Miracle-dz/UniFAR-FTUs huggingface dataset:
Decrease in Microbial Diversity Along a Pollution Gradient in Citarum River Sediment

Pollution of water resources is a major risk to human health and water quality throughout the world. Here, we studied the effect of river pollution on the microbial community composition in the Citarum River Basin, West Java, Indonesia. Sediment was collected at six sampling points along a gradient of pollution, from the pristine source of the river to the heavily polluted downstream site in the densely populated urban area of Bandung. After DNA extraction, microbial diversity and potential for nitrogen cycling were analyzed based on 16S rRNA gene amplicon sequencing and metagenomics. Comparing the pristine sediment to the polluted site showed a lower microbial diversity and higher dominance of anaerobic processes than at the polluted site. The most dominant phylum within the Bacteria were the Proteobacteria, which shifted from Beta- and Deltaproteobacteria in the pristine site to Alpha- and Gammaproteobacteria in the polluted sediment. With pollution Actinobacteria, Bacteroidetes, and Firmicutes increased in relative abundance. Relative high abundance of Soil Crenarchaeotic group was found in all sample sites, whilst the methanogenic archaea became more abundant with increased pollution and anaerobicity. The study of the nitrogen cycling potential revealed that ammonium oxidation and denitrification appeared to be abundant processes in the pristine site, whereas ammonification seemed to be more important in the polluted site. Increased water treatment would restore water quality and microbial diversity in Citarum river sediments.
Survival of some Probiotics in Bio-Yoghurt Production

Viability of Lactobacillus acidophilus (L. acidophilus) and Bifidobacterium bifidum (B. bifidum) incorporated with yoghurt culture in three combinations of starter cultures; Treatment 1 (yoghurt culture + L. acidophilus), T2 (yoghurt culture + B. bifidum) and T3 (yoghurt culture + L. acidophilus + B. bifidum) were studied. Analyses of pH, titratable acidity (TA), syneresis, acetaldehyde content and sensory evaluation after 1, 3, 7, 14 and 21 days of cold storage of yoghurt were under taken. Counts of L. acidophilus was recorded 5.85 log10 cfu g -1 in T1 which were higher than counts in T3 (5.79 log10 cfu g ) at the end of storage period. On the other hand, the viability of L. acidophilus and B. bifidum was stable until 14 days of storage period. The results showed that the addition of B. bifidum to yoghurt culture (T2) increased TA of bio-yoghurt comparing with addition of L. acidophilus (T1). Syneresis in all treatments was in the range of 20 to 33% and it was found higher in T3 than control. The highest sensory values were in control, T1 and T2 until the end of 14 days of storage period.
Histologi Tubulus Seminiferus dan Kadar Testosteron Tikus yang Diberi Pakan Imbuhan Tepung Daun Kaliandra dan Kulit Nanas (HISTOLOGY OF SEMINIFEROUS TUBULES AND TESTOSTERONE LEVEL OF RAT GIVEN CALLIANDRA LEAF MEAL AND PINEAPPLE PEELS IN THE DIETS)

Calliandra calothyrsus leaf contains 17-28% protein which is hihly potential for use as source of protein supplement for animal feed. However, the plants also contain high level (>10%) of condensed tannins as antinutritional effects which may reduce consumtion efficiency of diet. The addition of protease (bromelain) into feed containing tannin is expected to decrease the negative effects of tannins. Bromelain can be obtained from the pineapple plant (Ananas comosus) including on the peels. This study was conducted to determine the effect of calliandra tannin combined with bromelain protease of pineapple peels in the feed on testicular histology and testosterone level of rats feeded during the growth period. The feeding experiment on post-weaning male rats was conducted using a completely randomized factorial design (4 main factors x 4 subfactors). The main factors were calliandra leaf meal substitution of 0; 10; 17.5 and 25% in the diets and subfactors were addition of pineapple peels, 0; 4.35; 8.70 and 13.05 g/rat/day. Rats were divided into 16 groups and were feeded the diets for two months (during the growth period). The Jurnal Veteriner September 2017 Vol. 18 No. 3 : 369-377 pISSN: 1411-8327; eISSN: 2477-5665 DOI: 10.19087/jveteriner.2017. 18.3. 369 Terakreditasi Nasional, Dirjen Penguatan Riset dan Pengembangan, online pada http://ojs.unud. ac.id/php.index/jvet Kemenristek Dikti RI S.K. No. 36a/E/KPT/2016
Antioxidant and antimicrobial activity of bacteriocin-producing strains of lactic acid bacteria isolated from the human gastrointestinal tract

