Miracle-dz/UniFAR-FTUs huggingface dataset:
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?

Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame with “regulatory” codons, cognate to the amino acid that is synthesized by the enzymes encoded by the operon. When the amino acid is in short supply, translation of the regulatory codons is slow, which allows transcription to continue into the structural genes of the operon. When amino acid supply is in excess, translation of regulatory codons is rapid, which leads to termination of transcription. We use a discrete master equation approach to formulate a probabilistic model for the positioning of the RNA polymerase and the ribosome in the attenuator leader sequence. The model describes how the current rate of amino acid supply compared to the demand in protein synthesis (signal) determines the expression of the amino acid biosynthetic operon (response). The focus of our analysis is on the sensitivity of operon expression to a change in the amino acid supply. We show that attenuation of transcription can be hyper-sensitive for two main reasons. The first is that its response depends on the outcome of a race between two multi-step mechanisms with synchronized starts: transcription of the leader of the operon, and translation of its regulatory codons. The relative change in the probability that transcription is aborted (attenuated) can therefore be much larger than the relative change in the time it takes for the ribosome to read a regulatory codon. The second is that the general usage frequencies of codons of the type used in attenuation control are small. A small percentage decrease in the rate of supply of the controlled amino acid can therefore lead to a much larger percentage decrease in the rate of reading a regulatory codon. We show that high sensitivity further requires a particular choice of regulatory codon among several synonymous codons for the same amino acid. We demonstrate the importance of a high fraction of regulatory codons in the control region. Finally, our integrated model explains how differences in leader sequence design of the trp and his operons of Escherichia coli and Salmonella typhimurium lead to high basal expression and low sensitivity in the former case, and to large dynamic range and high sensitivity in the latter. The model clarifies how mechanistic and systems biological aspects of the attenuation mechanism contribute to its overall sensitivity. It also explains structural differences between the leader sequences of the trp and his operons in terms of their different functions.
Delay-Based Back-Pressure Scheduling in Multihop Wireless Networks

Scheduling is a critical and challenging resource allocation mechanism for multihop wireless networks. It is well known that scheduling schemes that favor links with larger queue length can achieve high throughput performance. However, these queue-length-based schemes could potentially suffer from large (even infinite) packet delays due to the well-known last packet problem, whereby packets belonging to some flows may be excessively delayed due to lack of subsequent packet arrivals. Delay-based schemes have the potential to resolve this last packet problem by scheduling the link based on the delay the packet has encountered. However, characterizing throughput optimality of these delay-based schemes has largely been an open problem in multihop wireless networks (except in limited cases where the traffic is single-hop.) In this paper, we investigate delay-based scheduling schemes for multihop traffic scenarios with fixed routes. We develop a scheduling scheme based on a new delay metric and show that the proposed scheme achieves optimal throughput performance. Furthermore, we conduct simulations to support our analytical results and show that the delay-based scheduler successfully removes excessive packet delays, while it achieves the same throughput region as the queue-length-based scheme.
Programmable ExG Biopotential Front-End IC for Wearable Applications

This paper presents a configurable CMOS integrated circuit front-end for the recording of a wide range of biopotentials (ExG). The system offers a choice between a single-differential or double-differential recording channel topology, wide continuously adjustable gain range (37-66 dB), selectable CMOS or BJT input stages, offset compensation, differential and buffered single-ended voltage output. Measured results from a prototype manufactured in 0.35 μm CMOS technology are presented. Practical recording examples of the electrocardiogram (ECG) and electromyogram (EMG) confirm its operation. The chip consumes between 110 and 324 μW depending on configuration, occupies a core area of 0.16 mm2, achieves a CMRR > 97 dB, and 21 nV/√Hz input-referred noise. The chip is suited for combination with a microcontroller in long-term wearable physiological sensing applications.
Data mining effect in peer-to-peer queries routing

