Miracle-dz/UniFAR-FTUs huggingface dataset:
Insertional activation of cepA leads to high-level beta-lactamase expression in Bacteroides fragilis clinical isolates

Bacteroides fragilis is an important opportunistic pathogen of humans and is resistant to many drugs commonly used to treat anaerobic infections, including beta-lactams. A strain set comprised of B. fragilis isolates producing either low or high levels of the endogenous cephalosporinase activity, CepA, has been described previously (M. B. Rogers, A. C. Parker, and C. J. Smith, Antimicrob. Agents Chemother. 37:2391-2400, 1993). Clones containing cepA genes from each of seven representative strains were isolated, and the DNA sequences were determined. Nucleotide sequence comparisons revealed that there were few differences between the cepA coding sequences of the low- and high-activity strains. The cepA coding sequences were cloned into an expression vector, pFD340, and analyzed in a B. fragilis 638 cepA mutant. The results of beta-lactamase assays and ampicillin MICs showed that there was no significant difference in the enzymatic activity of structural genes from the high- or low-activity strains. Comparison of sequences upstream of the cepA coding region revealed that 50 bp prior to the translation start codon, the sequence for high-activity strains change dramatically. This region of the high-activity strains shared extensive homology with IS21, suggesting that an insertion was responsible for the increased expression of cepA in these isolates. Northern (RNA) blot analysis of total RNA by using cepA-specific DNA probes supported the idea that differential cepA expression in low- and high-activity strains was controlled at the level of transcription. However, the insertion did not alter the cepA transcription start site, which occurred 27 bp upstream of the ATG translation start codon in both expression classes. Possible mechanisms of cepA activation are discussed.
Implementing a model-based design and test workflow

A model-based design workflow for embedded control systems can accelerate product development, improve performance, increase reliability, and reduce engineering cost. Several current technology trends are driving engineering organizations to establish model-based workflows that enable concurrent and collaborative engineering. In this way, embedded controls engineers can quickly develop reliable products of the highest performance. This paper discusses trends in automotive embedded controls and explains the use of model-based engineering workflows to accelerate embedded controls development. These trends include: platform-based requirements, systems/HW/SW codesign, agile methods, rapid prototyping needs, growing software content, integrated data systems, greater system complexity, and growing engineering needs. A model-based design workflow improves product development processes in the current engineering paradigm. Methods to accelerate development of model-based controls through the V cycle are described. Unconstrained prototyping with constrained design is shown as an effective means to converge on an implementation. Pros and cons of product development processes are contrasted. Model-based workflows provide a framework for controls engineers to incrementally create requirements, evaluate algorithms, develop architectures, coordinate designs, and facilitate requirements-based systems verification and validation testing. A framework that integrates requirements and testing improves system reliability and reduces development risks. Industry standards, such as ISO26262 and DO-178C, enforce such a framework. Tools and technologies that can be used to support modelbased development from functional requirements to automated testing are outlined. Readers gain an understanding of how to establish and deploy a model-based design workflow into their organizations to effectively and efficiently manage the development lifecycle of embedded controls.
The Ability of a Novel Algorithm for Automatic Estimation of the Respiratory Variations in Arterial Pulse Pressure to Monitor Fluid Responsiveness in the Operating Room

