Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Vegetation Composition and the Indicator Species Around Water Source Areas in a Pine Forest Plantation: A Case Study from Watujali and Silengkong Catchments, Kebumen, Indonesia

This research aimed to assess vegetation composition and the indicator species around water source areas of pine forest plantation. Data were collected through interview and vegetation survey. Vegetation communities were first compared using multi-response permutation procedure (MRPP) analysis. Indicator species analysis was then employed to determine the indicator species for each condition by considering historical data from the interview. Canonical correspondence analysis (CCA) and simple correlation analysis were also included. The result showed significant differences in species composition between water source areas in Watujali (lower low flow) and Silengkong (higher low flow) catchments, indicated by T = −5.104, p = 0.000. Pinus merkusii was dominant in Watujali (important value = 78%, D′ = 0.62) compared to Silengkong (important value = 41%, D' = 0.21), and in becoming an indicator species (value = 52.1, p = 0.042) for Watujali. Meanwhile, Laportea sinuata, as the specific tree of water source areas, was an indicator for Silengkong (value = 29.4, p = 0.004). At a smaller level, indicator species differentiated the two catchments, even though they shared similar in D′ and H′. Among specific plants of water source areas, only Ficus septica was an indicator for Watujali (value = 29.4, p = 0.004), given its adaptability. Specific plants of water source areas, including Laportea sinuata, Coctus spicatus, and Calocassia gigantea, were significant indicators for Silengkong catchments, illustrated by 34.6, 35.9, and 33.0 of indicator values, respectively. These results also reflected the relationship among tree vegetation change, environmental features, and the growth of smaller species, as implied by both CCA and simple correlation. This finding could be used as basic information for early assessment of environmental change and environmental restoration efforts around water source areas on pine forest plantations. Repetition of this study is suggested to be carried out in other pine forest areas, as each region sometimes has its own specific native and natural species.
Discrete event system formal approaches contribution onto global reliability markov chain generation

This research aims to synthesize a global reliability model, by applying Automata Theory to Model Based Safety Assessment (MBSA). Failure logic expression issued from conventional Reliability Block Diagram or Fault tree Analysis will identify specific Total breakdown States (TBS) and express requirement restricting the Global Faulty Automata (GFA) onto Global Reliability Automata (GRA) establishment thanks to formal composition. The main contributions are relevant to automata translation, requirement expression, TBS identification and TBS treatment.
First report of Telenomus remus parasitizing Spodoptera frugiperda and its natural parasitism in South China

The fall armyworm, Spodoptera frugiperda, is a lepidopteran pest that feeds on many economically important cereal crops such as corn, rice, sorghum, and sugarcane. Native to the Americas, it has become a serious invasive pest in Africa and Asia. Recently, this pest was found invaded China and has spread exceptionally fast across the country. As S. frugiperda will most likely become a major pest in China, Integrated Pest Management strategies, including biological control methods, should be developed to win the battle against it. Here, we report the detection of Telenomus remus parasitizing S. frugiperda eggs in cornfields in South China based on morphological and molecular evidence. Our preliminary surveys indicated that the natural parasitism rates of T. remus on S. frugiperda could reach 30% and 50% for egg masses and per egg mass, respectively. Further application of T. remus against S. frugiperda in biological control programs are discussed.
Short-Term Synaptic Plasticity Makes Neurons Sensitive to the Distribution of Presynaptic Population Firing Rates

Visual Abstract The ability to discriminate spikes that encode a particular stimulus from spikes produced by background activity is essential for reliable information processing in the brain. We describe how synaptic short-term plasticity (STP) modulates the output of presynaptic populations as a function of the distribution of the spiking activity and find a strong relationship between STP features and sparseness of the population code, which could solve this problem. Furthermore, we show that feedforward excitation followed by inhibition (FF-EI), combined with target-dependent STP, promote substantial increase in the signal gain even for considerable deviations from the optimal conditions, granting robustness to this mechanism. A simulated neuron driven by a spiking FF-EI network is reliably modulated as predicted by a rate analysis and inherits the ability to differentiate sparse signals from dense background activity changes of the same magnitude, even at very low signal-to-noise conditions. We propose that the STP-based distribution discrimination is likely a latent function in several regions such as the cerebellum and the hippocampus.
Avaliação da qualidade microbiológica de carnes de peito de frangos de corte submetidas a diferentes temperaturas do ambiente de processamento

