Miracle-dz/UniFAR-FTUs huggingface dataset:
Double Tubular Contractile Structure of the Type VI Secretion System Displays Striking Flexibility and Elasticity

The cell wall is a physical scaffold that all transenvelope complexes have to cross for assembly. However, the cell wall-deficient state has been described as a common condition found in both Gram-negative and Gram-positive pathogens during persistent infections. Loss of cell wall is known to have pleiotropic physiological effects, but how membrane-anchored large cellular organelles adapt to this unique state is less completely understood. Our study examined the assembly of the T6SS in cell wall-deficient spheroplast cells. We report the elastic nature of contractile T6SS tubules under such conditions, providing key insights for understanding how large intracellular structures such as the T6SS accommodate the multifaceted changes in cell wall-deficient cells. ABSTRACT Antimicrobial treatment can induce many bacterial pathogens to enter a cell wall-deficient state that contributes to persistent infections. The effect of this physiological state on the assembly of transenvelope-anchored organelles is not well understood. The type VI secretion system (T6SS) is a widespread molecular weapon for interspecies interactions and virulence, comprising a long double tubular structure and a transenvelope/baseplate complex. Here, we report that cell wall-deficient spheroplasts assembled highly flexible and elastic T6SS structures forming U, O, or S shapes. Upon contacting the inner membrane, the T6SS tubes did not contract but rather continued to grow along the membrane. Such deformation likely results from continual addition of sheath/tube subunits at the distal end. Induction of TagA repressed curved sheath formation. Curved sheaths could also contract and deliver T6SS substrates and were readily disassembled by the ClpV ATPase after contraction. Our data highlight the dramatic effect of cell wall deficiency on the shape of the T6SS structures and reveal the elastic nature of this double tubular contractile injection nanomachine. IMPORTANCE The cell wall is a physical scaffold that all transenvelope complexes have to cross for assembly. However, the cell wall-deficient state has been described as a common condition found in both Gram-negative and Gram-positive pathogens during persistent infections. Loss of cell wall is known to have pleiotropic physiological effects, but how membrane-anchored large cellular organelles adapt to this unique state is less completely understood. Our study examined the assembly of the T6SS in cell wall-deficient spheroplast cells. We report the elastic nature of contractile T6SS tubules under such conditions, providing key insights for understanding how large intracellular structures such as the T6SS accommodate the multifaceted changes in cell wall-deficient cells.
Transcriptome Sequencing of Two Kentucky Bluegrass (Poa pratensis L.) Genotypes in Response to Heat Stress

Kentucky bluegrass (Poa pratensis L.) (KBG) is a major cool-season turfgrass. However, as its complex genetic background and production modes, limited genomic and transcriptomic information of KBG was known so far. In this study, a transcriptome study between wild type material Ninglan (summer stress sensitive) and cultivar material KBG03 (summer stress tolerant) was conducted, under optimal (25 °C) and high (40 °C) temperatures. A total of 81.42 Gb clean reads were generated and de novo assembled into 110,784 unigenes with an average length of 1,105 bp. About 50% KBG unigenes were similar to the non-redundant (NR) database. Among the NR BLASTx top hits, 27.47% unigenes were matched to Brachypodium distachyon. After heat stress, a massive amount of unigenes showed significantly differential expression in both genotypes. After 2h heat stress, more specially up-regulated differentially expressed unigenes (DEGs) and less down-regulated DEGs were detected in Ninglan than in KBG03. At 24h, the expression of 1710 and 730 unigenes were increased and decreased uniquely in Ninglan, and 1361 up-regulated DEGs and 757 down-regulated DEGs were just found in KBG03. More heat shock proteins (HSPs) and heat shock transcription factors (HSFs) DEGs were also identified at 2h than 24h in both genotypes. In addition, by Gene Ontology (GO) enrichment analysis, three core terms (“protein folding”, “response to heat”, and “response to hydrogen peroxide”) of biological process (BP) ontology were found in both genotypes under different heat stress time. The DEGs shared in both genotypes might be related to the basic mechanism of thermal response in KBG.
Short Communication: Morphological characterizations of Aphis passeriniana (Del Guercio) (Hemiptera: Aphididae) living on common sage in Turkey