Background: cancer patients require special attention to maintenance therapy of their organism vital activity. Distribution of nutritional deficiency in cancer patients not only limits the possibilities of application of modern treatment methods, but can also be the direct cause of life-threatening complications and premature death. Objective: to study the use of bioactive peptide complexes with low molecular weight and probiotic strains isolated from the human gastrointestinal tract in food products intended for patients with cancer during their treatment and rehabilitation. Material and Methods: 14 strains of lactic acid bacteria were pre-selected and identified for this study. They were allocated from the gastrointestinal tract of 500 healthy people and people with cancer, who presented different age groups. The study of antagonistic activity of lactic acid bacteria was carried out by using the MRS medium and Lysogeny broth (LB). Biocompatibility study was performed through the co-culture method on solid MRS medium. Results: Research results proved that the isolated metabolites belonged to bacteriocins, as the studied microorganisms were resistant both to their inhibitors and mutually resistant to the single-type synthesized substances. Conclusions. Probiotics have a positive effect on the immune system, as the gastro-intestinal flora they reduce the impact of mutagens and carcinogens.
Malaria and Burkitt’s Lymphoma: An In Silico Analysis of Gene Expression Links between Malaria and Burkitt’s Lymphoma and Potential Anticancer Activity of Artemisinin Derivatives

Background Burkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic subtype of the disease showed a remarkable statistical and epidemiological association with malaria infection. Despite the numerous studies performed to explain this association; molecular mechanisms underlie such coincidence still remain unclear. Dissecting molecular mechanisms which link Malaria infection and Burkitt’s lymphoma can provide insights about reported anticancer action of certain antimalarial drugs, namely artemisinin derivatives. Methods Here we applied an integrative approach to investigate for potential links between malaria infection and endemic Burkitt’s lymphoma regarding their gene expression, and further explore common molecular mechanisms through which artemisinin compounds might act in endemic Burkitt’s lymphoma. Using gene expression data of malaria (Plasmodium falciparum infected erythroblasts) and endemic Burkitt’s lymphoma from Gene Expression Omnibus database, expression patterns in the two conditions were examined through clustering analysis using Self Organizing Maps, and then by significance testing of differentially expressed genes in each condition followed by Functional annotation using Gene Ontology clustering and Pathways analysis. Results Clustering analysis identified a significant overlap between the expression patterns in endemic Burkitt’s lymphoma and Plasmodium falciparum infected cells. Four out of the 12 identified clusters contained genes with similar expression patterns in both conditions. Differential expression analysis identified 1689 genes as significantly differentially expressed in endemic Burkitt’s lymphoma and 405 in malaria. Those genes were found to be related to important Gene Ontology terms and pathways. Interestingly 65% of the identified pathways in Malaria were overlapped with those identified in endemic Burkitt’s lymphoma. Several of these pathways reported to be related to actions of artemisinin derivatives. Conclusion Our In-silico analysis showed a significant molecular convergence between endemic Burkitt’s lymphoma and malaria. A number of 43pathways which demonstrated enrichment in tumour were shared with Plasmodium falciparum infected erythrocytes. Such pathways represent potential targets for antimalarial drugs to exert therapeutic effects in such malignancy.
Quantitative and Fourier Transform Infrared Analysis of Saponins from Three Kenyan Ruellia Species viz Ruellia prostrata, Ruellia linearibracteolata and Ruellia bignoniiflora

