoters for heterologous gene expression. Although increasing the gene dosage is a common strategy to improve recombinant protein productivities, P. pastoris strains harboring more than two copies of a Rhizopus oryzae lipase gene (ROL) have previously shown a decrease in cell growth, lipase production, and substrate consumption, as well as a significant transcriptional downregulation of methanol metabolism. This pointed to a potential titration effect of key transcriptional factors methanol expression regulator 1 (Mxr1) and methanol‐induced transcription factor (Mit1) regulating methanol metabolism caused by the insertion of multiple expression vectors. To prove this hypothesis, a set of strains carrying one and four copies of ROL (1C and 4C, respectively) were engineered to coexpress one or two copies of MXR1*, coding for an Mxr1 variant insensitive to repression by 14‐3‐3 regulatory proteins, or one copy of MIT1. Small‐scale cultures revealed that growth, Rol productivity, and methanol consumption were improved in the 4C‐MXR1* and 4C‐MIT1, strains growing on methanol as a sole carbon source, whereas only a slight increase in productivity was observed for re‐engineered 1C strains. We further verified the improved performance of these strains in glycerol‐/methanol‐limited chemostat cultures.
Introducing substrate limitations to overcome catabolite repression in a protease producing Bacillus licheniformis strain using membrane‐based fed‐batch shake flasks
Authors: Habicher Tobias , John Arian , Scholl Niklas , Daub Andreas , Klein Tobias , Philip Priya , Büchs Jochen
Published: February 2019

To overcome catabolite repression, industrial fermentation processes are usually operated in substrate‐limited fed‐batch mode. Therefore, the implementation of such an operating mode at small scale is crucial to maintain comparable process conditions. In this study, Bacillus licheniformis, a well‐known producer of proteases, was cultivated with carbon (glucose)‐ and nitrogen (ammonium)‐limited fed‐batch conditions using the previously introduced membrane‐based fed‐batch shake flasks. A repression of protease production by glucose and ammonium was thus avoided and yields increased 1.5‐ and 2.1‐fold relative to batch, respectively. An elevated feeding rate of glucose caused depletion of ammonium, which was recognizable within the oxygen transfer rate (OTR) signal measured with the Respiration Activity MOnitoring System (RAMOS). Ammonium limitation was prevented by feeding ammonium simultaneously with glucose. The OTR signal clearly indicated the initiation of the fed‐batch phase and gave direct feedback on the nutrient release kinetics. Increased feeding rates of glucose and ammonium led to an elevated protease activity without affecting the protease yield (YP/Glu). In addition to YP/Glu, protease yields were determined based on the metabolized amount of oxygen . The results showed that the protease production correlated with the amount of consumed glucose as well as with the amount of consumed oxygen. The membrane‐based fed‐batch shake flask in combination with the RAMOS device is a powerful combination to investigate the effect of substrate‐limited fed‐batch conditions.
Chemical, Antioxidant, and Antimicrobial Evaluation of Essential Oils and an Anatomical Study of the Aerial Parts from Baccharis Species (Asteraceae)
Authors: Zuccolotto Tatiana , Bressan Jaqueline , Lourenço Allan V. F. , Bruginski Estevan , Veiga Andressa , Marinho Jane V. N. , Raeski Paola A. , Heiden Gustavo , Salvador Marcos J. , Murakami Fabio S. , Budel Jane M. , Campos Francinete R.
Published: February 2019

The aim of this study was to evaluate the chemical, antioxidant, and antimicrobial activity of the essential oils as well as the anatomy of the aerial parts from Baccharis aracatubaensis, Baccharis burchellii, and Baccharis organensis owing to the therapeutic potential of Baccharis. The volatile constituents were analyzed using GC/MS, the antioxidant activity was evaluated by oxygen radical absorbance capacity (ORACFL) and DPPH assays, and the antimicrobial activity by a microdilution technique. Of the 56 compounds identified, only seven (β‐caryophyllene, γ‐muurolene, bicyclogermacrene, β‐germacrene, spathulenol, τ‐muurolol, and α‐cadinol) were common in the three specimens studied. Of these, γ‐muurolene was found abundantly in B. aracatubaensis, while bicyclogermacrene was abundant in B. burchellii and B. organensis. The essential oils exhibited antioxidant activity in the ORACFL (>500.0 μmol TE g−1) and DPPH assays. However, they did not exhibit any antimicrobial activity. Secretory ducts and flagelliform glandular trichomes were observed in the anatomical study of all the Baccharis species studied.
TAVR for aortic valve regurgitation: Ready for a randomized trial?
Authors: Belardi Jorge , Lamelas Pablo
Published: February 2019

Key Points

Transcatheter aortic valve replacement has been used successfully to treat native aortic valve regurgitation.

