Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

Metagenome sequence predicted the culture conditions required for successful isolation of a marsupial gut bacterium. The Tammar wallaby (Macropus eugenii) harbors unique gut bacteria and produces only one-fifth the amount of methane produced by ruminants per unit of digestible energy intake. We have isolated a dominant bacterial species (WG-1) from the wallaby microbiota affiliated with the family Succinivibrionaceae and implicated in lower methane emissions from starch-containing diets. This was achieved by using a partial reconstruction of the bacterium’s metabolism from binned metagenomic data (nitrogen and carbohydrate utilization pathways and antibiotic resistance) to devise cultivation-based strategies that produced axenic WG-1 cultures. Pure-culture studies confirm that the bacterium is capnophilic and produces succinate, further explaining a microbiological basis for lower methane emissions from macropodids. This knowledge also provides new strategic targets for redirecting fermentation and reducing methane production in livestock.
Isocyanate-Free Routes to Polyurethanes and Poly(hydroxy Urethane)s.

Greener routes to polyurethanes are required and arouse a growing interest in the academic and industrial communities. To this purpose, the depletion of fossil resources exacerbates the need of renewable materials. This review details two main routes to phosgene-free and isocyanate-free pathways to polyurethanes: the transurethanization and the cyclic carbonate/amine routes. A focus is also made on bio-based synthons toward non-phosgene and non-isocyanate PUs.
Participatory Assessment of Factors Influencing Nutrition and Livelihoods in Rural Ethiopia: Implications for Measuring Impacts of Multisector Nutrition Programs

Agricultural interventions more effectively improve nutrition when they are adapted to local contexts and engage multiple sectors. However, evidence is limited for how to design and measure the impacts of such interventions. We piloted a participatory methodology to collect community feedback to inform the design and selection of measures for a multisector nutrition intervention in Ethiopia. Study participants were purposively recruited from 6 rural districts in Tigray and the Southern Nations, Nationalities, and Peoples’ regions. Qualitative data were collected from 12 focus group discussions with smallholder farmers (men and women) participating in a nutrition-sensitive agriculture intervention. The Sustainable Livelihoods Approach (SLA) combined with an ecological systems model informed the survey tool and analyses. Analyses revealed 3 key findings. First, there were regional differences in how communities defined assets important for nutrition. Second, when asked to prioritize which assets were most important, communities selected every SLA capital category; however, the types of assets within each category differed by region. Third, the most commonly reported barriers to good nutrition were traditional feeding behaviors (eg, men eating before women) and lack of nutrition knowledge. How households use assets to enhance nutrition is influenced by diverse and dynamic cultural, social, economic, and ecological factors. The participatory methods piloted in this study present a novel approach to identify contextually relevant household, community, and institutional assets used to support food and nutrition security.
RNAP II CTD Phosphorylated on Threonine-4 Is Required for Histone mRNA 3′ End Processing

Phosphorylation of a single conserved amino acid in higher eukaryotes plays a specific role in processing histone messenger RNA genes. The RNA polymerase II (RNAP II) largest subunit contains a C-terminal domain (CTD) with up to 52 Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 consensus repeats. Serines 2, 5, and 7 are known to be phosphorylated, and these modifications help to orchestrate the interplay between transcription and processing of messenger RNA (mRNA) precursors. Here, we provide evidence that phosphorylation of CTD Thr4 residues is required specifically for histone mRNA 3′ end processing, functioning to facilitate recruitment of 3′ processing factors to histone genes. Like Ser2, Thr4 phosphorylation requires the CTD kinase CDK9 and is evolutionarily conserved from yeast to human. Our data thus illustrate how a CTD modification can play a highly specific role in facilitating efficient gene expression.
Surface Organometallic and Coordination Chemistry toward Single-Site Heterogeneous Catalysts: Strategies, Methods, Structures, and Activities.

