Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin

ABSTRACT The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.
Location privacy for crowdsourcing applications

This paper contributes to mobile crowdsourcing applications by developing a privacy preserving framework that enables users to contribute content to the community while controlling their privacy exposure. One fundamental challenge in such applications is how to preserve user privacy, as participants may end up revealing a great deal of user-identified, geo-located data, which can easily unfold user trajectories or sensitive locations (e.g., user's home or work location). In this paper we develop PROMPT, a highly efficient privacy preserving framework that runs locally on mobile devices. PROMPT relies on a novel geometric approximation approach to preserve user privacy, by evaluating the privacy exposure of users before sharing their geo-located data. Our detailed experimental evaluation using real-world datasets illustrates that our approach is effective, practical and has low overhead on smartphones.
Crystal structure of (4Z)-4-[(dimethylamino)methylidene]-3,5-dioxo-2-phenylpyrazolidine-1-carbaldehyde

In the title compound, C13H13N3O3, the pyrazolidine ring adopts a shallow envelope conformation, with the carbonyl C atom closest to the benzene ring as the flap [deviation of 0.126 (1) Å from the plane through the remaining atoms (r.m.s. deviation = 0.011 Å)]. The dihedral angle between the pyrazolidine ring (all atoms) and the benzene ring is 51.09 (4)°. An extremely short (2.08 Å) intramolecular C—H⋯O contact is seen. In the crystal, molecules are linked by C—H⋯O bonds, generating [010] chains. Extremely weak C—H⋯π interactions are also observed.
DNA binding sites: representation and discovery

The purpose of this article is to provide a brief history of the development and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be conveniently divided into two subproblems. The first is, given a collection of known binding sites, develop a representation of those sites that can be used to search new sequences and reliably predict where additional binding sites occur. The second is, given a set of sequences known to contain binding sites for a common factor, but not knowing where the sites are, discover the location of the sites in each sequence and a representation for the specificity of the protein.
Progressive alterations in microstructural organization and biomechanical response in the ApoE mouse model of aneurysm

AAA is a complex disease that leads to a localized dilation of the infrarenal aorta that develops over years. Longitudinal information in humans has been difficult to obtain for this disease, therefore mouse models have become increasingly used to study the development of AAAs. The objective of this study was to determine any changes that occur in the biomechanical response and fiber microstructure in the ApoE−/− AngII mouse model of aneurysm during disease progression. Adult ApoE−/− AngII infused mice along with wild-type controls were taken at 14 and 28 d. Aortas were excised and tested simultaneously for biaxial mechanical response and ECM organization. Data sets were fit to a Fung-type constitutive model to give peak strains and stiffness values. Images from two photon microscopy were quantified in order to assess the preferred fiber alignment and degree of fiber orientation. Biomechanical results found significant differences that were present at 14 d had returned to normal by 28 d along with significant changes in fiber orientation and dispersion indicating remodeling occurring within the aneurysmal wall. This return of some of the normal biomechanical function, in addition the continuing changes that occur in the microstructure suggest a restorative response that occurs in the ApoE−/− AngII infused model after the initial aneurysm formation.
Human T-Cell Leukemia Virus Type 1 Tax Oncoprotein Suppression of Multilineage Hematopoiesis of CD34+ Cells In Vitro

ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) and HTLV-2 are highly related viruses that differ in disease manifestation. HTLV-1 is the etiologic agent of adult T-cell leukemia and lymphoma, an aggressive clonal malignancy of human CD4-bearing T lymphocytes. Infection with HTLV-2 has not been conclusively linked to lymphoproliferative disorders. We previously showed that human hematopoietic progenitor (CD34+) cells can be infected by HTLV-1 and that proviral sequences were maintained after differentiation of infected CD34+ cells in vitro and in vivo. To investigate the role of the Tax oncoprotein of HTLV on hematopoiesis, bicistronic lentiviral vectors were constructed encoding the HTLV-1 or HTLV-2 tax genes (Tax1 and Tax2, respectively) and the green fluorescent protein marker gene. Human hematopoietic progenitor (CD34+) cells were infected with lentivirus vectors, and transduced cells were cultured in a semisolid medium permissive for the development of erythroid, myeloid, and primitive progenitor colonies. Tax1-transduced CD34+ cells displayed a two- to fivefold reduction in the total number of hematopoietic clonogenic colonies that arose in vitro, in contrast to Tax2-transduced cells, which showed no perturbation of hematopoiesis. The ratio of colony types that developed from Tax1-transduced CD34+ cells remained unaffected, suggesting that Tax1 inhibited the maturation of relatively early, uncommitted hematopoietic stem cells. Since previous reports have linked Tax1 expression with initiation of apoptosis, lentiviral vector-mediated transduction of Tax1 or Tax2 was investigated in CEM and Jurkat T-cell lines. Ectopic expression of either Tax1 or Tax2 failed to induce apoptosis in T-cell lines. These data demonstrate that Tax1 expression perturbs development and maturation of pluripotent hematopoietic progenitor cells, an activity that is not displayed by Tax2, and that the suppression of hematopoiesis is not attributable to induction of apoptosis. Since hematopoietic progenitor cells may serve as a latently infected reservoir for HTLV infection in vivo, the different abilities of HTLV-1 and -2 Tax to suppress hematopoiesis may play a role in the respective clinical outcomes after infection with HTLV-1 or -2.
Pain intensity rating training: results from an exploratory study of the ACTTION PROTECCT system

Abstract Clinical trial participants often require additional instruction to prevent idiosyncratic interpretations regarding completion of patient-reported outcomes. The Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION) public–private partnership developed a training system with specific, standardized guidance regarding daily average pain intensity ratings. A 3-week exploratory study among participants with low-back pain, osteoarthritis of the knee or hip, and painful diabetic peripheral neuropathy was conducted, randomly assigning participants to 1 of 3 groups: training with human pain assessment (T+); training with automated pain assessment (T); or no training with automated pain assessment (C). Although most measures of validity and reliability did not reveal significant differences between groups, some benefit was observed in discriminant validity, amount of missing data, and ranking order of least, worst, and average pain intensity ratings for participants in Group T+ compared with the other groups. Prediction of greater reliability in average pain intensity ratings in Group T+ compared with the other groups was not supported, which might indicate that training produces ratings that reflect the reality of temporal pain fluctuations. Results of this novel study suggest the need to test the training system in a prospective analgesic treatment trial.
Unveiling smart city implementation challenges: The case of Ghent

The 'smart city' label is internationally used by cities, researchers and technology providers with different meanings. As a popular concept it is widely used by city administrators and politicians to promote their efforts to prepare their cities for the future. There are decent definitions for what a smart city is, but it is much harder to find a trustworthy description of what it takes to become a smart city and how a city administration is impacted by that effort. This paper sets out to investigate how a city, aspiring to become a 'smart city', can manage its internal organization to realize that ambition. Specifically, it describes the case of the City of Ghent, Belgium, and the key challenges it has been facing in its ongoing efforts to be a smart city. Based on in depth interviews with city representatives six key challenges for smart city realization were identified and tested with a panel of representatives from five European cities that are in the process of becoming a smart city. The study contributes to a more professional pursuit of the smart city concept and elaborates the academic body of knowledge on smart city development, as an instance of IT-enabled transformation in public services.
Calcium promotes activity and confers heat stability on plant peroxidases

In this paper we demonstrate how peroxidase (PO) activities and their heat stability correlate with the availability of free Ca2+ ions. Calcium ions work as a molecular switch for PO activity and exert a protective function, rendering POs heat stable. The concentration ranges of these two activities differ markedly. POs are activated by µM Ca2+ concentration ranges, whereas heat stabilization is observed in the nM range. This suggests the existence of different Ca2+ binding sites. The heat stability of POs depends on the source plant species. Terrestrial plants have POs that exhibit higher temperature stability than those POs from limnic and marine plants. Different POs from a single species can differ in terms of heat stability. The abundance of different POs within a plant is dependent on age and developmental stage. The heat stability of a PO does not necessarily correlate with the maximum temperature the source species is usually exposed to in its natural habitat. This raises questions on the role of POs in the heat tolerance of plants. Consequently, detailed investigations are needed to identify and characterize individual POs, with regard to their genetic origin, subcellular expression, tissue abundance, developmental emergence and their functions in innate and acquired heat tolerance.
Functional Downregulation of P2X3 Receptor Subunit in Rat Sensory Neurons Reveals a Significant Role in Chronic Neuropathic and Inflammatory Pain