— Ruellia (syn. Dipteracanthus ) species are wild perennial creepers belonging to the Acanthaceae family. These species are reported to possess anti-inflammatory, analgesic, antioxidant, gastroprotective, anticancer, and immuno-stimulant properties. Phytochemical screening of both aqueous and methanolic extracts of Ruellia species revealed the presence of saponins. Saponins have been reported to possess anti-inflammatory, antioxidant, immuno-stimulant, antihepatotoxic, antibacterial, anticarcinogenic, and antiulcerogenic activities. The objective of this study was to quantify and analyze the Fourier transform infrared (FTIR) spectra of saponins in crude extracts of three Kenyan Ruellia species namely Ruellia prostrata (RPM), Ruellia lineari-bracteolata (RLB) and Ruellia bignoniiflora (RBK). Sequential organic extraction of the ground whole plant material was done using petroleum ether (PE), chloroform, ethyl acetate (EtOAc), and absolute methanol by cold maceration, while aqueous extraction was by hot maceration. The plant powders and extracts were mixed with spectroscopic grade KBr and compressed into a pellet. The infrared spectra were recorded using a Shimadzu FTIR spectrophotometer of 8000 series in the range of 3500 cm -1 - 500 cm -1 . Quantitative determination of the saponins was done using standard procedures. Quantitative analysis of saponins showed that RPM had the highest quantity of crude saponins (2.05% ± 0.03), followed by RLB (1.4% ± 0.15) and RBK (1.25% ± 0.11), respectively. FTIR spectra revealed the spectral peaks characteristic for saponins in RPM, RLB, and RBK plant powders, aqueous and methanol extracts; O-H absorption (3265 - 3393 cm -1 ), C-H absorption ranging from 2851 to 2924 cm -1 , C=C absorbance (1628 - 1655 cm -1 ), oligosaccharide linkage (C-O-C) absorption due to sapogenins (1036 - 1042 cm -1 ). The crude saponins from RPM, RLB and RBK showed similar peaks to their respective extracts. The presence of the saponins in extracts of RPM, RLB and RBK may be responsible for some of the biological activities reported in the Ruellia species.1
Antibacterial potential of catechin of tea (Camellia sinensis) and its applications

By reviewing various works of research by many experts on tea, this mini review elaborates the picture of catechins in tea, especially green tea, and their applications as potential antimicrobial agents. Tea originated in China as a drink with medicinal purposes and to be grew a worldwide beverage. Green tea undergoes minimum oxidation process compared to black tea, thus it may contain the same pharmacological bioactive components, but in different concentrations, except for theaflavins and thearubigens that are mainly found in black tea. Phytochemical screening of green tea leaves revealed various polyphenols, mainly catechins, which play multiple essential roles in plant physiology and have potential health properties and benefits on human health, such as antioxidants, as well as anti-allergic, anti-inflammatory, anticancer, antihypertensive, and as antimicrobial agents. Green tea polyphenolic EGCG has the capability to cross-link with many proteins which grants it a wide range of antimicrobial activities possibly by damaging microbial cytoplasmic lipids and proteins. The high concentrations of catechins in tea (Camellia sinensis) were reported to have antimicrobial activities against many pathogens including Listeria monocytogenes, a gram-positive bacterium known to be isolated from red meat, therefore making tea catechin an effective antimicrobial agent. In a study model applying up to 1000 ppm tea catechin extract to a biodegradable film, it proved beneficial for home-use wraps for meat, poultry, and seafood, thus expressing the strong potential of tea catechin as an organic antimicrobial agent.
Analysis of the complete organellar genomes of the rockweed Fucus spiralis (Fucaceae, Phaeophyceae) supports its infraspecific recognition as Fucus vesiculosus var. spiralis

Abstract Fucus spiralis L. is a broadly distributed monoecious intertidal seaweed. The specific status of F. spiralis however is debatable. Here, we contribute to the bioinformatics and systematics of F. spiralis by analysing the complete mitochondrial and plastid genomes of a specimen from California, U.S.A. The F. spiralis mitogenome is 36,396 base pairs (bp) in length and contains 67 genes, and the plastid genome is 125,066 bp in length and contains 171 genes. The F. spiralis genomes are 99.7% and 99.8% similar in nucleotide sequence to F. vesiculosus, and support the revised classification of F. spiralis to Fucus vesiculosus var. spiralis.
Effects of water table on cellulose and lignin degradation of Carex cinerascens in a large seasonal floodplain

