bluuebunny/crossref_metadata_2025 huggingface dataset:
Ex situ Conservation of Diospyros spp. (Ebenaceae) in the Bogor Botanic Gardens, Indonesia
Authors: Wanda I F , peniwidiyanti  , Oksari A A
Published: September 2019

Diospyros spp. is one of the genera of the Ebenaceae that has the highest distribution in tropical Asia and Africa. The high rate of deforestation in the tropics, so we need for preservation of species in conservation ex-situ at the Botanical Gardens. Research on the basic information and potential of Diospyros spp., the collection of the Bogor Botanical Gardens has been carried out through direct observation of all the Gardens’ Diospyros collections, both in the field and in the nursery. The results obtained as many as 32 species of Diospyros spp. which have been collected with the most specimens of the species Diospyros celebica, D. buxifolia, and D. maritima. Meanwhile, the source collection Diospyros spp. mostly from Sulawesi. The general potential of Diospyros spp. used as a valuable timber (ebony) and edible fruit.
The Effect of PVA and PEG Infusion on Titania Antibacterial Coating
Authors: Margaretta D O , Permadi K W , Rahman D Y , Utami F D , Viridi S , Abdullah M
Published: September 2019

Indonesia has great potential of the Solar energy, irradiated by the Sun throughout the years. Cotton textiles antibacterial has been prepared by coating Titania (TiO2) with Polyethylene glycol (PEG) and Polyvinyl alcohol (PVA) as adhesives. The method of depositing cotton using a simple dip coating. Cotton dry for 15 minutes with a halogen lamp, after the deposition process. Then, we do the antibacterial activity test using Plate Count Method. As a result, the coated cotton textiles with Polyvinyl alcohol (PVA), Polyethylene glycol (PEG) has antibacterial properties. Characterization by the Attenuated Total Reflectance (ATR) obtained that Titania (TiO2) surely adhere on the sample. From Attenuated Total Reflectance (ATR) characterization we conclude that Polyvinyl alcohol (PVA) and Polyethylene glycol (PEG) is not affecting the antibacterial ability of Titania (TiO2). But the infusion of Polyvinyl alcohol (PVA) and Polyethylene glycol (PEG) on Cotton increases the stiffness value of Cotton.
Agent-based Model and its Potential in Simulating Some Physical Systems
Authors: Viridi S , Haryanto F
Published: September 2019

Agent-based model (ABM) is very flexible in defining types of interaction between agents including non-physical ones, which can be used to simulate social interaction, economy, until city development. Only our abstraction in defining the interactions is the limitation. For a physical system, an agent can be considered as a particle and interaction between them is simply the interaction force, e.g. nuclear force between nucleons, electrostatic force between ions, gravitation force between asteroids, and contact force between granular particles. In this work, simple rule for the interaction between particle is proposed and several materials phases such as solid, liquid, gas, and granular can be obtained, but only qualitatively.
Synthesis and Characterization of Hydroxyapatite-Zinc Oxide (HAp-ZnO) as Antibacterial Biomaterial
Authors: Charlena  , Suparto Irma Herawati , Kurniawan Eldora
Published: September 2019

Hydroxyapatite (HAp) is an important biomaterial widely used as implants for bone and teeth. Biomaterial with antibacterial activities beneficial to prevent infection post implantation. Therefore, the present study aims to synthesized and characterized HAp composite with zinc oxide (ZnO) that has antibacterial properties. The HAp was synthesized through wet precipitation method using shell of Bellamya javanica as source of calcium. The zinc oxide was added with HAp using in situ method. The crystallinity of the material was decreased after added with ZnO which indicate Zn ion suppressed the crystal growth. Antibacterial abilities were tested against Eschericia coli and Staphylococcus aureus. Inhibition against bacteria increased when the HAp was composited with ZnO. The HAp-ZnO composite showed better inhibition toward Escherichia coli.
Flexural Property and Water Content of Unidirectional Polypropylene/Subang Pineapple Leaf Fiber Composites
Authors: Nugraha A , Juwono A L
Published: September 2019

The development of natural fiber reinforced composite research has shown significant results. Pineapple leaf fiber reinforced composites for non-structural application provide added value for Subang pineapple leaf fiber (PALF) waste. This study aimed to observe flexural strength, water absorption and desorption of composites which referred to the Indonesian National Standard (SNI) for composite board. Alkali treatment on Subang PALF was performed to improve the interface bonding between PALF with polypropylene (PP), in which the PALF was soaked in 5% NaOH solution for 24 hours. Treated PALF and PP sheets were fabricated using compression molding (hot press) technique with the variation of fiber fraction to polypropylene were 20 wt%, 30 wt% and 40 wt%. Flexural property, desorption and absorption water tests were conducted on PP and PP/PALF composites, and Optical Microscope (OM) observation was performed on the surfaces after the flexural test was conducted. The highest flexural strength and flexural modulus were (4.89 ± 0.37) MPa and (1.13 ± 0.43) Mpa respectively, these values shown an increased respectively by 153,37% compared to the pure PP. Then the desorption and the absorption water tests-were (1.08 ± 0,12) % and (8,83 ± 3,35) % respectively. The morphology of flexural tested composites indicated that matrix failure; and it showed that there was a strong interface bonding between the fiber and matrix.
Hydrogen Gas Production using Electro-activated Carbon Catalyst from Coconut Shells
Authors: Rustana C E , Khaerudini D S , Junia D , Dirgantara F D , Badruzzaman A , Marsya V
Published: September 2019

