Miracle-dz/UniFAR-FTUs huggingface dataset:
NopC Is a Rhizobium-Specific Type 3 Secretion System Effector Secreted by Sinorhizobium (Ensifer) fredii HH103

Sinorhizobium (Ensifer) fredii HH103 is a broad host-range nitrogen-fixing bacterium able to nodulate many legumes, including soybean. In several rhizobia, root nodulation is influenced by proteins secreted through the type 3 secretion system (T3SS). This specialized secretion apparatus is a common virulence mechanism of many plant and animal pathogenic bacteria that delivers proteins, called effectors, directly into the eukaryotic host cells where they interfere with signal transduction pathways and promote infection by suppressing host defenses. In rhizobia, secreted proteins, called nodulation outer proteins (Nops), are involved in host-range determination and symbiotic efficiency. S. fredii HH103 secretes at least eight Nops through the T3SS. Interestingly, there are Rhizobium-specific Nops, such as NopC, which do not have homologues in pathogenic bacteria. In this work we studied the S. fredii HH103 nopC gene and confirmed that its expression was regulated in a flavonoid-, NodD1- and TtsI-dependent manner. Besides, in vivo bioluminescent studies indicated that the S. fredii HH103 T3SS was expressed in young soybean nodules and adenylate cyclase assays confirmed that NopC was delivered directly into soybean root cells by means of the T3SS machinery. Finally, nodulation assays showed that NopC exerted a positive effect on symbiosis with Glycine max cv. Williams 82 and Vigna unguiculata. All these results indicate that NopC can be considered a Rhizobium-specific effector secreted by S. fredii HH103.
Construct Control Meshes of Helicoids over Trapezium Domain

In this paper, we present a geometric construction of control meshes of helicoids over trapezium domain. We flrst introduce the quasi-Bezier basis in the space spanned by f1;t;cost;sint;tsint;tcostg; with t 2 (0;fi);fi 2 (0;2…). We denote the curves ex- pressed by the quasi-Bezier basis as algebraic-trigonometric Bezier curves, for short AT- Bezier curves. Then we flnd out the transform matrices between the quasi-Bezier basis and f1;t;cost;sint;tsint;tcostg. Finally, we present the control mesh representation of the heli- coids and the geometric construction of the control mesh. In detail, we construct the control polygon of the planar Archimedean solenoid, which is also expressed with the quasi-Bezier basis, and then generate the mesh vertices by translating points of the control polygon.
Foxp1 regulation of neonatal vocalizations via cortical development

Usui et al. show that deletion of Foxp1 in the developing forebrain leads to impairments in neonatal vocalizations as well as neocortical cytoarchitectonic alterations via neuronal positioning and migration. Sumoylation of Foxp1 affects neuronal differentiation and migration in the developing neocortex.
Atomic Cross-Chain Swaps

An atomic cross-chain swap is a distributed coordination task where multiple parties exchange assets across multiple blockchains, for example, trading bitcoin for ether. An atomic swap protocol guarantees (1) if all parties conform to the protocol, then all swaps take place, (2) if some coalition deviates from the protocol, then no conforming party ends up worse off, and (3) no coalition has an incentive to deviate from the protocol. A cross-chain swap is modeled as a directed graph D, whose vertexes are parties and whose arcs are proposed asset transfers. For any pair (D, L), where D = (V,A) is a strongly-connected directed graph and L ⊂ V a feedback vertex set for D, we give an atomic cross-chain swap protocol for D, using a form of hashed timelock contracts, where the vertexes in L generate the hashlocked secrets. We show that no such protocol is possible if D is not strongly connected, or if D is strongly connected but L is not a feedback vertex set. The protocol has time complexityO(diam(D)) and space complexity (bits stored on all blockchains) O(|A|2).
Prostate organogenesis: tissue induction, hormonal regulation and cell type specification