BACKGROUND: Respiratory variations in arterial pulse pressure (&Dgr;PPman) are accurate predictors of fluid responsiveness in mechanically ventilated patients. However, they cannot be continuously monitored. In our study, we assessed the clinical utility of a novel algorithm for automatic estimation of &Dgr;PP (&Dgr;PPauto). METHODS: We studied 25 patients referred for coronary artery bypass grafting. &Dgr;PPauto was continuously displayed using a method based on automatic detection algorithms, kernel smoothing, and rank-order filters. All patients were under general anesthesia, mechanical ventilation, and were also monitored with a pulmonary artery catheter. &Dgr;PPman and &Dgr;PPauto were recorded simultaneously at eight steps during surgery including before and after intravascular volume expansion (500 mL hetastarch). Responders to volume expansion were defined as patients whose cardiac index increased by more than 15% after volume expansion. RESULTS: Agreement between &Dgr;PPman and &Dgr;PPauto over the 200 pairs of collected data was 0.7% ± 3.4% (mean bias ± sd). Seventeen patients were responders to volume expansion. A threshold &Dgr;PPman value of 12% allowed discrimination of responders to volume expansion with a sensitivity of 88% and a specificity of 100%. A threshold &Dgr;PPauto value of 10% allowed discrimination of responders to volume expansion with a sensitivity of 82% and a specificity of 88%. CONCLUSION: &Dgr;PPauto is strongly correlated to &Dgr;PPman is an accurate predictor of fluid responsiveness, and allows continuous monitoring of &Dgr;PP. This novel algorithm has potential clinical applications.
Iron–sulfur cluster biogenesis and trafficking in mitochondria

The biogenesis of iron–sulfur (Fe/S) proteins in eukaryotes is a multistage, multicompartment process that is essential for a broad range of cellular functions, including genome maintenance, protein translation, energy conversion, and the antiviral response. Genetic and cell biological studies over almost 2 decades have revealed some 30 proteins involved in the synthesis of cellular [2Fe-2S] and [4Fe-4S] clusters and their incorporation into numerous apoproteins. Mechanistic aspects of Fe/S protein biogenesis continue to be elucidated by biochemical and ultrastructural investigations. Here, we review recent developments in the pursuit of constructing a comprehensive model of Fe/S protein assembly in the mitochondrion.
An innovative prostheses design for rehabilitation of severely mutilated dentition: a case report

Partial edentulism has multiple implications in relation to function, esthetics and future rehabilitative treatment. This case report illustrates the management of a patient with extreme consequences of partial edentulism. The main clinical findings were unopposed remaining teeth, overeruption of the remaining teeth, loss of vertical dimension of occlusion, and significant disfigurement of the occlusal plane. Following the diagnostic procedure, a well-coordinated prosthodontic treatment involving liaison with other dental disciplines was indicated. The management involved an innovative combination of fixed and removable prostheses in conjunction with crown lengthening surgery and strategic implant placement. Series of provisional prostheses were applied to facilitate the transition to the final treatment.
New Constraints on Additional Satellites of the Pluto System

Observations of Pluto and its solar-tidal stability zone were made using the Advanced Camera for Surveys (ACS) Wide Field Channel (WFC) on the Hubble Space Telescope on UT 2005 May 15 and May 18. Two small satellites of Pluto, provisionally designated S/2005 P1 and S/2005 P2, were discovered, as discussed by Weaver et al. and Stern et al. Confirming observations of the newly discovered moons were obtained using the ACS in the High Resolution Channel (HRC) mode on 2006 February 15 (Mutchler et al.). Both sets of observations provide strong constraints on the existence of any additional satellites in the Pluto system. Based on the 2005 May observations using the ACS WFC, we place a 90% confidence lower limit of mV = 26.8 (mV = 27.4 for a 50% confidence lower limit) on the magnitude of undiscovered satellites greater than 5″ (1.1 × 105 km) from Pluto. Using the 2005 February 15 ACS HRC observations we place 90% confidence lower limits on the apparent magnitude of any additional satellites of mV = 26.4 between 3″ and 5″ (6.9 × 104-1.1 × 105 km) from Pluto, mV = 25.7 between 1″ and 3″ (2.3 × 104-6.9 × 104 km) from Pluto, and mV = 24 between 0. ″3 and 1″ (6.9 × 103-2.3 × 104 km) from Pluto. The 90% confidence magnitude limits translate into upper limits on the diameters of undiscovered satellites of 29 km outside of 5″ from Pluto, 36 km between 3″ and 5″ from Pluto, 49 km between 1″ and 3″ from Pluto, and 115 km between 0. ″3 and 1″ for a comet-like albedo of pV = 0.04. If potential satellites are assumed to have a Charon-like albedo of pV = 0.38, the diameter limits are 9, 12, 16, and 37 km, respectively.
Facilitating Lifetime Creative Processes—A Think Piece