The synthesis of heterogeneous carbon catalyst using electro-activation method has been carried out to assess the effect of temperature on surface morphology of hydrogen production and the surface area of the carbon catalyst as well as characterization of hydrogen production that was resulted. The electrolyte solution of NaOH with a concentration of 2.7 M which was produced from 2 grams of carbon and 25 ml of distilled water was used for electro-activation process. The activation process was taken place with a current of 3 A for 120 minutes and the variation of carbonization temperature of 1000, 1100 and 1200 °C. The electrode system that was used in the process comprised a carbon cathode and copper anode. The results of carbon mass yield testing indicated that purification of charcoal applied at high temperature. The optimum amount of gas with an average rate of 9.19 ml/min/gr Al for a time of 1 hour was produced from carbonized catalyst at carbonization temperature of 1200 °C. The SEM-EDS examination indicated that the reacted product consisted of a mixture of Al(OH)3 and carbon catalysts which would be reprocessed through the re-electro-activation. The characterization of Brunauer-Emmet-Teller (BET) of the surface area of catalyzed carbon shown a value of 394.456 m2/g; while the result test of Scanning Electron Microscope (SEM) shown that the morphology of surface layer tends to be more pores after carbon catalyzed was used with the concentration of NaOH electrolyte solution of 2.7 M. Results of Fourier Transform Infra-Red (FTIR) analysis also shown the formation of new carboxyl functional groups (O-H) in the wavelength range 464.41 cm−1.
TiO2 Photocatalytic Degradation of Methylene Blue Using Simple Spray Method
Authors: Utami F D , Rahman D Y , Margareta D O , Rahmayanti H D , Munir R , Sustini E , Abdullah M
Published: September 2019

The present work focused on the effects of TiO2 in degrading organic wastewater. Technical TiO2 of anatase crystalline phase was used. TiO2 photocatalyst showed a powerful result in destroying organic effluent. Spray coating was conducted to immobilize the TiO2 particles onto the plastic buffer followed with heat-treatment process. As a result, 30 mL of 25 mg L−1 methylene blue (MB) used in the photocatalyst test was sucessfully degraded after 4 hours of irradiation. Repetitive use of the TiO2 films still has a great photodecomposition ability of removing 99% of the organic contaminant after 5 times use.
Agarose Cleaning Optimization for DGT Devices Specific for Cesium
Authors: Sadewo PH , Suzuki-Muresan T , Widiharto A , Muresan B
Published: September 2019

Agarose gels commonly used in electrophoresis are regularly checked by its manufacturers for the absence of contaminating nucleases or residual sulfates. It is also tested for several metals and trace elements: Pb, Cd, Co, Cu, Zn, K, Ca, Cr Mg, Mn, Fe, Ni, Na, and Cl. However, no data are available for Cs-impurity measurements. A Diffusive Gradients in Thin films (DGT) device specific for cesium (Cs) is intended to be developed. Therefore, it is important to assess the impurity degree of agarose with Cs. Direct dissolution of agarose in 4 mol·L−1 HNO3 gives a concentration of 2.1×10−8 mol·L−1 of Cs, which is higher than that is found in natural environments (e.g. [Cs]<1×10−8 mol·L−1 in water). Two methods of Cs impurity removal have been tested, involving acidic cleaning with HCl and extraction by exchanger resin (KCuFC). Agarose powder was mixed with HCl in different concentrations, rinsed and dried. This method shows that the HCl-cleaning method is not quite efficient in removing the Cs impurity compared to untreated agarose gel. The second method, KCuFC resin was mixed with agarose powder in ultra-pure water, heated afterwards, and filtered. This method was able to reduce the amount of Cs by 99% compared to the untreated agarose gel. It appears that acceptable Cs levels (i.e. with respect to ambient Cs concentration in natural waters) are achievable by the removal of preexisting Cs in the agarose powder.
Microwave-Assisted Cationic Polymerization of Turpentine: Change in Infrared and Ultraviolet Spectra
Authors: Farid Muhamad , Soegijono Bambang , Mas’ud Zainal Alim , Herlambang Surya
Published: September 2019

Indonesia is a turpentine producer country. So far, only one factory is carrying out turpentine fractionation to increase its selling price. Chemical conversion is necessary to produce more valuable derivatives of this renewable biomass-based material. In this experiment, turpentine as the raw material and the four products: α-pinene, β-pinene, limonene, and δ-carene were reacted successively with sulfuric acid, hydrochloric acid, nitric acid, and ethereal boron trifluoride, respectively. The reaction products were further irradiated using a commercial microwave oven. The raw material composition, functional group, and ultraviolet absorption were analyzed using a gas chromatograph, Fourier transforms infrared spectrophotometer, and UV-Vis spectrophotometer, respectively. Half of the reaction products were neutralized with sodium bicarbonate whether or not it irradiated. All products which viscous colored liquid was examined on their ultraviolet and infrared spectrum. The turpentine reacted with sulfuric acid and boron trifluoride ethereal produced a brownish viscous liquid, but did not react with hydrochloric acid and nitric acid. The reaction products with sulfuric acid and boron trifluoride ethereal and microwave irradiation processes showed some shifts on the infrared spectra, particularly in C=C band due to to the polymerization and C=C reforming reaction. The products also demonstrate the presence of OH group in the infrared spectra.
An Optimization Method to Determine Optimum Carbonization Temperature of Banana Stems Based Activated Carbon for Supercapacitors
Authors: Taer Erman , Purnama Agrandi , Apriwandi  , Agustino  , Taslim Rika , Mustika Widya Sinta
Published: September 2019