O controle da temperatura do ambiente de processamento e um dos principais fatores relacionados a producao de alimentos seguros e com qualidade microbiologica. Com o objetivo de avaliar a influencia da temperatura ambiente durante o corte e a desossa da carne de frango sobre a qualidade microbiologica dos produtos finais, foram coletadas 288 amostras de carne de peito de frango sem pele, obtidas em uma sala de cortes climatizada submetida a quatro diferentes temperaturas ambientes (12oC, 14oC, 16oC e 18oC). Para avaliacao da contaminacao ambiental foi realizada a contagem de micro-organismos mesofilos aerobios e para a avaliacao da qualidade microbiologica da carne foram realizadas a contagem de coliformes totais e termotolerantes e pesquisa de Salmonella spp. Os resultados encontrados demonstraram um aumento da contaminacao ambiental (P=0,01) a medida que a temperatura da sala foi aumentada. Porem, nos cortes carneos, nao foram observadas diferencas significativas (P 0,05) na contagem de coliformes totais, nos termotolerantes e na pesquisa de Salmonella spp. Foi concluido que, apesar da elevacao da contaminacao ambiental, o aumento da temperatura ambiente da sala de cortes nao comprometeu a qualidade microbiologica do produto final.
A Krüppel-like factor 1 (KLF1) Mutation Associated with Severe Congenital Dyserythropoietic Anemia Alters Its DNA-Binding Specificity

Krüppel-like factor 1 (KLF1/EKLF) is a transcription factor that globally activates genes involved in erythroid cell development. Various mutations are identified in the human KLF1 gene. The E325K mutation causes congenital dyserythropoietic anemia (CDA) type IV, characterized by severe anemia and non-erythroid-cell-related symptoms. The CDA mutation is in the second zinc finger of KLF1 at a position functionally involved in its interactions with DNA. ABSTRACT Krüppel-like factor 1 (KLF1/EKLF) is a transcription factor that globally activates genes involved in erythroid cell development. Various mutations are identified in the human KLF1 gene. The E325K mutation causes congenital dyserythropoietic anemia (CDA) type IV, characterized by severe anemia and non-erythroid-cell-related symptoms. The CDA mutation is in the second zinc finger of KLF1 at a position functionally involved in its interactions with DNA. The molecular parameters of how CDA-KLF1 exerts its biological effects have not been addressed. Here, using an in vitro selection strategy, we determined the preferred DNA-binding site for CDA-KLF1. Binding to the deduced consensus sequence is supported by in vitro gel shifts and by in vivo functional reporter gene studies. Two significant changes compared to wild-type (WT) binding are observed: G is selected as the middle nucleotide, and the 3′ portion of the consensus sequence is more degenerate. As a consequence, CDA-KLF1 did not bind the WT consensus sequence. However, activation of ectopic sites is promoted. Continuous activation of WT target genes occurs if they fortuitously contain the novel CDA site nearby. Our findings provide a molecular understanding of how a single mutation in the KLF1 zinc finger exerts effects on erythroid physiology in CDA type IV.
Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis

Differential signalling of the WNT and Notch pathways regulates proliferation and differentiation of Lgr5+ crypt-based columnar cells (CBCs) into all cell lineages of the intestine. We have recently shown that high mitochondrial activity in CBCs is key in maintaining stem cell function. Interestingly, while high mitochondrial activity drives CBCs, it is reduced in the adjacent secretory Paneth cells (PCs). This observation implies that during differentiation towards PCs, CBCs undergo a metabolic rewiring involving downregulation of mitochondrial number and activity, through a hitherto unknown mechanism. Here we demonstrate, using intestinal organoids that FoxO transcription factors and Notch signalling functionally interact in determining CBC cell fate. In agreement with the organoid data, combined Foxo1 and 3 deletion in mice increases PC number in the intestine. Importantly, we show that FOXO and Notch signalling converge onto regulation of mitochondrial fission, which in turn provokes stem cell differentiation into the secretory types; Goblet cells and PCs. Finally, mapping intestinal stem cell differentiation based on pseudotime computation of scRNA-seq data further supports the role of FOXO, Notch and mitochondria in determining secretory differentiation. This shows that mitochondria is not only a discriminatory hallmark of CBCs and PCs, but that its status actively determines lineage commitment during differentiation. Together, our work describes a new signalling-metabolic axis in stem cell differentiation and highlights the importance of mitochondria in determining cell fate.
Soil niche of rain forest plant lineages: Implications for dominance on a global scale

Why some lineages are species‐rich and widespread, while others are species‐poor and localized, is a fundamental question in evolutionary biology and ecology. Diversification and range expansion relate to lineage‐specific niche characters, but this link has seldom been quantified across multiple lineages and environments. This study explored the link between local dominance and soil niche in rain forest plants, and tested the hypothesis that local soil niche patterns can be used to predict the global diversity and occupancy of equal‐aged plant lineages.
Identification and evolution of avian endogenous foamy viruses

A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (C. boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
Machine Translation Using Syntactic Analysis