Data mining has been used to extract hidden information from large databases. In peer-to-peer context, a challenging problem is how to find the appropriate peer to deal with a given query without overly consuming bandwidth? Different methods proposed routing strategies of queries taking into account the p2p network at hand. We consider an unstructured P2P system based on an organization of peers around super-peers that are connected to meta-super-peer according to their semantic domains. This paper integrates decision trees in P2P architectures for predicting Query-Suitable super-peers representing a community of peers where one among them is able to answer the given query. In fact by analyzing the queries log file, we construct a predictive model that avoids flooding queries in the p2p network by predicting the appropriate super-peer, and hence the peer to answer the query. A challenging problem in a schema-based peer-to-peer (P2P) system is how to locate peers that are relevant with respect to a given query. In this paper, we propose an architecture, based on (super-) peers, and we focus on query routing. Our approach considers that (super-) peers having similar interests are grouped together for an efficient query routing method. In such groups, called Meta-Super-Peers (MSP), super-peers submit queries that are often processed by members of this group. A MSP is a specific super-peer which contains knowledge about: 1. its super-peers and 2. The others MSP. Knowledge is extracted by using data mining techniques (e.g. decision tree algorithms) starting from queries of peers that transit on the network. The advantage of this distributed knowledge is that, it avoids making semantic mapping, between heterogeneous data sources owned by (super-)peers, each time the system decides to route query to other (super-)peers. The set of MSP improves the robustness in queries routing mechanism and scalability in P2P Network. Compared with a baseline approach, our proposal architectures show the effect of the data mining with better performance with respect to response time and precision.
Site Effects in Structural Response Predictions of Inelastic SDOF Oscillators

We study how the inelastic structural response predicted via synthetic seismograms is affected by the selection of site response models in ground motion simulations. We first generate synthetics for multiple scenarios and site conditions in Southern California using attenuation relations, site specific linear, vis-coelastic and nonlinear analyses, and estimate the ground motion variability that results from the soil model selection. We next use bilinear single degree-of-freedom oscillators to demonstrate how this variability propagates to the inelastic structural response predictions. Results show high bias and scatter of the inelastic displacement ratio predicted using the empirical and linear elastic site response models relative to the nonlinear, for periods close to the fundamental period of the site. For the synthetic motions and sites used, we derive empirical correlations between the amount of bias and period range where it manifests, and selected input motion and site parameters.
Molecular Models of Hydroxide, Oxyhydroxide, and Clay Phases and the Development of a General Force Field

The fate of chemical and radioactive wastes in the environment is related to the ability of natural phases to attenuate and immobilize contaminants through chemical sorption and precipitation processes. Our understanding of these complex processes at the atomic level is provided by a few experimental and analytical methods such as X-ray absorption and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental atomic-level understanding, interpretation, and prediction of these phenomena. In this effort, we have developed a general force field, CLAYFF, suitable for the simulation of hydrated and multicomponent mineral systems and their interfaces with aqueous solutions. Interatomic potentials were derived from parametrizations incorporating structural and spectroscopic data for a variety of simple hydrated compounds. A.
Finite Element Modeling of Vocal Fold Vibration in Normal Phonation and Hyperfunctional Dysphonia: Implications for the Pathogenesis of Vocal Nodules

A computer model of the vocal fold was developed using finite element modeling technology for studying mechanical stress distribution over vibrating vocal fold tissue. In a simulated normal phonation mode, mechanical stress was found to be lowest at the midpoint of the vocal fold and highest at tendon attachments. However, when other modes predominated, high mechanical stress could occur at the midpoint of the vocal folds. When a vocal fold mass was modeled, high shearing stress occurred at the base of the modeled vocal fold mass, suggesting that the presence of a vocal nodule or polyp is associated with high mechanical stress at the margins of the mass. This finding supports a hypothesis that mechanical intraepithelial stress plays an important role in the development of vocal nodules, polyps, and other lesions that are usually ascribed to hyperfunctional dysphonia.
Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection

Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China. Many significant trait-marker associations (P < 0.001) were detected in both association analyses. Five markers of Waxy gene, including the (CT)n repeats, the G/T SNP of intron 1, the 23 bp sequence duplication (InDel) of exon 2, the A/C SNP of exon 6, and the C/T SNP of exon 10, were found to be primarily associated with starch traits related to apparent amylose content (AAC), and two markers targeting the 4,329–4,330 bp GC/TT SNPs and 4,198 bp G/A SNP of SSIIa gene were mainly associated with traits related to gelatinization temperature (GT). Two new haplotypes were found in the mini-core collection based on the combinations of the 23 bp InDel and three SNPs (G/T of intron 1, A/C of exon 6, and C/T of exon 10) of Waxy gene. Furthermore, our analyses indicated that the (CT)n polymorphisms of Waxy gene had a non-negligible effect on AAC related traits, as evidenced by significant variation in AAC related traits among rice accessions with the same Waxy SNPs but different (CT)n repeats. As the five Waxy markers and the two SSIIa markers showed consistent major effects on starch quality traits across studies, these markers should have priority for utilization in marker-assisted breeding.
Inductively Coupled Coils for Local SNR-Enhancement during MR-guided Prostate Biopsy