Current observational evidence shows promising results in terms of procedural success while outcome data are difficult to interpret given the observational nature of the evidence.

We are ready for a randomized trial, which will be very challenging to run.
Fractional flow reserve from intravascular ultrasound imaging: Computational fluid dynamics to the rescue?
Authors: Kern Morton J. , Seto Arnold H.
Published: February 2019

Key Points

IVUS measurements of luminal area have only modest correlations to FFR.

This study used IVUS 3D anatomical data in a computational fluid dynamic model to estimate FFR with a reasonable degree of accuracy.

Further studies are needed to refine the models to make them more accurate and practical for routine use.
Techno‐economic feasibility of phosphorus recovery as a coproduct from corn wet milling plants
Authors: Juneja Ankita , Sharma Navneet , Cusick Roland , Singh Vijay
Published: February 2019

Background and objectives

Wet milling (WM) plants contribute to both point source and nonpoint source phosphorus (P) pollution by concentrating P in the coproduct corn gluten feed (CGF), the majority of which is undigested when consumed by ruminants, leading to manure management concerns. Phosphorus runoff from the manure consequently causes eutrophication in the water bodies downstream. This study investigates the economic feasibility of recovering the phosphorus at the front end from light steepwater to reduce P in CGF.

Findings

The amount of phosphorus in CGF was observed to reduce from 11.94 mg/g (db) to 2.44 mg/g (db), with phosphorus removal in the recovery unit calibrated with laboratory experiments. Direct fixed capital cost of $6.9 MM was estimated for the phosphorus recovery unit in an existing WM plant.

Conclusions

With a phosphorus recovery rate of 0.17 MT/hr, the operating cost of P recovery at the front end was estimated to be $1.23/kg‐P removed.

Significance and novelty

Ramifications of excess phosphorus in CGF on environment are an important understudied area. This study provided economic and technical feasibility of phosphorus recovery from CGF in WM industry, consequently producing a new coproduct and reducing the environmental burden.
Model‐less digital workflow for the replication of an existing complete fixed implant‐supported prosthesis using an intraoral scanner
Authors: Markarian Roberto A. , Feitosa Filho Marco , Vasconcelos Ednaria
Published: February 2019

Key Clinical Message

The use of an intraoral scanner was efficient to produce a full‐contour zirconia CAFIP, with improved esthetics when compared to the original prosthesis.
SnS2 Nanosheets/H‐TiO2 Nanotube Arrays as a Type II Heterojunctioned Photoanode for Photoelectrochemical Water Splitting
Authors: Lin Jianfei , Liu Yong , Liu Yongping , Huang Chen , Liu Wenhui , Mi Xihong , Fan Dayong , Fan Fengtao , Lu Huidan , Chen Xiaobo
Published: February 2019

Improving the separation efficiency of photogenerated electron–hole pairs and the conductivity of electrons to photoanode substrates are critical to achieve high‐performance photoelectrochemical (PEC) water splitting. Here, a SnS2/H‐TiO2/Ti heterojunction photoanode was fabricated with SnS2 nanosheets vertically grown on hydrogen‐treated TiO2 (H‐TiO2) nanotube arrays on a Ti substrate. It showed a significantly enhanced photocurrent of 4.0 mA cm−2 at 1.4 V (vs. reversible hydrogen electrode) under AM 1.5 G illumination, 70 times higher than that of SnS2/TiO2/Ti. Kelvin probe force microscopy measurements indicated that photogenerated electrons could be easily transported through the SnS2/H‐TiO2 interface but not through the SnS2/TiO2 interface. Through hydrogen treatment, defects were created in H‐TiO2 nanotubes to convert type I junctions to type II with SnS2 nanosheets. As a result, a high efficiency of electron–hole separation at the SnS2/H‐TiO2 interface and a high electron conductivity in H‐TiO2 nanotubes were achieved and improved PEC performance. These findings show an effective route towards high‐performance photoelectrodes for water splitting.
A comparative evaluation of five common pairwise tests of species association
Authors: Lavender Thomas Michael , Schamp Brandon S. , Arnott Shelley E. , Rusak James A.
Published: February 2019

