bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution of protein fractions in tofu whey wastewater and its potential influence on anaerobic digestion
Authors: Widyarani  , Butar Butar E S , Dara F , Hamidah U , Sriwuryandari L , Hariyadi H R , Sintawardani N
Published: June 2019

Wastewater from tofu (soybean curd) production contains a high organic concentration that might pollute the environment if it is not treated properly. Among the major organic constituents of tofu wastewater are proteins. Degradation of proteins generates ammonia and H2S gases, and if this occurs in an anaerobic digester might hamper the digester’s performance. On the other hand, proteins can potentially be recovered as value-added products. This research aimed to identify protein amounts in different fractions of tofu wastewater, as a basis of designing a process to recover the proteins. Furthermore, the influence of a lower protein concentration to anaerobic digestion of tofu wastewater was calculated. Tofu wastewater was fractionated by gravity settlement and filtration into settleable, suspended, and dissolved fractions. Subsequently, total solids, protein, and COD concentrations of each fraction were analysed. Our results show that tofu wastewater contained 2.9 g-protein/L, equivalent to 4 g-COD/L. While most of the proteins were dissolved, 9% of the proteins were settleable. This might be recovered via a settling chamber. Using the protein-separated wastewater in anaerobic digestion might reduce NH3 and H2S by 10% while only reduce biogas production by 2%.
Design of conventional mixer for biogas digester
Authors: Fahriansyah  , Andrianto M , Sriharti
Published: June 2019

The aim of this research is to design the mixer for a digester to produce biogas. The mixer is designed to mix various sludge types in all anaerobic digestion applications, in order to achieve a homogeneous mixture in tanks. It has four main parts consisting of lever players, two sets of the support frame, and two sets of blades. The mixer is enclosed in a dome-type digester made from fiberglass with 2.2-meter height, 1.8-meter diameter, and 5.6 cubic meter digester volume. The mixed volume in the stirred digester is 5 cubic meters. With small size, it is suitable for small and medium enterprises in sewage treatment to produce biogas.
Biogas development: Dissemination and barriers
Authors: Dyah S , Sriharti
Published: June 2019

Biogas as alternative energy has long been developed in Indonesia since 1970, however, the utilization of biogas as fuel has not been optimum even can be said is still low compared to the potential. Biogas can be produced from wastes (agriculture, household, farm, etc.), but from various studies and experiments, the best biogas is produced from livestock manure. Initially, the biogas produced from livestock manure was not approved by the community because of the public’s perception that cow dung/manure is dirty and inappropriate to be used for lighting and cooking. Over time these perceptions have changed and biogas is more accepted, but the utilization of biogas is still not optimal, various obstacles arise. This paper provides an overview of the barriers in biogas dissemination in West Java-Indonesia, among others, the investment is expensive, the process is considered complicated, the reluctance to manage the digester like filling cow dung, etc. Knowledge of these barriers can be used for designing the method in disseminating also the pattern/model of biogas development and application in a community to be accepted and sustainable. Information was extracted by observation and survey, interview and learning from various studies and reports. In addition, action research was also conducted in Subang, Sumedang, Bandung of West Java. Results from the studies and action research, show that biogas is actually needed by society, especially in rural areas, if its price is affordable and its operation is easy or not complicated, and also supported by policy.
Preliminary study for 9,10-anthraquinone residue analysis in tea-based functional beverage: GC-ECD optimization and method development
Authors: Pitoi M M , Ariyani M , Koesmawati T A , Yusiasih R
Published: June 2019

9,10-Anthraquinone, a possible carcinogenic compound, is recently detected above the regulated limit in tea samples sourced from Asian countries. Its occurrence is previously neglected. The European Union has set a limit of 0.02 mg/kg for anthraquinone residue in tea. The available analysis methods for anthraquinone are mostly by gas chromatography (GC) coupled with mass spectrophotometer (MS). This study was aimed to analyse anthraquinone in an infusion of tea-based functional beverage based on low volume liquid-liquid extraction followed by a GC-μECD quantification. The experiment included optimisation of GC-μECD for anthraquinone quantification. The result showed that GC-μECD was able to detect anthraquinone at 1 μg/L with good repeatability showed by %RSD of 6.68. The calibration curve at the range of 1 to 10 μg/L showed good linearity (r=0.9973). The low volume liquid-liquid extraction sample preparation was able to extract anthraquinone from the infusion samples as low as 0.67 μg/L.
The use of oxidation reactor for water sample preparation in the total phosphate determination using Segmented Flow Analysis
Authors: Ardeniswan  , Janetasari S A , Muchlis  , Priantoro E A , Sembiring T
Published: June 2019

