Miracle-dz/UniFAR-FTUs huggingface dataset:
Brucella Induces an Unfolded Protein Response via TcpB That Supports Intracellular Replication in Macrophages

Brucella melitensis is a facultative intracellular bacterium that causes brucellosis, the most prevalent zoonosis worldwide. The Brucella intracellular replicative niche in macrophages and dendritic cells thwarts immune surveillance and complicates both therapy and vaccine development. Currently, host-pathogen interactions supporting Brucella replication are poorly understood. Brucella fuses with the endoplasmic reticulum (ER) to replicate, resulting in dramatic restructuring of the ER. This ER disruption raises the possibility that Brucella provokes an ER stress response called the Unfolded Protein Response (UPR). In this study, B. melitensis infection up regulated expression of the UPR target genes BiP, CHOP, and ERdj4, and induced XBP1 mRNA splicing in murine macrophages. These data implicate activation of all 3 major signaling pathways of the UPR. Consistent with previous reports, XBP1 mRNA splicing was largely MyD88-dependent. However, up regulation of CHOP, and ERdj4 was completely MyD88 independent. Heat killed Brucella stimulated significantly less BiP, CHOP, and ERdj4 expression, but induced XBP1 splicing. Although a Brucella VirB mutant showed relatively intact UPR induction, a TcpB mutant had significantly compromised BiP, CHOP and ERdj4 expression. Purified TcpB, a protein recently identified to modulate microtubules in a manner similar to paclitaxel, also induced UPR target gene expression and resulted in dramatic restructuring of the ER. In contrast, infection with the TcpB mutant resulted in much less ER structural disruption. Finally, tauroursodeoxycholic acid, a pharmacologic chaperone that ameliorates the UPR, significantly impaired Brucella replication in macrophages. Together, these results suggest Brucella induces a UPR, via TcpB and potentially other factors, that enables its intracellular replication. Thus, the UPR may provide a novel therapeutic target for the treatment of brucellosis. These results also have implications for other intracellular bacteria that rely on host physiologic stress responses for replication.
Putative ATP-Binding Cassette Transporter Is Essential for Brucella ovis Pathogenesis in Mice

ABSTRACT Brucella ovis is a major cause of reproductive failure in sheep, which is associated with epididymitis and infertility in rams. Importantly, B. ovis is one of the few Brucella species that is not zoonotic. Due to the scarcity of studies on B. ovis infection, a murine model of infection was developed. The roles of B. ovis genes encoding a putative hemagglutinin and an ABC transporter were investigated in the mouse model. The kinetics of B. ovis infection were similar in BALB/c and C57BL/6 mice, and both strains of mice developed multifocal microgranulomas in the liver and spleen, but only minimal colonization and histopathological changes were observed in the genital tract. Therefore, the mouse was considered a suitable infection model for B. ovis but not for B. ovis-induced genital disease. Two mutant strains were generated in this study (the ΔabcAB and Δhmg strains). The B. ovis ΔabcAB strain was attenuated in the spleens and livers of BALB/c mice compared to the wild-type (WT) strain (P < 0.001). Conversely, the Δhmg strain infected mice at the same level as WT B. ovis, suggesting that a putative hemagglutinin is not required for B. ovis pathogenesis. Additionally, the ΔabcAB strain did not survive in peritoneal macrophages, extracellularly in the peritoneal cavity, or in RAW 264.7 macrophages. Moreover, infection with the ΔabcAB strain was not lethal for male regulatory factor 1-knockout mice, whereas infection with the B. ovis WT strain was 100% lethal within 14 days postinfection. These results confirm that the predicted ABC transporter is required for the full virulence and survival of B. ovis in vivo.
Interior-Point Methodology for Large-Scale Regularized Maximum Likelihood Reconstruction in Emission Tomography

