Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatic Analysis of the Type VI Secretion System and Its Potential Toxins in the Acinetobacter Genus

Several Acinetobacter strains are important nosocomial pathogens, with Acinetobacter baumannii as the species of greatest concern worldwide due to its multi-drug resistance and recent appearance of hyper-virulent strains in the clinical setting. Acinetobacter colonization of the environment and the host is associated with a multitude of factors which remain poorly characterized. Among them, the secretion systems (SS) encoded by Acinetobacter species confer adaptive advantages depending on the niche occupied. Different SS have been characterized in this group of microorganisms, including T6SS used by several Acinetobacter species to outcompete other bacteria and in some A. baumannii strains for Galleria mellonella colonization. Therefore, to better understand the distribution of the T6SS in this genus we carried out an in-depth comparative genomic analysis of the T6SS in 191 sequenced strains. To this end, we analyzed the gene content, sequence similarity, synteny and operon structure of each T6SS loci. The presence of a single conserved T6SS-main cluster (T6SS-1), with two different genetic organizations, was detected in the genomes of several ecologically diverse species. Furthermore, a second main cluster (T6SS-2) was detected in a subgroup of 3 species of environmental origin. Detailed analysis also showed an impressive genetic versatility in T6SS-associated islands, carrying VgrG, PAAR and putative toxin-encoding genes. This in silico study represents the first detailed intra-species comparative analysis of T6SS-associated genes in the Acinetobacter genus, that should contribute to the future experimental characterization of T6SS proteins and effectors.
Interactive effects of belowground organic matter input, increased precipitation and clipping on soil carbon and nitrogen mineralization in a temperate steppe

This ms describes a manipulative fi ld experiment conducted in a temp rate grassland steppe, in which organic matter input (clipping and direct incorporation into soil) and precipitation were the main factors. The authors examined the resulting effects on soil C and N mineralization and microbial community structure. This is an interesting subject, the approach taken has novel aspects, and in general is appropriate for Biogeosciences.
The Synergetic Effect of Ni and Fe Bi-metal Single Atom Catalysts on Graphene for Highly Efficient Oxygen Evolution Reaction

Oxygen evolution reaction (OER) is key for electrochemical water splitting. Catalysts minimized in single-atom level (SACs) anchored on two-dimensional substances are highly active for various electrocatalytic reactions, but so far represent the limited performance for OER. Herein we report a general strategy for the fabrication of bi-metal Ni and Fe SACs loaded on graphene to significantly boost the OER activity. Notably, this unique structure of single Ni and Fe atoms co-existed on graphene has a strong synergetic effect, which can substantially elevate the charge transfer of catalysts. As a result, the obtained bi-metal SACs with the appropriate ratio of 4 for single Ni and Fe atoms show a small overpotential of 247 mV at 10 mA·cm−2 of OER current density in KOH electrolyte, outperforming individual-metal Ni (329 mV) or Fe (384 mV) SACs. Furthermore, such catalyst exhibits excellent stability without significant decay with increasing time at high current of 20 mA·cm−2 continuously for 48 hours. This work provides a new avenue for regulating the properties of transition metal SACs on graphene for water electrolysis.
Topology trivialization transition in random non-gradient autonomous ODEs on a sphere

We calculate the mean total number of equilibrium points in a system of N random autonomous ODEs introduced by Cugliandolo et al [] to describe non-relaxational glassy dynamics on the high-dimensional sphere. In doing it we suggest a new approach which allows such a calculation to be done most straightforwardly, and is based on efficiently incorporating the Langrange multiplier into the Kac–Rice framework. Analysing the asymptotic behaviour for large N we confirm that the phenomenon of ‘topology trivialization’ revealed earlier for other systems holds also in the present framework with nonrelaxational dynamics. Namely, by increasing the variance of the random ‘magnetic field’ term in dynamical equations we find a ‘phase transition’ from the exponentially abundant number of equilibria down to just two equilibria. Classifying the equilibria in the nontrivial phase by stability remains an open problem.
Human Motives , Incentives and Non-market Mechanisms of Research Allocation

We report here on recent results from one phase of a collaborative program of analytical and empirical research on the economic organization, performance and viability of the free/libre and open source (F/LOSS) mode of software production. The focus of this inquiry concerns the interplay of decentralized, micro-level decisions that shape the allocation of individual voluntary software development effort on the part of individual agents, distributing these among the distinct ‘modules’ (or ‘packages’ of code) that form large and complex “open source” system products.
COMMUNITY COMPOSITION AND POLYCYCLIC AROMATIC HYDROCARBON (PAH) BIODEGRA -DATION POTENTIAL OF MICROORGANISM ISOLATED FROM OILY SLUDGE

