Top Loop Research Articles

Flow field characteristic in a novel cyclone-granular bed coupled separator

The three-dimensional flow field in a novel cyclone-granular bed coupled separator was discussed experimentally with a five-hole probe system. The airflow behaviors in the annular space, separation space, and central outlet were addressed. Several significant phenomena (the squeezing effect, the top flow loop, and the rectification effect) were observed and analyzed. By comparing the three-dimensional velocity distribution in the coupled separator with different structure parameters (the coupling space index, rc=0.37/0.44), the combined effect between the two efficient gas purifiers was demonstrated and the importance of the tangential velocity was clarified. For this purpose, the equations for the tangential velocity at four circumferential positions were fitted using regression analysis with a wide array of experimental data and effectively characterized prior experimental outcomes.

Molecular basis of TMPRSS2 recognition by Paeniclostridium sordellii hemorrhagic toxin

Hemorrhagic toxin (TcsH) is a major virulence factor produced by Paeniclostridium sordellii, which is a non-negligible threat to women undergoing childbirth or abortions. Recently, Transmembrane Serine Protease 2 (TMPRSS2) was identified as a host receptor of TcsH. Here, we show the cryo-EM structures of the TcsH-TMPRSS2 complex and uncover that TcsH binds to the serine protease domain (SPD) of TMPRSS2 through the CROP unit-VI. This receptor binding mode is unique among LCTs. Five top surface loops of TMPRSS2SPD, which also determine the protease substrate specificity, constitute the structural determinants recognized by TcsH. The binding of TcsH inhibits the proteolytic activity of TMPRSS2, whereas its implication in disease manifestations remains unclear. We further show that mutations selectively disrupting TMPRSS2-binding reduce TcsH toxicity in the intestinal epithelium of the female mice. These findings together shed light on the distinct molecular basis of TcsH-TMPRSS2 interactions, which expands our knowledge of host recognition mechanisms employed by LCTs and provides novel targets for developing therapeutics against P. sordellii infections.

Probing the role of the C2F domain of otoferlin.

Afferent synapses of cochlear inner hair cells (IHCs) employ a unique molecular machinery. Otoferlin is a key player in this machinery, and its genetic defects cause human auditory synaptopathy. We employed site-directed mutagenesis in mice to investigate the role of Ca2+ binding to the C2F domain of otoferlin. Substituting two aspartate residues of the C2F top loops, which are thought to coordinate Ca2+-ions, by alanines (OtofD1841/1842A) abolished Ca2+-influx-triggered IHC exocytosis and synchronous signaling in the auditory pathway despite substantial expression (~60%) of the mutant otoferlin in the basolateral IHC pole. Ca2+ influx of IHCs and their resting membrane capacitance, reflecting IHC size, as well as the number of IHC synapses were maintained. The mutant otoferlin showed a strong apex-to-base abundance gradient in IHCs, suggesting impaired protein targeting. Our results indicate a role of the C2F domain in otoferlin targeting and of Ca2+ binding by the C2F domain for IHC exocytosis and hearing.

Variable eIF4E-binding sites and their synergistic effect on cap-independent translation in a novel IRES of wheat yellow mosaic virus RNA2 isolates

Some viral proteins are translated cap-independently via the internal ribosome entry site (IRES), which maintains conservative characteristic among different isolates of the same virus species. However, IRES activity showed a 7-fold variance in RNA2 of wheat yellow mosaic virus (WYMV) HC and LYJN isolates in this study. Based on RNA structure probing and mutagenesis assay, the loosened middle stem of H1 and the hepta-nucleotide top loop of H2 in the LYJN isolate synergistically ensured higher IRES activity than that in the HC isolate. In addition, the conserved top loop of H1 ensured basic IRES activity in HC and LYJN isolates. WYMV RNA2 5′-UTR specifically interacted with the wheat eIF4E, accomplished by the top loop of H1 in the HC isolate or the top loop of H1 and H2 in the LYJN isolate. The high IRES activity of the WYMV RNA2 LYJN isolate was regulated by two eIF4E-binding sites, which showed a synergistic effect mediated by the proximity of the H1 and H2 top loops owing to the flexibility of the middle stem in H1. This report presents a novel evolution pattern of IRES, which altered the number of eIF4E-binding sites to regulate IRES activity.

Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids.