ABSTRACT Water table affects litter decomposition in wetlands, but its effects on the degradation of cellulose and lignin are poorly understood. We performed a decomposition experiment in Poyang Lake Wetland, to determine how water table affected the degradation of cellulose and lignin. After 60 days of decomposition at a site with a relatively highly water table, 46.19% of initial cellulose and 41.95% of initial lignin remained. Decay rates of both cellulose and lignin increased as the depth of the water table increased. Principle component analysis showed that the decay rates of cellulose and lignin increased with increasing soil pH, but decreased with increasing contents of clay and fungi: bacteria ratio. The path model accounted for 66% and 79% of the variation in cellulose and lignin decay rates, respectively, and considered the effects of interactions between the water table and related factors. The cellulose decay rate was affected by the water table with a direct coefficient of 0.47, and an indirect coefficient of 0.65, but the lignin decay rate was indirectly affected by water table (coefficient, 1.25) and directly affected by soil property (coefficient, 0.67). Thus, the water table affected the decomposition of cellulose and lignin via different mechanisms.
Molecular Cloning and Expression of Major Histocompatibility Complex Class Iα Gene of Swamp Eel (Monopterus albus)

Major histocompatibility complex (MHC) plays an important role in the immune response of vertebrates. In this study, we isolated MHC class Iα gene from swamp eel (Monopterus albus) by rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR). In order to study the function of MHC Iα in swamp eel, tissue distribution and immune response of the MHC Iα after bacterial challenge were analyzed. All the characteristic features of MHC Iα chain structure were identified by the deduced amino acid sequence, including the leader peptide, α1, α2, and α3 domains, connecting peptide, transmembrane and cytoplasmic regions, conserved cysteines, and Nglycosylation site. The deduced amino acid sequence of the MHC Iα shares 27.3% to 69.6% similarity with those of other vertebrates. Quantitative realtime PCR (qRT-PCR) demonstrated that MHC Iα gene was ubiquitously expressed in ten tissues, comparatively higher in immune related tissues, including the liver and intestine. Challenge of M. albus with the extracellular pathogen, Aeromonas hydrophila, resulted in a significant increase in the expression of MHC Iα within 72 h after infection and these high levels were maintained for 72 h in kidneys, spleen, and skin, whereas in the intestine and liver, it was found first in the form of up-regulated and then down-regulated gene. These results demonstrated that MHC Iα gene played an important role in response to bacterial infection in M. albus. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il/. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
When conservation becomes dangerous: Human-Crocodile conflict in Timor-Leste

In northern Australia and nearby Timor-Leste, saltwater crocodile (Crocodylus porosus) populations were seriously depleted historically but recovered rapidly after protection: 1969–1974 in northern Australia, and 2000–2005 in Timor-Leste. In both places, recovery caused increased rates of humancrocodile conflict (HCC). Within northern Australia, the crocodile recovery and HCC have been documented over time. In contrast, this has not been the situation in Timor-Leste, where we investigated HCC based on 130 attack records (1996–2014; 52% fatal). In 1996–2006, 0.55 attacks/year were reported in Timor-Leste. By 2007–2014, 9 years later, a 23-fold increase had occurred (13 attacks/year). Traditional subsistence fishing (82.5% of all attack records) is the highest risk activity, followed by bathing (7.5%) and water collecting (4.2%). Although the human population was correlated with crocodile attacks in TimorLeste, it likely does not explain the dramatic increase in crocodile attacks. Alternatively, crocodile numbers may have increased, either in the remnant resident crocodile population, or via migrants from elsewhere. Permanent crocodile habitat is limited, and limited breeding does not explain the high number of large crocodiles, and consequent increase in attacks in such a short time. A plausible explanation, consistent with traditional knowledge in Timor-Leste, is that the influx of large crocodiles attacking people are migrants from Australia. We examined this possibility from available sources. Within Australia crocodiles have recovered since protection and they regularly invade adjacent habitats, such as Darwin harbor, where they are removed to prevent attacks on people. Saltwater crocodiles have been sighted at oil rigs, in the open ocean, moving between northern Australia and the south coast of Timor-Leste. The likelihood of crocodiles migrating from Australia to Timor-Leste raises obvious conservation, moral, and ethical dilemmas when conserving a large dangerous predator in one country to increase abundance results in dispersal to another country, where the predator attacks and kills people. 2018 The Wildlife Society.
Not-so-working memory: Drift in fMRI pattern representations during maintenance predicts errors in a visual working memory task