Researchers have long viewed patterns of species association as key to understanding the processes that structure communities. Community‐level tests of species association have received the most attention; however, pairwise species associations may offer greater opportunity for linking patterns to specific mechanisms. Although several tests of pairwise association have been developed, there remain gaps in our understanding of their performance. Consequently, it is unclear whether these methods reliably detect patterns of association, or if any one method is superior. We maximized association patterns for single species pairs in synthetic community matrices and examined how accurately five pairwise association tests found that pair, while not finding others (i.e., type I and II error rates). All tests are more likely to miss patterns of association than to falsely detect them. When we maximized association for a species pair that included one or more rare or common species, tests were frequently unable to identify that pair as significantly associated. Consequently, these tests are best suited for identifying significant associations between pairs of species that occur in an intermediate number of samples; for such pairs, three of the five tests considered here detected 100% of the pairs for which we maximized associations.
Biogeochemical recuperation of lowland tropical forest during succession
Authors: Sullivan Benjamin W. , Nifong Rachel L. , Nasto Megan K. , Alvarez‐Clare Silvia , Dencker Camie M. , Soper Fiona M. , Shoemaker Kevin T. , Ishida F. Yoko , Zaragoza‐Castells Joana , Davidson Eric A. , Cleveland Cory C.
Published: February 2019

High rates of land conversion and land use change have vastly increased the proportion of secondary forest in the lowland tropics relative to mature forest. As secondary forests recover following abandonment, nitrogen (N) and phosphorus (P) must be present in sufficient quantities to sustain high rates of net primary production and to replenish the nutrients lost during land use prior to secondary forest establishment. Biogeochemical theory and results from individual studies suggest that N can recuperate during secondary forest recovery, especially relative to P. Here, we synthesized 23 metrics of N and P in soil and plants from 45 secondary forest chronosequences located in the wet tropics to empirically explore (1) whether there is a consistent change in nutrients and nutrient cycling processes during secondary succession in the biome; (2) which metrics of N and P in soil and plants recuperate most consistently; (3) if the recuperation of nutrients during succession approaches similar nutrient concentrations and fluxes as those in mature forest in ~100 yr following the initiation of succession; and (4) whether site characteristics, including disturbance history, climate, and soil order are significantly related to nutrient recuperation. During secondary forest succession, nine metrics of N and/or P cycling changed consistently and substantially. In most sites, N concentrations and fluxes in both plants and soil increased during secondary succession, and total P concentrations increased in surface soil. Changes in nutrient concentrations and nutrient cycling processes during secondary succession were similar whether mature forest was included or excluded from the analysis, indicating that nutrient recuperation in secondary forest leads to biogeochemical conditions that are similar to those of mature forest. Further, of the N and P metrics that recuperated, only soil total P and foliar δ15N were strongly influenced by site characteristics like climate, soils, or disturbance history. Predictable nutrient recuperation across a diverse and productive ecosystem may support future forest growth and could provide a means to quantify successful restoration of ecosystem function in secondary tropical forest beyond biomass or species composition.
Seed limitation in an Amazonian floodplain forest
Authors: Terborgh John , Zhu Kai , Alvarez Loayza Patricia , Cornejo Valverde Fernando
Published: February 2019

We monitored a close‐spaced grid of 289 seed traps in 1.44 ha for 8.4 yr in an Amazonian floodplain forest. In a tree community containing hundreds of species, a median of just three to four species of tree seeds falls annually into each 0.5‐m2 establishment site. The number of seed species reaching a given site increased linearly with time for the duration of the monitoring period, indicating a roughly random arrival of seed species in a given site‐year. The number of seed species captured each year over the entire grid ranged from one‐third to one‐half of the total captured over the 8.4 yr of monitoring, revealing a substantial temporal component of variation in the seed rain. Seed rain at the 0.5‐m2 scale displayed extreme spatial variability when all potentially viable seeds were tallied, whereas the rain of dispersed seeds was scant, more nearly uniform, and better mixed. Dispersal limitation, defined as failure of seeds to reach establishment sites, is ≥99% per year for a majority of species, explaining why seed augmentation experiments are often successful. Dispersal limitation has been evoked as an explanation for distance‐dependent species turnover in tropical tree communities, but that interpretation contrasts with the fact that many Amazonian tree species possess large geographical ranges that extend for hundreds or thousands of kilometers. A better understanding of the processes that bridge the gap between the scales of seedling establishment and the regulation of forest composition will require new methodologies for studying dispersal on scales larger than those yet achieved.
Carbon Membranes with Extremely High Separation Factors and Stability
Authors: Rodrigues Sandra C. , Andrade Márcia , Moffat Jamie , Magalhães Fernão D. , Mendes Adélio
Published: February 2019