There can be at least two &dquo;Golden Ages&dquo; in a lifetime: one the Golden Age of Youth; the second Golden Age can be the one of retirement, which is based upon a wealth of experience and a wealth of freedom and of time to think and to create. The American Medical Association has indicated that the American population is shifting towards the older age groups as the World War II baby boom cohorts move into their forties. The society has responded by postponing the age of mandatory retirement to 70. With the increase in life expectancy, Americans face years of non-job-centered existence in a work-and-consumer-oriented society. If older Americans lose the supervision, sense of community, and opportunity for self-fulfillment that a job provides, what inner resources can they mobilize in order to achieve the internal integration of personality that Ericson characterizes as the touchstone of maturity and self-sufficiency? Young persons who interact with gifted and talented teachers team to turn on their creative processes, and it is likely that they will become so habituated to creative thinking and living that they will use their creative processes throughout their entire life-an extreme example of this lifelong creativity was Picasso who focused a long and productive life on almost continually creating. However, if the creative potentials of young persons are neither challenged
ZooBP: Belief Propagation for Heterogeneous Networks

Given a heterogeneous network, with nodes of different types - e.g., products, users and sellers from an online recommendation site like Amazon - and labels for a few nodes ('honest', 'suspicious', etc), can we find a closed formula for Belief Propagation (BP), exact or approximate? Can we say whether it will converge? BP, traditionally an inference algorithm for graphical models, exploits so-called "network effects" to perform graph classification tasks when labels for a subset of nodes are provided; and it has been successful in numerous settings like fraudulent entity detection in online retailers and classification in social networks. However, it does not have a closed-form nor does it provide convergence guarantees in general. We propose ZooBP, a method to perform fast BP on undirected heterogeneous graphs with provable convergence guarantees. ZooBP has the following advantages: (1) Generality: It works on heterogeneous graphs with multiple types of nodes and edges; (2) Closed-form solution: ZooBP gives a closed-form solution as well as convergence guarantees; (3) Scalability: ZooBP is linear on the graph size and is up to 600× faster than BP, running on graphs with 3.3 million edges in a few seconds. (4) Effectiveness: Applied on real data (a Flipkart e-commerce network with users, products and sellers), ZooBP identifies fraudulent users with a near-perfect precision of 92.3 % over the top 300 results.
Hydroxyethyl starch–based preservation solutions enhance gene therapy vector delivery under hypothermic conditions

Isolated liver perfusion offers a unique prospect for safe, effective targeting of gene therapies that can be directed against allograft rejection or recurrent diseases such as reinfection by hepatitis C virus (HCV). We aimed to examine the effect of organ preservation solutions on vector‐based gene therapy delivery under hypothermic conditions. University of Wisconsin (UW) solution, histidine tryptophan ketoglutarate (HTK), EloHaes, sodium‐poly(ethylene glycol)‐UW solution [Institut Georges Lopez 1 solution (IGL‐1)], and Dulbecco's modified Eagle's medium (DMEM) culture medium (control) were tested at 2°C or 37°C for lentiviral vector transduction efficiencies to the hepatoma cell line Huh‐7 and primary human or mouse hepatocytes. Lentiviral vectors expressing short hairpin RNA were used to target HCV replication. With a potent short hairpin RNA vector, transductions were directly correlated to the therapeutic effect, with low transduction yielding low knockdown and vice versa. Green fluorescent protein (GFP) reporter gene expression was observed with vector incubation times as short as 10 minutes. The highest transductions were seen, after 2‐hour 37°C incubation, in UW (62% ± 6 SEM); they were significantly higher than those in HTK (21% ± 7 SEM). Neither adenosine nor glutathione, present in UW, provided any increase in transduction when supplemented to HTK, although the addition of hydroxyethyl starch (HES) significantly improved transductions. To rule out size exclusion as a mechanism of HES, IGL‐1 was tested but did not result in better transductions than HTK or DMEM. When supplemented to UW, anionic compounds reduced transduction, and this indicated a charge interaction mechanism of HES. In conclusion, this study demonstrates that effective vector delivery can be achieved under conditions of hypothermic liver perfusion. UW provides superior transduction to hepatocytes over nonstarch solutions. Liver Transpl 14:1708–1717, 2008. © 2008 AASLD.
Identifying Optimal Attributes in 3D Interface DevicesSite

