Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences (“markers”) and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph. harvard.edu/shortbred
Drawing Bers Embeddings of the Teichmüller Space of Once-Punctured Tori

We present a computer-oriented method of producing pictures of Bers embeddings of the Teichmüller space of once-punctured tori. The coordinate plane is chosen in such a way that the accessory parameter is hidden in the relative position of the origin. Our algorithm consists of two steps. For each point in the coordinate plane, we first compute the corresponding monodromy representation by numerical integration along certain loops. Then we decide whether the representation is discrete by applying Jørgensen's theory on the quasi-Fuchsian space of once-punctured tori.
Comparison of the CAM2 and NAL-NL2 Hearing Aid Fitting Methods

Objective: To compare preference judgments for sounds processed via a simulated five-channel compression hearing aid with gains and compression ratios selected according to two recently introduced fitting methods, CAMEQ2-HF (hereafter named CAM2) and NAL-NL2. Design: There were 15 participants with sloping sensorineural hearing loss. They had mild losses, typical of people who might be candidates for wide-bandwidth hearing aids. Within a given trial, the same segment of sound was presented twice in succession to one ear, once with CAM2 settings and once with NAL-NL2 settings, in random order. The participant had to indicate which one was preferred and by how much. Judgments of overall sound quality were obtained for female and male speech in quiet and for four types of music (classical, jazz, a man singing, and percussion). Judgments of speech clarity were obtained for female and male speech in speech-shaped noise, female speech in a male-talker background, and male speech in a female-talker background. Factors investigated included compression speed (slow or fast) and input sound level (50, 65, or 80 dB SPL). Results: The pattern of the results was reasonably consistent across participants, but the magnitude of the effects was small. For judgments of overall sound quality, nine participants preferred CAM2 relative to NAL-NL2, and the remainder showed no clear preference. There was a significant overall preference for CAM2. The preference for CAM2 over NAL-NL2 in overall sound quality was present for all types of stimuli, both compression speeds, and all three levels. For judgments of the clarity of speech in noise, five participants preferred CAM2 over NAL-NL2, one showed the opposite preference, and the remainder showed no clear preference. There was a significant overall preference for CAM2. The preference for CAM2 over NAL-NL2 in the context of clarity of speech in noise was present for all types of stimuli, both compression speeds, and all three levels. For judgments of the clarity of speech in a background talker, CAM2 was significantly preferred overall relative to NAL-NL2, but the effect was very small. Conclusions: For participants with mild sloping hearing loss, a simulated hearing aid unilaterally fitted using CAM2 was preferred over the same aid fitted using NAL-NL2 for overall sound quality and the clarity of speech in noise. Preferences differed only very slightly for the clarity of speech in a background talker. Further work is needed to establish whether similar preferences would be found in everyday life.
Universal Kinetic Modeling of RAFT Polymerization using Moment Equations

In the following text, we show that by introducing universal kinetic scheme, the origin of rate retardation and inhibition period which observed in dithiobenzoate-mediated RAFT polymerization can be described properly. We develop our model by utilizing the method of moments, then we apply our model to different monomer/RAFT agent systems, both homoand copolymerization. The modeling results are in an excellent agreement with experiments and imply the validity of universal kinetic scheme, not only for dithiobenzoate-mediated systems, but also for different types of monomer/RAFT agent ones. Keywords—RAFT Polymerization, Mechanism, Kinetics, Moment Equations, Modeling.
Will intelligent vehicles evolve into Human-peer Robots?

This paper aims at stimulating the discussion on the future of Intelligent Vehicles. It is a position paper, indicating converging technologies that, in our opinion, will have to be used in future Intelligent Vehicles. We present a vision according to which Intelligent Vehicles will evolve into Human-peer Robots, here called Co-Drivers. Co-Drivers will be able to “understand” human drivers and to form symbiotic systems with them. The general architecture of Co-Drivers, the building blocks and the technologies that are needed to bring them to life are discussed, pointing out which parts have been already researched and which gaps still remain. We clarify what “understanding driver” actually means and how a joint system can be obtained. The paper will identify research needs and paths, and hopefully trigger interest.
Comparison of Different Evaluation Methods to Determine Stray Load Losses in Induction Machines With Eh-Star Method