The excitation of nociceptive sensory neurons by ATP released in injured tissue is believed to be mediated partly by P2X3receptors. Although an analysis of P2X3 knock-out mice has revealed some deficits in nociceptive signaling, detailed analysis of the role of these receptors is hampered by the lack of potent specific pharmacological tools. Here we have used antisense oligonucleotides (ASOs) to downregulate P2X3 receptors to examine their role in models of chronic pain in the rat. ASOs and control missense oligonucleotides (180 μg/d) were administered intrathecally to naive rats for up to 7 d via a lumbar indwelling cannula attached to an osmotic minipump. Functional downregulation of the receptors was confirmed by αβ-methylene ATP injection into the hindpaw, which evoked significantly less mechanical hyperalgesia as early as 2 d after treatment with ASOs relative to controls. At this time point, P2X3 protein levels were significantly downregulated in lumbar L4 and L5 dorsal root ganglia. After 7 d of ASO treatment, P2X3 protein levels were reduced in the primary afferent terminals in the lumbar dorsal horn of the spinal cord. In models of neuropathic (partial sciatic ligation) and inflammatory (complete Freund's adjuvant) pain, inhibition of the development of mechanical hyperalgesia as well as significant reversal of established hyperalgesia were observed within 2 d of ASO treatment. The time course of the reversal of hyperalgesia is consistent with downregulation of P2X3 receptor protein and function. This study demonstrates the utility of ASO approaches for validating gene targets in in vivo pain models and provides evidence for a role of P2X3 receptors in the pathophysiology of chronic pain.
Is Domestic Abuse an Adult Social Work Issue?

Abstract Within a global profession with a stated definition that includes ‘promoting social change and development, social cohesion and the empowerment and liberation of people’ (online), it would be expected that the issue of domestic abuse would be integral to the training and role of all social workers. This article reports on research, which highlighted both a lack of understanding of the role of adult social worker within cases of domestic abuse and also a desire for further training around the issue. However, this article sets out how the current UK (in particular, English) context of social work marginalises the issue of domestic abuse within practice with adults. This marginalisation has been achieved through the construction of domestic abuse as a children and families issue and limited duties, powers and resources within statutory work to support victims/survivors in their own right, rather than as ‘failing’ parents. However, the article argues that the role of social work education should be wider than teaching to the current policy or procedures and instead encourage a wider appreciation of the social, historical and political context. The article concludes with tentative suggestions for how domestic abuse could be considered within the social work curriculum for adult practitioners. This is in acknowledgement that social workers can be well positioned for the detection, investigation and support of those experiencing abuse.
Performance of various training algorithms on scene illumination classification

The increasing number of training algorithms along with their convincing results will make this question that which algorithm will be more efficient. This study aims to perform some widespread tests on some well-known training algorithms (Levenberg-Marquardt, Resilient back propagation and Scaled conjugate gradient) to evaluate their performance for scene illumination classification. The results presented by this research can provide a reliable guide line for choosing the most appropriate training algorithm depends on the problem specification. The results of this study select the LM training method with the accuracy of 94.41% as the most accurate and RP as the most quick method with response time of 0.426 s.
Development of a Scale of Social Interest

n ＝149 ;average age 13.08)and university students ( n ＝329 ;average age 20.16),completed a questionnaire consisting of 24 items measuring social interest,college life anxiety,school adjustment,feelings of inferiority,psychological stress response,and narcissism. Factor analysis yielded 3 factors:feelings of belonging to society and trust in society, self-acceptance, and feelings of contribution. The reliability of the social interest scale was examined by measures of internal consistency and test-retest reliability,and was found to be high. The construct validity of the scale was examined in terms of relations between the scale and the participantsʼ scores on college life anxiety,school adjustment,feelings of inferiority,and psychological stress response. In addition,the data suggested that social interest and narcissism were positively correlated.
Peroxisomes in Saccharomyces cerevisiae: immunofluorescence analysis and import of catalase A into isolated peroxisomes