For some time, carbon molecular sieve membranes (CMSMs) have been promoted as energy‐efficient candidates for gas separation due to their high selectivity, permeability, and stability in chemically aggressive environments. Nevertheless, these membranes have not yet been made into commercial products due to a significant decrease in performance when exposed to humidity and/or oxygen. Herein, disruptive CMSMs with extremely high separation performance and stability, even in the presence of humidity, are reported. The carbon membranes are prepared from a renewable, low‐cost precursor with a single carbonization step. Water vapor adsorption/desorption studies demonstrate that these membranes have a linear water vapor adsorption isotherm, characteristic of a homogeneous distribution of hydrophilic sites on the pore surfaces, allowing for water molecules to hop continuously between sites and avoiding the formation of pore‐blocking water clusters. These results are a breakthrough toward bringing this new type of membrane to a commercial level.
Role of community resource persons in improving use of modern family planning methods among women of reproductive age in a rural area in Ebonyi State, Nigeria
Authors: Akamike Ifeyinwa C. , Mbachu Chinyere , Onwasigwe Chika , Okedo‐Alex Ijeoma , Eze Irene , Eze Nelson
Published: February 2019

Background

The study set out to determine the role of community resource persons in improving uptake of modern family planning methods among women of reproductive age in Ebonyi State.

Methods

A non‐randomized intervention study with control was done. A multistage sampling technique was used to select a sample of 484 in union women of reproductive age. Data were collected using a pretested structured questionnaire. Community resource persons were trained to provide culturally appropriate information on family planning to men and women in the community. Postintervention data were collected after a waiting period of 3 months.

Result

In the intervention arm, use of modern methods of family planning increased significantly by 7.4% at 3 months postintervention (P = 0.01) compared with the control arm. The most commonly used modern methods of family planning were pills, injectables, and barrier methods in the intervention arm and implant in the control arm. The major source of modern methods of family planning was health facility both before and after the intervention in both arms. Number of living children, increasing age and husband's education were predictors of current use of modern family planning methods.

Conclusion

Community‐driven strategies are useful for increasing uptake of modern methods of family planning and are recommended.
Heterogeneity in risk factors for ductal and lobular breast carcinomas: A case–control study
Authors: Dianatinasab Mostafa , Fararouei Mohammad , Daneshi Nima , Rezaian Shahab , Mohammadianpanah Mohammad , Chaman Reza , Ghiasvand Reza
Published: February 2019

Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) of the breast are the most common histological subtypes of breast cancer. However, the associations and heterogeneity between histological subtypes and their risk factors are not well established. This study aimed to investigate risk factors for IDC and ILC. This case–control study included 1,009 incident breast cancer cases and 1,009 hospital controls, frequency‐matched by age. Data were obtained from the patients’ medical files and an interview administered via a questionnaire. Multinomial logistic regression was used and odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. The heterogeneity of the associations was assessed using the Wald test. Family history of breast cancer was associated with IDC (OR 2.64, 95% CI: 1.97–3.55) but not ILC (OR 0.81, 95% CI: 0.42–1.57; p for heterogeneity <0.001). Conversely, a history of miscarriage was associated with ILC (OR 1.71, 95% CI: 1.17–2.51) but not IDC (OR 1.18, 95% CI: 0.95–1.46; p for heterogeneity = 0.04). Similarly, type 2 diabetes was associated with ILC but not IDC (p for heterogeneity = 0.02). Age at first delivery and breastfeeding were significantly associated with IDC but not ILC, though p values for heterogeneity did not reach the significance level. Deliberate weight loss and age at menarche were significantly associated with ILC but not IDC (p for heterogeneity ≥0.27). Smoking, history of benign breast disease and BMI were associated with both subtypes. The present study supports the hypothesis that IDC and ILC are etiologically distinct tumours.
Occurrence of human papillomavirus (HPV) type replacement by sexual risk‐taking behaviour group: Post‐hoc analysis of a community randomized clinical trial up to 9 years after vaccination (IV)
Authors: Gray Penelope , Luostarinen Tapio , Vänskä Simopekka , Eriksson Tiina , Lagheden Camilla , Man Irene , Palmroth Johanna , Pimenoff Ville N. , Söderlund‐Strand Anna , Dillner Joakim , Lehtinen Matti
Published: February 2019