Prostate organogenesis is a complex process that is primarily mediated by the presence of androgens and subsequent mesenchyme-epithelial interactions. The investigation of prostate development is partly driven by its potential relevance to prostate cancer, in particular the apparent re-awakening of key developmental programs that occur during tumorigenesis. However, our current knowledge of the mechanisms that drive prostate organogenesis is far from complete. Here, we provide a comprehensive overview of prostate development, focusing on recent findings regarding sexual dimorphism, bud induction, branching morphogenesis and cellular differentiation. Summary: This Review article provides a comprehensive overview of prostate development, focusing on recent findings regarding sexual dimorphism, bud induction, branching morphogenesis and cellular differentiation.
Widespread Volumetric Reductions in Schizophrenia and Schizoaffective Patients Displaying Compromised Cognitive Abilities

Objective Progress toward understanding brain mechanisms in psychosis is hampered by failures to account for within-group heterogeneity that exists across neuropsychological domains. We recently identified distinct cognitive subgroups that might assist in identifying more biologically meaningful subtypes of psychosis. In the present study, we examined whether underlying structural brain abnormalities differentiate these cognitively derived subgroups. Method 1.5T T1 weighted structural scans were acquired for 168 healthy controls and 220 patients with schizophrenia/schizoaffective disorder. Based on previous work, 47 patients were categorized as being cognitively compromised (impaired premorbid and current IQ), 100 as cognitively deteriorated (normal premorbid IQ, impaired current IQ), and 73 as putatively cognitively preserved (premorbid and current IQ within 1 SD of controls). Global, subcortical and cortical volume, thickness, and surface area measures were compared among groups. Results Whole cortex, subcortical, and regional volume and thickness reductions were evident in all subgroups compared to controls, with the largest effect sizes in the compromised group. This subgroup also showed abnormalities in regions not seen in the other patient groups, including smaller left superior and middle frontal areas, left anterior and inferior temporal areas and right lateral medial and inferior frontal, occipital lobe and superior temporal areas. Conclusions This pattern of more prominent brain structural abnormalities in the group with the most marked cognitive impairments-both currently and putatively prior to illness onset, is consistent with the concept of schizophrenia as a progressive neurodevelopmental disorder. In this group, neurodevelopmental and neurodegenerative factors may be important for cognitive function.
A Scheduling Algorithm for Hadoop MapReduce Workflows with Budget Constraints in the Heterogeneous Cloud

In recent years cloud services have gained much attention as a result of their availability, scalability, and low cost. One use of these services has been for the execution of scientific workflows as part of Big Data Analytics, which are employed in a diverse range of fields including astronomy, physics, seismology, and bioinformatics. There has been much research on heuristic scheduling algorithms for these workflows due to the problem's inherent complexity, however existing work has mainly considered execution in a utility grid environment using a generic distributed framework. For our research, we consider the ever-increasingly popular Apache Hadoop framework for scheduling workflow onto resources rented from cloud service providers. Contrary to other distributed frameworks, the Hadoop MapReduce model imposes a functional style onto application definition, and as such presents an interesting and unapproached challenge for workflow scheduling. Investigated in our work is budget-constrained workflow scheduling on the Hadoop MapReduce platform, wherein we devise both an optimal and a heuristic approach to minimize workflow makespan while satisfying a given budget constraint. We have implemented modifications to the Apache Hadoop framework to allow fully integrated workflow scheduling. These modifications are novel and have led to the completion of the first generic workflow scheduler fully integrated with the Apache Hadoop framework. Both the framework modifications and the proposed scheduler implementation have been extensively tested via execution on multiple workflow applications, which demonstrates the ability of our implementation to handle all possible workflow substructures. Results from our empirical studies further establish these facts.
Competition between a Lawn-Forming Cynodon dactylon and a Tufted Grass Species Hyparrhenia hirta on a South-African Dystrophic Savanna