To isolate peroxisomes from Saccharomyces cerevisiae of a quality sufficient for in vitro import studies, we optimized the conditions for cell growth and for cell fractionation. Stability of the isolated peroxisomes was monitored by catalase latency and sedimentability of marker enzymes. It was improved by (i) using cells that were shifted to oleic acid medium after growth to stationary phase in glucose precultures, (ii) shifting the pH from 7.2 to 6.0 during cell fractionation, and (iii) carrying out equilibrium density centrifugation with Nycodenz containing 0.25 M sucrose throughout the gradient. A concentrated peroxisomal fraction was used for in vitro import of catalase A. After 2 h of incubation, 62% of the catalase was associated with, and 16% was imported into, the organelle in a protease-resistant fashion. We introduced immunofluorescence microscopy for S. cerevisiae peroxisomes, using antibodies against thiolase, which allowed us to identify even the extremely small organelles in glucose-grown cells. Peroxisomes from media containing oleic acid were larger in size, were greater in number, and had a more intense fluorescence signal. The peroxisomes were located, sometimes in clusters, in the cell periphery, often immediately adjacent to the plasma membrane. Systematic immunofluorescence observations of glucose-grown S. cerevisiae demonstrated that all such cells contained at least one and usually several very small peroxisomes despite the glucose repression. This finding fits a central prediction of our model of peroxisome biogenesis: peroxisomes form by division of preexisting peroxisomes; therefore, every cell must have at least one peroxisome if additional organelles are to be induced in that cell.
Latent Feature Kernels for Link Prediction on Sparse Graphs

Predicting new links in a network is a problem of interest in many application domains. Most of the prediction methods utilize information on the network's entities, such as nodes, to build a model of links. Network structures are usually not used except for networks with similarity or relatedness semantics. In this paper, we use network structures for link prediction with a more general network type with latent feature models. The problem with these models is the computational cost to train the models directly for large data. We propose a method to solve this problem using kernels and cast the link prediction problem into a binary classification problem. The key idea is not to infer latent features explicitly, but to represent these features implicitly in the kernels, making the method scalable to large networks. In contrast to the other methods for latent feature models, our method inherits all the advantages of the kernel framework: optimality, efficiency, and nonlinearity. On sparse graphs, we show that our proposed kernels are close enough to the ideal kernels defined directly on latent features. We apply our method to real data of protein-protein interaction and gene regulatory networks to show the merits of our method.
Dose Response and Dose Equivalence of Antipsychotics

Abstract: We review evidence from randomized, placebo-controlled studies of patients with schizophrenia or schizoaffective disorder, which compared 2 or more doses of an antipsychotic to calculate the dose-response curve for each first-generation (typical) antipsychotic (FGA) or second-generation (atypical) antipsychotic (SGA) and as a group (based on dose equivalence). We identified the near-maximal effective dose (ED; ie, the threshold dose necessary to produce all or almost all the clinical responses for each drug). In randomized, fixed-dose studies of SGAs, the near-maximal efficacy dose for olanzapine may be greater than 16 mg; for risperidone, it is 4 mg; and for ziprasidone, it is 120 mg. Risperidone at 2 mg daily is 50% less efficacious than higher doses. Olanzapine at about 6 mg is approximately 33% less effective than higher doses. Aripiprazole at 10 mg daily was fully efficacious. Doses of clozapine well above 400 mg are necessary for optimal treatment of many schizophrenia patients. We found 3.3 to 10 mg haloperidol to be the near-maximal ED range. We find no evidence that doses higher than these are more effective. We failed to find that high doses of haloperidol (or all other first-generation comparison drugs converted to equivalent doses) were less effective than medium doses (3.3 to 10 mg). While high-dose FGAs are not less effective, we feel it is important not to avoid using high dose to avoid excessive toxicity.
On the capacity of free-space optical intensity channels

New upper and lower bounds are presented on the capacity of the free-space optical intensity channel. This channel is characterized by inputs that are nonnegative (representing the transmitted optical intensity) and by outputs that are corrupted by additive white Gaussian noise (because in free space the disturbances arise from many independent sources). Due to battery and safety reasons the inputs are simultaneously constrained in both their average and peak power. For a fixed ratio of the average power to the peak power the difference between the upper and the lower bounds tends to zero as the average power tends to infinity, and the ratio of the upper and lower bounds tends to one as the average power tends to zero. The case where only an average-power constraint is imposed on the input is treated separately. In this case, the difference of the upper and lower bound tends to 0 as the average power tends to infinity, and their ratio tends to a constant as the power tends to zero.