Oncogenic non‐vaccine human papillomavirus (HPV) types may conceivably fill the vacated ecological niche of the vaccine types. The likelihood of this may differ by the risk of acquiring HPV infections. We examined occurrence of HPV types among vaccinated and unvaccinated subgroups of 1992–1994 birth cohorts with differing acquisition risks up to 9 years post‐implementation of HPV vaccination in 33 Finnish communities randomized to: Arm A (gender‐neutral HPV16/18 vaccination), Arm B (girls‐only HPV16/18 vaccination and hepatitis B‐virus (HBV) vaccination of boys), and Arm C (gender‐neutral HBV vaccination). Out of 1992–1994 born resident boys (31,117) and girls (30,139), 8,618 boys and 15,615 girls were vaccinated, respectively, with 20–30% and 50% coverage in 2007–2009. In 2010–2013, 8,868 HPV16/18 and non‐HPV vaccinated females, and in 2014–2016, 5,574 originally or later (2010–2013) HPV16/18 vaccinated females attended two cervical sampling visits, aged 18.5 and 22‐years. The samples were typed for HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/66/68 using PCR followed by MALDI‐TOF MS. HPV prevalence ratios (PR) between Arms A/B vs. C were calculated for Chlamydia trachomatis positives (core‐group), and negatives (general population minus core group). At both visits the vaccine‐protected HPV type PRs did not significantly differ between the core‐group and non‐core group. Among the vaccinated 18‐year‐olds, HPV51 occurrence was overall somewhat increased (PRcore = 1.4, PRnon‐core. = 1.4) whereas the HPV52 occurrence was increased in the core‐group only (PRcore = 2.5, PRnon‐core = 0.8). Among the non‐HPV vaccinated 18‐year‐olds, the HPV51/52 PRs were higher in the core‐group (PRcore = 3.8/1.8, PRnon‐core = 1.2/1.1). The 22‐year‐olds yielded no corresponding observations. Monitoring of the sexual risk‐taking core‐group may detect early tendencies for HPV type replacement.
In search of definitions: Cancer‐associated fibroblasts and their markers
Authors: Nurmik Martin , Ullmann Pit , Rodriguez Fabien , Haan Serge , Letellier Elisabeth
Published: February 2019

The tumor microenvironment has been identified as one of the driving factors of tumor progression and invasion. Inside this microenvironment, cancer‐associated fibroblasts (CAFs), a type of perpetually activated fibroblasts, have been implicated to have a strong tumor‐modulating effect and play a key role in areas such as drug resistance. Identification of CAFs has typically been carried based on the expression of various “CAF markers”, such as fibroblast activation protein alpha (FAP) and alpha smooth muscle actin (αSMA), which separates them from the larger pool of fibroblasts present in the body. However, as outlined in this Review, the expression of various commonly used fibroblast markers is extremely heterogeneous and varies strongly between different CAF subpopulations. As such, novel selection methods based on cellular function, as well as further characterizing research, are vital for the standardization of CAF identification in order to improve the cross‐applicability of different research studies in the field. The aim of this review is to give a thorough overview of the commonly used fibroblast markers in the field and their various strengths and, more importantly, their weaknesses, as well as to highlight potential future avenues for CAF identification and targeting.
Digital Access is not Binary: The 5'A's of Technology Access in the Philippines
Authors: Roberts Tony , Hernandez Kevin
Published: February 2019