Interior-point methods possess strong theoretical properties and have been successfully applied to a wide variety of linear and nonlinear programming applications. This paper presents a class of algorithms, based on interior-point methodology, for performing regularized maximum likelihood reconstructions on 3-D emission tomography data. The algorithms solve a sequence of subproblems that converge to the regularized maximum likelihood solution from the interior of the feasible region (the non-negative orthant). We propose two methods, a primal method which updates only the primal image variables and a primal-dual method which simultaneously updates the primal variables and the Lagrange multipliers. Termination to a solution of desired accuracy is based on well-defined convergence measures. We demonstrate the rapid convergence of the interior-point methods using both data from a small animal scanner and Monte Carlo simulated data. We present a parallel implementation that permits the interior-point methods to scale to very large reconstruction problems.
An Application of Spike-Timing-Dependent Plasticity to Readout Circuit for Liquid State Machine

Liquid state machine (LSM) is a neural system based on spiking neurons that implements a mapping between functions of time. A typical application of LSM is classification of time functions obtained observing the state of the liquid by using a memoryless readout circuit, usually implemented by a linear perceptron. Due to the high number of neurons in the liquid the training of the readout is difficult. In this paper we show that using the Spike-Timing-Dependent Plasticity (STDP) a single neuron with short training session can be used to recognize the state of the liquid due to an input signal. Using STDP it is possible to identify the spikes timing of the neurons in the liquid and this allows to correctly classify a large set of input signals, the method is also robust to noise and amplitude variations.
PRISM: Policy-driven Risk-based Implicit locking for improving the Security of Mobile end-user devices

Nowadays, most mobile applications rely on device screen locking mechanisms for ensuring practical security, which expects the users to explicitly authenticate with a PIN or biometric irrespective of the perceived threats. Owing to this usability issues, many avoid using device locks potentially compromising the security. To overcome the limitations of this binary approach, we present an implicit authentication framework called PRISM (Policy-driven Risk-based Implicit locking for improving the Security of Mobile end-user devices). It provides risk based authentication by detecting anomalies in the usual behavior patterns of the users which include their expected locations, activities and application usage. Its device unlocking decisions are driven by policies that are defined either automatically by mining sensor data or manually by the end-users. Our experiments show that PRISM is able to discover useful behavior patterns efficiently even with limited data. The number of required explicit authentications is significantly reduced while assuring the preferred security for everyday scenarios.
Direct transcatheter aortic valve implantation – one-year outcome of a case control study

Introduction Transaortic valve implantation (TAVI) has a well-established position in the treatment of high-risk and inoperable patients with severe aortic stenosis (AS). The TAVI protocol requires a pre-dilatation for native valve preparation. Aim To assess the safety and feasibility of TAVI without pre-dilatation and to compare it with the procedure with pre-dilatation. Material and methods Out of 101 TAVI patients, in 10 the procedure was performed without balloon predilatation, and 8 patients were included in the analysis. The procedural, echocardiographic, and clinical outcomes were compared with a case control matched cohort (1: 2 ratio). A 12-month follow-up was done in all cases. Results The procedure was successfully completed in all patients in the study group (SG), but there was one procedural failure in the control group (CG). All patients received a CoreValve (Medtronic) bioprosthesis. There was a significant immediate decrease in transvalvular gradients (TG) in both study arms after the procedure (SG: mean TG: from 46.0 ±14.0 mm Hg to 10.0 ±4.8 mm Hg, p < 0.001; CG: mean TG: from 55.9 ±12.0 mm Hg to 9.9 ±2.9 mm Hg, p < 0.001). A marked increase in the effective orifice areas was observed in both cohorts (SG: 1.63 ±0.13 cm2 and CG: 1.67 ±0.25 cm2, p = 0.75). The periprocedural complication rate was equally distributed in both arms. The 12-month all-cause mortality was 12.5% in both groups. Conclusions The direct TAVI approach seams to be safe and feasible. The clinical and echocardiographic results are not different from those achieved in patients treated with standard TAVI protocol with pre-dilatation.
A systematized method for dream analysis in a group setting.