Zarkani A, Turanlı F. 2018. Short Communication: Morphological characterizations of Aphis passeriniana (Del Guercio) (Hemiptera: Aphididae) living on common sage in Turkey. Biodiversitas 19: 1319-1325. Aphis passeriniana (Del Guercio) (Hemiptera: Aphididae) living on sage plant in Turkey is already recorded, but some morphological characterizations are still needed to extend. Here, morphometrics data of A. passeriniana is described from apterous viviparous females (fundatrigeniae and fundatrices) attacking Salvia officinalis Linnaeus (Lamiaceae) in Turkey. Seventy specimens were collected in Izmir province between January 2015 and December 2017. The study revealed that apterous viviparous females of A. passeriniana turkish species have body lenght of 0.715-1.407 mm, rostal segment IV+V of 1.80-2.49 × hind tibia II, antennae processus terminalis/base of 1.4-1.8, siphunculus of 0.56-1.56 × cauda length and cauda of 3-6 setae. Biometric data of alate viviparous and intermediate individual between apterous and oviparous, and also a revision of identification key for the species within aphid species in Salvia are consisted.
Detection and Localization of FDIA on Distributed State Estimation in Two Operation Modes of Interconnected Power System

—As power systems will be increasingly interconnected in the future grid, it is practically infeasible to implement a centralized state estimator owing to the complexity scale of an interconnection. To address this issue, distributed state estimation (DSE) has become an important alternative to centralized and hierarchical solutions. Implementation of distributed options require the use of information and communication technology. However, reliance on ICT renders smart grid vulnerable to cyber-attacks with severe social, economic and physical consequences. One of the most widely studied attacks on the power system is false data injection attack (FDIA). In this paper a FDIA on DSE is proposed and it is proved that the attack can get through the existing robust estimators. Afterwards, a detection and localization algorithm is presented for two different ways of doing the DSE: 1) by one operator, and 2) by several operators. Speciﬁcally, a measure based on computing the error between estimates of the state variables and their actual value is utilized. When the system is operated by an operator, this error is compared to a threshold value for different areas. Also, when the system is operated by multiple operators, a controlled information dissemination method is used to inform all areas of each other’s error in a private manner. The tests are done on the IEEE 14-bus and the results
University of Birmingham Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling

38 Senescence is a tightly regulated developmental programme coordinated by transcription factors. 39 Identifying these transcription factors in crops will provide opportunities to tailor the senescence 40 process to different environmental conditions and regulate the balance between yield and grain 41 nutrient content. Here, we use ten time points of gene expression data along with gene network 42 modelling to identify transcription factors regulating senescence in polyploid wheat ( Triticum 43 aestivum L.). We observe two main phases of transcriptional changes during senescence: early 44 downregulation of housekeeping functions and metabolic processes followed by upregulation of 45 transport and hormone related genes. These two phases are largely conserved with Arabidopsis 46 ( Arabidopsis thaliana ), although the individual genes underlying these changes are often not 47 orthologous. We have identified transcription factor families associated with these early and later 48 waves of differential expression. Using gene regulatory network modelling, we identified candidate 49 transcription factors that may control senescence. Using independent, publicly available datasets, we 50 found that the most highly ranked candidate genes in the network were enriched for senescence-51 related functions compared to all genes in the network. We validated the function of one of these 52 candidate transcription factors in senescence using wheat chemically-induced mutants. This study lays 53 the groundwork to understand the transcription factors that regulate senescence in polyploid wheat 54 and exemplifies the integration of time-series data with publicly available expression atlases and 55 networks to identify candidate regulatory genes.
Terrestrial Passive Acoustic Monitoring: Review and Perspectives

Passive acoustic monitoring (PAM) is quickly gaining ground in ecological research, following global trends toward automated data collection and big data. Using unattended sound recording, PAM provides tools for long-term and cost-effective biodiversity monitoring. Still, the extent of the potential of this emerging method in terrestrial ecology is unknown. To quantify its application and guide future studies, we conducted a systematic review of terrestrial PAM, covering 460 articles published in 122 journals (1992–2018). During this period, PAM-related studies showed above a fifteenfold rise in publication and covered three developing phases: establishment, expansion, and consolidation. Overall, the research was mostly focused on bats (50%), occurred in northern temperate regions (65%), addressed activity patterns (25%), recorded at night (37%), used nonprogrammable recorders (61%), and performed manual acoustic analysis (58%), although their applications continue to diversify. The future agenda should include addressing the development of standardized procedures, automated analysis, and global initiatives to expand PAM to multiple taxa and regions.
Mycoplasma genitalium incidence, persistence, concordance between partners and progression: systematic review and meta-analysis