The optimization of carbonization temperature was obtained by experimental design, assisted by using a 3rd-order polynomial equation, for use in supercapacitor application. Activated carbon monoliths are produced based on the carbonization temperatures of 500 °C, 550 °C, 600 °C and 650 °C. The monolithic activated carbon samples were characterized based on their physical properties, including density, degree of crystallinity and surface morphology, and their electrochemical properties, including specific capacitance, energy and power. The optimum conditions, which yielded a minimum electrode density and steak height as well as a maximum combination of energy and power, were found to be at a temperature of approximately 550 °C. In addition, the exact minimum and maximum carbonization temperatures that correlated with density, steak height and a combination of energy and power were found by a simulated mathematical model to be 543 °C, 544 °C, and 553 °C, respectively. The surface morphology was analyzed and was used as supporting data. In conclusion, by experimental and mathematical simulation, the optimum carbonization condition was obtained more accurately.
A Study of Physical and Mechanical Properties of Nata de Coco in the Market
Authors: Rahmayanti Handika Dany , Amalia Nadya , Munir Rahmawati , Yuliza Elfi , Utami Fisca Dian , Sustini Euis , Abdullah Mikrajuddin
Published: September 2019

Nata de coco is a bacterial cellulose produced by Acetobacter xylinum in the process of fermenting coconut water. It is renowned for its high fiber content. The chewiness of nata de coco is proportional to the fiber content. There are many brands of nata de coco available in the market. Six different brands are included in this study. The mechanical strengths have been evaluated using a Universal Testing Machine. Based on the tensile test results, the lowest Young’s modulus is 3 MPa, attributed to the brand labeled as F as the most elastic nata de coco among the six brands. The degree of elasticity of nata de coco also corresponds to the sugar content. Further, the optical properties have been observed using a UV/Vis Spectrometer. Clearer nata de coco yields higher transmittance value. Meanwhile, the turbidity commensurate the nitrogen content.
Novel mathematical modelling of Saudi Arabian natural diatomite clay
Authors: Alsawalha Murad , Rao Chintaginjala Venkateswara , Al-Subaie Abeer Mohammed , Haque SK Manirul , Veeraraghavan Vishnu Priya , Surapaneni Krishna Mohan
Published: September 2019

Background: Diatomite is a clay material and a mineral that contains high content of silica and alumina and additional element traces. The characteristics and properties of the Saudi Arabian natural diatomite clay were studied using temperature programmed desorption of pyrrole. The relation between the particular mathematical parameters and the diatomite clay was also investigated, with a mathematical modelling of pyrrole adsorption by means of a regression analysis. Methods: The Polanyi-Wigner equation was computed for the analysis of Saudi Arabian diatomite clay, using temperature programmed desorption (TPD) of pyrrole together with a regression analysis. The correlation and regression analyses were conducted according to the following variables; 1. Temperature versus WLD-Signal- to ascertain the temperature dependence of WLD Signal. 2. Time versus WLD- to determine the time dependence of WLD. 3. 1/Temperature versus lnk to establish both the temperature dependence of the reaction rates and the time dependence of the desorption of pyrrole. Results: The results revealed that a cubic polynomial is the most suitable for the interpretation of the TCD signal of Pyrrole adsorption at a variety of temperature ranges. The findings in this study have determined that Polanyi-Wigner equation for the analysis of natural Saudi Arabian diatomite clay was computed successfully. Conclusion: The proposed equation shown in the current paper serves as the best model in the analysis of natural Saudi Arabian clay in the improvement of accuracy and efficacy of the Pyrrole- TPD. The proposed equation also greatly assists in achieving accurate results when calculating the desorbed amount of pyrrole and as compared to the traditional method, helps set a clear direction and a feedback mechanism for researchers during the investigation of clay samples. Importantly, using the equation can help to develop pyrrole-TPD software which in turn may assist scientists to clearly determine directly desorbed pyrrole amount of the clay samples during the experimental process. The findings conclude that the usefulness of the pyrrole equation can, in future, contribute greatly to the development of TPD-pyrol instrument software. It will also provide better control and quality feedback to investigators in the process of experimental design and during the run in terms of the behavior of clays and their capacity for gas desorption.
Rapid On-Site Evaluation With Telecytology Significantly Reduced Unsatisfactory Rates of Thyroid Fine-Needle Aspiration
Authors: Lin Diana M , Tracht Jessica , Rosenblum Frida , Kouba Erik , Bahl Deepti , Patel Anish , Eltoum Isam-Eldin
Published: September 2019

Objectives

We evaluated telecytology rapid on-site evaluation (ROSE) for thyroid ultrasound-guided fine-needle aspiration. To the best of our knowledge, this study is the first case-control clinical trial of thyroid telecytology.