This thesis describes our improvement of machine translation (MT), with a special focus on the English-Czech language pair, but using techniques applicable also to other languages. First, we present multiple improvements of the deep-syntactic system TectoMT. For instance, we implemented a novel context-sensitive translation model, comparing several machine learning approaches. We also adapted TectoMT to other domains and languages. Second, we present Transformer – a state-of-the-art end-to-end neural MT sys-tem. We analyzed in detail the effect of several training hyper-parameters. With our optimized training, the system outperformed the best result on the WMT2017 test set by +1.0 BLEU. We further extended this system by utilization of monolingual training data and by a new type of backtranslation (+2.8 BLEU compared to the baseline system). In addition, we leveraged domain adaptation and the effect of “translationese” (i.e which language in parallel data is the original and which is the translation) to optimize MT systems for original-language and translated-language data (gaining further +0.2 BLEU). Our improved neural MT system significantly (p¡0.05) out-performed all other systems in English-Czech and Czech-English WMT2018 shared tasks, in terms of both automatic and manual evaluation. It was even significantly better than the human reference translation according to the manual evaluation.
An efficient k-means algorithm for the cluster head selection based on SAW and WPM

A wireless sensor network (WSN) offers the aggregation of data for the communication and processing in the exterior area or the base station. The main purpose of this study was to efficiently select the cluster heads (CHs) and carry out the synchronous data sink operation for the efficient energy and time utilization. An efficient approach based on the k-means algorithm for the cluster head selection has been proposed. It also includes simple additive weighting (SAW) and weighted product method (WPM) for the data sink operation priority by the decision performance ranking. In this approach, weights are assigned and pre-processed on the basis of the node operations or the attribute values. These values are used for clustering of the nodes. K-means have been applied for the clustering. The resultant data are then processed with the decision performance ranking methods. We have used SAW and WPM for the selection of CHs from the clusters. The variations in SAW and WPM results are minor and these approaches are efficient in providing the proper CHs selection from the obtained clusters. The result of the random selection priority scale also offers an energy efficient system. The proposed approach results in less delay in packet delivery and offers efficient energy consumption in contrast to the traditional method.
Morphological and Molecular Characteristics of Kudoa viseuensis n. sp. (Myxosporea: Multivalvulida), Found in the Muscle of Batrachoides surinamensis (Teleostei: Batrachoididae) in the Brazilian Amazon Region

A new species of myxozoan, Kudoa viseuensis n. sp. (Myxosporea: Multivalvulida), is described based on specimens extracted from the musculature of the Pacuma toadfish, Batrachoides surinamensis, collected in the municipality of Viseu, in the northern Brazilian state of Para. A total of 60 specimens of B. surinamensis were examined, of which 52 (86%) presented whitish pseudocysts containing numerous rounded spores (7.2±0.2 μm in length and 5.2±0.2 μm in width). These spores have four polar capsules of equal size, measuring 1.8±0.2 μm x 1.3±0.1 μm in the apical view, and 2.7±0.2 μm x 1.3±0.1 μm in the lateral view. A partial sequence (1400 bps) of the small subunit ribosomal RNA gene was obtained and deposited in GenBank (access number: MK256272). The comparison of the morphological and molecular data with those of other Kudoa species supported the description of a new species of mixosporean from the Amazon region, which is denominated here as Kudoa viseuensis n. sp.
Evaluation of Amylase Activity Produced by Genetically Modified Bacillus Grown on Different Media Containing Sugar Crops Wastes

In this investigation, α-amylase gene region from a thermophilic Bacillus stearothermophilus isolated from sugar beet juice obtained from Dakahlia Sugar factory (Egypt) was cloned to competent Bacillus licheniformis ATCC 27811 cells. The original and modified Bacillus strains were spread on different media composition and enzyme activity was determined. According to the results, the α-amylase enzyme was seen to have highest activity at media containing sugarcane bagasse and/or sugar beet pulp. The results revealed that modified Bacillus surpassed the original one at all studied media. This obtained result proofed that gene transferred into BL had effective action on increase α-amylase activity. The thermo-stability studies revealed that enzyme activity of modified bacillus was high for the first 8 hours at 90°C, it was ranged from 95-90 % after 6 hours (enzyme activity decreased from 7.80 to 7.02 gm glucose/ml) then, decreased to 65-63 % at the end of 24 hours.
Analysis and prediction of hotel ratings from crowdsourced data

Crowdsourcing has become an essential source of information for tourism stakeholders. Every day, tourists leave large volumes of feedback data in the form of posts, likes, textual reviews, and ratings in dedicated crowdsourcing platforms. This behavior makes the analysis of crowdsourced information strategic, allowing the discovery of important knowledge regarding tourists and tourism resources. This paper presents a survey on the analysis and prediction of hotel ratings from crowdsourced data, covering both off‐line (batch) and on‐line (stream‐based) processing. Specifically, it reports multiple rating‐based profiling, recommendation, and evaluation techniques. While most of the surveyed works adopt entity‐based multicriteria profiling, prerecommendation filtering, and off‐line processing, the latest hotel rating prediction trends include feature‐based, trust and reputation modeling, postrecommendation filtering, and on‐line processing. Additionally, since the volume of crowdsourced ratings tends to increase, the deployment of profiling and recommendation algorithms on high‐performance computing resources should be further explored.
The complete chloroplast genome of Vaccinium fragile (Vacciniaceae), a shrub endemic to China