ABSTRACTThis paper presents a rationale and step-by-step procedure for the interpretation of dreams in a specifically dream-oriented group. Traditionally, dreams have been used across a broad spectrum of approaches to individual psychotherapy. As group methods have evolved, the group context has emerged as a particularly favorable medium for the analysts of dreams. Adherence to the Jungian approach to dream interpretation, together with theoretical insights from dream and imagery research, group research, and behavior modification form the basis of this four-step dream group model. This systematized procedure has utility for the training of professionals in basic psychodynamic dream work, for psychotherapeutic practice, and for research into the efficacy of the model.
When Good Randomness Goes Bad: Virtual Machine Reset Vulnerabilities and Hedging Deployed Cryptography

Random number generators (RNGs) are consistently a weak link in the secure use of cryptography. Routine cryptographic operations such as encryption and signing can fail spectacularly given predictable or repeated randomness, even when using good long-lived key material. This has proved problematic in prior settings when RNG implementation bugs, poor design, or low-entropy sources have resulted in predictable randomness. We investigate a new way in which RNGs fail due to reuse of virtual machine (VM) snapshots. We exhibit such VM reset vulnerabilities in widely-used TLS clients and servers: the attacker takes advantage of (or forces) snapshot replay to compromise sessions or even expose a server’s DSA signing key. Our next contribution is a backwards-compatible framework for hedging routine cryptographic operations against bad randomness, thereby mitigating the damage due to randomness failures. We apply our framework to the OpenSSL library and experimentally confirm that it has little overhead.
Extremum seeking control with fractional-order switching technique design for maximum power point tracking in photovoltaic systems

This paper considers a novel extremum seeking control with fractional-order switching technique (ESC-FOST) as a maximum power point tracking (MPPT) algorithm for a PV system. The proposed ESC-FOST combines extremum seeking controller with FO sliding mode dynamics, in which FO proportional-integral (PI) switching surface is adopted. The ESC-FOST can not only guarantee the output power is maintained around the maximum power point but that it will also have a faster tracking performance and higher accuracy than the ESC with integer-order switching technique (ESC-IOST). Simulation and experimental results demonstrate the effectiveness and benefit of the ESC-FOST for the PV plant.
Eddy transport of organic carbon and nutrients from the Chukchi Shelf : impact on the upper halocline of the western Arctic Ocean

[1] In September 2004 a detailed physical and chemical survey was conducted on an anticyclonic, cold-core eddy located seaward of the Chukchi Shelf in the western Arctic Ocean. The eddy had a diameter of ∼16 km and was centered at a depth of ∼160 m between the 1000 and 1500 m isobaths over the continental slope. The water in the core of the eddy (total volume of 25 km3) was of Pacific origin, and contained elevated concentrations of nutrients, organic carbon, and suspended particles. The feature, which likely formed from the boundary current along the edge of the Chukchi Shelf, provides a mechanism for transport of carbon, oxygen, and nutrients directly into the upper halocline of the Canada Basin. Nutrient concentrations in the eddy core were elevated compared to waters of similar density in the deep Canada Basin: silicate (+20 μmol L−1), nitrate (+5 μmol L−1), and phosphate (+0.4 μmol L−1). Organic carbon in the eddy core was also elevated: POC (+3.8 μmol L−1) and DOC (+11 μmol L−1). From these observations, the eddy contained 1.25 × 109 moles Si, 4.5 × 108 moles NO3−, 5.5 × 107 moles PO3−, 1.2 × 108 moles POC, and 1.9 × 109 moles DOC, all available for transport to the interior of the Canada Basin. This suggests that such eddies likely play a significant role in maintaining the nutrient maxima observed in the upper halocline. Assuming that shelf-to-basin eddy transport is the dominant renewal mechanism for waters of the upper halocline, remineralization of the excess organic carbon transported into the interior would consume 6.70 × 1010 moles of O2, or one half the total oxygen consumption anticipated arising from all export processes impacting the upper halocline.
Enhancing domain-specific software architecture recovery

Performing software architecture analysis and recovery on a large software system is expensive and time consuming; when it is done at all, it is often performed within a narrow context, focused on a few areas of particular concern. However, for a long-lived system within a well understood application domain, the costs for performing detailed architecture recovery may be amortized over several generations of the system; the resulting models can also be broadened and put into context by incorporating information about the history and anticipated future evolution of both the application and its underlying domain. This paper proposes a systematic approach for organizing application domain knowledge into a unified structure called the Architectural Domain Assets Set (ADAS). The ADAS structure builds on previous research, as well as our experience in performing an architecture recovery of IBM's DB2. Our initial experiences in using ADAS suggest that it brings needed focus to the recovery process and provides assistance to domain-specific architecture recovery.
The Impact of the Mobile Web in Developing Countries

