Miracle-dz/UniFAR-FTUs huggingface dataset:
Abundance of Reverse Tricarboxylic Acid Cycle Genes in Free-Living Microorganisms at Deep-Sea Hydrothermal Vents

ABSTRACT Since the discovery of hydrothermal vents more than 25 years ago, the Calvin-Bassham-Benson (Calvin) cycle has been considered the principal carbon fixation pathway in this microbe-based ecosystem. However, on the basis of recent molecular data of cultured free-living and noncultured episymbiotic members of the epsilon subdivision of Proteobacteria and earlier carbon isotope data of primary consumers, an alternative autotrophic pathway may predominate. Here, genetic and culture-based approaches demonstrated the abundance of reverse tricarboxylic acid cycle genes compared to the abundance of Calvin cycle genes in microbial communities from two geographically distinct deep-sea hydrothermal vents. PCR with degenerate primers for three key genes in the reverse tricarboxylic acid cycle and form I and form II of ribulose 1,5-bisphosphate carboxylase/oxygenase (Calvin cycle marker gene) were utilized to demonstrate the abundance of the reverse tricarboxylic acid cycle genes in diverse vent samples. These genes were also expressed in at least one chimney sample. Diversity, similarity matrix, and phylogenetic analyses of cloned samples and amplified gene products from autotrophic enrichment cultures suggest that the majority of autotrophs that utilize the reverse tricarboxylic acid cycle are members of the epsilon subdivision of Proteobacteria. These results parallel the results of previously published molecular surveys of 16S rRNA genes, demonstrating the dominance of members of the epsilon subdivision of Proteobacteria in free-living hydrothermal vent communities. Members of the epsilon subdivision of Proteobacteria are also ubiquitous in many other microaerophilic to anaerobic sulfidic environments, such as the deep subsurface. Therefore, the reverse tricarboxylic acid cycle may be a major autotrophic pathway in these environments and significantly contribute to global autotrophic processes.
Aerobic and Combined Exercise Sessions Reduce Glucose Variability in Type 2 Diabetes: Crossover Randomized Trial

Purpose To evaluate the effects of aerobic (AER) or aerobic plus resistance exercise (COMB) sessions on glucose levels and glucose variability in patients with type 2 diabetes. Additionally, we assessed conventional and non-conventional methods to analyze glucose variability derived from multiple measurements performed with continuous glucose monitoring system (CGMS). Methods Fourteen patients with type 2 diabetes (56±2 years) wore a CGMS during 3 days. Participants randomly performed AER and COMB sessions, both in the morning (24 h after CGMS placement), and at least 7 days apart. Glucose variability was evaluated by glucose standard deviation, glucose variance, mean amplitude of glycemic excursions (MAGE), and glucose coefficient of variation (conventional methods) as well as by spectral and symbolic analysis (non-conventional methods). Results Baseline fasting glycemia was 139±05 mg/dL and HbA1c 7.9±0.7%. Glucose levels decreased immediately after AER and COMB protocols by ∼16%, which was sustained for approximately 3 hours. Comparing the two exercise modalities, responses over a 24-h period after the sessions were similar for glucose levels, glucose variance and glucose coefficient of variation. In the symbolic analysis, increases in 0 V pattern (COMB, 67.0±7.1 vs. 76.0±6.3, P = 0.003) and decreases in 1 V pattern (COMB, 29.1±5.3 vs. 21.5±5.1, P = 0.004) were observed only after the COMB session. Conclusions Both AER and COMB exercise modalities reduce glucose levels similarly for a short period of time. The use of non-conventional analysis indicates reduction of glucose variability after a single session of combined exercises. Trial Registration Aerobic training, aerobic-resistance training and glucose profile (CGMS) in type 2 diabetes (CGMS exercise). ClinicalTrials.gov ID: NCT00887094.
Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK

Macroautophagy (herein referred to as autophagy) is an evolutionarily conserved self-digestive process cells adapt to starvation and other stress responses. Upon starvation, autophagy is induced, providing cells with needed nutrient supplies. We report here that Unc-51-like kinase 1 (Ulk1), a key initiator for mammalian autophagy, undergoes dramatic dephosphorylation upon starvation, particularly at serine 638 and serine 758. Phosphorylations of Ulk1 are mediated by mammalian target-of-rapamycin (mTOR) kinase and adenosine monophosphate activated protein kinase (AMPK). AMPK interacts with Ulk1 in a nutrient-dependent manner. Proper phosphorylations on Ulk1 are crucial for Ulk1/AMPK association, as a single serine-to-alanine mutation (S758A) at Ulk1 impairs this interaction. Compared to the wild-type ULK1, this Ulk1-S758A mutant initiates starvation-induced autophagy faster at an early time point, but does not alter the maximum capacity of autophagy when starvation prolongs. This study therefore revealed previously unnoticed acute autophagy response to environmental changes.
A New Mitigation Approach for Soft Errors in Embedded Processors

Embedded processors, like for example processor macros inside modern FPGAs, are becoming widely used in many applications. As soon as these devices are deployed in radioactive environments, designers need hardening solutions to mitigate radiation-induced errors. When low-cost applications have to be developed, the traditional hardware redundancy-based approaches exploiting m-way replication and voting are no longer viable as too expensive, and new mitigation techniques have to be developed. In this paper we present a new approach, based on processor duplication, checkpoint and rollback, to detect and correct soft errors affecting the memory elements of embedded processors. Preliminary fault injection results performed on a PowerPC-based system confirmed the efficiency of the approach.
Perceived parenting style and its relationship to hopefulness, happiness, and optimism in a college student sample

The purpose of this study was to investigate differences among positive psychology traits of happiness, hopefulness, and optimism, between three perceived parenting styles in 291 undergraduate college students. It was hypothesized that students identifying with the reared authoritative parenting style would endorse higher levels of hopefulness, happiness, and optimism than the permissive and authoritarian parenting styles. Multivariate and discriminant analyses were conducted to test the hypotheses. Data analysis in this study supported that the perceived authoritative parenting style contributed to higher levels of optimism than the authoritarian parenting style. The development of optimism or lack thereof can become a means of clinical intervention both individually and in providing parenting interventions. Based on the studies relating optimism to coping skills, identifying levels of optimism in students can help provide ideas for clinical intervention. The hypothesis that the perceived authoritative parenting style would contribute to the development of higher levels of optimism than the perceived permissive style were inconclusive due to the limitations of using multivariate analyses. The hypotheses suggesting that the perceived authoritative parenting style would also contribute to the development of higher levels of happiness and hopefulness were not supported in this study. Introduction As new generations of students enter into college, universities find ways to adjust to the unique issues presented with each changing generation of students. Since the era of the baby boomers becoming parents, universities are finding themselves adjusting to the unique issues brought about by over involved parents that have earned themselves the name of “helicopter parents” through their constant hovering (Lum, 2006, White, 2005). The term “helicopter parents” evolved from the idea of a hovering helicopter being like
Automatic bone parameter estimation for skeleton tracking in optical motion capture

Motion analysis is important in a broad range of contexts, including animation, bio-mechanics, robotics and experiments investigating animal behavior. For applications, in which tracking accuracy is one of the main requirements, passive optical motion capture systems are widely used. Many skeleton tracking methods based on such systems use a predefined skeleton model, which is scaled once in the initialization step to the individual size of the character to be tracked. However, there are remarkable differences in the bone length relations across gender and even more across mammal races. In practice, the optimal skeleton model has to be determined in a manual and time-consuming process. In this paper, we reformulate this task as an optimization problem aiming to rescale a rough hierarchical skeleton structure to optimize probabilistic skeleton tracking performance. We solve this optimization problem by means of state-of-the-art blackbox optimization methods based on sequential model-based Bayesian optimization (SMBO). We compare different SMBO methods on three real-world datasets with an animal and humans, demonstrating that we can automatically find skeleton structures for previously unseen mammals. The same methods also allow an automated choice of a suitable starting frame for initializing tracking.
Antibiotics for Local Delivery Systems Cause Skeletal Cell Toxicity In Vitro