South African savanna grasslands are often characterised by indigestible tufted grass species whereas lawn grasses are far more desirable in terms of herbivore sustenance. We aimed to investigate the role of nutrients and/or the disturbance (grazing, trampling) by herbivores on the formation of grazing lawns. We conducted a series of common garden experiments to test the effect of nutrients on interspecific competition between a typical lawn-forming grass species (Cynodon dactylon) and a species that is frequently found outside grazing lawns (Hyparrhenia hirta), and tested for the effect of herbivore disturbance in the form of trampling and clipping. We also performed a vegetation and herbivore survey to apply experimentally derived insights to field observations. Our results showed that interspecific competition was not affected by soil nutrient concentrations. C. dactylon did show much more resilience to disturbance than H. hirta, presumably due to the regenerative capacity of its rhizomes. Results from the field survey were in line with these findings, describing a correlation between herbivore pressure and C. dactylon abundance. We conclude that herbivore disturbance, and not soil nutrients, provide C. dactylon with a competitive advantage over H. hirta, due to vegetative regeneration from its rhizomes. This provides evidence for the importance of concentrated, high herbivore densities for the creation and maintenance of grazing lawns.
Specific adaptation to strong competitors can offset the negative effects of population size reductions

Competition plays a crucial role in determining adaptation of species, yet we know little as to how adaptation is affected by the strength of competition. On the one hand, strong competition typically results in population size reductions, which can hamper adaptation owing to a shortage of beneficial mutations; on the other hand, specificity of adaptation to competitors may offset the negative evolutionary consequences of such population size effects. Here, we investigate how competition strength affects population fitness in the bacterium Pseudomonas fluorescens. Our results demonstrate that strong competition constrains adaptation of focal populations, which can be partially explained by population size reductions. However, fitness assays also reveal specific adaptation of focal populations to particular competitors varying in competitive ability. Additionally, this specific adaptation can offset the negative effects of competitor-mediated population size reductions under strong competition. Our study, therefore, highlights the importance of opposing effects of strong competition on species adaptation, which may lead to different outcomes of colonization under intense and relaxed competitive environments in the context of population dispersal.
Evolution of the optical properties of PVA films filled with Sodium Iodide

Transparent films of polyvinyl alcohol with different doping Sodium Iodide concentrations were prepared by using solution cast technique. The optical absorption measurements were carried out for all samples at room temperature across the wavelength regions. The study has been also extended to include the changes in the optical parameters including the band tail width and band gap energies for the samples; It was found that the optical absorption is due to direct and indirect transitions, and the optical energy gaps values shifted to lower energies on sodium iodide concentration for all transitions. Also absorption spectrums after annealing for three hours at temperature are investigated. Moreover, the study of complex refractive index showed dependence on dopant concentrations.
Resistance to Thiacetazone Derivatives Active against Mycobacterium abscessus Involves Mutations in the MmpL5 Transcriptional Repressor MAB_4384

ABSTRACT Available chemotherapeutic options are very limited against Mycobacterium abscessus, which imparts a particular challenge in the treatment of cystic fibrosis (CF) patients infected with this rapidly growing mycobacterium. New drugs are urgently needed against this emerging pathogen, but the discovery of active chemotypes has not been performed intensively. Interestingly, however, the repurposing of thiacetazone (TAC), a drug once used to treat tuberculosis, has increased following the deciphering of its mechanism of action and the detection of significantly more potent analogues. We therefore report studies performed on a library of 38 TAC-related derivatives previously evaluated for their antitubercular activity. Several compounds, including D6, D15, and D17, were found to exhibit potent activity in vitro against M. abscessus, Mycobacterium massiliense, and Mycobacterium bolletii clinical isolates from CF and non-CF patients. Similar to TAC in Mycobacterium tuberculosis, the three analogues act as prodrugs in M. abscessus, requiring bioactivation by the EthA enzyme, MAB_0985. Importantly, mutations in the transcriptional TetR repressor MAB_4384, with concomitant upregulation of the divergently oriented adjacent genes encoding an MmpS5/MmpL5 efflux pump system, accounted for high cross-resistance levels among all three compounds. Overall, this study uncovered a new mechanism of drug resistance in M. abscessus and demonstrated that simple structural optimization of the TAC scaffold can lead to the development of new drug candidates against M. abscessus infections.
Human papillomavirus genome integration in squamous carcinogenesis: what have next‐generation sequencing studies taught us?