Online political participation has been presented as a possible solution to declining levels of trust in traditional politics. However, the most marginalised communities are often the least connected and participate least in digital citizenship programmes. Much existing literature rests on a binary understanding of citizens as being either connected or unconnected. Progress is therefore often understood simply as a process of “connecting the unconnected.” This paper presents primary empirical research from the Philippines, which suggests that such binary understandings disguise more than they reveal. We argue that it is descriptively more accurate and more analytically useful to recognise that multiple classes of technology access exist, which limit digital citizenship in multiple ways. Qualitative methods were used to learn from non‐users and the least connected about the barriers to online civic participation that they experience. The 5'A's of Technology Access was employed as a framework to analyse those barriers and reveal the social and economic factors that they reflect, reproduce, and amplify. Findings suggest that nonbinary and nontechnical understandings of the barriers to digital inclusion are essential to any effective attempt to remove the remaining obstacles to genuinely inclusive digital citizenship.
Remarkable shifts of Csp2‐H and O‐H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes
Authors: Trung Nguyen Tien , Khanh Pham Ngoc , Carvalho Alfredo J. Palace , Nguyen Minh Tho
Published: February 2019

Thirty‐six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH3, NH2. All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C‐H···S to C‐H···O to O‐H···S and finally to O‐H···O. Remarkably, a significant blueshift of Csp2‐H bond by 81–96 cm−1 in the Csp2‐H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O‐H stretching frequency by 206–544 cm−1 in the O‐H···O/S hydrogen bonds is also predicted. The obtained results in our present work and previous literatures support that a distance contraction and a stretching frequency blueshift of C‐H bond involving hydrogen bond depend mainly on its polarity and gas phase basicity of proton acceptor, besides the rearrangement of electron density due to complex formation. Markedly, we suggest the ratio of deprotonation enthalpy to proton affinity (R
c) as an indicator to prospect for classification of hydrogen bonds. The symmetry adapted perturbation theory results show a larger role of attractive electrostatic term in XO‐n as compared to that in XS‐n and the electrostatic interaction is overwhelming dispersion or induction counterparts in stabilizing XO‐n and XS‐n, with n = 1, 2, 3. © 2019 Wiley Periodicals, Inc.
Silencing MEKK3 attenuates cardiomyocyte injury caused by hypoxia/reoxygenation via the sonic hedgehog pathway
Authors: Wang Lei , Yan Weijun , Wang Jing
Published: February 2019

MEKK3 is a member of MAP3K, which plays a pivotal role in cardiac diseases. In this study, we aimed to investigate the effects and potential mechanisms of MEKK3 on hypoxia/reoxygenation (H/R) injury of cardiomyocytes. After exposing H9C2 cells to H/R insult, real‐time polymerase chain reaction and western blot analysis showed that MEKK3 was highly expressed. Cell viability, cell apoptosis, caspase 3/7 activity, and cleaved‐caspase 3 expression were tested using a CCK‐8 assay, Cell Death Detection PLUS ELISA, Caspase‐Glo 3/7 Assay Kit and western blot analysis, respectively. Mitochondrial membrane potential, cytochrome C expression, adenosine triphosphate (ATP), and reactive oxygen species also were measured using JC‐1 staining, western blot analysis, an ATP Assay Kit, and DCFH
2‐DA staining, respectively. The messenger RNA (mRNA) levels and secretions of TNF‐α, IL‐6, and IL‐1β were evaluated. The results revealed that MEKK3 silencing promoted cell survival and attenuated lactate dehydrogenase leakage, cell apoptosis, caspase 3/7 activity, and the protein level of cleaved‐caspase 3. Moreover, knockdown of MEKK3 blocked mitochondrial impairment by inhibiting the loss of mitochondrial membrane potential and cytochrome C expression as well as promoting ATP synthesis. MEKK3 deficiency led to a decrease in reactive oxygen species and malondialdehyde (MDA) generation and an increase in superoxide dismutase (SOD) activity. Deletion of MEKK3 led to reduced inflammatory cytokines in mRNA level and secretion. MEKK3 suppression activated the sonic hedgehog (Shh) signaling pathway in H9C2 cells. After blocking the Shh signaling pathway with a specific inhibitor, cyclopamine, the cardioprotective functions of MEKK3 downregulation were partly abolished. In conclusion, downregulation of MEKK3 prevented apoptosis and inflammation in H9C2 cells via the Shh signaling pathway.
LINC00052 functions as a tumor suppressor through negatively modulating miR‐330‐3p in pancreatic cancer
Authors: Xiong Xingcheng , Shi Qiao , Yang Xiaojia , Wang Weixing , Tao Jing
Published: February 2019