The eh-star method is a simple and economical alternative test for stray-load-loss assessment in induction machines, also for higher efficiency above 96%. It is an asymmetrical circuit where two machine phases are connected in parallel through an auxiliary ohmic resistance Reh without coupling of the machine and without needing any dynamometer. This resistance shall be adjusted, so that the positive sequence current I1 stays below 30% of negative sequence current I2. If this pure ldquoohmicrdquo resistance is not available, the eh-star measurement can be done with an impedance Z-eh, preferably ohmic inductive. The determination of stray load losses must be done from the measured losses by decomposition into positive and negative sequence losses. Negative sequence losses at slip 2 - s ap 2 correspond to stray load losses similar to the standardized reverse-rotation test (RRT). For this evaluation, the phase angles of measured currents and voltages must be known. This can be done by calculation with three different methods A, B, and C, which yield identical results for ideal ohmic resistance Reh. Method A is only useful for an ohmic resistance Reh for determination of loss separation. Method B is based on the measured two line-to-line motor-input-power values Pe, in_UV and Pe, in_WV. Instead of Reh, also an impedance Z-eh (inductor, capacitor, or resistor) may be used. Method C is similar to method B, but only the measured total motor input power Pe, in is needed. A comparison of evaluated stray load losses with the three evaluation methods is given with theoretical examples and measurements. This is compared to stray load losses and measured with RRT and input-output method according to IEEE-112.
Improving entrepreneurial research methodology: When research design fails

The diverse endeavours undertaken by entrepreneurs have the potential to positively impact communities, and yet this population appears notoriously difficult to recruit for research. This paper reflects on declining research participation, particularly noted in top executives and the entrepreneurial community; and introduces a Master’s dissertation study which failed to recruit significant numbers of entrepreneurs for quantitative research purposes. While ‘failed’ research may lack allure, it does provide valuable learning insights for students undertaking new research projects. Quite apart from not repeating past mistakes, outlining research challenges may assist students to develop more creative and robust projects. As such, this paper highlights two significant points regarding barriers to recruiting amongst entrepreneurs. First, we present evidence that entrepreneurs are often over-worked and time poor, and this impacts on their research participation; secondly, we highlight how entrepreneurs respond differently to research activities, and hereby, we offer some recommendations for improved research design.
Whole-body motion control for capturing a tumbling target by a free-floating space robot

This paper discusses a control strategy of a free- floating space robot for capturing a non-cooperative target. It is desirable that the base attitude deviation of the robot is minimized for accurate operation by a manipulator arm mounted on it, for communication with the earth, and the ideal contact with the target so that the target would not be pushed away, impedance control and Distributed Momentum Control are reasonable for the above two requirements. The proposed strategy includes both control methods simultaneously using the manipulator's redundancy. Moreover, a control law for reaction wheels is proposed so that the singularity problem would not happened. The proposed strategy is verified from results of numerical simulations that compare the different degree of freedom manipulator.
Optimal single-session flow routing for wireless sensor networks

Wireless sensor networks are becoming increasingly important in recent years due to their ability to detect and convey real-time in-situ scenes for many civil and military applications. A major technical challenge for a wireless sensor network lies in the energy constraint at each node, which poses a fundamental limit on the network lifetime. We consider two-tiered wireless sensor networks and address the network lifetime problem for upper-tier aggregation and forwarding nodes (AFNs). Prior efforts have formulated the network lifetime problem into a linear programming (LP) that results in a multi-session flow routing solution. Under multi-session flow routing, each AFN must be equipped with multiple transmitter to reach various destinations at the same time, which poses a scalability problem in practice. This paper shows that, by exploiting dynamic power control at an AFN's transmitter, a multi-session flow routing solution can be converted into an equivalent single-session flow routing solution (requiring only a single transmitter at each AFN). Consequently, it shows that it is possible to design a single-session flow routing solution that has the same optimal network lifetime as a multi-session flow routing solution.
AGC tuning of interconnected reheat thermal systems with particle swarm optimization

This paper demonstrates the use of particle swarm optimization for optimizing the parameters of automatic generation control systems (AGC). An integral controller and a proportional-plus-integral controller are considered. A two-area reheat thermal system is considered to exemplify the optimum parameter search. The optimal AGC parameters search is formulated as an optimization problem with a standard infinite time quadratic objective function. A time domain simulation of the system is then used in conjunction with the particle swarm optimizer to determine the controller gains. The integral square of the error and the integral of time-multiplied absolute value of the error performances indices are considered. The results reported in this paper demonstrate the effectiveness of the particle swarm optimizer in the tuning of the AGC parameters. The enhancement in the dynamic response of the power system is verified through simulation results.
The grounding and sharing of symbols

The double function of language, as a social/communicative means, and as an individual/cognitive capability, derives from its fundamental property that allows us to internally re-represent the world we live in. This is possible through the mechanism of symbol grounding, i.e., the ability to associate entities and states in the external and internal world with internal categorical representations. The symbol grounding mechanism, as language, has both an individual and a social component. The individual component, called the “Physical Symbol Grounding”, refers to the ability of each individual to create an intrinsic link between world entities and internal categorical representations. The social component, called “Social Symbol Grounding”, refers to the collective negotiation for the selection of shared symbols (words) and their grounded meanings. The paper discusses these two aspects of symbol grounding in relation to distributed cognition, using examples from cognitive modeling research on grounded agents and robots.
LOXL4 Is Induced by Transforming Growth Factor β1 through Smad and JunB/Fra2 and Contributes to Vascular Matrix Remodeling