Site Heterogeneous Catalysts: Strategies, Methods, Structures, and Activities Christophe Copeŕet,*,† Aleix Comas-Vives,† Matthew P. Conley,† Deven P. Estes,† Alexey Fedorov,† Victor Mougel,† Haruki Nagae,†,‡ Francisco Nuñ́ez-Zarur,† and Pavel A. Zhizhko†,§ †Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1−5, CH-8093 Zürich, Switzerland ‡Department of Chemistry, Graduate School of Engineering Science, Osaka University, CREST, Toyonaka, Osaka 560-8531, Japan A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28, 119991 Moscow, Russia
Three Periods of Regulatory Innovation During Vertebrate Evolution

Patterns of vertebrate gene regulation have changed during the course of evolution. The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
Knockdown of MMP12 inhibits the growth and invasion of lung adenocarcinoma cells

Matrix metalloproteinase-12 (MMP12) is involved in many pathological processes including cancer. The expression and function of MMP12 in lung adenocarcinoma (LAC) remain unclear. The present study aimed to investigate the correlation of MMP12 expression with LAC patients and clarify its role in growth and invasion of LAC cells. The expression of MMP12 in human LAC was examined by immunohistochemical assay using a tissue microarray procedure. A loss-of-function experiment was used for observing the effects of lentiviral vector-mediated MMP12 shRNA (shMMP12) on cell growth and invasion in LAC cell lines (A549), indicated by MTT and Transwell assays. We found that the expression of MMP12 protein was significantly increased in LAC tissues compared with that in adjacent non-cancerous tissues (ANCT) (57.69% vs. 32.69%, P = 0.019), and was closely correlated with the pathological stage and lymph node metastasis of LAC patients (P = 0.01; P = 0.003). Knockdown of MMP12 inhibited proliferation and invasion of LAC cells followed by the downregulation of proliferating cell nuclear antigen (PCNA) and vascular endothelial growth factor (VEGF). In conclusion, our findings show that high expression of MMP12 is correlated with the pathological stage and tumor metastasis of LAC patients, and knockdown of MMP12 suppresses the development of LAC cells, suggesting that MMP12 may be a promising therapeutic target for the treatment of LAC.
Thinking PubMed: an Innovative System for Mental Health Domain

Information regarding mental illness is dispersed over various resources but even within a specific resource, such as PubMed, it is difficult to link this information, to share it and find specific information when needed. Specific and targeted searches are very difficult with current search engines as they look for the specific string of letters within the text rather than its meaning. In this paper we present thinking PubMed as a system that results from synergy of ontology and data mining technologies and performs intelligent information searches using the domain ontology. Furthermore, the thinking PubMed analyzes and links the retrieved information, and extracts hidden patterns and knowledge using data mining algorithms. This is a new generation of information-seeking tool where the ontology and data-mining work in concert to increase the value of the available information.
The Hedgehog Pathway Promotes Blood-Brain Barrier Integrity and CNS Immune Quiescence

Hedgehog signaling is required for maintaining the integrity of the blood-brain barrier. The blood-brain barrier (BBB) is composed of tightly bound endothelial cells (ECs) and perivascular astrocytes that regulate central nervous system (CNS) homeostasis. We showed that astrocytes secrete Sonic hedgehog and that BBB ECs express Hedgehog (Hh) receptors, which together promote BBB formation and integrity during embryonic development and adulthood. Using pharmacological inhibition and genetic inactivation of the Hh signaling pathway in ECs, we also demonstrated a critical role of the Hh pathway in promoting the immune quiescence of BBB ECs by decreasing the expression of proinflammatory mediators and the adhesion and migration of leukocytes, in vivo and in vitro. Overall, the Hh pathway provides a barrier-promoting effect and an endogenous anti-inflammatory balance to CNS-directed immune attacks, as occurs in multiple sclerosis.
Control of Local Protein Synthesis and Initial Events in Myelination by Action Potentials