Methods

We introduced on-site ROSE in our institution’s thyroid clinic for 6 months, followed by telecytology for 12 months. Our institution’s ultrasound clinic, where ROSE is not provided, was used as a control group for each period.

Results

Both groups had similar initial unsatisfactory rates (thyroid clinic: 8.8%; ultrasound clinic: 8.0%) before the study began. The thyroid clinic’s unsatisfactory rate was significantly reduced to 1.6% after on-site ROSE (P = .001) and to 3.8% after telecytology ROSE (P = .010), with no significant difference between on-site and telecytology ROSE periods (P > .05). The ultrasound clinic’s unsatisfactory rate was unchanged for both periods. Concordance between telecytology ROSE and final adequacy was 97% (κ = 0.699).

Conclusions

Telecytology ROSE reduces unsatisfactory rates for ultrasound-guided fine-needle aspiration without compromising patient care.
Clinicopathologic Characterization of Post–Renal Transplantation BK Polyomavirus-Associated Urothelial CarcinomaSingle Institutional Experience
Authors: Chu Ying-Hsia , Zhong Weixiong , Rehrauer William , Pavelec Derek M , Ong Irene M , Arjang Djamali , Patel Sanjay S , Hu Rong
Published: September 2019

Objectives

To review rare cases of BK polyomavirus (BKPyV) associated urologic carcinomas in kidney transplant recipients at one institution and in the literature.

Methods

We describe the clinicopathologic features of BKPyV-associated urologic carcinomas in a single-institution cohort.

Results

Among 4,772 kidney recipients during 1994 to 2014, 26 (0.5%) and 26 (0.5%) developed posttransplantation urothelial carcinomas (UCs) and renal cell carcinomas (RCCs), respectively, as of 2017. Six (27%) UCs but none of the RCCs expressed large T antigen (TAg). TAg-expressing UCs were high grade with p16 and p53 overexpression (P < .05 compared to TAg-negative UCs). Tumor genome sequencing revealed BKPyV integration and a lack of pathogenic mutations in 50 cancer-relevant genes. Compared to TAg-negative UCs, TAg-expressing UCs more frequently presented at advanced stages (50% T3-T4) with lymph node involvement (50%) and higher UC-specific mortality (50%).

Conclusions

Post-renal transplantation BKPyV-associated UCs are aggressive and genetically distinct from most non-BKPyV–related UCs.
Genome organization via loop extrusion, insights from polymer physics models
Authors: Ghosh Surya K , Jost Daniel
Published: September 2019

Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
Identifying enhancer–promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism
Authors: Hong Zengyan , Zeng Xiangxiang , Wei Leyi , Liu Xiangrong
Published: September 2019

Motivation

Identification of enhancer–promoter interactions (EPIs) is of great significance to human development. However, experimental methods to identify EPIs cost too much in terms of time, manpower and money. Therefore, more and more research efforts are focused on developing computational methods to solve this problem. Unfortunately, most existing computational methods require a variety of genomic data, which are not always available, especially for a new cell line. Therefore, it limits the large-scale practical application of methods. As an alternative, computational methods using sequences only have great genome-scale application prospects.

Results

In this article, we propose a new deep learning method, namely EPIVAN, that enables predicting long-range EPIs using only genomic sequences. To explore the key sequential characteristics, we first use pre-trained DNA vectors to encode enhancers and promoters; afterwards, we use one-dimensional convolution and gated recurrent unit to extract local and global features; lastly, attention mechanism is used to boost the contribution of key features, further improving the performance of EPIVAN. Benchmarking comparisons on six cell lines show that EPIVAN performs better than state-of-the-art predictors. Moreover, we build a general model, which has transfer ability and can be used to predict EPIs in various cell lines.

Availability and implementation

The source code and data are available at: https://github.com/hzy95/EPIVAN.
scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data
Authors: Ye Congting , Zhou Qian , Wu Xiaohui , Yu Chen , Ji Guoli , Saban Daniel R , Li Qingshun Q
Published: September 2019

Motivation

Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 3′ enriched strategy in library construction, the most commonly used scRNA-seq protocol—10× Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data.

Results

Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.

Availability and implementation

The scDAPA package is implemented in Shell and R, and is freely available at https://scdapa.sourceforge.io.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genetic and epigenetic study of an Alzheimer’s disease family with monozygotic triplets
Authors: Zhang Ming , Dilliott Allison A , Khallaf Roaa , Robinson John F , Hegele Robert A , Comishen Michael , Sato Christine , Tosto Giuseppe , Reitz Christiane , Mayeux Richard , George-Hyslop Peter St , Freedman Morris , Rogaeva Ekaterina
Published: September 2019