Background Mycoplasma genitalium is increasingly seen as an emerging sexually transmitted pathogen, and has been likened to Chlamydia trachomatis, but its natural history is poorly understood. The objectives of this systematic review were to determine M. genitalium incidence, persistence, concordance between sexual partners and the risk of pelvic inflammatory disease (PID). Methods We searched Medline, EMBASE, LILACS, IndMed and African Index Medicus from 1 January 1981 until 17 March 2018. Two independent researchers screened studies for inclusion and extracted data. We examined results in forest plots, assessed heterogeneity and conducted meta-analysis where appropriate. Risk of bias was assessed for all studies. Results We screened 4634 records and included 18 studies; six (4201 women) reported on incidence, five (636 women) on persistence, 10 (1346 women and men) on concordance and three (5139 women) on PID. Incidence in women in two very highly developed countries was 1.07 per 100 person-years (95% CI 0.61 to 1.53, I2 0%). Median persistence of M. genitalium was estimated from one to three months in four studies but 15 months in one study. In 10 studies measuring M. genitalium infection status in couples, 39%–50% of male or female sexual partners of infected participants also had M. genitalium detected. In prospective studies, PID incidence was higher in women with M. genitalium than those without (risk ratio 1.73, 95% CI 0.92 to 3.28, I2 0%, two studies). Discussion Incidence of M. genitalium in very highly developed countries is similar to that for C. trachomatis, but concordance might be lower. Taken together with other evidence about age distribution and antimicrobial resistance in the two infections, M. genitalium is not the new chlamydia. Synthesised data about prevalence, incidence and persistence of M. genitalium infection are inconsistent. These findings can be used for mathematical modelling to investigate the dynamics of M. genitalium. Registration numbers CRD42015020420, CRD42015020405
Recent Advances in Virus-host Coevolution and Protective Mechanisms against Plant Viruses

In plant pathology, the study of the interaction between the plant host and the viral pathogen has been a very active area of research in the last few decades. The infection process of a plant pathogen usually begins with the exchange of molecular signals. With particular emphasis on plant virus evolution, and focusing on quantitative and population genetics, plant virus-host interactions and coevolution allow understanding of the major factors favoring disease emergence. The Review Article exploitation of viral interaction phenomena will improve established genetic engineering strategies for viral cross-protection in plants. Also, the study of plant immunity against viral infection, both innate and adaptive (e.g. RNA silencing), has helped in the development of resistant varieties to several plant viruses based on genetic engineering. This review summarizes the recent advances in plant-virus interactions and co-evolution as well as current developments in resistant crop investigations.
Pencegahan Viktimisasi Pencurian Data Pribadi

Penelitian ini membahas strategi pencegahan viktimisasi pencurian data pribadi di Indonesia. Dengan keberadaan internet, kehidupan manusia tidak lagi berlangsung hanya di dunia fisik saja tetapi sudah merambah ke dunia maya, begitu pula dengan kejahatan. Transisi kejahatan didukung oleh keberadaan internet yang mendukung akses ke dunia maya lewat smartphone. Penelitian ini bertujuan untuk meningkatkan kesadaran keamanan masyarakat dan mencegah masyarakat menjadi korban kejahatan pencurian data pribadi. Penelitian dilakukan dengan mixed-method kuantitatif dan kualitatif menggunakan kuesioner terstandar dan survei viktim serta self-report mengenai pengetahuan, persepsi, dan perilaku masyarakat. Terdapat 179 responden dengan batasan: berusia dewasa, berdomisili di Jabodetabek, dan menggunakan smartphone pribadi. Hasil penelitian menunjukkan bahwa nilai kesadaran keamanan responden terhadap alat (smartphone), sistem, dan ruang (internet) cukup baik yaitu 67,03% pada tingkat kesadaran tinggi. Namun jika dinilai secara terpisah, penilaian terhadap kesadaran menjadi semakin menurun dan berada di tingkat rendah-menengah dengan nilai paling rendah pada kesadaran terhadap ruang. Kemudian penilaian kesadaran terhadap data pribadi, yaitu 56,98% pada tingkat kesadaran menengah dan jika dinilai secara terpisah antara pengetahuan, sikap, dan persepsi dengan perilaku hasilnya semakin menurun. 44,69% responden memiliki kesadaran dengan nilai nol pada perilaku terhadap data pribadi umum. Tidak mengherankan jika hasil survei menunjukkan 94,97% responden pernah menjadi korban pencurian data pribadi, terutama pada kejahatan pencurian data dengan tingkat rendah. Untuk itu, strategi pencegahan viktimisasi yang terbaik adalah dengan memperbaiki aspek penentu kesadaran keamanan terutama dalam berperilaku dalam kepemilikan data pribadi dan smartphone, juga dalam menggunakan sistem, aplikasi, dan internet.
EFEKTIVITAS KOMPRES JAHE TERHADAP PERUBAHAN SKALA NYERI SENDI ASAM URAT (Gout) PADA LANSIA DI UPT PANTI SOSIAL TRESNA WERDHA KABUPATEN MAGETAN