Pancreatic cancer is a serious solid malignant tumor worldwide. Increasing evidence has pointed out that abnormal expressions of long noncoding RNAs are involved in various tumors. Meanwhile, LINC00052 is reported as a famous tumor regulator in several cancers. Nevertheless, the biological role of LINC00052 in pancreatic cancer progression is still unknown. Our study was to explore the specific mechanism of LINC00052 in pancreatic cancer. First, we observed that the LINC00052 was obviously downregulated in several pancreatic cancer cell lines. Overexpression of LINC00052 greatly repressed AsPC‐1 and SW1990 cell proliferation, triggered the apoptosis and prevented cell cycle in the G1 phase. For another, AsPC‐1 and SW1990 cell migration and invasion capacity were also obviously repressed by LINC00052 upregulation. Moreover, miR‐330‐3p was elevated in pancreatic cancer cells and can function as a target of LINC00052 confirmed by luciferase reporter and RNA Immunoprecipitation (RIP) experiments. Inhibition of miR‐330‐3p could depress pancreatic cancer progression while overexpressed miR‐330‐3p exhibited an opposite process. Finally, our data indicated that the LINC00052 also remarkably suppressed pancreatic tumor growth via modulating miR‐330‐3p in vivo. To conclude, our study revealed that the LINC00052 might provide a new perspective for pancreatic cancer therapy.
Identification of microRNA expression in sentinel lymph nodes from patients with breast cancer via RNA sequencing for diagnostic accuracy
Authors: Sun Desheng , Zhong Jieyu , Wei Wei , Chen Xiangmei , Liu Jun , Hu Zhengming
Published: February 2019

Background

Sentinel lymph node (SLN) property assessment (with or without metastasis) is important when deciding the surgery for breast cancer; however, the current diagnosis of SLN metastasis remains to be studied. microRNAs (miRNAs) have been confirmed previously as a molecular marker for the diagnosis, development and prognosis of tumors. However, the detailed role of miRNAs in the diagnosis of SLN metastasis has not been reported.

Methods

The present study aimed to explore the potential use of miRNAs in the diagnosis of SLN using RNA sequencing (RNA‐seq) and a quantitative real‐time polymerase chain reaction (qRT‐PCR) to compare the expression profiles of miRNAs in patients with breast cancer with or without SLN metastasis.

Results

The RNA‐seq results revealed that 1993 miRNAs were differentially expressed in patients with breast cancer with SLN metastasis. Among these miRNAs, 1960 were up‐regulated and 33 were down‐regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that these differentially expressed miRNAs were associated with tumor growth and metastasis and were also predicted to regulate a series of tumorigenesis and metastasis genes. In particular, the most differentially expressed miRNAs were validated by qRT‐PCR, such that miR‐200a‐3p and miR‐96‐5p were up‐regulated and miR‐1‐3p and miR‐486‐3p were down‐regulated in patients with breast cancer with SLN metastasis.

Conclusions

The findings of the present study suggest that there is an association of miRNAs with SLN metastasis and also that miRNAs function as biomarkers with respect to the choice of therapy and disease prognosis.
Analysis of HBV X gene quasispecies characteristics by next‐generation sequencing and cloning‐based sequencing and its association with hepatocellular carcinoma progression
Authors: Mei Fanbiao , Ren Jingjing , Long Long , Li Jilin , Li Kezhi , Liu Haizhou , Tang Yanping , Fang Xiang , Wu Hanghang , Xiao Chanchan , Huang Tianren , Deng Wei
Published: February 2019

Objectives

This study aimed to describe the differences between next‐generation sequencing (NGS) and cloning‐based sequencing (CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and hepatocellular carcinoma (HCC).

Methods

A total of 12 serum samples were collected. Serum hepatitis B virus (HBV) DNA was extracted, and the HBV X‐region (HBX) was amplified by nested polymerase chain reaction (PCR). The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX.