Antimicrobial resistance is a persistent challenge in human and veterinary medicine, which is often encoded on plasmids which are transmissible between bacterial cells. Incompatibility is the inability of two plasmids to be stably maintained in one cell which is caused by the presence of identical or closely related shared determinants between two plasmids originating from partition or replication mechanisms. For I-complex plasmids in Enterobacteriacae, replication- based incompatibility is caused by the small antisense RNA stem-loop structure called RNAI. The I-complex plasmid group IncK consists of two compatible subgroups, IncK1 and IncK2, for which the RNAI differs only by five nucleotides. In this study we focussed on the interaction of the IncK1 and IncK2 RNAI structures by constructing minireplicons containing the replication region of IncK1 or IncK2 plasmids coupled with a kanamycin resistance marker. Using minireplicons excludes involvement of incompatibility mechanisms other than RNAI. Additionally, we performed single nucleotide mutagenesis targeting the five nucleotides that differ between the IncK1 and IncK2 RNAI sequences of these minireplicons. The obtained results show that a single nucleotide change in the RNAI structure is responsible for the compatible phenotype of IncK1 with IncK2 plasmids. Only nucleotides in the RNAI top loop and interior loop have an effect on minireplicon incompatibility with wild type plasmids, while mutations in the stem of the RNAI structure had no significant effect on incompatibility. Understanding the molecular basis of incompatibility is relevant for future in silico predictions of plasmid incompatibility.

Two-loop bottom mass effects on the Higgs transverse momentum spectrum in top-induced gluon fusion

We compute bottom mass (mb) corrections to the transverse momentum (qT) spectrum of Higgs bosons produced by gluon fusion in the regime qT ∼ mb ≪ mH at leading power in mb/mH and qT/mH, where the gluons couple to the Higgs via a top loop. To this end we calculate the quark mass dependence of the transverse momentum dependent gluon beam functions (aka gluon TMDPDFs) at two loops in the framework of SCET. These functions represent the collinear matrix elements in the factorized gluon-fusion cross section for small qT. We discuss in detail technical subtleties regarding rapidity regulators and zero-bin subtractions in the calculation of the virtual corrections present for massive quarks. Combined with the known soft function for mb ≠ 0 our results allow to determine the resummed Higgs qT distribution in the top-induced gluon fusion channel at NNLL′ (and eventually N3LL) with full dependence on mb/qT. We perform a first phenomenological analysis at fixed order, where the new corrections to the massless approximation lead to percent-level effects in the peak region of the Higgs qT spectrum. Upon resummation they may thus be relevant for state-of-the-art precision predictions for the LHC.

Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids

Antimicrobial resistance is a persistent challenge in human and veterinary medicine, which is often encoded on plasmids which are transmissible between bacterial cells. Incompatibility is the inability of two plasmids to be stably maintained in one cell which is caused by the presence of identical or closely related shared determinants between two plasmids originating from partition or replication mechanisms. For I-complex plasmids in Enterobacteriacae, replication- based incompatibility is caused by the small antisense RNA stem-loop structure called RNAI. The I-complex plasmid group IncK consists of two compatible subgroups, IncK1 and IncK2, for which the RNAI differs only by five nucleotides. In this study we focussed on the interaction of the IncK1 and IncK2 RNAI structures by constructing minireplicons containing the replication region of IncK1 or IncK2 plasmids coupled with a kanamycin resistance marker. Using minireplicons excludes involvement of incompatibility mechanisms other than RNAI. Additionally, we performed single nucleotide mutagenesis targeting the five nucleotides that differ between the IncK1 and IncK2 RNAI sequences of these minireplicons. The obtained results show that a single nucleotide change in the RNAI structure is responsible for the compatible phenotype of IncK1 with IncK2 plasmids. Only nucleotides in the RNAI top loop and interior loop have an effect on minireplicon incompatibility with wild type plasmids, while mutations in the stem of the RNAI structure had no significant effect on incompatibility. Understanding the molecular basis of incompatibility is relevant for future in silico predictions of plasmid incompatibility.

How relevant are top loops in VBS at the LHC?

We present the contributions to the imaginary part of the W+W− elastic scattering from top and bottom quark one-loop diagrams. The computation is performed within the context of HEFT, where we compare them with the boson-loop corrections. We argue that the often neglected (top and bottom) fermion contributions may in fact be relevant.

Top-Yukawa-induced corrections to Higgs pair production

Higgs-boson pair production at hadron colliders is dominantly mediated by the loop-induced gluon-fusion process gg → HH that is generated by heavy top loops within the Standard Model with a minor per-cent level contamination of bottom-loop contributions. The QCD corrections turn out to be large for this process. In this note, we derive the top-Yukawa-induced part of the electroweak corrections to this process and discuss their relation to an effective trilinear Higgs coupling with integrated out top-quark contributions.

Binding of Ca2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study

SummaryC2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins.

An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA.

The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.