We measured the precision and ease of use of three separate interface devices designed to be operated in 3D space, specifically with 3D environments and tasks. A gyroscopic, handheld mouse, a finger mounted gyroscopic mouse and a wired glove accompanied with a Microsoft Kinect were used to see which attributes of the devices were most important in their use. Results found interfaces with the closest analogue to typical computer usage performed the best, with participants commenting mainly on the importance of precision and accuracy over the 'naturalness' or appropriateness of the style of interface. We conclude that usability factors and maximizing user effectiveness in an environment far outweigh UX concerns of immersion or closeness to interface paradigm.
We Are Not All the Same: Arab and Muslim Students Forging Their Own Campus Communities in a Post-9/11 America

Abstract The study investigates Arab and Muslim students’ social relationships on 21 community college campuses in the USA (N = 753), with comparison groups of African Americans, Latinos, Asians, and Whites (N = 567). Survey findings revealed a positive relationship between campus friendships and sense of belonging, controlling for ethnic and religious identities, and perceived discrimination on campus. Individual group differences were found among Arab Christians, Arab Muslims, and non-Arab Muslims, and the comparison group. As an earlier publication based on the same study revealed, 75% of Arab and Muslim students’ campus friendships were either same ethnic and/or same faith, with only a quarter of campus friendships being of different ethnicity and different religion. Although such results suggest the existence of ethno-religious enclaves, this paper concludes that Arab and Muslim students are not purposely enacting their own ethno-religious balkanization, but—like other ethnic groups—forging their own campus communities within the larger campus community.
Actuator With Angle-Dependent Elasticity for Biomimetic Transfemoral Prostheses

Despite tremendous improvements in recent years, lower-limb prostheses are still inferior to their biological counterparts. Most powered knee joints use impedance control, but it is unknown which impedance profiles are needed to replicate physiological behavior. Recently, we have developed a method to quantify such profiles from conventional gait data. Based on this method, we derive stiffness requirements for knee prostheses, and we propose an actuation concept where physical actuator stiffness changes in function of joint angle. The idea is to express stiffness and moment requirements as functions of angle, and then to combine a series elastic actuator (SEA) with an optimized nonlinear transmission and parallel springs to reproduce the profiles. By considering the angle-dependent stiffness requirement, the upper bound for the impedance in zero-force control could be reduced by a factor of two. We realize this ANGle-dependent ELAstic Actuator (ANGELAA) in a leg, with rubber cords as series elastic elements. Hysteresis in the rubber is accounted for, and knee moment is estimated with a mean error of 0.7 Nm. The nonlinear parallel elasticity creates equilibria near 0° as well as 90° knee flexion, frequent postures in daily life. Experimental evaluation in a test setup shows force control bandwidth around 5-9 Hz, and a pilot experiment with an amputee subject shows the feasibility of the approach. While weight and power consumption are not optimized in this prototype, the incorporated mechatronic principles may pave the way for cheaper and lighter actuators in artificial legs and in other applications where stiffness requirements depend on kinematic configuration.
Order constraints for single machine scheduling with non-linear cost

Typically in a scheduling problem we are given jobs of different processing times pj and different priority weights wj, and need to schedule them on a single machine in order to minimize a specific cost function. In this paper we consider the non-linear objective function ΣwjCβj, where Cj is the completion time of job j and β > 0 is some arbitrary real constant. Except for β = 1 the complexity status of this problem is open. Past research mainly focused on the quadratic case (β = 2) and proposed different techniques to speed up exact algorithms. This paper proposes new pruning rules and generalizations of existing rules to non-integral β. An experimental study evaluates the impact of the proposed rules on the exact algorithm A*
A Defense of Publishing Nonsignificant (ns) Results

An argument is advanced for the propositions that a lack of statistically significant findings does not automatically justify rejecting a scientific article for publication or mean that the findings are necessarily uninformative. Systematically declining publication for nonsignificant results leads to negative consequences that include distorting scientific literatures, making hypotheses and theories less falsifiable, depriving meta-analyses of an accurate sample of prior findings, and encouraging questionable research practices. Providing effect sizes and confidence intervals can make findings more informative, regardless of whether the finding is p < . 05.
Duality of large N Yang-Mills Theory on T 2 × R n .