Zhang, Dilliott et al. examine a unique family with early- and late-onset Alzheimer’s disease phenotypes, as well as disease-discordant monozygotic triplets. The triplets and the patient with early-onset disease are carriers of the APOE ε4-allele plus rare substitutions in other genes. Epigenetic analyses suggest accelerated ageing in the early-onset patient.
Recessive Charcot-Marie-Tooth and multiple sclerosis associated with a variant in MCM3AP
Authors: Sedghi Maryam , Moslemi Ali-Reza , Cabrera-Serrano Macarena , Ansari Behnaz , Ghasemi Majid , Baktashian Mojtaba , Fattahpour Ali , Tajsharghi Homa
Published: September 2019

Variants in MCM3AP, encoding the germinal-centre associated nuclear protein, have been associated with progressive polyneuropathy with or without intellectual disability and ptosis in some cases, and with a complex phenotype with immunodeficiency, skin changes and myelodysplasia. MCM3AP encoded protein functions as an acetyltransferase that acetylates the replication protein, MCM3, and plays a key role in the regulation of DNA replication. In this study, we report a novel variant in MCM3AP (p.Ile954Thr), in a family including three affected individuals with characteristic features of Charcot-Marie-Tooth neuropathy and multiple sclerosis, an inflammatory condition of the central nervous system without known genetic cause. The affected individuals were homozygous for a missense MCM3AP variant, located at the Sac3 domain, which was predicted to affect conserved amino acid likely important for the function of the germinal-centre associated nuclear protein. Our data support further expansion of the clinical spectrum linked to MCM3AP variant and highlight that MCM3AP should be considered in patients with accompaniment of recessive motor axonal Charcot-Marie-Tooth neuropathy and multiple sclerosis.
Epigenetic silencing of microRNA-204 by Helicobacter pylori augments the NF-κB signaling pathway in gastric cancer development and progression
Authors: Chen Peizhan , Guo He , Wu Xuming , Li Jingquan , Duan Xiaohua , Ba Qian , Wang Hui
Published: September 2019

Helicobacter pylori infection induces gastric cancer (GC) development through a progressive cascade; however, the roles of the microRNAs that are involved in the cascade and the underlying mechanisms are still unclear. Here, we found that microRNA-204 was suppressed in gastric mucosal cells in response to H.pylori infection and downregulated in GC tissues due to aberrant methylation of the promoter of its host gene, TRPM3. Helicobacter pylori induced a progressive downregulation of microRNA-204 from superficial gastritis to intestinal metaplasia, with an accompanying increment of the methylated levels of CpG sites in the TRPM3 promoter. With the GC cellular models of AGS, MGC-803 or BGC-823, we found that microRNA-204 suppressed the tumor necrosis factor (TNF)-α-induced activation of NF-κB signaling pathways and, in animal models, inhibited tumor growth and metastasis. The conditional supernatant of microRNA-204 overexpression GC cells led to reduced tube formation of human umbilical vein endothelial cells. A target gene for microRNA-204 was BIRC2, and in GC cells, BIRC2 knockdown recapitulated the biological phenotype of microRNA-204 overexpression. BIRC2 overexpression promoted the metastasis of GC cells and rescued the inhibition activities of microRNA-204 on cell migration and the NF-κB signaling pathway. Moreover, lower microRNA-204 and higher BIRC2 expression levels were associated with a poorer prognosis of GC patients. These results demonstrate that epigenetic silencing of microRNA-204 induced by H.pylori infection augments the NF-κB signaling pathway in H.pylori-induced gastritis and GC, potentially providing novel intervention targets for these diseases.

MicroRNA-204 was epigenetically down-regulated by H. pylori infection in gastric mucosal cells. It led to enhanced BIRC2 expression level and BIRC2/TNF-a/NF-kB signaling pathway activities, which promoted angiogenesis and metastasis of gastric cancer cells.
“My zines, so far, aren't as political as other works I've produced”: Communicative Capitalism Among Queer Feminist Zinesters
Authors: Reynolds Chelsea
Published: September 2019

Self-published zines have been celebrated by some feminist communication scholars for offering an emancipatory outlet for women and queer people. But under the logics of late capitalism, zines cannot reach truly transgressive potentials. This study situates zinester politics within a framework of communicative capitalism: the current era of command individuality and “woke” representational politics. I also historicize zines’ proliferation through punk, do-it-yourself (DIY), and White, feminist communities. Using critical discourse analysis as my analytical approach, I illustrate the interpellation of capitalist ideology in online questionnaires completed by 11 queer, White, feminist zinesters from Chicago. By harnessing a DIY production model, respondents said they resisted mass-mediated expectations of normative sexuality and gender identity, but zinesters also reflect and reify the systems they attempt to transcend.
AMPA Induces NO-Dependent cGMP Signals in Hippocampal and Cortical Neurons via L-Type Voltage-Gated Calcium Channels
Authors: Giesen Jan , Füchtbauer Ernst-Martin , Füchtbauer Annette , Funke Klaus , Koesling Doris , Russwurm Michael
Published: September 2019