Mobile phone penetration in the developing world shows remarkable growth patterns, which triggers competition among mobile operators and service providers. As a consequence, this has made mobile communications more affordable for people in developing countries. At the beginning, people use mobile phones only for audio or text communications. Later, people start using their mobiles to access the World Wide Web, which is called mobile Web. Despite rapid mobile Web adoption in the developing world, there has been no comprehensive research methodology to define, identify, and measure the impact of mobile Web use. In the context of Web Science research, the methodology is needed by various mobile Web stakeholders to enable the advancement of mobile Web technology, as well as to anticipate the potential impact on society. In this paper we describe a proposed methodology to measure the impact of mobile Web in developing countries. The methodology will be tried in Kenya and Indonesia this year. Then it will be evaluated, refined, and tested again in 2011.
A High-Resolution Study of Two Galactic H I Halo Clouds in the Ophiuchus Superbubble

Two compact HI clouds which seem to belong to the Ophiuchus superbubble were studied at ∼30  resolution using the Very Large Array (VLA) in C and D configurations together with the Green Bank Telescope (GBT) providing the short-spacing flux. Here we present preliminary results of the data analysis.
Treatment of Paroxysmal Supraventricular Tachycardia in Infancy with Digitalis, Adenosine‐5′‐Triphosphate, and Verapamil: A Comparative Study

The treatment of paroxysmal supraventricular tachycardia (PSVT) in infancy with digitalis, adenosine triphosphate (ATP) and verapamil is reported. Treatment was successful in about 90% of the patients treated with ATP and verapamil and in 61-71% of the patients treated with digitalis (Lanatoside C). Verapamil terminated the tachycardia within 2 minutes of administration in most instances and ATP less than 1 minute. Digitalis, however, took as long as 2 hours; it was therefore excluded as the drug of first choice in emergencies, and is better suited for treating patients with poor hemodynamics.Side effects with ATP are common but short-lived. With verapamil, side effects are rare, but may serious if certain contraindications are not taken into account. Digitalis in the dose used in this trial rarely produced side effects.We conclude that ATP or verapamil is the drug of first choice for quick termination of PSVT in infancy.
Parameters affecting HS emissions removal and re-circulating water quality in a pilot-scale sequential biological treatment system at a wastewater lift station in Brownsville, Texas, USA

In this study, a pilot-scale sequential biological treatment system combining a biotrickling filter and biofilter was used to optimize the removal of variable emission H2S loadings ranging from 30 to 120 g m−3 h−1at a wastewater lift station in Brownsville, Texas USA. The biotrickling filter recycle water pH remained between 2.0 to 3.0 during the four months of unit operation and the overall removal efficiency for H2S was >99%. The biotrickling filter removal efficiency was 70 ± 8%, with an elimination capacity of 10 to 80 g m−3 h−1 while the biofilter elimination capacity ranged from 10 to 40 g m−3 h−1. The sequential treatment system was operated initially at an Empty Bed Residence Time (EBRT) of 120 s (50 s for the biotrickling filter and 70 s for biofilter) for two months and then at an EBRT of 60 s (25 s for biotrickling filter and 35s for biofilter) for the remainder of the operating period; remarkably, there was only a slight decrease in removal efficiency at 60 s EBRT. In order to qualitatively evaluate the changes in recycle water quality in the system on the performance of the unit in precipitating sulfur species, the equilibrium chemical model, Visual MINTEQ was employed. The model predicted speciation results based on the feed water quality and sulfur loadings, and also forecast some iron-sulfur complexes which have potential to form some complex precipitates. This research demonstrated that low pH re-circulating water quality in the biological treatment of H2S was possible without compromising the high removal efficiency, and that an improved understanding of the recycle water chemistry of the trickling unit of a sequential treatment system could be useful in the overall optimization of the process.
RNA-directed DNA methylation