ABSTRACT Transforming growth factor β1 (TGF-β1) is a pleiotropic factor involved in the regulation of extracellular matrix (ECM) synthesis and remodeling. In search for novel genes mediating the action of TGF-β1 on vascular ECM, we identified the member of the lysyl oxidase family of matrix-remodeling enzymes, lysyl oxidase-like 4 (LOXL4), as a direct target of TGF-β1 in aortic endothelial cells, and we dissected the molecular mechanism of its induction. Deletion mapping and mutagenesis analysis of the LOXL4 promoter demonstrated the absolute requirement of a distal enhancer containing an activator protein 1 (AP-1) site and a Smad binding element for TGF-β1 to induce LOXL4 expression. Functional cooperation between Smad proteins and the AP-1 complex composed of JunB/Fra2 accounted for the action of TGF-β1, which involved the extracellular signal-regulated kinase (ERK)-dependent phosphorylation of Fra2. We furthermore provide evidence that LOXL4 was extracellularly secreted and significantly contributed to ECM deposition and assembly. These results suggest that TGF-β1-dependent expression of LOXL4 plays a role in vascular ECM homeostasis, contributing to vascular processes associated with ECM remodeling and fibrosis.
Prevalence and impact of worsening renal function in patients hospitalized with decompensated heart failure: results of the prospective outcomes study in heart failure (POSH).

AIMS To determine the prevalence and risk factors for worsening renal function (WRF) among patients hospitalized for decompensated heart failure (HF) and the association with subsequent re-hospitalization and mortality. METHODS AND RESULTS We prospectively enrolled 299 patients across eight European countries (mean age 68, 74% men). HF was defined using the European Society of Cardiology criteria, but only patients with a history of ejection fraction < or =40% on echocardiography were recruited. WRF was defined as an increase in serum creatinine >26 micromol/L ( approximately 0.3 mg/dL) from admission. Follow-up was 95% complete to 6 months. Nearly one-third of patients [72 of 248 patients, 29% (95% CI 26-32%)] developed WRF during hospitalization, excluding patients who had a major in-hospital complication likely to compromise renal function. The risk of WRF in this group was independently associated with serum creatinine levels on admission [odds ratio (OR) 3.02 (95% CI 1.58-5.76)], pulmonary oedema [OR 3.35 (1.79-6.27)], and a history of atrial fibrillation [OR 0.35 (0.18-0.67)]. Although the mortality of WRF patients was not increased significantly, the length of stay was 2 days longer [median 11 days (90% range (4-41) vs. 9 days (4-34), P=0.006]. The re-hospitalization rate was similar in both groups. CONCLUSION WRF is common in patients admitted to European hospitals with decompensated HF. Such patients have longer duration admissions, but a similar mortality and re-hospitalization rate to those without WRF (if patients experiencing a major in-hospital complication are excluded).
Controls on soil microbial community stability under climate change

Soil microbial communities are intricately linked to ecosystem functioning because they play important roles in carbon and nitrogen cycling. Still, we know little about how soil microbial communities will be affected by disturbances expected with climate change. This is a significant gap in understanding, as the stability of microbial communities, defined as a community's ability to resist and recover from disturbances, likely has consequences for ecosystem function. Here, we propose a framework for predicting a community's response to climate change, based on specific functional traits present in the community, the relative dominance of r- and K-strategists, and the soil environment. We hypothesize that the relative abundance of r- and K-strategists will inform about a community's resistance and resilience to climate change associated disturbances. We also propose that other factors specific to soils, such as moisture content and the presence of plants, may enhance a community's resilience. For example, recent evidence suggests microbial grazers, resource availability, and plant roots each impact on microbial community stability. We explore these hypotheses by offering three vignettes of published data that we re-analyzed. Our results show that community measures of the relative abundance of r- and K-strategists, as well as environmental properties like resource availability and the abundance and diversity of higher trophic levels, can contribute to explaining the response of microbial community composition to climate change-related disturbances. However, further investigation and experimental validation is necessary to directly test these hypotheses across a wide range of soil ecosystems.
La qualité éducative en pouponnière : évaluation des besoins de formation des éducatrices des 0 à 18 mois.