The nitric oxide (NO)/cGMP signaling cascade has an established role in synaptic plasticity. However, with conventional methods, the underlying cGMP signals were barely detectable. Here, we set out to confirm the well-known NMDA-induced cGMP increases, to test the impact of AMPA on those signals, and to identify the relevant phosphodiesterases (PDEs) using a more sensitive fluorescence resonance energy transfer (FRET)-based method. Therefore, a “knock-in” mouse was generated that expresses a FRET-based cGMP indicator (cGi-500) allowing detection of cGMP concentrations between 100 nM and 3 μM. Measurements were performed in cultured hippocampal and cortical neurons as well as acute hippocampal slices. In hippocampal and cortical neurons, NMDA elicited cGMP signals half as high as the ones elicited by exogenous NO. Interestingly, AMPA increased cGMP independently of NMDA receptors and dependent on NO synthase (NOS) activation. NMDA- and AMPA-induced cGMP signals were not additive indicating that both pathways converge on the level of NOS. Accordingly, the same PDEs, PDE1 and PDE2, were responsible for degradation of NMDA- as well as AMPA-induced cGMP signals. Mechanistically, AMPAR induced calcium influx through L-type voltage-gated calcium channels leading to NOS and finally NO-sensitive guanylyl cyclase activation. Our results demonstrate that in addition to NMDA also AMPA triggers endogenous NO formation and hence cGMP production.
Typhoid and the Military in the Early 20th Century
Authors: Gradmann Christoph , Harrison Mark , Rasmussen Anne
Published: September 2019

Background

In the decades following the discovery of the bacillus causing typhoid, in 1880, understanding of the disease formerly known as enteric fever was transformed, offering new possibilities for prevention. Gradually, measures that aimed to prevent infection from human carriers were developed, as were inoculations designed to confer immunity against typhoid and paratyphoid fevers. These were initially introduced in European armies that were regularly ravaged by typhoid, especially garrisons stationed in the colonies. This article reviews the research undertaken in the armed forces and the measures that they implemented in the years up to and during the First World War.

Methods

The article is based on an analytical review of scientific literature from the early 19th century, focusing on the United Kingdom, Germany, and France.

Results

The armies of the United Kingdom, Germany, and France undertook important work on the transmission of typhoid in the years between 1890 and 1918. Many preventive measures were introduced to deal with the spread of typhoid but these varied between the 3 countries, depending largely on their political traditions. Inoculation was particularly successful in preventing typhoid and greatly reduced the number of casualties from this disease during the First World War. Despite this, it proved difficult to prevent paratyphoid infection, and debates continued over which vaccines to use and whether or not immunization should be voluntary.

Conclusions

By the end of the First World War, the value of inoculation in preventing the spread of typhoid had been proven. Its successful implementation demonstrates the importance of vaccination as a public health intervention during times of conflict and social upheaval.
Controlled Human Infection With Bordetella pertussis Induces Asymptomatic, Immunizing Colonization
Authors: de Graaf Hans , Ibrahim Muktar , Hill Alison R , Gbesemete Diane , Vaughan Andrew T , Gorringe Andrew , Preston Andrew , Buisman Annemarie M , Faust Saul N , Kester Kent E , Berbers Guy A M , Diavatopoulos Dimitri A , Read Robert C
Published: September 2019

Background

Bordetella pertussis is among the leading causes of vaccine-preventable deaths and morbidity globally. Human asymptomatic carriage as a reservoir for community transmission of infections might be a target of future vaccine strategies, but has not been demonstrated. Our objective was to demonstrate that asymptomatic nasopharyngeal carriage of Bordetella pertussis is inducible in humans and to define the microbiological and immunological features of presymptomatic infection.

Methods

Healthy subjects aged 18–45 years with an antipertussis toxin immunoglobin G (IgG) concentration of <20 international units/ml were inoculated intranasally with nonattenuated, wild-type Bordetella pertussis strain B1917. Safety, colonization, and shedding were monitored over 17 days in an inpatient facility. Colonization was assessed by culture and quantitative polymerase chain reaction. Azithromycin was administered from Day 14. The inoculum dose was escalated, aiming to colonize at least 70% of participants. Immunological responses were measured.

Results

There were 34 participants challenged, in groups of 4 or 5. The dose was gradually escalated from 103 colony-forming units (0% colonized) to 105 colony-forming units (80% colonized). Minor symptoms were reported in a minority of participants. Azithromycin eradicated colonization in 48 hours in 88% of colonized individuals. Antipertussis toxin IgG seroconversion occurred in 9 out of 19 colonized participants and in none of the participants who were not colonized. Nasal wash was a more sensitive method to detect colonization than pernasal swabs. No shedding of Bordetella pertussis was detected in systematically collected environmental samples.

Conclusions

Bordetella pertussis colonization can be deliberately induced and leads to a systemic immune response without causing pertussis symptoms.