Introduction It has been shown that both MRI and MRS can improve specificity in the detection of prostate cancer [1]. During MR-guided prostate biopsies suspect prostate areas can be identified on T2w MR images, and MRS metabolic information can further help to decide from which areas biopsy samples need to be harvested. Since the quality of MR data crucially depends on the local signal-to-noise ratio (SNR), typically local endorectal coils are utilized. To harvest the biopsy samples a commercial needle holder with a passive marker is available, which completely fills the available space in the rectum, and the integration of an endorectal coil becomes difficult. Inductively coupled rf coils with no direct connection to the MR system can be realized with significantly smaller space requirements, and usage of the coils is greatly simplified. We therefore examined two inductively coupled coil designs for possible integration into the commercial biopsy system to improve the local SNR at or near the biopsy sample area.
System-level Synthesis Of Low-power Hard Real-time Systems

We present a system-level approach for power optimization undera set of user specified costs and timing constraints of hard real-timedesigns. The approach optimizes all three degrees of freedom forpower minimization, namely switching activity, effective capacityand voltage supply.We first define two key associated optimization problems, processorallocation and task assignment, and establish their computationalcomplexity. Efficient algorithms are developed for bothsystem design problems. The statistical analysis of comprehensiveexperimental results and their comparison with the developed conservativeand optimistic sharp lower bounds, clearly indicates thequality of the proposed optimization techniques.
Activity in the Primate Rostral Superior Colliculus during the “Gap Effect” for Pursuit and Saccades

The latencies of both pursuit and saccadic eye movements are reduced when a fixated visual target is extinguished several hundred milliseconds before a new target appears. 1–6 One possible neural substrate for this “gap effect” is the rostral superior colliculus (SC), which has recently been shown to participate in pursuit eye movements, in addition to its established role in the control of saccades. The discharge rate of buildup neurons in the rostral SC (rSC) is related to the retinal position of targets during pursuit, as well as during the preparation and execution of saccades. 7,8 In addition, microstimulation of the rSC disrupts the initiation of both types of eye movements. 9 To test whether these rostral buildup neurons could underlie the “gap effect,” we have now studied their activity with this paradigm during both pursuit and saccades. Monkeys tracked a target stimulus that appeared either immediately after the offset of the fixation spot (no-gap trials) or 200 msec after the offset of the fixation spot (gap trials). On saccade trials, the target stimulus was stationary and was presented at an eccentricity of 3.5 o along the horizontal meridian. On pursuit trials, the target stimulus appeared at an eccentricity of 2 o and moved toward the center of the display at 15 o /sec. We adjusted the starting position of the stimulus to produce saccadefree pursuit and chose neurons with appropriate response fields. We identified the neurons in our sample (n = 72) as rostral buildup neurons on the basis of criteria described previously. 7 The activity of most rostral buildup neurons showed a “gap effect” for both pursuit and saccades. For example, on no-gap trials, the firing rate of the neuron illustrated in FIGURE 1 remained nearly constant at 25 spikes/sec until 50–100 msec after target onset, at which point the firing rate increased to more than 100 spikes/sec. However, on gap trials, the firing rate of this neuron increased after the offset of the fixation spot, reaching a firing rate of 40–50 spikes/sec. These changes in activity
A clearer view of the insect brain—combining bleaching with standard whole-mount immunocytochemistry allows confocal imaging of pigment-covered brain areas for 3D reconstruction

In the study of insect neuroanatomy, three-dimensional (3D) reconstructions of neurons and neuropils have become a standard technique. As images have to be obtained from whole-mount brain preparations, pigmentation on the brain surface poses a serious challenge to imaging. In insects, this is a major problematic in the first visual neuropil of the optic lobe, the lamina, which is obstructed by the pigment of the retina as well as by the pigmented fenestration layer. This has prevented inclusion of this major processing center of the insect visual system into most neuroanatomical brain atlases and hinders imaging of neurons within the lamina by confocal microscopy. It has recently been shown that hydrogen peroxide bleaching is compatible with immunohistochemical labeling in insect brains, and we therefore developed a simple technique for removal of pigments on the surface of insect brains by chemical bleaching. We show that our technique enables imaging of the pigment-obstructed regions of insect brains when combined with standard protocols for both anti-synapsin-labeled as well as neurobiotin-injected samples. This method can be combined with different fixation procedures, as well as different fluorophore excitation wavelengths without negative effects on staining quality. It can therefore serve as an effective addition to most standard histology protocols used in insect neuroanatomy.
ClubMED: Coordinated Multi-Exit Discriminator Strategies for Peering Carriers