Distributed Control Strategy with Smith's Predictor in a Pilot‐Scale Diabatic Distillation Unit

AbstractIntrinsic characteristics of distillation such as dead time and high nonlinearities do not allow the complete elimination of transient times when any external disturbance or set‐point change occurs. Thus, aiming at the use of easy‐tuning systems, a distributed‐action control in trays of a diabatic distillation unit with Smith's predictor was implemented in the Simulink environment to further reduce transient times and out‐of‐specification product. The distributed‐action strategy with Smith's predictor led to a reduction of 33.3 min (33 %) in the transient time of the top temperature control loop and 66 % in out‐of‐specification product, when compared with the conventional strategy, and thus is shown to be an efficient approach to increasing the productivity of distillation plants.

Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.

Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play distinct roles in the viral life cycle. During reverse transcription, HIV-1 NC facilitates the rearrangement of nucleic acid secondary structures, allowing the transactivation response (TAR) RNA hairpin to be transiently destabilized and annealed to a complementary RNA hairpin. In contrast, during viral assembly, NC, as a domain of the group-specific antigen (Gag) polyprotein, binds the genomic RNA and facilitates packaging into new virions. It is not clear how the same protein, alone or as part of Gag, performs such different RNA binding functions in the viral life cycle. By combining single-molecule optical tweezers measurements with a quantitative mfold-based model, we characterize the equilibrium stability and unfolding barrier for TAR RNA. Comparing measured results with a model of discrete protein binding allows us to localize affected binding sites, in addition to quantifying hairpin stability. We find that, while both NCp7 and Gag∆p6 destabilize the TAR hairpin, Gag∆p6 binding is localized to two sites in the stem, while NCp7 targets sites near the top loop. Unlike Gag∆p6, NCp7 destabilizes this loop, shifting the location of the reaction barrier toward the folded state and increasing the natural rate of hairpin opening by ~104. Thus, our results explain why Gag cleavage and NC release is an essential prerequisite for reverse transcription within the virion.

Investigation of on-chip integrated inductors fabricated in SOI-MUMPs for RF MEMS ICs

This paper presents for the first time implementation of zig–zag and solenoidal on-chip inductors in standard and cost effective SOI-MUMPs fabrication process. The solenoidal inductor offers high Q-factor and inductance as compared to planar zig–zag inductor. Bonding wires are used to construct the top conductor loop of the solenoidal inductor. The inductors are also characterized at elevated temperature for performance investigation in harsh environment. The mechanical resonance frequency of the inductors are characterized using the Finite element software COMSOL. The inductors are characterized using a vector network analyzer from 60 MHz to 3 GHz, and the results of both inductors are compared. The total size of the device is 2 × 0.7 mm2.

EMT Conversion of Composite Broadband Absorbent Metamaterials for Stealth Application Over X-Bands

A validating approach for electromagnetic thermal (EMT) conversion of a composite broadband absorbent metamaterials (AMs) is proposed in this paper. The integrated multilayer AMs consisting of top square loop (Q-loops) array layer, middle metal plate-polymer sandwich, bottom Q-loops array layer stacked vertically is analyzed with finite-different time-domain (FDTD) algorithm and fabricated by High Density Interconnector (HDI) process and Micro-electromechanical Systems (MEMS) technology. The implemented composite layered structure with the dielectrics and subsequent multi metal loops has broadband bandwidth over 2.5GHz in X-bands. High absorption performance in various incident waves with different polarizations and incident angles basically maintains a fixed efficient level of the AMs with diverse absorbing states in wide operating band. Electromagnetics and thermal multiphysics analysis validates the EMT conversion of the AMs in induced strong electromagnetic resonance. The integrated thermal conduction device is loaded on the back of AMs to transfer the converted thermal energy in time, which effectively reduces the surface thermal distribution. Finally, absorbent properties tested by free space methods and thermocouple and infrared thermal imaging (ITI) system shows the polarization independent energy transformation in greatly accordance with numerical analysis. This investigation shows the potential application of AMs in stealth systems to achieve both electromagnetic stealth and infrared thermal stealth through EMT energy conversion.

Design and Performance of an Experimental Cooled Perch System for Heat Stress Relief of Laying Hens