Clinical Trials Registration

NCT03751514.
A Survey on Prediction of Suicidal Ideation Using Machine and Ensemble Learning
Authors: Chadha Akshma , Kaushik Baijnath
Published: September 2019

Suicide is a major health issue nowadays and has become one of the highest reason for deaths. There are many negative emotions like anxiety, depression, stress that can lead to suicide. By identifying the individuals having suicidal ideation beforehand, the risk of them completing suicide can be reduced. Social media is increasingly becoming a powerful platform where people around the world are sharing emotions and thoughts. Moreover, this platform in some way is working as a catalyst for invoking and inciting the suicidal ideation. The objective of this proposal is to use social media as a tool that can aid in preventing the same. Data is collected from Twitter, a social networking site using some features that are related to suicidal ideation. The tweets are preprocessed as per the semantics of the identified features and then it is converted into probabilistic values so that it will be suitably used by machine learning and ensemble learning algorithms. Different machine learning algorithms like Bernoulli Naïve Bayes, Multinomial Naïve Bayes, Decision Tree, Logistic Regression, Support Vector Machine were applied on the data to predict and identify trends of suicidal ideation. Further the proposed work is evaluated with some ensemble approaches like Random Forest, AdaBoost, Voting Ensemble to see the improvement.
Epidermal collagenase activity and its induction by 20-hydroxyecdysone in the fiddler crab Uca pugilator
Authors: Toups Erin A. , Zou Enmin
Published: September 2019

The epidermal collagenase activity and its induction by 20- hydroxyecdysone in Uca pugilator were investigated. Zymographic electrophoresis showed four bands of collagenase activity, 16, 19, 22 and 29 kDa in molecular weight, with the former two accounting for 60% and 36%, respectively, of the total collagenase activity. The collagenase activity varies during the molting cycle. Among the molt stages tested, Premolt Stage D0 exhibited the highest epidermal collagenase activity for both the 16 and 19 kDa isoenzymes and, as the molt stage proceeded, the enzymatic activity of these two isoenzymes decreased, with the lowest activity for both found in Premolt Stage D3-4. Injection of 20-hydroxyecdysone significantly induced the activity of the 16 kDa collagenase in the epidermis of Uca pugilator, suggesting that the activity of this isoenzyme is under molting hormone control. Although 20-hydroxyecdysone injection did not result in a statistically significant increase in the activity of the 19 kDa isoenzyme, a tendency of the induction was nonetheless demonstrated. This is the first report on epidermal collagenase activity and its induction by the molting hormone in a crustacean.
Maternal investment and reproductive success in Chinese water deer
Authors: Mauget Christiane , Mauget Robert
Published: September 2019

Among cervids, maternal investment, estimated as the amount of resources and care allocated to the offspring, was expected to be related to species body size. Therefore, maternal investment in a herd of captive Chinese water deer Hydropotes inermis, a relatively small species of cervid, was investigated over 3 years. Except during the lactation period, reproductive females spent about 2-fold more time resting than feeding. During lactation, the amount of time spent feeding increased highly (25.3 min/h during lactation vs 17.3 min/h during the gestation period). Females spent less than 30% of time in communal behaviours with offspring. They did not reject alien fawns during this care period. Frequency and duration of suckling events decreased exponentially from the second week onwards. More than 10% of suckling bouts were non-filial. Prenatal investment leads to a mean litter mass (about 12% of maternal mass) higher than in most cervid species. Postnatal investment in fawns represents a daily mass gain of ca. 85 g/d during the first 2 weeks, without any sexual difference. Female production, timing and synchrony of births and survival of fawns characterized reproductive success. Seventy percent of mature females gave birth, with a mean of 1.9 offspring per female. The sex ratio was even. Births were synchronous, 80% of births occurring in 25 days. In this herd, 0.74 fawn per female was successfully weaned and 0.56 fawn per female survived through their first year. Based on these results we conclude that reproductive strategy of Chinese water deer was efficient and characterized by mother-offspring relationships typical of hiders and high levels of pre- and postnatal investments. This strategy seems typical of small species of cervids without marked sexual dimorphism.
A populational survey of 45S rDNA polymorphism in the Jefferson salamander Ambystoma jeffersonianum revealed by fluorescence in situ hybridization (FISH)
Authors: Bi Ke , Bogart James P. , Fu Jinzhong
Published: September 2019

The chromosomal localization of 45S ribosomal RNA genes in Ambystoma jeffersonianum was determined by fluorescence in situ hybridization with 18S rDNA fragment as a probe (FISH-rDNA). Our results revealed the presence of rDNA polymorphism among A. jeffersonianum populations in terms of number, location and FISH signal intensity on the chromosomes. Nine rDNA cytotypes were found in ten geographically isolated populations and most of them contained derivative rDNA sites. Our preliminary study provides strong indication of karyotypic diversification of A. Jeffersonianum that is demonstrated by intraspecific variation of 45S rDNA cytotypes. rDNA cytotype polymorphism has been described in many other caudate amphibians. We predict that habitat isolation, low dispersal ability and decline of effective population size could facilitate the fixation and accumulation of variable rDNA cytotypes during their chromosome evolution.
Population structure of the Atlantic sand fiddler crab Uca pugilator along the eastern coast of US revealed by molecular data
Authors: Weese David A. , Mclain Denson K. , Pratt Ann E. , Fang Quentin Q.
Published: September 2019

