bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genomic dating tool resolves the origins of ancient Eurasian genomes
Authors: Esposito U. , Holland G. , Alshehab G. , Dobre A. M. , Pirooznia M. , Brimacombe C. S. , Elhaik E. 
Published: November 2019

AbstractRadiocarbon dating is the gold-standard in archaeology to estimate the age of skeletons, a key to studying their origins. Nearly half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we developed the Temporal Population Structure (TPS), the first DNA-based dating method for ancient genomes ranging from the Upper Palaeolithic to modern-day samples and applied it to 1559 ancient Europeans, Asians, and Caucasus individuals and to 2117 modern worldwide individuals. We show that TPS predictions for dated skeletons align with their known dates and correctly account for kin relationships. The TPS-dating of poorly dated Eurasian samples resolves conflicts and sheds new light on disputed findings, as illustrated by four test cases. We discuss the phenotypic traits of the Time Informative Markers (TIMs) that underlie TPS.SummaryTPS is a novel method to date humans from the Upper Palaeolithic to modern time from their DNA sequences.Accurate dating is essential to the interepretation of paleogemonic data.. The gold-standard method in archaeology is radiocarbon dating1. However, a major limitation of radiocarbon dating is the high amount of collagen extraction (500 mg) involved in the process2. Consequently, half of all published ancient human genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we present the Temporal Population Structure (TPS), the first genomic dating method for ancient genomes ranging from the Upper Palaeolithic to modern-day samples. We show that TPS predictions for 961 radiocarbon-dated Eurasian skeletons align with their known dates. We replicate these findings on 598 other Europeans, Asians and Caucasus individuals. Using kin-pairs, we demonstrate that TPS has produced more accurate results than radiocarbon and other dating. We show how our findings resolve conflicts and sheds new light on disputed findings as illustrated by four test cases. Finally, we discuss the phenotypic traits of the Time Informative Markers (TIMs) that underlie TPS. TPS is a novel dating technique, which can be used when radiocarbon dating is unfeasible or uncertain or to develop alternative hypotheses. TPS cannot be used for older (<14,000 years ago) samples, and its accuracy depends on the temporal and geographical breadth of radiocarbon-dated samples in the training dataset, though this limitation can be improved over time. Overall, TPS can improve the accuracy of archeological and paleogenomic studies.
Disinfection exhibits systematic impacts on the drinking water microbiome
Authors: Dai Zihan , Sevillano-Rivera Maria C. , Calus Szymon T. , Bautista-de los Santos Q. Melina , Eren A. Murat , van der Wielen Paul W.J.J. , Ijaz Umer Z. , Pinto Ameet J. 
Published: November 2019

ABSTRACTLimiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without the use of a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We utilized genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiomes across multiple full-scale drinking water systems utilizing these two-distinct microbial growth control strategies. Microbial communities cluster together at the structural- and functional potential-level based on the presence or absence of a disinfectant residual. Disinfectant residual concentrations alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including samples from multiple drinking water systems with variable source waters and source water communities, treatment strategies, and chemical compositions. The drinking water microbiome is structurally and functionally less diverse and less variable across disinfected systems as compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems which may be associated with the recycling of amino acids. Metagenome-assembled genome-level analyses for a subset of phylogenetically related microorganisms suggests that disinfection may select for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic and consistent selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection inactivated microorganisms.
Single-molecule nanopore sensing of actin dynamics and drug binding
Authors: Wang Xiaoyi , Wilkinson Mark D. , Lin Xiaoyan , Ren Ren , Willison Keith , Ivanov Aleksandar P. , Baum Jake , Edel Joshua B. 
Published: November 2019

AbstractActin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, drug-binding and filament-growth events at the single-molecule level. This enabled us to calculate binding stoichiometries and to propose a model for protein dynamics using unmodified, native actin molecules, demostrating the promise of nanopores sensing for in-depth understanding of protein folding landscapes and for drug discovery.
High-resolution Introgressive Region Map Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication
Authors: Ohyanagi Hajime , Goto Kosuke , Negrão Sónia , Wing Rod A. , Tester Mark A. , McNally Kenneth L. , Bajic Vladimir B. , Mineta Katsuhiko , Gojobori Takashi 
Published: November 2019