The pollution in surface waters such as rivers, lakes/reservoirs and estuarine is mostly caused by domestic waste; one of them is detergent. Detergents used in households contain phosphate that disrupts the ecosystem. In the determination of detergents, sample preparation is one of the most important stages. This study describes the use of an oxidation reactor with UV radiation for the destruction of total phosphate compounds in detergent into dissolved phosphates in the preparation stage of detergent determination. With this method, the destruction of total phosphate in detergent samples required a very short time and could be connected directly to the Segmented Flow Analysis device. In this study, the oxidation reactor was tested on artificial samples containing 0.5% detergent and water samples from the Citarum and Cikapundung Rivers (Bandung, Indonesia) which were estimated to be contaminated with detergent. The average concentrations of total phosphate of the samples from Cikapundung and Citarum were 4.5773 ± 0.2286 mg-PO43-/l and 4.1841 ± 0.0361 mg-PO43-/l, respectively. Meanwhile, the average concentration of total phosphate of the artificial sample was 5.5727 ± 0.1830 mg-PO43-/l. The results show that the sample digestion method using UV radiation in the oxidation reactor can provide excellent results with a high recovery at 94.51%.
Remediation of Ni2+ in a nickel-contaminated water sample using magnetic nanoprobes prepared via green process by Psidium guajava leaves extract
Authors: Capangpangan R Y , Corpuz M J B , Alguno A C
Published: June 2019

Rapid detection of toxic metal ions is of paramount importance in environmental studies for efficient environmental remediation. The use of effective nanomaterials that facilitate fast detection and cost-effective analysis is one of the active areas of research nowadays. Plant-based magnetic nanoparticles (MNPs) were prepared via a reverse chemical co-precipitation method using guava leaves extract as a reducing agent. The prepared MNPs were utilized as an adsorbent for the remediation of Ni2+ ions in aqueous solution. Batch adsorption experiment was conducted to evaluate the amount of Ni2+ ions being adsorbed in the surface of the MNPs. Results revealed that 98% of the Ni2+ ions were adsorbed in the surface of the MNPs when 5.0 mg of the MNP adsorbent was utilized. Likewise, it was observed that the maximum adsorption was achieved even at 10 minutes incubation time using 1.597 ppm initial Ni2+ concentration and the use of 5.0 mg of MNP. The adsorption behavior and mechanism of MNPs as the adsorbent is probably dominated by electron-electron interaction, and the data can be correlated with the functional group analysis using Fourier-Transform Infrared Spectroscopy (FT-IR). It was also observed that higher adsorption capacity (~8.5 mg/g) was attained when 5.0 mg of MNP was used. Importantly, the equilibrium data perfectly fit in the Langmuir isotherm with a slight deviation in the Freundlich isotherm.
Can Electrical Resistance Tomography be Used to Monitor the Distribution of Moisture in Cement-Based Materials?
Authors: Jiang Yong , Qin Lei , Ren Hongwei
Published: June 2019

It is important to develop a tool to monitor moisture distribution in cement-based materials, because freeze-thaw of concrete, corrosion of steel bars, carbonization and other problems occur in the presence of water. In this paper, the feasibility of monitoring water distribution in cement-based materials by electrical resistance imaging (ERT) is studied. In ERT technology, the resistivity distribution is reconstructed by detecting the voltage at the boundary of the test block, and the structure and state of the object are presented by the image. The experimental results show that ERT technology can monitor the moisture distribution and outline in cement-based materials.
Stability Analysis and Reinforcement Treatment of Open Pit Slope
Authors: Liu Yunqiu , Wang Xiaofei , Gao Jiaxing
Published: June 2019

The construction of mine surface facilities shall be carried out according to the scope of mining rights and ease of use. The underground mining of Shirengou Iron Mine uses filling method mining, and the filling station needs to be built on the surface. According to the design, it is constructed near the open pit. Based on the protection of the filling station system, the stability analysis of the open slope is needed. The failure mode of iron ore open slope is circular arc sliding failure mode. The calculation model of the stability analysis is calculated by the residual thrust method. The maximum residual thrust of the I-I section is 128.9 tons/meter, and the maximum residual thrust of the II-II section is 75.39 tons/meter. According to the calculation results, the safety measures such as slope dressing and masonry retaining wall are carried out on the open slope, and the grouting prestressed anchor cable is selected to reinforce the slope. The anchor cables are connected by reinforced concrete frame and beam, and the concrete is used. The beam acts as an anchor pier. In order to effectively consolidate the slope stability, the grouting method is combined to effectively treat the slope. After a series of slope reinforcement measures, the stability of the open slope and the safety of the filling station can be guaranteed.
Research Progress on Self-Healing and Repairing Technology of Asphalt Mixture Crack
Authors: Hui Jia , Gu Yunhui , Wang Tong , Jiang Ruinan , Zhu Baolin
Published: June 2019