Double-stranded RNAs (dsRNAs) and their `diced' small RNA products can guide key developmental and defense mechanisms in eukaryotes. Some RNA-directed mechanisms act at a post-transcriptional level to degrade target messenger RNAs. However, dsRNA-derived species can also direct changes in the chromatin structure of DNA regions with which they share sequence identity. For example, plants use such RNA species to lay down cytosine methylation imprints on identical DNA sequences, providing a fundamental mark for the formation of transcriptionally silent heterochromatin. Thus, RNA can feed backwards to modulate the accessibility of information stored in the DNA of cognate genes. RNA triggers for DNA methylation can come from different sources, including invasive viral, transgene or transposon sequences, and in some cases are derived from single-stranded RNA precursors by RNA-dependent RNA polymerases. The mechanism by which RNA signals are translated into DNA methylation imprints is currently unknown, but two plant-specific types of cytosine methyltransferase have been implicated in this process. RNA can also direct heterochromatin formation in fission yeast and Drosophila, but in these organisms the process occurs in the absence of DNA methylation.
Does the Number of Cancer Patients' Close Social Ties Affect Cancer-Related Information Seeking Through Communication Efficacy? Testing a Mediation Model

This study addresses whether having a broad social network of close friends equips cancer patients with increased efficacy to engage in communication about their cancer, which then leads to an increased likelihood of patients actively seeking cancer-related information. Guided by the theory of motivated information management, the study also tests whether the effect of the number of close social ties on information seeking is mediated, in part, by communication efficacy. Results are based on data collected from a randomly drawn sample from the Pennsylvania Cancer Registry of 2,013 cancer patients who completed mail surveys in the Fall of 2006. Results are consistent with a cross-sectional mediation effect in which the number of close social ties in one's social network is positively associated with communication efficacy (b = .17, p = .001), which, in turn, is positively associated with cancer-related information seeking (b = .13, p < .001).
Astaxanthin Inhibits PC-3 Xenograft Prostate Tumor Growth in Nude Mice

Prostate cancer (PCa), the most common malignancy in men, is a major cause of cancer deaths. A better understanding of the mechanisms that drive tumor initiation and progression may identify actionable targets to improve treatment of this patient group. As a dietary carotenoid, astaxanthin has been demonstrated to exert beneficial effects against inflammation, cardiovascular disease, oxidative damage, or different cancer sites. This study used intragastric administration of astaxanthin to detect its role on tumor proliferation, apoptosis, microRNA (miRNA) overexpression, and microbacteria composition change by establishing androgen-independent PCa cell PC-3 xenograft nude mice. Nude mice were inoculated with androgen-independent prostate cancer PC-3 cells subcutaneously. The intervention was started when tumors reached 0.5–0.6 cm in diameter. Mice were intragastrically administered 100 mg/kg astaxanthin (HA), 25 mg/kg astaxanthin (LA), or olive oil (TC). The results showed that 100 mg/kg astaxanthin significantly inhibited tumor growth compared to the TC group, with an inhibitory rate of 41.7%. A decrease of Ki67 and proliferating cell nuclear antigen (PCNA) as well as an increase of cleaved caspase-3 were observed in HA-treated tumors, along with increasing apoptotic cells, obtained by TUNEL assay. The HA significantly elevated the levels of tumor suppressors miR-375 and miR-487b in tumor tissues and the amount of Lactobacillus sp. and Lachnospiraceae in mice stools, while there was no significant difference between LA and TC groups. These results provide a promising regimen to enhance the therapeutic effect in a dietary supplement manner.
C3: Lightweight Incrementalized MCMC for Probabilistic Programs using Continuations and Callsite Caching

Lightweight, source-to-source transformation approaches to implementing MCMC for probabilistic programming languages are popular for their simplicity, support of existing deterministic code, and ability to execute on existing fast runtimes. However, they are also slow, requiring a complete re-execution of the program on every Metropolis Hastings proposal. We present a new extension to the lightweight approach, C3, which enables efficient, incrementalized re-execution of MH proposals. C3 is based on two core ideas: transforming probabilistic programs into continuation passing style (CPS), and caching the results of function calls. We show that on several common models, C3 reduces proposal runtime by 20-100x, in some cases reducing runtime complexity from linear in model size to constant. We also demonstrate nearly an order of magnitude speedup on a complex inverse procedural modeling application.