AbstractDomestication is anthropogenic evolution that fulfills mankind’s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new food resources including crops. With the aim of understanding the long-term domestication process of Asian rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian rice domestication model, we scrutinized past genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and the so-called selective sweep regions, we provide a definitive answer to a long-standing controversy over the evolutionary origin of Asian rice domestication, single or multiple origins: It heavily depends upon which regions you pay attention to, implying that wider genomic regions represent immediate short history of Asian rice domestication as a likely support to the single origin, while its ancient history is interspersed in narrower traces throughout the genome as a possible support to the multiple origin.
Magnetic resonance image‐guided focal laser ablation in clinically localized prostate cancer: safety and efficacy
Authors: Al‐Hakeem Yasser , Raz Orit , Gacs Zita , Maclean Fiona , Varol Celi 
Published: November 2019

AbstractBackgroundTo evaluate the safety and efficacy of focal laser ablation (FLA) in low‐intermediate risk prostate cancer.MethodsInclusion criteria were men aged 50–75 years, prostate‐specific antigen (PSA) ≤15 ng/mL, clinical stage T1c–T2a, one or two lesions (PI‐RADS ≥3) on magnetic resonance imaging (MRI), and Gleason score 6 (>3 mm) or Gleason 7 on targeted biopsy. Treatment success was defined as no clinically significant cancer in ablated areas. The study is prospective. Under MRI guidance, laser ablation was applied to the visible lesion(s). International Prostate Symptoms Score, Sexual Health Inventory in Men score and PSA levels were assessed at baseline and repeated at 1, 3, 6, 12 and 18 months. MRI was repeated at 3 and 12 months. Cancer control was assessed at 6 months using targeted and systematic biopsies.ResultsFLA was performed in 49 patients. Gleason scores were 3 + 3 in 13 patients (26.5%), 3 + 4 in 29 (59.2%) and 4 + 3 in 7 (14.3%). No significant complications were noticed. International Prostate Symptoms Score measurements up to 18 months were not different from baseline (all P > 0.05). Sexual Health Inventory in Men scores dropped in the first year (all P < 0.05), but were not different from baseline levels at 18 months (P = 0.097). PSA levels dropped significantly at 3–18 months (all P < 0.05). Treatment was successful in 39 patients (79.6%). Persistent cancer in treated areas was found in 10 patients (20.4%).ConclusionsFLA is safe with no impact on urinary and sexual functions at 18 months follow‐up. Oncologic control is encouraging. Larger scale studies and longer follow‐up are required.
The grade index model as a rationale for autogenic nonequilibrium responses of deltaic clinoform to relative sea‐level rise
Authors: Wang Junhui , Naruse Hajime , Muto Tetsuji 
Published: November 2019

AbstractGrade index (Gindex) is a dimensionless number given as the volume‐in‐unit‐time ratio of subaerial allocation to both subaerial and subaqueous allocations of sediment supplied to a delta from upstream. It was originally proposed for understanding the effect of basin water depth on the morphodynamics of delta distributary channels under stationary relative sea level. We here examine how rising relative sea level modulates the Gindex, using geometrical reasoning and numerical simulations. We find that the grade index model can account for autoretreat of the deltaic shoreline, autodrowning of the whole system, and autobreak of the deltaic sedimentation, all of which are the consequences of autogenic nonequilibrium responses to steadily rising relative sea level. The regressive‐to‐transgressive threshold (i.e. the onset of autoretreat) is crossed when the delta plain's dimensionless basal area (At*) encounters a critical value that is expressed in terms of Gindex: regression and transgression are sustained when At* is below and above the threshold, respectively. The mode of transgression depends on the slope conditions. If the hinterland slope (γ) is steeper than the foreset slope (β), both At* and Gindex decrease as the relative sea‐level rises. Eventually, the depositional system experiences autodrowning when At* = Gindex = 0. If γ < β; on the other hand, both At* and Gindex increase. This latter slope condition eventually causes autobreak of the deltaic sedimentation, afterward of which At* = Gindex = 1. The grade index model is useful for interpreting and predicting the stratigraphic responses of natural deltaic clinoforms in conditions of rising relative sea level.
Cortical responses to tactile stimuli in preterm infants
Authors: Leikos Susanna , Tokariev Anton , Koolen Ninah , Nevalainen Päivi , Vanhatalo Sampsa 
Published: November 2019