The latest research results at home and abroad have comprehensively analyzed the self-healing and repairing technology of asphalt mixture, and introduced the self-healing mechanism of asphalt and self-healing behavior of asphalt. Active and passive healing methods are mainly discussed. Both methods can effectively enhance the healing properties of asphalt materials and achieve the purpose of repairing cracks and looseness of asphalt concrete pavement. The development of self-healing asphalt concrete technology at home and abroad is expounded, and the application significance and application prospect of the technology are analyzed. The conclusion is that the environmental and social benefits of self-healing asphalt concrete technology are outstanding, and the promotion is of great significance and good development prospects.
The Dynamic Mechanics Behavior on Triaxial Compression of the Recycled Aggregate Concrete
Authors: He Z. J. , Ding M. J.
Published: June 2019

The tests under triaxial compression states were conducted on recycled aggregate concrete (RAC) by different stress ratios (-0.1: -0.1: -1; -0.1: -0.25: -1; -0.1: -0.5: -1; -0.1: -0.75: -1; -0.1: -1: -1) at the strain rates of 10-5/s, 10-4/s, 10-3/s, and 10-2/s. This study was accomplished in the servo-hydraulic multi-axial testing system. The experimental phenomena and failure modes of recycled aggregate concrete under triaxial compression are described, the results of triaxial compressive strength of recycled aggregate concrete are presented, the effects of the strain rate and stress ratio on the triaxial compressive strength of recycled aggregate concrete are studied. This paper built a new dynamic strength criterion. The strength criterion describes the characteristics of structural RAC at different stress ratios and strain rates. The feature of the model is that it can consider the influence of strain rates.
Analysis’s Research Status of Reinforcement Technology of PP-Bands in Masonry Structures
Authors: Zhou Qiang , Min Quanhuan , Wu Shuang
Published: June 2019

Reinforcement with polypropylene bands is a newly arisen seismic technique. it can effectively improve the ultimate shear and flexural capacity and seismic performance of the structure, sudden collapse of whole structure can also be avoided, so it is especially suitable for the seismic reinforcement of rural masonry structures. In recent years, it has been gradually applied in the reinforcement and restoration of masonry structures. Based on the latest development of research, the influence of reinforcement with polypropylene bands (pp-bands) on the shear, flexural and seismic behavior of masonry structure were systematically introduced. The influence of the main reinforcement parameters such as mesh size, grid layout direction, connection mode, connection strength and mortar layer on the reinforcement effect were summarized. Deficiency of the current research and the key problems that need to be solved were pointed out. Through the study on research status of reinforcement technology of pp-bands in masonry structures, references for further research on the strengthening technology of pp-bands and the seismic reinforcement of rural masonry buildings in China were given.
Influence of Shield Propulsion on Longitudinal Soil Mass Near Subway Structure
Authors: Zhang Zhaoran , Guo Yixian , Jiao Weigang , Tong Wenjing
Published: June 2019

Metro construction has important significance to the safety of the structure, based on a line existing Beijing subway, with air shaft and station structure as the background, research on soil displacement near the existing structure. The results show that: (1)The shield to the main structure from about 28.8m-7.2m (except for the shield at the center line testing point), the displacement and the shield is the same direction, the displacement changes generally decrease from the surface to the deep level, the variation is in the range of 1-5mm, with a linear distribution; (2) The displacement direction is as same as shield direction from 7.2m-3.6m, the displacement increases continuously is in the range of 5-15mm, the displacement accord with normal distribution; (3) 1 times diameter range and the shield to the existing structure of 7.2m-3.6m range should be regarded as significant influence area in the process of shield construction. The displacement of soil increases with the approach of shield, the maximum displacement point appears at the center of shield or above the top of shield of 1m. The above results can provide reference for shield driving parameters.
Application and Effect of Underground Magnetic Fluid Detection Technology to Detect Groundwater of Highway Slope
Authors: Yang Chao , Wang Kai , Cao Yunjiang
Published: June 2019

The dynamic information such as water level, supply source and motion direction of groundwater in slope engineering have an important influence on the selection of water drainage project. It is important to quickly and effectively ascertain the groundwater information of slope engineering. The underground magnetic fluid detection technology uses the groundwater flow system to continuously cut the magnetic force lines in the geomagnetic field to form the underground magnetic fluid and then generate induced electromagnetic fields. The dynamic information of groundwater can be detected quickly and efficiently by testing the electromagnetic field. The application results of groundwater detection technology in Shang-San Expressway in Zhejiang province to K290 + 400 slope show that: the results of exploration are basically consistent with the results of underground magnetic fluid detection; and groundwater distribution of slope which is tested by underground magnetic fluid detection technology is reliable. The underground magnetic fluid detection technology provides a quick and effective means for groundwater exploration of slope engineering.
A Nation of Immigrants?
Authors: Minich Julie Avril
Published: June 2019

With US immigration policy seeming ever more brutal with each new headline, it becomes increasingly tempting to advocate for the rights of migrants and asylum seekers by presenting the current situation as extraordinary and questioning the legitimacy of the Trump administration’s border enforcement tactics. Jay Timothy Dolmage, Katherine Benton-Cohen, and Beth Lew-Williams, however, show that the contemporary moment is far from exceptional; rather, immigration restriction in North America has long mobilized exclusionary nativist logics and shifting constructions of legality. Timely without being ripped from the headlines, their latest books offer much-needed historical context for a current humanitarian crisis along with important lessons from previous crises.
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors
Authors: Wu Jiansheng , Liu Ben , Chan Wallace K B , Wu Weijian , Pang Tao , Hu Haifeng , Yan Shancheng , Ke Xiaoyan , Zhang Yang
Published: June 2019