Resume: L’enquete quebecoise sur la qualite des services de garde educatifs Grandir en qualite (2015a) demontre que la qualite d’ensemble des services educatifs offerts aux poupons est jugee d’acceptable a bonne, sans plus. Le niveau de formation et de scolarite du personnel educateur etant un des facteurs determinants de la qualite des services de garde educatifs (Clarke-Stewart, Vandell, Burchinal, O’Brien & McCartney, 2002; Goelman, Doherty, Lero, LaGrange & Tougas, 2000; Harme & Pianta, 2001; Howes & Ritchie, 2003; NICHD, 2000, 2006), la mise en place d’une formation continue axee sur la pratique reflexive pour les educatrices en pouponniere serait souhaitable, etant donne la complexite de leur travail. Cet article porte donc sur l’evaluation des besoins de formation chez les educatrices en pouponniere, dans le but de bonifier la qualite du processus, et s’inscrit dans la phase origine de la recherche d’une recherche-developpement inspiree du modele de Loiselle et Harvey (2009). Abstract: A Quebec survey on the quality of educational childcare services Grandir en qualite (2015a) shows that the overall quality of educational services offered to infants is considered acceptable to good, no more. The level of training and education of educators is one of the determining factors in the quality of educational childcare (Clarke-Stewart, Vandell, Burchinal, O'Brien & McCartney, 2002; Goelman, Doherty, Lero, LaGrange & Tougas, 2000; Harme & Pianta, 2001; Howes & Ritchie, 2003; NICHD, 2000, 2006) Additionally, reflexion practice-based continuing education for toddlers educators would be desirable given the complexity of their work. This articletherefore focuses on the assessment of training needs of toddler educators, with the aim of improving the quality of the process, and is part of the original phase of the search for research development inspired by Loiselle and Harvey’s model (2009).
Topology Discovery on Unicast Networks : A Hierarchical Approach Based on End-to-End Measurements

In this paper we address the problem of topology discovery in unicast logical tree networks using endto-end measurements. Without any cooperation from the internal routers, topology estimation can be formulated as hierarchical clustering of the leaf nodes based on pair-wise correlations as similarity metrics. We investigate three types of similarity metrics: queueing delay measured by sandwich probes, delay variance measured by packet pairs, and loss rate measured also by packet pairs. Unlike previous work which first assumes the network topology is a binary tree and then tries to generalize to a non-binary tree, we provide a framework which directly deals with general logical tree topologies. Based on our proposed finite mixture model for the set of similarity measurements we develop a penalized hierarchical topology likelihood that leads to a natural clustering of the leaf nodes level by level. A hierarchical algorithm to estimate the topology is developed in a similar manner by finding the best partitions of the leaf nodes. Our simulations show that the algorithm is more robust than binary-tree based methods. The three types of similarity metrics are also evaluated under various network load conditions using ns-2.
Inhibition of TNF in the Brain Reverses Alterations in RAS Components and Attenuates Angiotensin II-Induced Hypertension

Dysfunction of brain renin-angiotensin system (RAS) components is implicated in the development of hypertension. We previously showed that angiotensin (Ang) II-induced hypertension is mediated by increased production of proinflammatory cytokines (PIC), including tumor necrosis factor (TNF), in brain cardiovascular regulatory centers such as the paraventricular nucleus (PVN). Presently, we tested the hypothesis that central TNF blockade prevents dysregulation of brain RAS components and attenuates Ang II-induced hypertension. Male Sprague-Dawley rats were implanted with radio-telemetry transmitters to measure mean arterial pressure (MAP) and subjected to intracerebroventricular (ICV) infusion of etanercept (10 µg/kg/day) with/without concurrent subcutaneous 4-week Ang II (200 ng/kg/min) infusion. Chronic Ang II infusion resulted in a significant increase in MAP and cardiac hypertrophy, which was attenuated by inhibition of brain TNF with etanercept. Etanercept treatment also attenuated Ang II-induced increases in PIC and decreases in IL-10 expression in the PVN. Additionally, Ang II infusion increased expression of pro-hypertensive RAS components (ACE and AT1R), while decreasing anti-hypertensive RAS components (ACE2, Mas, and AT2 receptors), within the PVN. ICV etanercept treatment reversed these changes. Ang II-infusion was associated with increased oxidative stress as indicated by increased NAD(P)H oxidase activity and super oxide production in the PVN, which was prevented by inhibition of TNF. Moreover, brain targeted TNF blockade significantly reduced Ang II-induced NOX-2 and NOX-4 mRNA and protein expression in the PVN. These findings suggest that chronic TNF blockade in the brain protects rats against Ang II-dependent hypertension and cardiac hypertrophy by restoring the balance between pro- and anti-hypertensive RAS axes and inhibiting PIC and oxidative stress genes and proteins in the PVN.