Human papillomavirus (HPV) infection is associated with ∼5% of all human cancers, including a range of squamous cell carcinomas. Persistent infection by high‐risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an important event in HPV‐associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation, and further genomic instability. However, the mechanisms by which HRHPV integration occur and by which the subsequent gene expression changes take place are incompletely understood. The advent of next‐generation sequencing (NGS) of both RNA and DNA has allowed powerful interrogation of the association of HRHPVs with human disease, including precise determination of the sites of integration and the genomic rearrangements at integration loci. In turn, these data have indicated that integration occurs through two main mechanisms: looping integration and direct insertion. Improved understanding of integration sites is allowing further investigation of the factors that provide a competitive advantage to some integrants during disease progression. Furthermore, advanced approaches to the generation of genome‐wide samples have given novel insights into the three‐dimensional interactions within the nucleus, which could act as another layer of epigenetic control of both virus and host transcription. It is hoped that further advances in NGS techniques and analysis will not only allow the examination of further unanswered questions regarding HPV infection, but also direct new approaches to treating HPV‐associated human disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Development of gastroretentive systems for famotidine: in vitro characterization

Floating tablets of famotidine were developed to prolong gastric residence time, leading to an increase in drug bioavailability. Tablets were prepared by direct compression technique, using polymers hydroxypropyl methylcellulose (HPMC K4M and HPMC K15M). Tablets were evaluated for physical characteristics, weight, thickness, hardness and friability; drug content, swelling, floating properties and in vitro drug release characteristics for 12 h. Tablets exhibited sustained and prolonged drug release profiles while floating over the dissolution medium. The release pattern followed was anomalous non4fickian type, indicating that water diffusion and polymer rearrangement played an essential role in drug release. The best formulation was selected based on in vitro characteristics and was subjected for in vivo radiographic studies. These studies revealed that the tablets remained in stomach for more than 4.5 h in fed condition indicated that gastric retention time was increased by floating principle.
Pathways limiting warming to 1.5°C: a tale of turning around in no time?

We explore the feasibility of limiting global warming to 1.5°C without overshoot and without the deployment of carbon dioxide removal (CDR) technologies. For this purpose, we perform a sensitivity analysis of four generic emissions reduction measures to identify a lower bound on future CO2 emissions from fossil fuel combustion and industrial processes. Final energy demand reductions and electrification of energy end uses as well as decarbonization of electricity and non-electric energy supply are all considered. We find the lower bound of cumulative fossil fuel and industry CO2 emissions to be 570 GtCO2 for the period 2016–2100, around 250 GtCO2 lower than the lower end of available 1.5°C mitigation pathways generated with integrated assessment models. Estimates of 1.5°C-consistent CO2 budgets are highly uncertain and range between 100 and 900 GtCO2 from 2016 onwards. Based on our sensitivity analysis, limiting warming to 1.5°C will require CDR or terrestrial net carbon uptake if 1.5°C-consistent budgets are smaller than 650 GtCO2. The earlier CDR is deployed, the more it neutralizes post-2020 emissions rather than producing net negative emissions. Nevertheless, if the 1.5°C budget is smaller than 550 GtCO2, temporary overshoot of the 1.5°C limit becomes unavoidable if CDR cannot be ramped up faster than to 4 GtCO2 in 2040 and 10 GtCO2 in 2050. This article is part of the theme issue ‘The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels’.
aspeCTos aTUais da biodisponibilidade de FÁRMaCos CoM baiXa solUbilidade: UM enFoQUe sobRe a sinVasTaTina