Motivation

Accurate prediction and interpretation of ligand bioactivities are essential for virtual screening and drug discovery. Unfortunately, many important drug targets lack experimental data about the ligand bioactivities; this is particularly true for G protein-coupled receptors (GPCRs), which account for the targets of about a third of drugs currently on the market. Computational approaches with the potential of precise assessment of ligand bioactivities and determination of key substructural features which determine ligand bioactivities are needed to address this issue.

Results

A new method, SED, was proposed to predict ligand bioactivities and to recognize key substructures associated with GPCRs through the coupling of screening for Lasso of long extended-connectivity fingerprints (ECFPs) with deep neural network training. The SED pipeline contains three successive steps: (i) representation of long ECFPs for ligand molecules, (ii) feature selection by screening for Lasso of ECFPs and (iii) bioactivity prediction through a deep neural network regression model. The method was examined on a set of 16 representative GPCRs that cover most subfamilies of human GPCRs, where each has 300–5000 ligand associations. The results show that SED achieves excellent performance in modelling ligand bioactivities, especially for those in the GPCR datasets without sufficient ligand associations, where SED improved the baseline predictors by 12% in correlation coefficient (r2) and 19% in root mean square error. Detail data analyses suggest that the major advantage of SED lies on its ability to detect substructures from long ECFPs which significantly improves the predictive performance.

Availability and implementation

The source code and datasets of SED are freely available at https://zhanglab.ccmb.med.umich.edu/SED/.

Supplementary information

Supplementary data are available at Bioinformatics online.
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
Authors: Junge Alexander , Jensen Lars Juhl
Published: June 2019

Motivation

Information extraction by mining the scientific literature is key to uncovering relations between biomedical entities. Most existing approaches based on natural language processing extract relations from single sentence-level co-mentions, ignoring co-occurrence statistics over the whole corpus. Existing approaches counting entity co-occurrences ignore the textual context of each co-occurrence.

Results

We propose a novel corpus-wide co-occurrence scoring approach to relation extraction that takes the textual context of each co-mention into account. Our method, called CoCoScore, scores the certainty of stating an association for each sentence that co-mentions two entities. CoCoScore is trained using distant supervision based on a gold-standard set of associations between entities of interest. Instead of requiring a manually annotated training corpus, co-mentions are labeled as positives/negatives according to their presence/absence in the gold standard. We show that CoCoScore outperforms previous approaches in identifying human disease–gene and tissue–gene associations as well as in identifying physical and functional protein–protein associations in different species. CoCoScore is a versatile text mining tool to uncover pairwise associations via co-occurrence mining, within and beyond biomedical applications.

Availability and implementation

CoCoScore is available at: https://github.com/JungeAlexander/cocoscore.

Supplementary information

Supplementary data are available at Bioinformatics online.
Polyamine-stimulation of arsenic-transformed keratinocytes
Authors: Alexander Eric T , Mariner Kelsey , Borodyanskaya Yelizaveta , Minton Allyson , Gilmour Susan K
Published: June 2019

Tumor promotion is strongly associated with inflammation and increased polyamine levels. Our understanding of relevant mechanisms responsible for arsenic-induced cancer remains limited. Previous studies suggest that arsenic targets and dysregulates stem cell populations that remain dormant in the skin until promoted to be recruited out of the bulge stem cell region, thus giving rise to skin tumors. In this study, we explored a possible mechanism by which increased keratinocyte polyamine biosynthesis promotes tumorsphere formation and invasiveness of arsenic-transformed HaCaT keratinocytes (As-HaCaT). Unlike parental HaCaT cells, As-HaCaT cells were tumorigenic in athymic nude mice, and the CD45negative epithelial tumor cells had enriched expression of Toll-Like Receptor 4 (TLR4), CD34 and CXCR4 as did As-HaCaT tumorsphere cultures compared to As-HaCaT monolayer cultures. Ornithine decarboxylase (ODC) overexpressing keratinocytes (Ker/ODC) release increased levels of the alarmin high mobility group box 1 (HMGB1). Ker/ODC conditioned medium (CM) stimulated As-HaCaT but not parental HaCaT tumorsphere formation, and this was inhibited by glycyrrhizin, an inhibitor of HMGB1, and by TAK242, an inhibitor of the HMGB1 receptor TLR4. Compared to parental HaCaT cells, As-HaCaT cells demonstrated greater invasiveness across a Matrigel-coated filter using either fibroblast CM or SDF-1α as chemoattractants. Addition of Ker/ODC CM or HMGB1 dramatically increased As-HaCaT invasiveness. Glycyrrhizin and TAK242 inhibited this Ker/ODC CM-stimulated invasion of As-HaCaT cells but not HaCaT cells. These results show that polyamine-dependent release of HMGB1 promotes the expansion of stem cell-like subpopulations in arsenic-transformed keratinocytes while also increasing their invasiveness, suggesting that polyamines may be a potential therapeutic target for the prevention and treatment of arsenic-initiated skin cancers.
STDP Forms Associations between Memory Traces in Networks of Spiking Neurons
Authors: Pokorny Christoph , Ison Matias J , Rao Arjun , Legenstein Robert , Papadimitriou Christos , Maass Wolfgang
Published: June 2019