Antibiotic concentrations associated with antibiotic bone cements may cause skeletal cell toxicity and prevent fracture healing. We investigated toxicity effects of dose and treatment time after exposure to three antibiotics commonly used in orthopaedic local drug delivery systems. We hypothesized a threshold exists for toxicity of osteoblasts and chondrocytes after treatment with ciprofloxacin, vancomycin, or tobramycin. To test this hypothesis, we first determined whether treatment with antibiotics caused differences in cellular morphology. Cells exposed to ciprofloxacin showed considerable changes in spread, cell membrane, and extensions. We next asked what dosage of antibiotic would cause reductions in osteoblast and chondrocyte cell numbers. Ciprofloxacin at a dose greater than 100 μg/mL and vancomycin and tobramycin at doses greater than 2000 μg/mL severely decreased cellular proliferation. Finally, we questioned whether observed decreases in cell numbers were the result of increased cellular toxicity or senescence. Released lactate dehydrogenase ratios were severely increased in osteoblasts. These data suggest the balance between the targeted microbicidal effects and host cellular toxicity is critical for skeletal cell survival and function.
Deep Structured Models For Group Activity Recognition

This paper presents a deep neural-network-based hierarchical graphical model for individual and group activity recognition in surveillance scenes. Deep networks are used to recognize the actions of individual people in a scene. Next, a neural-network-based hierarchical graphical model refines the predicted labels for each class by considering dependencies between the classes. This refinement step mimics a message-passing step similar to inference in a probabilistic graphical model. We show that this approach can be effective in group activity recognition, with the deep graphical model improving recognition rates over baseline methods.
Joint formation of QSOs and spheroids: QSOs as clocks of star formation in spheroids

Direct and indirect observational evidence leads to the conclusion that high-redshift QSOs did shine in the core of early-type protogalaxies during their main episode of star formation. Exploiting this fact, we derive the rate of formation of this kind of stellar system at high redshift by using the QSO luminosity function. The elemental proportions in elliptical galaxies, the descendants of the QSO hosts, suggest that the star formation was more rapid in more massive objects. We show that this is expected to occur in dark matter haloes, when the processes of cooling and heating are considered. This is also confirmed by comparing the observed submm counts with those derived by coupling the formation rate and the star formation rate of the spheroidal galaxies with a detailed model for their SED evolution. In this scenario SCUBA galaxies and Lyman-break galaxies are early-type protogalaxies forming the bulk of their stars before the onset of QSO activity.
Secrecy capacity maximization for secure cooperative ad-hoc networks

This paper investigates secure cooperative communication with the involvement of multiple malicious eavesdroppers. By characterizing the security performance of the system by secrecy capacity, we study the secrecy capacity maximization problem in cooperative communication aware ad hoc networks. Specifically, we propose a system model where secrecy capacity enhancement is achieved by the assignment of cooperative relays. We theoretically present a corresponding formulation for the problem and discuss the security gain brought by the relay assignment process. Then, we develop an optimal relay assignment algorithm to solve the secrecy capacity maximization problem in polynomial time. The basic idea behind our proposed algorithm is to boost the capacity of the primary channel by simultaneously decreasing the capacity of the eavesdropping channel. To further increase the system secrecy capacity, we exploit the jamming technique and propose a smart jamming algorithm to interfere the eavesdropping channels. Analysis and experimental results reveal that our proposed algorithms significantly increase the system secrecy capacity under various network settings.
Echinocandin Treatment of Pneumocystis Pneumonia in Rodent Models Depletes Cysts Leaving Trophic Burdens That Cannot Transmit the Infection