No âmbito farmacêutico, é necessário um profundo conhecimento sobre as características moleculares dos fármacos, uma vez que essas propriedades influenciam diretamente a eficácia terapêutica dos medicamentos, a partir deles produzidos. Nesse contexto, esta revisão pre‐ tende abordar os aspectos biofarmacêuticos, apresentan‐ do conceitos clássicos e novas abordagens utilizadas para aprimorar a biodisponibilidade de fármacos com baixa solubilidade em meio aquoso. O enfoque será dado ao fármaco sinvastatina, cuja absorção pode ser fortemente influenciada pelos excipien‐ tes presentes na formulação, devido à sua baixa solubili‐ dade. Este fármaco antilipêmico representa uma terapia bastante empregada na atualidade e cuja demanda magis‐ tral é crescente. Dessa forma, reflexões sobre a escolha de excipientes empregados na produção magistral de cápsu‐ las de sinvastatina são necessárias para que se garanta a qualidade terapêutica dessas preparações. palaVRas‐CHaVe: biofarmácia, características físi‐ co‐químicas de fármacos, biodisponibilidade, sinvastati‐ na, manipulação de cápsulas.
Suche in aufgezeichneten Vorträgen und Vorlesungen

Durch den immer starker werdenden Trend, Vortrage und Vorlesungen automatisch aufzuzeichnen und Studenten zur spateren Verwendung zur Verfugung zu stellen, entsteht auch ein zunehmender Bedarf an Suchverfahren fur die derart entstandenen Dokumente. Dieser Artikel geht der Frage nach, wie sich eine Suchmaschine fur aufgezeichnete Vortrage und Vorlesungen realisieren lasst, was die speziellen Probleme und Besonderheiten sind und welche Losungsansatze hierfur existieren. Neben einer detaillierten Einfuhrung in die Problematik werden erste Ergebnisse prasentiert und mogliche kunftige Forschungsthemen aufgezeigt.
A Content Store-Based Module for Congestion Control Algorithms of Named Data Networking

NDN (Named Data Networking) is an increasingly important topic with the realm of the future Internet architecture research. Naturally, a new congestion control mechanism is important for a new Internet architecture. Existing research on NDN congestion control mainly considers the one-Interest-one-Data transport mode, internally, they control the Data sending rate by adjusting the Interest sending rate, thus to realize the congestion control. However, as one of the key features in NDN, in-network storage is rarely exploited. Furthermore, the problem of bursty traffic is also not fully considered and corresponding resolution is absent. Therefore, in this paper, we propose a novel congestion control module based on interacting with Content Store (CS-based) in NDN network to reduce packet loss caused by bursty traffic by taking advantage of the characteristic of in-network storage of NDN. CS-based is an independent module which can combine with existing NDN congestion control mechanisms (non-CS-based) to further reduce the packet loss rate caused by congestion especially by bursty traffic, increase throughput and improve the network resource utilization. Simulation results based on ndnSIM indicate that, compared with non-CS-based, CS-based has better performance under the circumstances that bursty traffic occurs and can mitigate NDN congestion better.
3C-SiC Epitaxy on Deeply Patterned Si(111) Substrates

The growth morphology of epitaxial 3C-SiC crystals grown on hexagonal pillars deeply etched into Si (111) substrates is presented. Different growth velocities of side facets let the top crystal facet evolve from hexagonal towards triangular shape during growth. The lateral size and separation between Si pillars determine the onset of fusion between neighboring crystals during growth at a height tailoring of which is crucial to reduce the stacking fault (SF) density of the coalesced surface. Intermediate partial fusion of neighboring crystals is shown as well as a surface of fully coalesced crystals.
Cervical Spondylotic Myelopathy

The inconsistent use of nomenclature to describe this entity has plagued both the reporting and understanding of CSM. Progress has similarly been stifled by the waxing and waning of symptoms that so often accompany the clinical presentation of CSM. Surgical approaches have, therefore, been chosen in situations in which an optimal result may not be expected and, conversely, they have not been chosen when a good result could have been expected. This confuses the student of CSM and further perverts the literature. The aforementioned waxing and waning clinical course presents significant decision-making dilemmas. This is particularly so in the elderly, in whom the risks of surgery may be significant and the benefits difficult to appreciate.