We find aspects of electrically confining large N Yang-Mills theories on T 2 × R d−2 which are consistent with a GL(2, Z) duality. The modular parameter associated with this GL(2, Z) is given by m N + iΛ 2 A, where A is the area of the torus, m is the t'Hooft twist on the torus, and Λ 2 is the string tension. N is taken to infinity keeping m N and g 2 N fixed. This duality may be interpreted as T-duality of the QCD string if one identifies the magnetic flux with a two-form background in the string theory. Our arguments make no use of supersymmetry. While we are not able to show that this is an exact self duality of conventional QCD, we conjecture that it may be applicable within the universality class of QCD. We discuss the status of the conjecture for the soluble case of pure two dimensional Euclidean QCD on T 2 , which is almost but not exactly self dual. For higher dimensional theories, we discuss qualitative features consistent with duality. For m = 0, such a duality would lead to an equivalence between pure QCD on R 4 and QCD on R 2 with two adjoint scalars. When Λ 2 A << m 2 /N 2 , the proposed duality includes exchanges of rank with twist. This exchange bears some resemblance, but is not equivalent, to Nahm duality. A proposal for an explicit perturbative map which implements duality in this limit is discussed.
Growth and band-gap modulation in single-crystalline Si1-xGex nanowires for nanophotonics applications

We report growth of single crystalline Si1-xGex nanowires, whose relative composition is controllably tuned over the entire composition range by Au-catalyst assisted chemical vapor syntheses. We also present experimental demonstration of the band-gap modulation from near infrared to ultraviolet regions with alloying of Si and Ge, and their spatial confinement at the nanometer scale. Our finding demonstrates that the energy band-gap of Si1-xGex nanowires can be modulated in a wider energy range, and suggests implications for group IV semiconductor nanophotonics.
Classification of states of bi-stable oscillator using deep learning

Study of critical transitions and early warning measures are of great importance for dealing with any complex system. Manually selected statistical features with handpicked parameters have been used in a wide variety of fields for this purpose. We envision the use of deep learning architectures like simple feed forward networks (FFN), convolutional neural networks (CNN) and long short-term memory networks (LSTM) to predict these critical transitions from raw time-series data obtained from complex systems with minimal human interference in parameter choosing. As a first step towards this goal, in this study we use the above mentioned deep learning architectures to classify the states of a modified Van der Pol oscillator. We observe that the deep learning architectures produce good classification results and show promise as a tool for detection of critical transitions from raw time-series data.
An allelic series reveals essential roles for FY in plant development in addition to flowering-time control

The autonomous pathway functions to promote flowering in Arabidopsis by limiting the accumulation of the floral repressor FLOWERING LOCUS C (FLC). Within this pathway FCA is a plant-specific, nuclear RNA-binding protein, which interacts with FY, a highly conserved eukaryotic polyadenylation factor. FCA and FY function to control polyadenylation site choice during processing of the FCA transcript. Null mutations in the yeast FY homologue Pfs2p are lethal. This raises the question as to whether these essential RNA processing functions are conserved in plants. Characterisation of an allelic series of fy mutations reveals that null alleles are embryo lethal. Furthermore, silencing of FY, but not FCA, is deleterious to growth in Nicotiana. The late-flowering fy alleles are hypomorphic and indicate a requirement for both intact FY WD repeats and the C-terminal domain in repression of FLC. The FY C-terminal domain binds FCA and in vitro assays demonstrate a requirement for both C-terminal FY-PPLPP repeats during this interaction. The expression domain of FY supports its roles in essential and flowering-time functions. Hence, FY may mediate both regulated and constitutive RNA 3′-end processing.