The Atlantic sand fiddler crab Uca pugilator is an extremely abundant crab found along the eastern coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30 - 90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However, a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U. pugilator and to determine whether these differences may have a genetic basis. The population structure of the fiddler crab was analyzed using 472 individuals collected from 12 sites along the eastern coast. PCR-based single stand conformation polymorphism (SSCP) was used to investigate between-site variation in the mitochondrial 16S rRNA gene of these individuals. Analysis of genetic variation indicated frequent gene flow between nearby localities' but much reduced levels between populations separated by larger geographic distances. Thus, despite the potential for high dispersal by planktonic larvae, population differentiation and isolation by distance is evident between northern and southern populations of U. pugilator. A high amount of genetic differentiation (FST = 0.3468) was found between northern and southern regions suggesting that the morphological and behavioral differences between these two regions have a genetic basis and may represent subspecies.
Melatonin and schistosomal antigens ameliorate the anti-oxidative and biochemical response to Schistosoma mansoni infection in hamster
Authors: El-Shenawy Nahla S. , Soliman Maha F. M. , Abel-Rahman Shimaa E.
Published: September 2019

The present study was designed to investigate the potential protective effect of melatonin as an antioxidant separately or in combination with antigens (cercarial; CAP or soluble worm; SWAP) against Schistosoma mansoni infection in hamsters. Each hamster was sensitized with an initial immunization of 0.6 ml of the extracted antigen (30 μg protein/mL). After four days, a second injection of 0.4 mL was given (20 μg protein/mL). Then, each hamster was exposed to 260 ± 20 S. mansoni cercariae followed with melatonin treatment (3.5 mg/ kg) for thirty days from the 1st day of post infection. Levels of lipid peroxidation (LPO) products, catalase (CAT) activity, hepatic glutathione (GSH) and biochemical changes in the liver and kidneys functions were investigated. The results revealed a high significant increasing of LPO and decreasing of CAT and GSH in liver of infected hamsters. Biochemical observations showed severe damage in the liver enzyme activities and increasing cholesterol level in infected animals. Melatonin co-treatment with antigen to the infected-hamster attenuated the increase of LPO and restored the activity of CAT and levels of hepatic GSH. Also, the biochemical damages in the liver and kidneys functions were reduced. The present study suggests that melatonin may be useful in combating free radical-induced damage due to infection toxicity. The immunization with previous antigens resulted in a remarkable improvement on the liver enzyme activities, which were increased after infection. Thus, vaccination of hamsters with antigens (both CAP and SWAP) and melatonin treatment has more potent effect on the enhancement of antioxidant and biochemical of S. mansoni infected-hamster than each treatment separately. Immunization of the hamster with SWAP followed by melatonin was the best way among the other regime treatments to improve the biochemical and antioxidant parameters of the infected-hamsters.
Are local plague endemicity and ecological characteristics of vectors and reservoirs related? A case study in north-east Tanzania
Authors: Laudisoit Anne , Neerinckx Simon , Makundi Rhodes H. , Leirs Herwig , Krasnov Boris R.
Published: September 2019

The pattern of plague endemicity in Tanzania is characterized by continuous re-appearance of the disease in some locations, while in other neighbouring villages the disease has never or seldom been observed. To understand the reasons for this pattern, we studied small mammal and flea species composition, diversity and relative abundances in two plague-endemic and two plague-free locations. We asked (a) whether fleas more abundant in plague-endemic locations differ in their characteristic abundance and the degree of their host specificity from fleas more abundant in plague-free locations and (b) whether hosts most abundant in plague- endemic locations differ in the diversity of their flea assemblages from hosts most abundant in plague-free locations. We characterized (a) each host species by species richness and degree of taxonomic relatedness of its flea assemblages and (b) each flea species by its mean abundance and size, and degree of taxonomic relatedness of its host spectrum and compared their relative abundances between locations. No significant difference between plague- endemic and plague-free locations in either host density or any variable related to flea abundance or diversity was found. However, there was marginally significant effect of taxonomic distinctness of a flea assemblage harboured by a host on its probability to be more abundant in either plague-endemic or plague-free locations. Furthermore, hosts more abundant in plague-endemic locations tended to harbour closely-related fleas. Finally. while opportunistic and specialist fleas were equally distributed in both sets of locations, fleas exploiting distantly-related hosts were found mainly in plague-free locations during the rainy season. We suggest that the observed patterns might arise due to seasonal and spatial differences in local microclimatic conditions and landscape connectivity.
Age effect of deafening on stereotyped song maintenance in adult male bengalese finches Lonchura striata domestica
Authors: Sun Yingyu , Wang Rui , Shao Shuli , Zeng Shaoju , Zuo Mingxue
Published: September 2019

Birdsong is a complex learned vocal behavior that relies on auditory experience for development. However, it appears that among different species of close-ended songbirds, there are some variations in the necessity of auditory feedback for maintaining stereotyped adult song. In zebra finches, the deterioration of adult songs following deafness depends on the birds’ age. It is unknown whether this age effect is a general rule in other avian species as well. Therefore, we chose Bengalese finches, whose songs show more complexity and have much heavier dependency on auditory feedback than that of zebra finches, to compare the degree of song degradation after hearing loss in old (over 18 months old) and young adult birds (5 - 6 months old). We found that both syllable sequence and syllable phonology were much less severely affected by deafening in old adults than that in young ones. Moreover, young adults almost lost their capability to sing trills over 6 months following deafening, while old birds continued to sing plenty of trills and trilled syllables after the same period of deafening. Our results suggest that age plays an important role in affecting the dependency of adult song maintenance on auditory feedback in Bengalese finches. Furthermore, the age dependency may be a general phenomenon in different species of close-ended songbirds.