Memory traces and associations between them are fundamental for cognitive brain function. Neuron recordings suggest that distributed assemblies of neurons in the brain serve as memory traces for spatial information, real-world items, and concepts. However, there is conflicting evidence regarding neural codes for associated memory traces. Some studies suggest the emergence of overlaps between assemblies during an association, while others suggest that the assemblies themselves remain largely unchanged and new assemblies emerge as neural codes for associated memory items. Here we study the emergence of neural codes for associated memory items in a generic computational model of recurrent networks of spiking neurons with a data-constrained rule for spike-timing-dependent plasticity. The model depends critically on 2 parameters, which control the excitability of neurons and the scale of initial synaptic weights. By modifying these 2 parameters, the model can reproduce both experimental data from the human brain on the fast formation of associations through emergent overlaps between assemblies, and rodent data where new neurons are recruited to encode the associated memories. Hence, our findings suggest that the brain can use both of these 2 neural codes for associations, and dynamically switch between them during consolidation.
Immune Reconstitution Inflammatory Syndrome as a Posttransplantation Complication in Primary Immunodeficiency With Disseminated Mycobacterium avium
Authors: Manion Maura , Dimitrova Dimana , Pei Luxin , Gea-Banacloche Juan , Zelazny Adrian , Lisco Andrea , Zerbe Christa , Freeman Alexandra F , Holland Steven M , Kanakry Christopher G , Kanakry Jennifer A , Sereti Irini
Published: June 2019

Patients with primary immunodeficiencies undergoing allogeneic hematopoietic cell transplantation (HCT) for difficult-to-control infections can experience immune reconstitution inflammatory syndrome (IRIS) following engraftment. In 3 patients with post-HCT IRIS related to mycobacterial infection, in vitro data demonstrate the emergence of pathogen-specific immune responses and a concomitant rise in plasma inflammatory markers.
Photosynthesis and Survival of Young Carpotroche brasiliensis Endl. (Achariaceae) Plants Subjected to Flooding
Authors: Queiroz-Alves Laize , Leal Adrielle , Dalmolin Ândrea Carla , Schaffer Bruce , Mielke Marcelo Schramm
Published: June 2019

Carpotroche brasiliensis is a native tree of the Brazilian Atlantic Forest with potential economic value for cultivation in agroforestry systems. We conducted an experiment to determine the photosynthetic and survival responses of young C. brasiliensis plants to electrochemical changes in flooded soils as an indication of their flood tolerance and potential for cultivation in flood-prone areas. Soil flooding decreases the reduction–oxidation potential (redox) potential (Eh), pH, and electrical conductivity (Ec) of the soil, with subsequent recovery of the pH and Ec. Decreases in Eh negatively affect net photosynthesis (A). In flooded soil, decreased A was associated with decreased stomatal conductance (gs) and after 21 days was also associated with decreases in the instantaneous carboxylation efficiency (A/Ci) and potential quantum yield of photosystem II (Fv/Fm). Although flooded C. brasiliensis seedlings developed morphological structures known to increase flood tolerance, this was not enough to prevent severe signs of flooding stress. After 21 days of flooding, flooded plants were unflooded, and 17 days after plants were removed from flood, 90 percent of the unflooded plants died. Our results demonstrate that young plants of C. brasiliensis are suitable for planting in agroforestry systems only in areas with well-drained soils.
Enrichment of G4DNA and a Large Inverted Repeat Coincide in the Mitochondrial Genomes of Termitomyces
Authors: Nieuwenhuis Mathijs , van de Peppel Lennart J J , Bakker Freek T , Zwaan Bas J , Aanen Duur K
Published: June 2019

Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape, and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered that the mitochondrial genomes of a basidiomycete fungus (Termitomyces spp.) contain an inverted repeat (IR), a duplicated region half the size of the complete genome. In addition, we found an abundance of sequences capable of forming G-quadruplexes (G4DNA); structures that can disrupt the double helical formation of DNA. G4DNA is implicated in replication fork stalling, double-stranded breaks, altered gene expression, recombination, and other effects. To determine whether this occurrence of IR and G4DNA was correlated within the genus Termitomyces, we reconstructed the mitochondrial genomes of 11 additional species including representatives of several closely related genera. We show that the mtDNA of all sampled species of Termitomyces and its sister group, represented by the species Tephrocybe rancida and Blastosporella zonata, are characterized by a large IR and enrichment of G4DNA. To determine whether high mitochondrial G4DNA content is common in fungi, we conducted the first broad survey of G4DNA content in fungal mtDNA, revealing it to be a highly variable trait. The results of this study provide important direction for future research on the function and evolution of G4DNA and organellar IRs.
Deleterious Mutation Accumulation in Arabidopsis thaliana Pollen Genes: A Role for a Recent Relaxation of Selection
Authors: Harrison Mark C , Mallon Eamonn B , Twell Dave , Hammond Robert L
Published: June 2019

In many studies, sex-related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 Myr, A. thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity, and a dilution of masking in diploid expressed, sporophytic genes. In this study, we have investigated the relative strength of selection on pollen genes compared with sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible, positive selection was stronger on pollen genes than sporophytic genes for A. thaliana and 2) current polymorphism data indicate that selection is weaker on pollen genes compared with sporophytic genes. This weaker selection on pollen genes can in part be explained by their higher tissue specificity, which in outbreeding plants can be outweighed by the effects of haploid expression and pollen competition. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared with sporophytic genes.
Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans
Authors: Whitman Mary C , Miyake Noriko , Nguyen Elaine H , Bell Jessica L , Matos Ruiz Paola M , Chan Wai-Man , Di Gioia Silvio Alessandro , Mukherjee Nisha , Barry Brenda J , Bosley T M , Khan Arif O , Engle Elizabeth C
Published: June 2019

Oculomotor synkinesis is the involuntary movement of the eyes or eyelids with a voluntary attempt at a different movement. The chemokine receptor CXCR4 and its ligand CXCL12 regulate oculomotor nerve development; mice with loss of either molecule have oculomotor synkinesis. In a consanguineous family with congenital ptosis and elevation of the ptotic eyelid with ipsilateral abduction, we identified a co-segregating homozygous missense variant (c.772G>A) in ACKR3, which encodes an atypical chemokine receptor that binds CXCL12 and functions as a scavenger receptor, regulating levels of CXCL12 available for CXCR4 signaling. The mutant protein (p.V258M) is expressed and traffics to the cell surface but has a lower binding affinity for CXCL12. Mice with loss of Ackr3 have variable phenotypes that include misrouting of the oculomotor and abducens nerves. All embryos show oculomotor nerve misrouting, ranging from complete misprojection in the midbrain, to aberrant peripheral branching, to a thin nerve, which aberrantly innervates the lateral rectus (as seen in Duane syndrome). The abducens nerve phenotype ranges from complete absence, to aberrant projections within the orbit, to a normal trajectory. Loss of ACKR3 in the midbrain leads to downregulation of CXCR4 protein, consistent with reports that excess CXCL12 causes ligand-induced degradation of CXCR4. Correspondingly, excess CXCL12 applied to ex vivo oculomotor slices causes axon misrouting, similar to inhibition of CXCR4. Thus, ACKR3, through its regulation of CXCL12 levels, is an important regulator of axon guidance in the oculomotor system; complete loss causes oculomotor synkinesis in mice, while reduced function causes oculomotor synkinesis in humans.
Universal standards for the concept of trust in online dispute resolution systems in e-commerce disputes
Authors: Abedi Fahimeh , Zeleznikow John , Bellucci Emilia
Published: June 2019

The need for an appropriate jurisdiction for electronic commerce disputes has led to the well-established mechanism for solving disputes through the internet known as the Online Dispute Resolution (ODR). Currently, there is no universal agreement about the concept of trust in ODR systems, although this issue has been widely discussed in the field of Alternative Dispute Resolution (ADR). The current study aimed to develop a set of standards to enhance trust and confidence in using ODR systems. In this study, we have adopted a new approach in the ODR field, and no similar research has been conducted. This study used a quantitative (online survey) and mainly qualitative approach (interview) for gathering data. After analysing data, this research identified three elements as standards to measure trust in ODR systems including knowledge, expectations of fairness and code of ethics. Finally, our findings provide several practical and methodological implications.
Smartphone photography as a possible method of post-validation trachoma surveillance in resource-limited settings
Authors: Snyder Blake M , Sié Ali , Tapsoba Charlemagne , Dah Clarisse , Ouermi Lucienne , Zakane S Alphonse , Keenan Jeremy D , Oldenburg Catherine E
Published: June 2019

Background

Validation of trachoma elimination requires monitoring after discontinuation of trachoma program activities, though such evaluations are not commonly done.

Methods

Conjunctival examinations and smartphone photography were performed on a random sample of pre-school children from 15 villages in a region of Burkina Faso thought to have eliminated trachoma.

Results

No clinically active trachoma was detected by in-field or photographic evaluation. Smartphone images demonstrated high agreement with field grading (>99% concordance).