Environmental pollution caused by petroleum and its associated products through accidental or deliberate release results in the calamitous consequences within the ecosystem. Microorganism based bioremediation technology is considered as an efficient, economic and versatile alternative to conventional treatment methods for the reclamation of oil contaminated sites. This study was conducted to assess the genetic diversity and catabolic potential of indigenous microorganism in a petroleum hydrocarbon contaminated sludge sample obtained from an oil storage facility. Twenty eight (28) indigenous bacterial strains were isolated from the oily sludge. Most of these strains were identified as gram-positive bacteria that were phylogenetically affiliated to the genera Bacillus (more than 46%), Paenibacillus (~11%), Micrococcus (7%), Brachybacterium (7%), Aerococcus (14%) and Zimmermannella. Among the gram-negative strains Pseudomonas sp. and Pseudoxanthomonas sp. were identified. One of these bacteria, Aerococcus sp. strain BPD- 6 was further characterized in terms of its heavy metal resistance and other hydrocarbon utilization potential. Naphthalene and anthracene degradation potential of Aerococcus sp. BPD-6 was studied over a wide concentration range and the kinetic parameters were estimated using four growth kinetic models. Overall observation indicated that the strain may be useful for bioremediation of Polycyclic Aromatic Hydrocarbons (PAHs).
Microsensor Development for the Study of Droplet Spreading

Droplet-Based Manufacturing (DBM) process can produce a functional part directly from raw material. The DBM process consists of generating and depositing molten metal microdroplets. Fundamental to the deposition process is droplet spreading on the substrate surface, for it determines geometric definition and properties of the product. The Uniform Droplet Spray (UDS) process is a novel method of DBM which generates droplets of a uniform size. The UDS process can accurately control the dynamic and thermal states of droplets, thereby creating an excellent opportunity to study the droplet impact behavior. The measurement techniques available today, however, are inadequate to monitor the highspeed impact behavior of micro-droplets due to limits on the temporal and spatial resolutions. A novel technique to capture the transient spreading of molten metal droplets has been developed using the Very Large Scale Integration (VLSI) technology. The microsensor consists of thin conducting lines (Au) finely spaced and mounted on a nonconducting base (Si). In order to verify the UDS process capability to control the impact conditions of droplets, molten tin droplets were sprayed with varied conditions such as orifice diameter, ejection pressure, and charging voltage. Velocity of the droplets was measured using a high speed camera at 6,000 frames per second. The simulation results were compared with the experimental results and the comparison showed fairly good agreement between them. Spreading behavior of a molten tin droplet was measured by depositing a 356 pm diameter droplet at the velocity of 4.84 m/s onto the microsensor. The initial speed of contact area expansion was found to be about 2.4 times the impact velocity. The spreading speed decreased dramatically afterwards and the spreading process lasted over 450 jis. The experimental results verified that the microsensor had satisfactorily monitored the transient spreading behavior of molten metal droplets. Thesis Supervisor: Dr. Jung-Hoon Chun Esther and Harold E. Edgerton Associate Professor of Mechanical Engineering
Prion-Like Propagation of Protein Misfolding and Aggregation in Amyotrophic Lateral Sclerosis

The discovery that prion protein can misfold into a pathological conformation that encodes structural information capable of both propagation and inducing severe neuropathology has revolutionized our understanding of neurodegenerative disease. Many neurodegenerative diseases with a protein misfolding component are now classified as “prion-like” owing to the propagation of both symptoms and protein aggregation pathology in affected individuals. The neuromuscular disorder amyotrophic lateral sclerosis (ALS) is characterized by protein inclusions formed by either TAR DNA-binding protein of 43 kDa (TDP-43), Cu/Zn superoxide dismutase (SOD1), or fused in sarcoma (FUS), in both upper and lower motor neurons. Evidence from in vitro, cell culture, and in vivo studies has provided strong evidence to support the involvement of a prion-like mechanism in ALS. In this article, we review the evidence suggesting that prion-like propagation of protein aggregation is a primary pathomechanism in ALS, focusing on the key proteins and genes involved in disease (TDP-43, SOD1, FUS, and C9orf72). In each case, we discuss the evidence ranging from biophysical studies to in vivo examinations of prion-like spreading. We suggest that the idiopathic nature of ALS may stem from its prion-like nature and that elucidation of the specific propagating protein assemblies is paramount to developing effective therapies.
Patient-Reported Prevalence of Non-motor Symptoms Is Low in Adult Patients Suffering From 5q Spinal Muscular Atrophy