This article summarizes the design and performance of a cooled perch system for laying hens during heat stress.Water flow rates, perch loop water temperatures, and system net heat gain are provided.The average daily net heat absorption data, useful for sizing thermal water storage and chiller capacity in future applications, is 256 W m-1 perch length, or 43.2 W per hen housed.This analysis provides a baseline for future cooled perch system design in other application settings.Abstract. This article summarizes the engineering design and performance of a cooled perch system used in a multi-year collaborative study to evaluate cooled perch effects on hen production, health, and welfare during heat stress. The cooled perch system consisted of two replicates (CP-1 and CP-2) of three-tier cage units with galvanized perch pipes forming a complete loop in each tier (top, middle, bottom) in which chilled water circulated. A total of 324 White Leghorns at 17 weeks of age were randomly assigned to 36 cages (76 cm × 52 cm × 48 cm) in six banks placed in the same room. Flow for each loop was provided by loop pumps that drew chilled water from an open thermal storage manifold and returned it to the same manifold. Each thermal storage was cooled by continuously circulating water through a water chiller. Each loop pump was thermostatically controlled based on the cage air temperature. The water inlet and outlet temperatures, cage air temperatures, and loop water flow rates during stable system operation were measured for performance evaluation. Mean water flow rates in 2015 were 5.19 and 5.45 kg min-1 for CP-1 and CP-2, respectively, but significantly declined to 3.91 and 4.03 kg min-1 in 2016. The mean loop water temperature rise was about 2°C for both replicates. The mean loop net heat gain of CP-1 and CP-2 ranged from 690 to 850 W and from 551 to 1,298 W, respectively, with a significant difference between CP-2 loops (p < 0.0001), indicating a discrepancy between the manufacturer’s pump curve and field performance. There was a correlation between room air temperature and net heat gain for all loops of CP-1 and the top loop of CP-2 (p < 0.0001), suggesting that natural convection and radiation from the room to the pipe were the major contributors to loop heat gain. The average daily net heat gain was approximately 2,334 W per replicate, 256 W m-1 perch length, or 43.2 W per hen housed. This analysis provides a baseline for future cooled perch system design in other application settings. An example is provided for sizing the thermal water storage and chiller capacity. In addition, a closed water system with a properly sized expansion tank is recommended for future energy-efficient cooled perch applications. Keywords: Alternative cooling, Heat stress, Heat transfer, Poultry.

Planar Double Box Integral for Top Pair Production with a Closed Top Loop to all orders in the Dimensional Regularization Parameter.

We compute systematically for the planar double box Feynman integral relevant to top pair production with a closed top loop the Laurent expansion in the dimensional regularization parameter ϵ. This is done by transforming the system of differential equations for this integral and all its sub-topologies to a form linear in ϵ, where the ϵ^{0} part is strictly lower triangular. This system is easily solved order by order in the dimensional regularization parameter ϵ. This is an example of an elliptic multiscale integral involving several elliptic subtopologies. Our methods are applicable to similar problems.

Analytic results for the planar double box integral relevant to top-pair production with a closed top loop

In this article we give the details on the analytic calculation of the master integrals for the planar double box integral relevant to top-pair production with a closed top loop. We show that these integrals can be computed systematically to all order in the dimensional regularisation parameter ε. This is done by transforming the system of differential equations into a form linear in ε, where the ε0-part is a strictly lower triangular matrix. Explicit results in terms of iterated integrals are presented for the terms relevant to NNLO calculations.

Singlet scalar top partners from accidental supersymmetry

We present a model wherein the Higgs mass is protected from the quadratic one-loop top quark corrections by scalar particles that are complete singlets under the Standard Model (SM) gauge group. While bearing some similarity to Folded Supersymmetry, the construction is purely four dimensional and enjoys more parametric freedom, allowing electroweak symmetry breaking to occur easily. The cancelation of the top loop quadratic divergence is ensured by a Z3 symmetry that relates the SM top sector and two hidden top sectors, each charged under its own hidden color group. In addition to the singlet scalars, the hidden sectors contain electroweak-charged supermultiplets below the TeV scale, which provide the main access to this model at colliders. The phenomenology presents both differences and similarities with respect to other realizations of neutral naturalness. Generally, the glueballs of hidden color have longer decay lengths. The production of hidden sector particles results in quirk or squirk bound states, which later annihilate. We survey the possible signatures and corresponding experimental constraints.

Probing extra Yukawa couplings by precision measurements of Higgs boson properties

If one removes any \emph{ad hoc} symmetry assumptions, the general two Higgs doublet model should have additional Yukawa interactions independent from fermion mass generation, in general involving flavor changing neutral Higgs couplings. These extra couplings can affect the discovered Higgs boson $h$ through fermion loop contributions. We calculate the renormalized $hZZ$ coupling at one-loop level %by on-shell and minimal subtraction scheme, and evaluate the dependence on heavy Higgs boson mass and extra Yukawa coupling $\rho_{tt}$. Precision measurements at future colliders can explore the parameter space, and can give stronger bound on $\rho_{tt}$ than the current bound from flavor experiments. As a side result, we find that if $\rho_{tt}\cos\gamma < 0$, where $\cos\gamma$ is the exotic Higgs component of $h$, the $\rho_{tt}$-induced top loop contribution cancels against bosonic loop contributions, and one may have alignment without decoupling, namely $\sin(-\gamma) \simeq 1$, but exotic scalar bosons could have masses at several hundred GeV.