Working memory (WM) is critical to many aspects of cognition, but it frequently fails. Much WM research has focused on capacity limits, but even for single, simple features, the fidelity of individual representations is limited. Why is this? We used fMRI and a pattern-based index of “representational drift” to investigate how ongoing changes in brain activity patterns throughout the WM maintenance period predicted performance, using a delayed-match-to-sample task for a single item with a single critical feature: orientation. In trials where the target and probe stimuli matched, participants incorrectly reported more non-matches when their activity patterns drifted away from the target. In trials where the target and probe did not match, participants incorrectly reported more matches when their activity patterns drifted towards the probe. Our results suggest that WM errors are not simply due to unstructured noise, but also drift within representation space that can be indexed by neuroimaging.
The complete mitochondrial genome of the Pink dentex Dentex gibbosus (Perciformes: Sparidae)

Abstract The Pink dentex (Dentex gibbosus, Rafinesque 1810) is one of the most commercially important Sparidae species and it is often subjected to fraud. Here, we report the complete mitochondrial genome of D. gibbosus. The mitogenome is 16,771 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. The overall base composition of D. gibbosus mtDNA is: 27.8% for A, 28.60% for C, 16.5% for G, 27.05% for T.
Comparative Ultrastructures of the Fertilized Egg Envelopes in Nothobranchius guentheri and Nothobranchius patrizii, Nothobranchiidae, Teleostei

Nothobranchius guentheri and Nothobranchius patrizii have special life cycle to sustain the dry season. So, we investigated the fertilized eggs morphology, and compared ultrastructures of surface structures and the cross section of fertilized egg envelopes using light and electron microscopes to determine whether these fertilized eggs and egg envelopes show the species specificity or have special structure to sustain the dry season. These fertilized eggs were spherical, yellowish, demersal and adhesive, and had a one-sided large oil droplet. The whip-like structures, adhesive filament were distributed throughout egg envelope in both species. But, that of N. guentheri was covered with fibrous structures, and that of N. patrizii was smooth. The egg envelope consisted of two distinct layers: an outer, electron-dense layer containing adhesive filaments and an inner layer of 16 to 17 horizontal electron-dense lamellae alternating with 15 to 16 interlamellae of lower electron density in both species. The external shapes of fertilized egg and section of fertilized egg envelope were same, but ultrastructure of adhesive filaments on the outer surface was concluded to show species specificity. Our data indicate that the ultrastructural differences of adhesive filament and outer surface of fertilized egg envelope show species specificity although these species belong to same genus.
Preface: Natural hazard impacts on technological systems and infrastructures

Critical infrastructures and other technological systems such as transportation systems, telecommunication networks, power lines, pipelines, and reservoirs are at risk of natural hazards (e.g., earthquakes, floods, landslides) in many urban and rural areas worldwide. A key to the safe and affordable operations of these types of infrastructure is an in-depth knowledge of their exposure and vulnerability to natural hazards and the impact of damage experienced either locally or across the network. A fundamental understanding of hazard and risk involves (a) systematic identification, monitoring, and mapping of potential infrastructure exposure, (b) integrated assessment of impact as a result of damage, repair, and/or mitigation, (c) indirect losses from infrastructure disruption and synergistic effects, and (d) consideration of interactions between hazards and/or cascades of hazards. The special issue (SI) “Natural hazard impacts on technological systems and infrastructures” was organized in the aftermath of two sessions of the same name at the European Geosciences Union (EGU) general assemblies of 2018 and 2019 held in Vienna, Austria. The special issue aims at raising awareness of this topical and increasing problem by summarizing and analyzing relationships between natural events and technological accidents, collecting experiences, and finding out new methods of assessing the vulnerability of technological and infrastructure objects to natural hazards. This SI includes contributions with a focus on natural hazard risk assessment for critical infrastructure and technological systems, as well as a compilation of databases that record the impacts and elements at risk. The SI is dedicated to contributions with national, regional, and local perspective, covering a wide range of different geographic regions. In Sect. 2 of this preface, there is a brief overview of each contribution to the special issue. This is followed by a summary of the research in Sect. 3.