AbstractThe conventional assessment of preterm somatosensory functions using averaged cortical responses to electrical stimulation ignores the characteristic components of preterm somatosensory evoked responses (SERs). Our study aimed to systematically evaluate the occurrence and development of SERs after tactile stimulus in preterm infants. We analysed SERs performed during 45 electroencephalograms (EEGs) from 29 infants at the mean post‐menstrual age of 30.7 weeks. Altogether 2,087 SERs were identified visually at single‐trial level from unfiltered signals capturing also their slowest components. We observed salient SERs with a high‐amplitude slow component at a high success rate after hand (95%) and foot (83%) stimuli. There was a clear developmental change in both the slow wave and the higher‐frequency components of the SERs. Infants with intraventricular haemorrhage (IVH; eleven infants) had initially normal SERs, but those with bilateral IVH later showed a developmental decrease in the ipsilateral SER occurrence after 30 weeks of post‐menstrual age. Our study shows that tactile stimulus applied at bedside elicits salient SERs with a large slow component and an overriding fast oscillation, which are specific to the preterm period. Prior experimental research indicates that such SERs allow studying both subplate and cortical functions. Our present findings further suggest that they might offer a window to the emergence of neurodevelopmental sequelae after major structural brain lesions and, hence, an additional tool for both research and clinical neurophysiological evaluation of infants before term age.
Survey on Bactrocera spp. (Tephritidae, Diptera) in Austria
Authors: Egartner A. , Lethmayer C. , Gottsberger R. A. , Blümel S. 
Published: November 2019

Fruit fly species (Diptera: Tephritidae) of the genus Bactrocera are among the most serious orchard pests worldwide but are not native to Austria. The unexpected finding of one Bactrocera zonata adult in Vienna in 2011 initiated increasing survey efforts in Austria since 2012. Traps with male attracting lures were employed at several sites during the fruiting periods and catches were analysed. At sites in Vienna (urban area) Bactrocera specimens were trapped between 2012 and 2018, whereas no Bactrocera specimens were caught in agricultural areas or commercial orchards outside the city. Twelve specimens were identified as B. zonata and nine specimens as B. dorsalis sensu lato, though for the latter it was not possible to distinguish between B. dorsalis s.l. and B. carambolae using molecular analysis (ITS1). Molecular sequencing showed that the specimens caught were genetically different (with only a few exceptions), indicating genetically different origins. It is evident that the repeated findings of Bactrocera specimens in Vienna, where winter temperatures do not allow the establishment of tropical fruit flies, are linked to repeated entries of juveniles with infested fruits (in luggage or consignments). The results of our study reveal the need to strengthen phytosanitary import requirements for fruit commodities and travellers’ luggage in order to protect fruit production in Austria and probably in other countries.
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori
Authors: Song He , Dharmasena Madushini N. , Wang Chao , Shaw Gary X. , Cherry Scott , Tropea Joseph E. , Jin Ding J. , Ji Xinhua 
Published: November 2019

Rapid adaptation to environmental changes is crucial for bacterial survival. Almost all bacteria possess a conserved stringent response system to prompt transcriptional and metabolic responses toward stress. The adaptive process relies on alarmones, guanosine pentaphosphate (pppGpp), and tetraphosphate (ppGpp), to regulate global gene expression. The ppGpp is more potent than pppGpp in the regulatory activity, and pppGpp phosphohydrolase (GppA) plays a key role in (p)ppGpp homeostasis. Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX), which mediates the metabolism of cellular inorganic polyphosphate. Here, our phylogenetic analysis of PPX/GppA homologs in bacteria shows a wide distribution with several distinct subfamilies, and our structural and functional analysis of Escherichia coli GppA and Helicobacter pylori PPX/GppA reveals unique properties of each homolog. These results explain how each homolog possesses its distinct functionality.
Sequencing two Tyr::CreERT2 transgenic mouse lines
Authors: Aktary Zackie , Corvelo Andre , Estrin Camille , Larue Lionel 
Published: November 2019