Background: 5q spinal muscular atrophy (SMA) is an autosomal recessive lower motoneuron disease caused by deletion or mutations in the survival motor neuron 1 gene (SMN1) which results in reduced expression of full-length SMN protein. The main symptoms are caused by spinal motor neuron demise leading to muscle atrophy, and medical care mostly refers to motor symptoms. However, new insights of recent studies in severe SMA type I revealed disease involvement of several non-motor regions, for example cardiac, vascular, sensory nerve involvement, and thalamic lesions. Non-motor symptoms (NMS) were previously described in many neurodegenerative diseases i.e., Parkinson's disease and, importantly, also amyotrophic lateral sclerosis. Methods: We screened for NMS in 70 adult patients with SMA type II (SMAII) and type III (SMAIII) and 59 age/sex-matched healthy controls (controls) in a multicenter cross-sectional study including 5 different centers with specialized expertise in medical health care of motoneuron diseases. We used a self-rating questionnaire including 30 different items of gastrointestinal, autonomic, neuropsychiatric, and sleep complaints [NMS questionnaire (NMSQuest)], which is a validated tool in Parkinson's disease. Results: Total NMS burden was low in adult SMA (median: 3 items) and not significantly different compared to controls (median: 2 items). Total NMS of SMA patients did not correlate with disease severity scores. However, the items “swallowing difficulties,” “falling,” and particularly “swelling legs” were significantly more frequently reported in SMA. Neuropsychiatric symptoms were reported in a frequency comparable to controls and were not significantly increased in SMA. Conclusion: Patient-reported prevalence of NMS in adult SMA was low, which does not argue for a clinically relevant multisystemic disorder in SMAII/III. Importantly, adult SMA patients do not seem to suffer more frequently from symptoms of depression or adaptive disorders compared to controls. Our results yield novel information on previously underreported symptoms and will help to improve the medical guidance of these patients.
Radical Spatial Practices/ Radical Public Spheres

Architects, architectural critics, and public sphere theorists share an overlapping verbal language. Public sphere theorists often speak metaphorically of "sites," "theaters," and "arenas" of citizen interaction while architects gloss their work with claims of democratic values without actually specifying the conception of democracy that they wish their work to advance. Although there is a problem in transferring the tenn "public" from one discussion to another, the relations spun by language perversely invite the translation of what might be inerely an analogy into a methodology where the one acts as the lens and the other as the object of analysis. The need for inore precision in our discussions about democracy and its relation to public space was exemplified by a provocative symposium, "From Public to Social Space(s)," that took place at the Harvard School of Design in 1994. ' On the one hand, the value of public space in democratic societies was taken as a given. On the other, the architects and designers who participated were reluctant to address how design might play a role in advancing specific types of social interaction that might serve particular democratic interests. The discussion, in fact, suggested a reluctance on the part of the architects and designers to claim an active role for design, which rendered moot the need for them to specify the type of democracy they believed that particular fomis of public spaces might advance. Taken to its logical conclusions, the symposium suggested either that design has no role to play in fijrthering democracy, or that it is not possible to develop productive discourse about the role of design, given that architecture effects, and is effected by, socially and culturally diverse individuals. For purposes of argument against the latter position, I shall take a page from Martha Nussbaum's suggestive little book. Poetic Justice: The Literary Imagination and Public Life, in which she proposes the value of the novel as a means to develop public reasoning.Nussbaum does not claim that the novel should replace political theory, or vice versa; nor is she focusing on the individual reading the novel. Rather, she argues that discussion Radical Spatial Practices/ Radical Public Spheres
Lactate in the Regulation of Tumor Microenvironment and Therapeutic Approaches

Tumor cells must generate sufficient ATP and biosynthetic precursors in order to maintain cell proliferation requirements. Otto Warburg showed that tumor cells uptake high amounts of glucose producing large volumes of lactate even in the presence of oxygen, this process is known as “Warburg effect or aerobic glycolysis. ” As a consequence of such amounts of lactate there is an acidification of the extracellular pH in tumor microenvironment, ranging between 6.0 and 6.5. This acidosis favors processes such as metastasis, angiogenesis and more importantly, immunosuppression, which has been associated to a worse clinical prognosis. Thus, lactate should be thought as an important oncometabolite in the metabolic reprogramming of cancer. In this review, we summarized the role of lactate in regulating metabolic microenvironment of cancer and discuss its relevance in the up-regulation of the enzymes lactate dehydrogenase (LDH) and monocarboxilate transporters (MCTs) in tumors. The goal of this review is to expose that lactate is not only a secondary product of cellular metabolic waste of tumor cells, but also a key molecule involved in carcinogenesis as well as in tumor immune evasion. Finally, the possible targeting of lactate production in cancer treatment is discussed.
PRODUCTION AND CHARACTERIZATION OF FISH OIL METHYL ESTER