Fungi in the genus Pneumocystis cause pneumonia (PCP) in hosts with debilitated immune systems and are emerging as co-morbidity factors associated with chronic diseases such as COPD. Limited therapeutic choices and poor understanding of the life cycle are a result of the inability of these fungi to grow outside the mammalian lung. Within the alveolar lumen, Pneumocystis spp. , appear to have a bi-phasic life cycle consisting of an asexual phase characterized by binary fission of trophic forms and a sexual cycle resulting in formation of cysts, but the life cycle stage that transmits the infection is not known. The cysts, but not the trophic forms, express β -1,3-D-glucan synthetase and contain abundant β -1,3-D-glucan. Here we show that therapeutic and prophylactic treatment of PCP with echinocandins, compounds which inhibit the synthesis of β -1,3-D-glucan, depleted cysts in rodent models of PCP, while sparing the trophic forms which remained in significant numbers. Survival was enhanced in the echincandin treated mice, likely due to the decreased β -1,3-D-glucan content in the lungs of treated mice and rats which coincided with reductions of cyst numbers, and dramatic remodeling of organism morphology. Strong evidence for the cyst as the agent of transmission was provided by the failure of anidulafungin-treated mice to transmit the infection. We show for the first time that withdrawal of anidulafungin treatment with continued immunosuppression permitted the repopulation of cyst forms. Treatment of PCP with an echinocandin alone will not likely result in eradication of infection and cessation of echinocandin treatment while the patient remains immunosuppressed could result in relapse. Importantly, the echinocandins provide novel and powerful chemical tools to probe the still poorly understood bi-phasic life cycle of this genus of fungal pathogens.
Effects of Exposure of Clostridium difficile PCR Ribotypes 027 and 001 to Fluoroquinolones in a Human Gut Model

ABSTRACT The incidence of Clostridium difficile infection is increasing, with reports implicating fluoroquinolone use. A three-stage chemostat gut model was used to study the effects of three fluoroquinolones (ciprofloxacin, levofloxacin, and moxifloxacin) on the gut microbiota and two epidemic C. difficile strains, strains of PCR ribotypes 027 and 001, in separate experiments. C. difficile total viable counts, spore counts, and cytotoxin titers were determined. The emergence of C. difficile isolates with reduced antibiotic susceptibility was monitored with fluoroquinolone-containing medium, and molecular analysis of the quinolone resistance-determining region was performed. C. difficile spores were quiescent in the absence of fluoroquinolones. Instillation of each fluoroquinolone led to C. difficile spore germination and high-level cytotoxin production. High-level toxin production occurred after detectable spore germination in all experiments except those with C. difficile PCR ribotype 027 and moxifloxacin, in which marked cytotoxin production preceded detectable germination, which coincided with isolate recovery on fluoroquinolone-containing medium. Three C. difficile PCR ribotype 027 isolates and one C. difficile PCR ribotype 001 isolate from fluoroquinolone-containing medium exhibited elevated MICs (80 to ≥180 mg/liter) and possessed mutations in gyrA or gyrB. These in vitro results suggest that all fluoroquinolones have the propensity to induce C. difficile infection, regardless of their antianaerobe activities. Resistant mutants were seen only following moxifloxacin exposure.
Conceptual grounding of expertise

Finding ways in which communities of experts can benefit from each other is a question shared by the machine learning community and social sciences alike. Considerable research in machine learning methods has shown that communities of experts can provide consistently better classifications and decisions than single experts in various tasks and domains. Our aim is to extend the perspective on communities of experts to cover the wider context of socio-cognitive research. In particular, we discuss the sociocognitive research on the formation and use of expertise in relation to the modeling of concept formation, integration and use in human and artificial agents. We present three case studies related to problem solving and decision making in environmental policy, medical care, and consumer research. We present a methodological framework for the computational modeling of the phenomena described above. A specific emphasis is on unsupervised statistical machine learning of heterogeneous conceptual spaces in multi-agent systems and on the application of such conceptual expert knowledge.
Combined thrombolysis with abciximab and rtPA in patients with middle cerebral artery occlusion

Background – In patients with acute middle cerebral artery (MCA) occlusion, recanalization rates with intravenous (IV) recombinant tissue plasminogen activator (rtPA) are limited. Aim– We evaluated the feasibility and safety of combined IV thrombolysis with abciximab and reduced dose rtPA in a 3‐ to 6‐h time window.
Toward understanding CMB anisotropies and their implications.