AbstractThe Cre/loxP system is a powerful tool that has allowed the study of the effects of specific genes of interest in various biological settings. The Tyr::CreERT2 system allows for the targeted expression and activity of the Cre enzyme in the melanocyte lineage following treatment with tamoxifen, thus providing spatial and temporal control of the expression of specific target genes. Two independent transgenic mouse models, each containing a Tyr::CreERT2 transgene, have been generated and are widely used to study melanocyte transformation. In this study, we performed whole genome sequencing (WGS) on genomic DNA from the two Tyr::CreERT2 mouse models and identified their sites of integration in the C57BL/6 genome. Based on these results, we designed PCR primers to accurately, and efficiently, genotype transgenic mice. Finally, we discussed some of the advantages of each transgenic mouse model.
Zero Hunger and Sustainable Development Goals: Model of Food Bank Centre By Lembaga Zakat Negeri Kedah
Authors: Zainal Hafizah , Mustaffa Mohd Faisal , Othman Zakaria 
Published: November 2019

Food banks are normally owned by non-profit organizations which responsible for distributes food items to a person or charitable organizations in need. The implementation of Food Bank Centre is very suitable as the Malaysia government’s focus to ease burden among the B40 group in 11th Malaysia Plan. In addition, Malaysia also focuses on Sustainable Development Goals (SDGs) whereby to ensure everyone can access food and end hunger by 2030. However, poverty rates are higher in rural area especially in Kedah, Malaysia. This article explores Model of Food Bank Centre offer to the needy and poor by Lembaga Zakat Negeri Kedah (LZNK). In 2019, The Food Bank covering 574 mosques in Kedah, to cover 17,220 families of the needy and poor in need to access food every month. Maqasid shariah theory is used as a guideline and conjunction to implement the SDGs 2030 as maqasid syariah itself already highlight on the elements of SDGs. The result of this program created aid to the needy and the poor in term of virtuous and moral matters. Furthermore, it also gives a positive impact to stakeholder towards LZNK. Therefore, it is suggested stakeholders should engage and do a collaboration with LZNK in order to sustain supplying food for Food Bank Centre.
The Role of War Game in Educating and Training the Commanders
Authors: Almuqati Mislat Safar , Marni Nurazmallail 
Published: November 2019

The war game is considered to be the most effective means of military training due to the fact that it simulates the reality since it provides a semi-real picture of the weapons and equipment used in the training. Consequently, it provides the trainee with the appropriate environment to freely deal with such weapons as well as military equipment which in turn help the trainee become acquainted with all aspects of use and significantly instill confidence in him when such equipment are actually needed in war. More importantly, war game provides environment similar to what is going on in the actual battlefields allowing the commanders to exercise the training as if they were in a real war. Based on this perspective, the war game has emerged as an advanced training means which provides an analogy of the battle atmosphere to a great extent and gives commanders the opportunity to make decisions. It also helps in providing the commanders with a future view which enables them to plan their future and to deal with any challenges they might encounter. In fact, the role of war play is not only limited to training, but also extends to the aspects of military education, preparation, and development. The notion of war game is not only a means for the commander to have knowledge about the war before it occurs so as to be able to realize whether the decisions taken are right or wrong, but also it has become an effective means on which the armies depend when they train and polish the commanders' capabilities as well as skills. In fact, the concept of war play is not exclusive to the military field but also it is employed by all agencies and departments that require a future vision in training or planning. This paper sheds some light on the notion of war game and its role in training and educating the commanders and staff.
Rangelia vitalii infection in a dog from São Paulo city, Brazil: case report
Authors: Silva Bruna Regina Figura da , Labruna Marcelo Bahia , Marcili Arlei , Santos Caio Rodrigues dos , Bastos Bárbara Buff Blumer , Bordin Jessica Tainá , Moraes-Filho Jonas 
Published: November 2019

Canine rangeliosis is an extravascular hemolytic disease caused by the protozoan Rangelia vitalii, which is transmitted by ticks of the species Amblyomma aureolatum. Te most common clinical signs are apathy, hyperthermia and spontaneous bleeding. Anemia and thrombocytopenia are the most common hematological fndings. Tis work reports a clinical case of canine Rangeliosis treated at a private veterinary hospital, in São Paulo city in 2017. A dog was treated at a veterinary hospital in the north of São Paulo, with progressive weight loss, apathy and tail injury. Anemia and thrombocytopenia were observed on the hemogram. Rangelia vitalii DNA was detected in animal blood by real-time PCR (qPCR). In addition to the supportive treatment, doxycycline and subcutaneous imidocarb applications were used. Te sample collected afer treatment with the antibiotic continued to present protozoal DNA. Te disease should be considered as a diferential diagnosis and there is a great need for further studies about the therapy used.