Nyeri sendi merupakan penyakit yang sering dialami oleh lansia. Asam urat (gout) merupakan suatu penyakit peradangan pada persendian yang dapat diakibatkan oleh kelebihan kadar senyawa asam urat di dalam tubuh, baik karena produksi berlebih atau peningkatan asupan purin. Salah satu terapi non farmakologi yang bisa dilakukan untuk meredakan nyeri adalah dengan kompres hangat tumbukkan jahe. Tujuan penelitian ini untuk Mengidentifikasi Efektivitas Kompres Jahe Terhadap Perubahan Skala Nyeri Sendi Asam Urat (Gout) Pada Lansia di UPT Panti Sosial Tresna Werdha Kabupaten Magetan. Metode penelitian ini menggunakan quasy eksperimental dengan desain one group pretest-posttest dengan jumlah sampel 21 responden dengan teknik sampling yang digunakan adalah purposive sampling. Hasil penelitian menunjukan bahwa dari 21 responden didapatkan adanya penurunan rata-rata skala nyeri responden sebelum diberikan kompres hangat dengan tumbukan jahe sebesar 6,14 (nyeri sedang), namun setelah diberikan kompres hangat dengan tumbukan jahe rata-rata skala nyeri responden sebesar 3,29 (nyeri ringan). Hasil penelitian dengan uji Paired t test menunjukkan nilai signifikansi p value sebesar 0,000 karena (p < 0,05) disimpulkan Ho ditolak. Dengan demikian dapat dinyatakan ada pengaruh kompres hangat tumbukkan jahe terhadap perubahan skala nyeri sendi asam urat (gout) pada lansia di UPT Panti Sosial Tresna Werdha Kabupaten. Kompres jahe diharapkan dapat menjadi salah satu terapi non farmakologi yang dapat digunakan untuk meringankan nyeri sendi yang dialami lansia. Sehingga dapat meminimalkan terjadinya nyeri sendi dan meningkatkan kualitas hidupnya. Kepada perawat maupun tenaga kesehatan lainnya sangat penting untuk memberikan informasi dan edukasi tentang pemberian kompres jahe pada lansia penderita nyeri sendi asam urat (gout)
Forage sorghum-legumes intercropping: effect on growth, yields, nutritional quality and economic returns