Axons signal through both glutamate and adenosine triphosphate release to regulate their insulating wraps. Formation of myelin, the electrical insulation on axons produced by oligodendrocytes, is controlled by complex cell-cell signaling that regulates oligodendrocyte development and myelin formation on appropriate axons. If electrical activity could stimulate myelin induction, then neurodevelopment and the speed of information transmission through circuits could be modified by neural activity. We find that release of glutamate from synaptic vesicles along axons of mouse dorsal root ganglion neurons in culture promotes myelin induction by stimulating formation of cholesterol-rich signaling domains between oligodendrocytes and axons, and increasing local synthesis of the major protein in the myelin sheath, myelin basic protein, through Fyn kinase-dependent signaling. This axon-oligodendrocyte signaling would promote myelination of electrically active axons to regulate neural development and function according to environmental experience.
Structural Basis for Tail-Anchored Membrane Protein Biogenesis by the Get3-Receptor Complex

Docking of cytoplasmic and membrane receptors facilitates conformational changes that drive protein insertion. Tail-anchored (TA) proteins are involved in cellular processes including trafficking, degradation, and apoptosis. They contain a C-terminal membrane anchor and are posttranslationally delivered to the endoplasmic reticulum (ER) membrane by the Get3 adenosine triphosphatase interacting with the hetero-oligomeric Get1/2 receptor. We have determined crystal structures of Get3 in complex with the cytosolic domains of Get1 and Get2 in different functional states at 3.0, 3.2, and 4.6 angstrom resolution. The structural data, together with biochemical experiments, show that Get1 and Get2 use adjacent, partially overlapping binding sites and that both can bind simultaneously to Get3. Docking to the Get1/2 complex allows for conformational changes in Get3 that are required for TA protein insertion. These data suggest a molecular mechanism for nucleotide-regulated delivery of TA proteins.
Global DNA Demethylation During Mouse Erythropoiesis in Vivo

Erythroblasts undergoing differentiation into red cells lose one-third of DNA methylation marks at nearly all genomic loci. In the mammalian genome, 5′-CpG-3′ dinucleotides are frequently methylated, correlating with transcriptional silencing. Genome-wide demethylation is thought to occur only twice during development, in primordial germ cells and in the pre-implantation embryo. These demethylation events are followed by de novo methylation, setting up a pattern inherited throughout development and modified only at tissue-specific loci. We studied DNA methylation in differentiating mouse erythroblasts in vivo by using genomic-scale reduced representation bisulfite sequencing (RRBS). Demethylation at the erythroid-specific β-globin locus was coincident with global DNA demethylation at most genomic elements. Global demethylation was continuous throughout differentiation and required rapid DNA replication. Hence, DNA demethylation can occur globally during somatic cell differentiation, providing an experimental model for its study in development and disease.
Population Policy in Transition in the Developing World

Population growth remains rapid in the poorest countries, particularly in sub-Saharan Africa, despite substantial AIDS mortality. Voluntary family-planning programs reduce unplanned pregnancies by providing access to and information about contraception and by reducing socioeconomic obstacles to use. With sufficient political will and resources, well-run voluntary programs have been shown to bring about sustained declines in fertility and population growth across much of Asia, the Middle East, and Latin America, simply by permitting people to realize their individual reproductive goals. Such programs represent a cost-effective approach to relieving population pressures, stimulating economic development, improving health, and enhancing human freedom.
Resolution of robot redundancy in the Cartesian space by criteria optimization

A computationally efficient control law for a redundant robot in the Cartesian space is presented. This approach uses a decomposition of the joint acceleration into primary and secondary joint acceleration. The joint acceleration solution is searched in order to compute the dynamic control law which can achieve the desired task in the Cartesian space with smaller tracking errors, little calculation, and good system behavior. The extra degrees of freedom are used to optimize a quadratic criterion by a direct or a gradient method. The results are compared to the dynamic control proposed by Hsu and colleagues in 'Dynamic control of redundant manipulator', Proc. IEEE Conf. on Robotics and Automation, 1988, p.183-7 for a 3-joint planar robot. Similar results are obtained with less calculation. <<ETX>>
Enniatin B and beauvericin are common in Danish cereals and show high hepatotoxicity on a high‐content imaging platform