Inter-domain peering links represent nowadays the real bottleneck of the Internet. On peering links carriers may coordinate to efficiently balance the load, but the current practice is often based on an uncoordinated selfish routing supported by the peer relationship. We present a novel game theoretical routing framework to efficiently coordinate the routing on peering links while modelling the non-cooperative carrier behaviour. It relies on a collaborative use of the Multi-Exit Discriminator (MED) attribute of BGP, hence it is nicknamed ClubMED (Coordinated MED). The incentives are the minimization of carrier routing costs, the control of peering link congestions and peering route stability. For the ClubMED game, we define the Nash Equilibrium Multi-Path (NEMP) routing policy that shall be implemented upon Nash equilibria and Pareto-efficient profiles. Intra-domain Interior Gateway Protocol (IGP) weight optimizations are consistently integrated into the framework. We emulated the peering settlement between the Internet2 and the Geant2 networks, employing real datasets, comparing the ClubMED results to the current BGP practice. The results show that the global routing cost can be reduced of roughly 17%, that the peering link congestion can be avoided and that the stability of the routes can significantly be reinforced.
Changes in Deep Water Oxygenation of the South China Sea Since the Last Glacial Period

The Pacific meridional overturning circulation is thought to have a significant influence on global climate. However, the extent to which intermediate and deep circulations have changed in the Pacific Ocean since the Last Glacial Maximum (LGM) is not well known. At present, the South China Sea Deep Water (SCSDW) is fed by the upper Pacific Deep Water. Here we present new benthic foraminiferal δ13C and redox‐sensitive elemental data from a sediment core retrieved from the southern deep SCS to reconstruct the oxygenation history of the SCSDW since the LGM. Oxygenation records from the deep SCS and intermediate and deep waters in the Pacific Ocean demonstrate that the SCSDW deeper than 1,600 m has been sourced by the Pacific Deep Water since the LGM. Our data suggest that the well‐ventilated North Pacific Intermediate Water would not have influenced the SCSDW during cold stadials of the last deglacial period.
Approximation of Distances and Shortest Paths in the Broadcast Congest Clique

We study the broadcast version of the CONGEST CLIQUE model of distributed computing. In this model, in each round, any node in a network of size $n$ can send the same message (i.e. broadcast a message) of limited size to every other node in the network. Nanongkai presented in [STOC'14] a randomized $(2+o(1))$-approximation algorithm to compute all pairs shortest paths (APSP) in time $\tilde{O}(\sqrt{n})$ on weighted graphs, where we use the convention that $\tilde{\Omega}(f(n))$ is essentially $\Omega(f(n)/$polylog$f(n))$ and $\tilde{O}(f(n))$ is essentially $O(f(n) $polylog$f(n))$. We complement this result by proving that any randomized $(2-o(1))$-approximation of APSP and $(2-o(1))$-approximation of the diameter of a graph takes $\tilde\Omega(n)$ time in the worst case. This demonstrates that getting a negligible improvement in the approximation factor requires significantly more time. Furthermore this bound implies that already computing a $(2-o(1))$-approximation of all pairs shortest paths is among the hardest graph-problems in the broadcast-version of the CONGEST CLIQUE model and contrasts a recent $(1+o(1))$-approximation for APSP that runs in time $O(n^{0.15715})$ in the unicast version of the CONGEST CLIQUE model. On the positive side we provide a deterministic version of Nanongkai's $(2+o(1))$-approximation algorithm for APSP. To do so we present a fast deterministic construction of small hitting sets. We also show how to replace another randomized part within Nanongkai's algorithm with a deterministic source-detection algorithm designed for the CONGEST model presented by Lenzen and Peleg at PODC'13.
Spectral Analysis and Long-Time Behaviour of a Fokker-Planck Equation with a Non-Local Perturbation

In this article we consider a Fokker-Planck equation with a non-local, mass preserving perturbation. We show that the perturbed Fokker-Planck operator generates a $C_0$-semigroup on an exponentially weighted $L^2$-space. Surprisingly, the spectrum of the Fokker-Planck operator is not affected by the perturbation. In particular there still exists a unique (normalized) stationary solution of the perturbed equation. And we have convergence towards the stationary state with exponential rate -1, the same rate as for the unperturbed Fokker-Planck equation. Moreover, for any $k\in\mathbb N$ there exists an invariant subspace with finite codimension in which the exponential decay rate equals $-k$. As a byproduct of our analysis we characterize the spectrum of the Fokker-Planck operator in $L^2$-spaces with exponential weights.