Abstract Vaccinium fragile, an endemic species in China, is a plant of the family Vacciniaceae. It is an evergreen shrubby tree distributed in Sichuan, Guizhou, Yunnan, and Tibet province of China. The chloroplast (cp) genome of V. fragile is 169,480 bp in size containing 123 unique genes, including 8 rRNA genes, 38 tRNA genes, and 77 protein-coding genes (PCGs). Phylogenetic analysis exhibited that both V. macrocarpon and V. fragile were phylogenetically closer to Arbutus unedo than other taxa in this study.
PREVALENCE OF ESBL PRODUCING OXIDASE POSITIVE NON FERMENTING GRAM NEGATIVE BACTERIA ISOLATED FROM VARIOUS CLINICAL SPECIMENS AT A TERTIARY CARE HOSPITAL IN CHENNAI

, 10 isolates Oxidase positive nonfermenting bacteria (NFGNB) have emerged as potential nosocomial pathogens and are becoming resistant to commonly used antimicrobial agents, therefore the present study was under taken to investigate the prevalence of Extended Spectrum Beta Lactamases (ESBLs) production in various species of oxidase positive Non Fermenting Gram Negative Bacteria (NFGNB). Isolates of oxidase positive NFGNB from various clinical specimens were obtained from Department of Microbiology, Madras Medical College & Hospital, Chennai and speciated using conventional biochemical methods and antibiotic susceptibility testing was done as per CLSI guidelines. ESBL production was detected by phenotypic conﬁrmatory disc diﬀusion test (PCT). ESBL phenotypes were subjected bla TEM screening using PCR. Out of 40 isolates from various clinical samples, Pseudomonas aeruginosa was the commonest accounting for 70% followed by Pseudomonas ﬂuorescens 15%. Among the 40 isolates, 35% were multidrug resistant, 27.5% of the isolates were found to be ESBL producers. ESBL producers were negative for bla TEM gene by PCR assay. To conclude signiﬁcant percentage of NFGNB were found to be ESBL producers in our study. To know the actual incidence of ESBLs in these organisms, all the NFGNB should be speciated and screened for ESBL production to avoid the spread of drug resistance. ABSTRACT
Adult dentate gyrus neurogenesis: a functional model

In adult dentate gyrus neurogenesis, the link between maturation of newborn neurons and their function, such as behavioral pattern separation, has remained puzzling. By analyzing a theoretical model, we show that the switch from excitation to inhibition of the GABAergic input onto maturing newborn cells is crucial for their proper functional integration. When the GABAergic input is excitatory, cooperativity drives the growth of synapses such that newborn cells become sensitive to stimuli similar to those that activate mature cells. When GABAergic input switches to inhibitory, competition pushes the configuration of synapses onto newborn cells towards representations that are away from previously stored memories. This enables the maturing newborn cells to code for concepts that are novel, yet similar to familiar ones. Our theory of newborn cell maturation explains how adult newborn cells integrate into the preexisting network and why they promote separation of similar patterns.
The complete chloroplast genome of Pedicularis alaschanica (Orobanchaceae)

Abstract The complete chloroplast genome sequence of Pedicularis alaschanica was determined and described. The complete chloroplast was 146,989 bp in length with typical quadripartite structure and overall GC content of 38.4%, which encompassed 68 protein-coding genes, 22 tRNAs, 4 rRNAs, and 11 pseudogenes. The functions of ndh genes were lost. The phylogenetic analysis indicated that P. alaschanica was close to other species of Pedicularis. This study would contribute to enrich the Pedicularis chloroplast genome resource and promote the biological research.
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.
Using Genetic Algorithms in Designing Substation Lightning Shielding

This paper introduces application of genetic algorithm (GA) in designing air-termination system of the highvoltage open-air substation external lightning protection system (LPS). The air-termination system, as a part of the external LPS of high-voltage substation, is known to be cumbersome to design using traditional techniques, where optimization is often relegated to the trial-and-error approach. In addition, traditional methods are often associated with geometric constraints and various implementation difficulties. This paper proposes a novel approach which utilizes a combination of statistical LPS efficiency and GA in designing techno-economically optimal external LPS of open-air substations. Proposed approach offers a LPS designer unique and valuable assistance in optimally arranging elements of air-termination system for obtaining maximum lightning shielding effects with minimum total investments. Keywords—Genetic algorithm; Lightning protection; LPS; Substation shielding; EGM