Mycotoxins are fungi‐born metabolites that can contaminate foods through mould‐infected crops. They are a significant food/feed‐safety issue across the globe and represent a substantial financial burden for the world economy. Moreover, with a changing climate and fungal biota, there is now much discussion about emerging mycotoxins that are measurable at significant levels in crops world‐wide. Unfortunately, we still know very little about the bioavailability and toxic potentials of many of these less characterized mycotoxins, including the large family of enniatins. In this study, we present new occurrence data for enniatin A, A1, B, B1 and beauvericin in four Danish crops: oat, wheat, and barley from the 2010 harvest, and rye from 2011 harvest. The occurrence of the four enniatins were B > B1 > A1 > A. Enniatin B was detected in 100% of tested samples regardless of crop type. In addition to occurrence data, we report a proof‐of‐concept study using a human‐relevant high‐content hepatotoxicity, or “quadroprobe,” assay to screen mycotoxins for their cytotoxic potential. The assay was sensitive for most cytotoxic compounds in the 0.009–100 µM range. Among eight tested mycotoxins (enniatin B, beauvericin, altenariol, deoxynivalenol, aflatoxin B1, andrastin A, citrinin, and penicillic acid), enniatin B and beauvericin showed significant cytotoxicity at a concentration lower than that for aflatoxin B1, which is the archetypal acute hepatotoxic and liver‐carcinogenic mycotoxin. Hence, the quadroprobe hepatotoxicity assay may become a valuable assessment tool for toxicity assessment of mycotoxins in the future. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1658–1664, 2017.
Protection of Nrf2 against arsenite‐induced oxidative damage is regulated by the cyclic guanosine monophosphate‐protein kinase G signaling pathway

Arsenite has been shown to induce a variety of oxidative damage in mammalian cells. However, the mechanisms underlying cellular responses to its adverse effects remain unknown. We previously showed that the level of Nrf2, a nuclear transcription factor significantly increased in arsenite‐treated human bronchial epithelial (HBE) cells suggesting that Nrf2 is involved in responding to arsenite‐induced oxidative damage. To explore how Nrf2 can impact arsenite‐induced oxidative damage, in this study, we examined Nrf2 activation and its regulation upon cellular arsenite exposure as well as its effects on arsenite‐induced oxidative damage in HBE cells. We found that Nrf2 mRNA and protein levels were significantly increased by arsenite in a dose‐ and time‐dependent manner. Furthermore, we showed that over‐expression of Nrf2 significantly reduced the level of arsenite‐induced oxidative damage in HBE cells including DNA damage, chromosomal breakage, lipid peroxidation and depletion of antioxidants. This indicates a protective role of Nrf2 against arsenite toxicity. This was further supported by the fact that activation of Nrf2 by its agonists, tertiary butylhydroquinone (t‐BHQ) and sulforaphane (SFN) resulted in the same protective effects against arsenite toxicity. Moreover, we demonstrated that arsenite‐induced activation of Nrf2 was mediated by the cyclic guanosine monophosphate (cGMP)‐protein kinase G (PKG) signaling pathway. This is the first evidence showing that Nrf2 protects against arsenite‐induced oxidative damage through the cGMP‐PKG pathway. Our study suggests that activation of Nrf2 through the cGMP‐PKG signaling pathway in HBE cells may be developed as a new strategy for prevention of arsenite toxicity. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 2004–2020, 2017.
Association of UGT2B7 polymorphisms with risk of induced liver injury by anti-tuberculosis drugs in Chinese Han