Results

A total of 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity, it was found that the quasispecies complexity value of HBV X‐region obtained by NGS was higher than CBS (P < 0.05). The diversity values, including
d,
dS,
dN, an
d d N/
dS obtained by NGS were lower than by CBS (all of
P < 0.01). The relativity of Spearman(rs) in
d,
dS, and
dN were statistically significant (rs_
d = 0.865,
P = 0.001; rs_
dS = 0.722,
P = 0.014; and rs_
dN = 0.738,
P = 0.011, respectively). There were 21 different bases between the HBX quasispecies of case A and control B.

Conclusion

The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high‐risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration.
Effects of future sea level rise on coastal habitat
Authors: Von Holle Betsy , Irish Jennifer L. , Spivy Annette , Weishampel John F. , Meylan Anne , Godfrey Matthew H. , Dodd Mark , Schweitzer Sara H. , Keyes Tim , Sanders Felicia , Chaplin Melissa K. , Taylor Nick R.
Published: February 2019

Sea level rise (SLR) and disturbances from increased storm activity are expected to diminish coastal ecosystems available to nesting species by removing habitat and inundating nests during incubation. We updated the United States Geological Survey's (USGS) Coastal Vulnerability Index, which provides a qualitative and relative assessment of a coastal area's vulnerability to erosion and shoreline retreat as a function of SLR and other factors, for the South Atlantic Bight. We considered a eustatic SLR projection of 14 cm by 2030. We linked long‐term survey data for 3 sea turtle species, 3 shorebird species, and 5 seabird species to future coastal erosion vulnerability to SLR to understand effects of future SLR on nesting habitats. Over 2,000 km (43%) of the South Atlantic Bight coastline is projected to have an increase in coastal erosion vulnerability by the 2030s, with respect to its present vulnerability. Future vulnerability of SLR‐induced erosion along the South Atlantic Bight is spatially variable, and the 11 coastal study species also varied in their use of coastal habitats with high future coastal vulnerability to SLR. For example, only 23% of high‐density nesting habitat for the brown pelican (Pelecanus occidentalis) is expected to be at increased vulnerability to SLR, whereas >70% of the high‐nesting density habitat for 2 seabird species (gull‐billed tern [Gelochelidon nilotica], sandwich tern [Thalasseus sandvicensis]) is predicted to have higher future coastal erosion vulnerability by 2030. We provide predictions for the level of susceptibility of the study species to erosion from future SLR, which is the first step in managing coastal species for the changing environmental conditions associated with climate change and SLR. © 2019 The Authors. Journal of Wildlife Management Published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.
Abundance and ecological associations of small mammals
Authors: Weldy Matthew J. , Epps Clinton W. , Lesmeister Damon B. , Manning Tom , Linnell Mark A. , Forsman Eric D.
Published: February 2019

Effective conservation and management of small mammals require knowledge of the population dynamics of co‐occurring species. We estimated the abundances, autocorrelations, and spatiotemporal associations of 4 small‐mammal species from 2011–2016 using live‐trapping mark‐recapture methods on 9 sites across elevation and canopy openness gradients of a late‐successional forest in the H. J. Andrews Experimental Forest, on the west slope of the Oregon Cascades. We also quantified species‐specific spatial variation in adult sex ratios and body mass. We used Huggins closed capture models to estimate site‐ and year‐specific abundances of 4 target species: Humboldt's flying squirrels (Glaucomys oregonensis), Townsend's chipmunks (Neotamias townsendii), western red‐backed voles (Myodes californicus), and deer mice (Peromyscus maniculatus). We estimated the temporal autocorrelations among site‐ and species‐specific abundance estimates and used generalized linear mixed effects models to investigate the effects of 7 spatiotemporal covariates on species‐specific mean abundance estimates. Species‐specific adult sex ratios, juvenile to adult ratios, and adult body masses were not widely variable among study sites. Abundance estimates varied by as much as 4‐fold among years and 6‐fold among sites. Humboldt's flying squirrel abundance was temporally autocorrelated at intervals of 1 and 5 years, Townsend's chipmunk abundance was temporally autocorrelated at intervals of 1–4 years, and western red‐backed vole abundance was temporally autocorrelated at 1, 4, and 5 years. Mean fall abundance estimates were associated with elevation and climate and in some cases, canopy openness and berry‐producing shrubs, but the direction of the association differed among species for some covariates. Our findings could provide additional management tools for small‐mammal abundance objectives, and highlight the importance of careful covariate selection in studies using indices of small‐mammal abundance. © 2019 The Authors. Journal of Wildlife Management Published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.