Working toward a model-independent understanding of cosmic microwave background (CMB) anisotropies and their significance, we undertake a comprehensive and self-contained study of scalar perturbation theory. Initial conditions, evolution, thermal history, matter content, background dynamics, and geometry all play a role in determining the anisotropy. By employing analytic techniques to illuminate the numerical results, we are able to separate and identify each contribution. We thus bring out the nature of the total Sachs-Wolfe effect, acoustic oscillations, diffusion damping, Doppler shifts, and reionization, as well as their particular manifestation in a critical curvature, or cosmological-constant-dominated universe. By studying the full angular and spatial content of the resultant fluctuations, we isolate the signature of these effects from the dependence on initial conditions. Whereas structure in the Sachs-Wolfe anisotropy depends strongly on the underlying power spectra, the acoustic oscillations provide features which are nearly model independent. This may allow for future determination of the matter content of the Universe as well as the adiabatic and/or isocurvature nature of the initial fluctuations.
Oncogenic targets, magnitude of benefit, and market pricing of antineoplastic drugs.

PURPOSE The relationship between market pricing of new anticancer drugs and the magnitude of clinical benefit caused by them has not been reported. PATIENTS AND METHODS Randomized clinical trials (RCTs) that evaluated approved new agents for solid tumors by the U.S. Food and Drug administration since the year 2000 were assessed. Hazard ratios (HRs) and 95% CIs were extracted for time-to-event end points described for each RCT. HRs were pooled for three groups: agents directed against a specific molecular target, for which the target population is selected by a biomarker (group A); less specific biologic targeted agents (group B); and chemotherapeutic agents (group C). Monthly market prices of these different drugs were compared. RESULTS For overall survival (OS), the pooled HR was 0.69 (95% CI, 0.59 to 0.81) for group A (six drugs, six trials); it was 0.78 (95% CI, 0.74 to 0.83) for group B (seven drugs, 14 trials); and it was 0.84 (95% CI, 0.79 to 0.90) for group C (eight drugs, 12 trials). For progression-free survival (PFS), the pooled HR was 0.42 (95% CI, 0.36 to 0.49) for group A (six drugs, seven trials); it was 0.57 (95% CI, 0.51 to 0.64) for group B (seven drugs, 14 trials); and it was 0.75 (95% CI, 0.66 to 0.85) for group C (six drugs, 10 trials). Tests for heterogeneity between subgroups were highly significant for PFS (P < .001) and OS (P = .02). The median monthly prices for standard doses of drugs were $5375 for group A, $5644 for group B, and $6584 for group C (P = .87). CONCLUSION New agents with specific molecular targets are clinically the most beneficial, but their monthly market prices are not significantly different from those of other anticancer agents.
Towards Realizing the Performance and Availability Benefits of a Global Overlay Network

Prior analyses of the benefits of routing overlays are based on platforms consisting of nodes located primarily in North America, on the academic Internet, and at the edge of the network. This paper is the first global study of the benefits of overlays on the commercial Internet in terms of round trip latencies and availability, using measurements from diverse ISPs distributed across all tiers, and over 1100 locations (77 countries, 630 cities and 6 continents). Our study shows that while overlays provide some improvements in North America, their benefits are especially significant for paths with Asian endpoints. For example, overlays reduce latencies of a quarter of the paths in Asia by over 50%, while the latencies of over half the paths globally are improved by at least 10%. Furthermore, overlays increase availability in North America and Europe by up to 0.5%, whereas improvements in Asia are significantly larger at 3.25%. Our study also focuses on practical considerations in constructing overlay routes. We show that a simple algorithm that randomly chooses a small number of alternate redundant paths achieves an availability of over 99.5%. We also propose and evaluate a simple predictive scheme that achieves almost optimal latency using only 2-3 paths. Finally, we demonstrate that this is achievable with surprisingly persistent routing choices.
SRLG-disjoint multi-path protection: When LP meets ILP

Multi-Path Routing routes the upcoming demand over multiple paths. This is feasible in networks where the demand can be split into multiple parallel flows, i.e., the network is capable to perform inverse multiplexing (e.g., ngSDH and OTN via VCat) and where the connectivity of the topology also allows it.