Anti-tuberculosis drug-induced liver injury (ATLI) is common during the treatment of tuberculosis (TB). As an important enzyme in the metabolism of many drugs, UGT2B7 (uridine diphosphate glucuronyl transferase 2B7) was associated with drug-induced liver disorder. This study investigated the association between the polymorphisms of UGT2B7 and ATLI in Chinese Han. Totally, 280 newly diagnosed TB patients had been followed up for 3 months after the prescription of anti-TB therapy. Tag-single-nucleotide polymorphism (tag-SNPs) (rs10028494 and rs7668282) were genotyped with the MassARRAY platform. The associations between tag-SNPs and ATLI risk were analyzed by logistic regression analysis adjusting for confounding factors. In this prospective study, 33 patients were lost to follow-up, and 24 patients were diagnosed with ATLI and considered as the case group. The remaining 223 subjects without ATLI were considered as the control group. No significant association was observed in allele and genotype frequencies of UGT2B7 between the two groups. This study is the first attempt to investigate the association of genetic polymorphisms of UGT2B7 with ATLI in Chinese Han. There is no significant association between UGT2B7 polymorphisms and ATLI in Chinese Han.
Flash Heating Leads to Low Frictional Strength of Crustal Rocks at Earthquake Slip Rates

Extreme temperatures generated over short distances may weaken faults during earthquakes. The sliding resistance of faults during earthquakes is a critical unknown in earthquake physics. The friction coefficient of rocks at slow slip rates in the laboratory ranges from 0.6 to 0.85, consistent with measurements of high stresses in Earth’s crust. Here, we demonstrate that at fast, seismic slip rates, an extraordinary reduction in the friction coefficient of crustal silicate rocks results from intense “flash” heating of microscopic asperity contacts and the resulting degradation of their shear strengths. Values of the friction coefficient due to flash heating could explain the lack of an observed heat flow anomaly along some active faults such as the San Andreas Fault. Nearly pure velocity-weakening friction due to flash heating could explain how earthquake ruptures propagate as self-healing slip pulses.
Different Effect of Growth Hormone on the Triglyceride Metabolism in Visceral and Subcutaneous AdiposeTissues of Rats

To clarify the mechanism by which visceral adipose tissue developed in growth hormone (GH) deficient patients, and was reduced by GH supplementation, the effects of GH on the triglyceride metabolism in the visceral and subcutaneous adipose tissues of the rats were compared.Visceral and subcutaneous adipose tissues were obtained from omentum and abdominal wall. [14C] deoxyglucose uptake and the triglyceride synthetic activity from [14C] oleic acid, and heparin-releasable lipoprotein lipase activity were not changed by the addition of GH (10ng/mL) in both visceral and subcutaneous adipose tissues, but the lipolysis by GH (10ng/mL) was much more remarkable in the visceral adipose tissue than in subcutaneous adipose tissue, whereas adrenaline-induced lipolysis occurred almost equally in both tissues.These results suggest that the preponderance of visceral adipose tissue in GH deficiency might partly be due to the lack of GH-preferential lipolysis in visceral adipose tissue.
The modular telerobot task execution system for space telerobotics

A telerobot task execution system that has been developed for space station Freedom applications is described. The modular telerobot task execution system (MOTES) provides the remote site task execution capability in a local-remote telerobotic system. The design addresses the constraints of limited computational power available at the remote site control system while providing a large range of control capabilities. The system provides supervised autonomous control, shared control, and teleoperation for a redundant manipulator. The system is capable of nominal task execution as well as monitoring and reflex motion. A command interpreter similar to one used on robotic spacecraft is used to interpret commands received from the local site. Execution utilizes multiple control modules which execute based upon command parameterization. The system controls a seven degree-of-freedom manipulator. <<ETX>>
Actuator and sensor fault diagnosis of nonlinear dynamic systems via genetic neural networks and adaptive parameter estimation technique

This paper presents a novel approach to the fault detection and diagnosis of actuators and sensors in nonlinear systems. First, a known nonlinear system is considered, where an adaptive diagnostic model incorporating the estimate of the fault is constructed. The diagnostic algorithm is then developed to minimise the possible modelling error. Furthermore, unknown nonlinear systems are studied and a feedforward neural network trained to estimate the system under healthy conditions. Genetic algorithms is proposed as a means of optimising the weighting connections of neural network and to assist the diagnosis of the fault.