Conclusions

Trachoma appears to have been eliminated from this area of Burkina Faso. Smartphone cameras may be a useful aid for monitoring in resource-limited settings.
Diffusion, implementation, and use of Research Electronic Data Capture (REDCap) in the Veterans Health Administration (VA)
Authors: Paris Bonnie L , Hynes Denise M
Published: June 2019

This case study describes the implementation of the Research Electronic Data Capture (REDCap) software at the United States Department of Veterans Affairs Veterans Health Administration (VA). VA REDCap enables secure and standardized data collection, fosters collaboration with external researchers through use of a widely used data management tool, facilitates multisite studies through use of data forms that can be shared across sites within and outside the VA, is well suited to health services research studies and quality improvement projects, and enables exporting data for analysis in the VA secure computing environment. Using a diffusion of innovation framework approach, authors explore organizational factors that shaped adoption of REDCap technology and constraints on its use within the VA. Lessons learned from the VA experience are discussed.
MiR-21 Regulates Keloid Formation by Downregulating Smad7 via the TGF-β/Smad Signaling Pathway
Authors: Wu Junliang , Fang Lu , Cen Ying , Qing Yong , Chen Junjie , Li Zhengyong
Published: June 2019

A keloid is a benign fibroproliferative skin tumor that results from abnormal wound healing after injury and tends to grow beyond the boundary of the original wound; the mechanism of keloid formation is still unclear. MicroRNA-21 (MiR-21) is a representative microRNA that plays a key role in a variety of fibrotic diseases via the transforming growth factor-β/Smad signaling pathway. The aim of our study was to explore the mechanism of keloid formation. First, we found that the expression of miR-21 in keloids and keloid fibroblasts was significantly upregulated by microRNA microarray and real-time polymerase chain reaction. Additionally, at the protein level, our study confirmed that the overexpression of miR-21 could promote the process of keloid fibrosis to some extent and also indicated that a low expression of miR-21 could inhibit the process of keloid fibrosis. Finally, the results proved that miR-21 could participate in the keloid fibrosis process through negative regulation of its downstream target gene Smad7 via the transforming growth factor-β/Smad signaling pathway, which provides a guiding framework for further studies and new theoretical support for keloid clinical treatment.
Influence of Menstrual Cycle Timing on Screening Breast MRI Background Parenchymal Enhancement and Diagnostic Performance in Premenopausal Women
Authors: Dontchos Brian N , Rahbar Habib , Partridge Savannah C , Lehman Constance D , DeMartini Wendy B
Published: June 2019

Purpose

To assess the influence of menstrual cycle timing on background parenchymal enhancement (BPE) and performance on screening breast magnetic resonance imaging (MRI) in premenopausal women at high risk for developing breast cancer.

Methods

After Institutional Review Board approval, all screening breast MRIs performed from January 2007 through November 2010 in premenopausal women in whom day from last menstrual period was recorded were identified. Prospectively recorded BPE levels and Breast Imaging Reporting and Data System MRI assessments were extracted from our database. Subject outcomes were determined by using biopsy, imaging follow-up, and linkage with the regional tumor registry (minimum 12-month follow-up). Associations of BPE levels (minimal/mild versus moderate/marked) with menstrual cycle phase (follicular [day 0–15] versus luteal [day 16–35]) and week (1, 2, 3, or 4) were compared. Differences in MRI performance metrics, including abnormal interpretation rate (AIR), positive biopsy rate (PBR), cancer yield, sensitivity, and specificity, were compared between menstrual cycle phase and menstrual cycle week.

Results

Three-hundred twenty examinations in 244 premenopausal women met inclusion criteria with nine cancers diagnosed. BPE levels were not associated with menstrual cycle phase or week (P > 0.05). MRI performance metrics (ie, AIR, PBR, cancer yield, sensitivity, or specificity) did not differ significantly based on menstrual cycle phase or menstrual cycle week (P > 0.05).

Conclusions

Obtaining screening breast MRI exams during specific phases or weeks of the menstrual cycle in premenopausal women does not reliably produce MRI examinations with lower BPE levels or improved performance.
Coffee, green tea and liver cancer risk: an evaluation based on a systematic review of epidemiologic evidence among the Japanese population
Authors: Tanaka Keitaro , Tamakoshi Akiko , Sugawara Yumi , Mizoue Tetsuya , Inoue Manami , Sawada Norie , Matsuo Keitaro , Ito Hidemi , Naito Mariko , Nagata Chisato , Kitamura Yuri , Sadakane Atsuko , Tsugane Shoichiro , Shimazu Taichi ,   for the Research Group for the Development and Evaluation of Cancer Prevention Strategies in Japan
Published: June 2019

Background

Coffee and green tea, two popular drinks in the Japanese, have recently drawn much attention as potential protective factors against the occurrence of liver cancer.