Cereal-legumes intercropping is among the most economical and effective agronomic strategies to boost forage biomass production, nutritional quality and monetary returns. This review synthesizes the research findings on how intercropping affects productivity, quality, competitiveness and economic viability of sorghum-legumes mixed, row and strip intercropping systems under varied pedo-climatic conditions. Though component crops show yield reductions in row (additive and row-replacement series), mixed (seed blended crops) and strip intercropping systems, in general overall productivity per unit land area increases to a great extent. The significantly higher resource capturing with better utilization efficacy by intercrops in temporal and spatial dimensions helps explain their greater productivity. In addition, forage intercrops result in improved nutritional quality as legumes contain protein in double quantity than cereals. Cereal-legumes intercropping systems yield CROP PRODUCTION AND MANAGEMENT Article Forage sorghum-legumes intercropping: effect on growth, yields, nutritional quality and economic returns Muhammad Aamir Iqbal1*, Abdul Hamid2, Tanvir Ahmad3, Muzammil Hussain Siddiqui1, Imtiaz Hussain4, Sajid Ali5, Anser Ali6, Zahoor Ahmad7 1.University of Poonch Rawalakot Department of Agronomy Rawalakot, Pakistan. 2.University of Poonch Rawalakot Department of Horticulture Rawalakot, Pakistan. 3.Ghazi University Department of Horticulture D. G. Khan, Pakistan. 4.University of Poonch Rawalakot Department of Food Science and Technology Rawalakot, Pakistan. 5.University of Punjab Institute of Agricultural Sciences Lahore, Pakistan. 6.Ghazi University Department of Agronomy Dera Ghazi Khan, Pakistan. 7.Islamia University Bahawalpur Department of Life Sciences Bahawalpur, Pakistan. *Corresponding author: muhammadaamir@upr.edu. pk Received: Oct. 18, 2017 – Accepted: Mar. 26, 2018 higher quantities of lush green forage with improved quality traits, which ultimately increase monetary benefits. Furthermore, legumes inclusion as an intercrop with cereals has the potential to serve as a nitrogen-saving strategy due to the biological nitrogen fixation (BNF) process. Moreover, cereal-legume intercropping systems are effective in reducing weed infestations and soil erosion by providing extended soil cover, as well as in increasing water use efficiency and improving soil fertility. However, despite a significant increase in overall productivity, component crops suffer yield losses in intercropping systems owing to competition for the finite divisible pool of growth resources. Thus, there is a dire need to optimize spatial and temporal arrangements in sorghum-legumes intercropping systems to achieve maximum productivity and economic returns.
Caractérisation structurale de la birnessite : influence du protocole de synthèse

La birnessite est un oxyde de manganese lamellaire dont les feuillets sont composes d'octaedres MnO6. La presence dans ces feuillets de cations Mn heterovalents ou de lacunes induit un deficit de charge compense par la presence de cations hydrates dans l'espace interfoliaire. Les oxydes de manganese jouent un role fondamental pour le devenir de nombreux polluants organiques ou metalliques dans l'environnement, mais la connaissance imparfaite de leur structure limite la modelisation de cet impact. Le but de ce travail etait de recenser et de classifier les differentes varietes de birnessites obtenues selon deux criteres pertinents (symetrie du feuillet et mode d'empilement) et de determiner la structure de plusieurs varietes essentielles par diffraction des rayons X et des electrons. La birnessite hydrothermale est caracterisee par un feuillet lacunaire de symetrie hexagonale et un empilement rhomboedrique 3R. Dans l'empilement des feuillets de la birnessite haute-temperature, les octaedres des feuillets successifs presentent une orientation inverse induisant un polytype a deux feuillets. La symetrie de ces feuillets, liee a l'origine du deficit de charge, depend de la temperature de synthese. A 800°C, le feuillet lacunaire possede une symetrie hexagonale (polytype 2H). A 1000°C, le deficit de charge est du a la presence de Mn3+ dans le feuillet. L'allongement systematique de ces octaedres selon l'axe a induit une symetrie orthogonale du feuillet (polytype 2O). Diverses heterogeneites chimiques et structurales ont egalement ete decrites dans ces echantillons, ainsi que l'occurrence originale d'un nouveau type de desordre structural. Nous avons enfin illustre le lien fondamental entre l'origine de la charge foliaire et la symetrie du feuillet, ainsi que l'influence des parametres physico-chimiques lors de la synthese (temperature, degre d'oxydation du manganese, nature du cation) sur la structure du compose obtenu, et compare leurs stabilites chimiques et thermiques.
DNA phenotyping and drug induce pigmentation: a theoretical approach

Human genetic variation has a high discriminatory power, so the prediction of phenotypes through genotype has been a topic of growing interest for study, and there is anticipation for its use in personalized medicine and in the area of forensic genetics, the latter having a greater interest in predicting externally visible traits. One of the areas of human genetic variation with more variants is the pigmentation, and for its multifactorial nature is of great interest to study the effect of pharmaceutical drugs on this characteristic, even more considering that drugs that have already been identified as related to induced pigmentation, are present in the environment and for that reason we are exposed to them even without knowledge. Drug influence in pigmentation is an area with almost no studies, having only a few that mention pigmentation but do not explore this any further mainly because the ones who focus on drugs effects on organisms normally are more related to pathologies being the pigmentation a characteristic that is easily discarded.