Limited availability of edible oils prevents it from being used as viable source of Biodiesel. Low cost and abundantly found fish oil produced from soap stock could be a better option for biodiesel processing. Such type of fish oil contains a higher amount of moisture and FFA and requires a pre-treatment prior to biodiesel production. In this study, refining of raw oil, optimization of process variables of transesterification, qualitative as well as quantitative aspects of fish oil methyl ester (FOME) has been evaluated. With optimized production process, it was found that almost complete conversion of fish oil to methyl ester has taken place. The fuel properties of FOME were found to be in accordance with the ASTM, IS and EN standards.
RELICT MINERALOGY OF SERPENTINITES FROM DEEP SEA DRILLING PROJECT LEG 84 1

Eleven serpentine samples from DSDP Leg 84 and four serpentinized ultramafic samples from Costa Rica and Guatemala were described and their relict mineral compositions measured by electron microprobe to try to determine the origin of the Leg 84 serpentinites and their relationship to the ultramafic rocks of the onshore ophiolites. The Leg 84 samples comprise more than 90% secondary minerals, principally serpentine, with hematitic and opaque oxides, and minor talc and smectites. Four distinct textural types can be identified according to the distribution of opaque phases and smectite. Remnants of spinel, olivine, orthopyroxene, and clinopyroxene occur variously in the samples; spinal occurs in all the samples. Textural evidence suggests that the serpentinites were originally clinopyroxene-bearing harzburgites. Relict mineral compositions are refractory and relatively uniform: olivine, Fo^ ^ ^ 9; orthopyroxene, E n ^ ^ ; clinopyroxene, Wo47 En50 Fs3; spinels, Cr/Cr + Al = 0.4-0.6. 567A-29-2, 30-35 cm has slightly more magnesian olivines (Fo92) and orthopyroxene, and more aluminous spinels (Cr/Cr + Al = 0.3). These compositions are similar to those inferred for refractory upper-mantle materials and also fall within the range of compositions for relict minerals in abyssal peridotites. They could be of oceanic origin. The onshore samples include serpentinites, a clinopyroxene-bearing harzburgite, and a clinopyroxenite. They too have magnesium-rich silicate assemblages, but relative to the drilled samples have more iron-rich olivines (Fogo) and more aluminous and sodic pyroxenes; spinels which are clearly relicts are very aluminum-rich (Cr/Cr + Al = 0.1-0.25). These samples are most likely mantle materials, but significantly less depleted. Their relationship to the drilled samples is unclear. Serpentinites were the most common basement materials recovered during Leg 84, and there appears to be a bimodal assemblage (basalt/diabase and serpentine) of igneous rocks sampled from the trench slope. Diapirism of serpentine throughout the trench slope and forearc is suggested as an explanation for this distribution of samples.
Corrosion Control in CO2 Enhanced Oil Recovery From a Perspective of Multiphase Fluids

Carbon capture and storage (CCS) combined with CO2-enhanced oil recovery (EOR), has been recently viewed as an economical and effective method for the reduction of carbon emissions. However, corrosion is a challenging issue in the whole chain process of CO2-EOR production if water presents and mild steel pipeline is used. In this paper, the corrosion risk of pipeline at different stages of CO2-EOR production is systematically assessed based on a detailed analysis of the fluid characteristics. According to the fluid state of CO2, water and crude oil, current understandings on the corrosion behavior of steel materials in multiphase flow conditions are reviewed. Furthermore, the intermittent water wetting phenomena and the fluid behavior of water droplets or clusters in an electrolyte/non-electrolyte emulsion are correlated with the steel corrosion performance, providing new insights into the corrosion phenomena. Besides application of corrosion resistant materials and selection of corrosion inhibitors, tailoring of processing parameters, such as enhancing the water entrainment, shortening the water contact time, and reducing the solution corrosivity, is highly recommended as an effective method for corrosion control in aggressive CO2-EOR production conditions. Based on these, some important future research topics on the corrosion in multiphase fluids are suggested.
Geographical indications and trademarks in Vietnam: confusion or real difference?

Geographical indications (GIs) in Vietnam are protected through a sui generis system involving a Statedriven management following a topdown approach. However, in practice, collective or certification trademarks (TMs) are increasingly used as origin labels, following the same path of a Statedriven process. This is mainly explained by the very demanding criteria to meet for proving the qualitative link with the origin in the case of GIs, which may be considered as going beyond the GI definition, and the sometimes arbitrary choice between TM and GIs to meet quotas. Drawing upon case studies, the paper shows that the choice between GIs or TMs is not the most relevant factor to contribute to local economic development, preserve traditional knowledge and conserve biodiversity. The marketing channels seem to be more significant. Yet the lack of consideration of the weaker level of protection of TMs compared to GIs might be a threat. Finally, it seems legitimate to question the EU's preferential policy for GIs over TMs in the bilateral agreement between Vietnam and the EU. (Resume d'auteur)