Methods

We systematically reviewed epidemiologic studies on coffee, green tea and liver cancer among Japanese populations. Original data were obtained by searching the MEDLINE (PubMed) and Ichushi databases, complemented with manual searches. The evaluation was performed in terms of the magnitude of association in each study and the strength of evidence (‘convincing’, ‘probable’, ‘possible’, or ‘insufficient’), together with biological plausibility.

Results

We identified four cohort and four case-control studies on coffee and liver cancer and six cohort and one case-control studies on green tea and liver cancer. All cohort and case-control studies on coffee reported a weak to strong inverse association, with a summary relative risk (RR) for one cup increase being 0.72 (95% confidence interval [CI] 0.66–0.79). Conversely, all studies but two cohort studies on green tea reported no association, with a corresponding summary RR of 0.99 (95% CI 0.97–1.01, P = 0.37).

Conclusion

Coffee drinking ‘probably’ decreases the risk of primary liver cancer among the Japanese population whereas the evidence on an association between green tea and liver cancer is ‘insufficient’ in this population.
The compliance dilemma: economic sanctions and the AIPN Model Form International Joint Operating Agreement
Authors: Derman Andrew B , Melsheimer Andrew , Auner Thomas J , Sikes Skyler K
Published: June 2019

The current AIPN Model Form International JOA (the ‘Model Form’) does not sufficiently address circumstances and issues arising from economic sanctions, and the global contemporary trend demonstrates a significant increase in the use of sanctions by both multi-national governing bodies and nation-states. The USA implements unilateral economic sanctions more than any other country, and because US sanctions are often designed to prevent petroleum-related business with targeted countries and parties. Accordingly, this article (i) analyzes the impact US economic sanctions may have on the ability of international JOA members to both comply with sanctions and protect their interests under the JOA, and (ii) proposes certain definitions and a number of additional provisions the Model Form can adopt to address the issues arising from economic sanctions and protect the each party's interests.
Music as Feminine Capital in Napoleonic France: Nancy Macdonald’s Musical Upbringing
Authors: Geoffroy-Schwinden Rebecca Dowd
Published: June 2019

This microhistory situates the musical activities of Nancy Macdonald, a French student at Madame Campan’s National Institute for Young Women and Napoleon Bonaparte’s school for daughters of Legion of Honour Recipients, in broader discourses about women and music in Napoleonic France. Drawing on Pierre Bourdieu’s theories of capital, it eschews a simplistic assessment of music as either constraining or liberating young women, by arguing instead that performance operated as a kind of ‘feminine capital’, accrued and then circulated to achieve tangible socio-economic ends. A feminine-capital framework exposes the paradoxes inherent in female music-making and reveals how values about music were enculturated from girlhood to womanhood in France. This approach contributes to recent scholarship that challenges the rigid binaries previously defining women’s musical labour during the Classical era and inserts France into historiographies of women’s musical practices in the early nineteenth century.
Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening
Authors: Lountos George T , Zhao Xue Zhi , Kiselev Evgeny , Tropea Joseph E , Needle Danielle , Pommier Yves , Burke Terrence R , Waugh David S
Published: June 2019

Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3′ end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.
The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo
Authors: Cucinotta Christine E , Hildreth A Elizabeth , McShane Brendan M , Shirra Margaret K , Arndt Karen M
Published: June 2019

The nucleosome core regulates DNA-templated processes through the highly conserved nucleosome acidic patch. While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo. We employed site-specific crosslinking to identify proteins that directly bind the acidic patch in Saccharomyces cerevisiae and demonstrated crosslinking of histone H2A to Paf1 complex subunit Rtf1 and FACT subunit Spt16. Rtf1 bound to nucleosomes through its histone modification domain, supporting its role as a cofactor in H2B K123 ubiquitylation. An acidic patch mutant showed defects in nucleosome positioning and occupancy genome-wide. Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.
Targeted DNA transposition in vitro using a dCas9-transposase fusion protein
Authors: Bhatt Shivam , Chalmers Ronald
Published: June 2019

Homology-directed genome engineering is limited by transgene size. Although DNA transposons are more efficient with large transgenes, random integrations are potentially mutagenic. Here we present an in vitro mechanistic study that demonstrates efficient Cas9 targeting of the mariner transposon Hsmar1. Integrations were unidirectional and tightly constrained to one side of the sgRNA binding site. Further analysis of the nucleoprotein intermediates demonstrated that the transposase and Cas9 moieties can bind their respective substrates independently or in concert. Kinetic analysis of the reaction in the presence of the Cas9 target–DNA revealed a delay between first and second strand cleavage at the transposon end. This step involves a significant conformational change that may be hindered by the properties of the interdomainal linker. Otherwise, the transposase moiety behaved normally and was proficient for integration in vitro and in Escherichia coli. Specific integration into the lacZ gene in E. coli was obscured by a high background of random integrations. Nevertheless, Cas9 is an attractive candidate for transposon-targeting because it has a high affinity and long dwell-time at its target site. This will facilitate a future optogenetic strategy for the temporal control of integration, which will increase the ratio of targeted to untargeted events.