Fat Links Research Articles

LASSO-derived model for the prediction of lean-non-alcoholic fatty liver disease in examinees attending a routine health check-up

Background Lean individuals with non-alcohol fatty liver disease (NAFLD) often have normal body size but abnormal visceral fat. Therefore, an alternative to body mass index should be considered for prediction of lean-NAFLD. This study aimed to use representative visceral fat links with other laboratory parameters using the least absolute shrinkage and selection operator (LASSO) method to construct a predictive model for lean-NAFLD. Methods This retrospective cross-sectional analysis enrolled 2325 subjects with BMI < 24 kg/m2 from medical records of 51,271 examinees who underwent a routine health check-up. They were randomly divided into training and validation cohorts at a ratio of 1:1. The LASSO-derived prediction model used LASSO regression to select 23 clinical and laboratory factors. The discrimination and calibration abilities were evaluated using the Hosmer–Lemeshow test and calibration curves. The performance of the LASSO model was compared with the fatty liver index (FLI) model. Results The LASSO-derived model included four variables—visceral fat, triglyceride levels, HDL-C-C levels, and waist hip ratio—and demonstrated superior performance in predicting lean-NAFLD with high discriminatory ability (AUC, 0.8416; 95% CI: 0.811–0.872) that was comparable with the FLI model. Using a cut-off of 0.1484, moderate sensitivity (75.69%) and specificity (79.86%), as well as high negative predictive value (95.9%), were achieved in the LASSO model. In addition, with normal WC subgroup analysis, the LASSO model exhibits a trend of higher accuracy compared to FLI (cut-off 15.45). Conclusions We developed a LASSO-derived predictive model with the potential for use as an alternative tool for predicting lean-NAFLD in clinical settings.

Distributed computing with the cloud

We investigate the effect of omnipresent cloud storage on distributed computing. To this end, we specify a network model with links of prescribed bandwidth that connect standard processing nodes, and, in addition, passive storage nodes. Each passive node represents a cloud storage system, such as Dropbox, Google Drive etc. We study a few tasks in this model, assuming a single cloud node connected to all other nodes, which are connected to each other arbitrarily. We give implementations for basic tasks of collaboratively writing to and reading from the cloud, and for more advanced applications such as matrix multiplication and federated learning. Our results show that utilizing node-cloud links as well as node-node links can considerably speed up computations, compared to the case where processors communicate either only through the cloud or only through the network links. We first show how to optimally read and write large files to and from the cloud in general graphs using flow techniques. We use these primitives to derive algorithms for combining, where every processor node has an input value and the task is to compute a combined value under some given associative operator. In the special but common case of “fat links,” where we assume that links between processors are bidirectional and have high bandwidth, we provide near-optimal algorithms for any commutative combining operator (such as vector addition). For the task of matrix multiplication (or other non-commutative combining operators), where the inputs are ordered, we present tight results in the simple “wheel” network, where procesing nodes are arranged in a ring, and are all connected to a single cloud node.

Circadian clock dysfunction in human omental fat links obesity to metabolic inflammation

To unravel the pathogenesis of obesity and its complications, we investigate the interplay between circadian clocks and NF-κB pathway in human adipose tissue. The circadian clock function is impaired in omental fat from obese patients. ChIP-seq analyses reveal that the core clock activator, BMAL1 binds to several thousand target genes. NF-κB competes with BMAL1 for transcriptional control of some targets and overall, BMAL1 chromatin binding occurs in close proximity to NF-κB consensus motifs. Obesity relocalizes BMAL1 occupancy genome-wide in human omental fat, thereby altering the transcription of numerous target genes involved in metabolic inflammation and adipose tissue remodeling. Eventually, clock dysfunction appears at early stages of obesity in mice and is corrected, together with impaired metabolism, by NF-κB inhibition. Collectively, our results reveal a relationship between NF-κB and the molecular clock in adipose tissue, which may contribute to obesity-related complications.

Network Anatomy Controlling Abrupt-like Percolation Transition

We virtually dissect complex networks in order to understand their internal structure, just as doctors do with the bodies of animals. Our novel method classifies network links into four categories: bone, fat, cartilage, and muscle, based on network connectivity. We derive an efficient percolation strategy from this new viewpoint of network anatomy, which enables abrupt-like percolation transition through removal of a small amount of cartilage links, which play a crucial role in network connectivity. Furthermore, we find nontrivial scaling laws in the relationships between four types of links in each cluster and evaluate power exponents, which characterize network structures as seen in the real large-scale network of trading business firms and in the Erdős-Rényi network. Finally, we observe changes in the transition point for random bond percolation process, demonstrating that the addition of muscle links enhances network robustness, while fat links are irrelevant. These findings aid in controlling the percolation transition for an arbitrary network.

Hidden Variant of ChREBP in Fat Links Lipogenesis to Insulin Sensitivity

The ChREBP transcription factor is regulated by glucose and plays a role in insulin sensitivity, but the mechanism underlying these effects remains unclear. In a recent Nature article, Herman etal. (2012) show that a shorter ChREBP isoform (ChREBP-β) links glucose transport to lipogenesis in white adipose tissue.

Logarithmic link smearing for full QCD

A Lie-algebra based recipe for smoothing gauge links in lattice field theory is presented, building on the matrix logarithm. With or without hypercubic nesting, this LOG/HYL smearing yields fat links which are differentiable with respect to the original ones. This is essential for defining UV-filtered (“fat link”) fermion actions which may be simulated with a HMC-type algorithm. The effect of this smearing on the distribution of plaquettes and on the residual mass of tree-level O ( a ) -improved clover fermions in quenched QCD is studied.

Fat link irrelevant clover overlap quark propagator

FLIC overlap fermions are a variant of the standard (Wilson) overlap action, with the FLIC (Fat Link Irrelevant Clover) action as the overlap kernel rather than the Wilson action. The structure of the FLIC overlap fermion propagator in momentum space is studied, and a comparison against previous studies of the Wilson overlap propagator in quenched QCD is performed. To explore the scaling properties of the propagator for the two actions, numerical calculations are performed in Landau Gauge across three lattices with different lattice spacing $a$ and similar physical volumes. We find that at light quark masses the acti ons agree in both the infrared and the ultraviolet, but at heavier masses some disagreement in the ultraviolet appears. This is attributed to the two action s having different discretisation errors with the FLIC overlap providing superior performance in this regime. Both actions scale reasonably, but some scaling violations are observed.

Improved chiral properties of FLIC fermions

The chiral properties of the fat-link irrelevant clover (FLIC) fermion action are examined. The improved chiral properties of fermion actions incorporating smoothed links are realised in the FLIC action where only the irrelevant operators of the fermion action are constructed with smoothed links. In particular, the histogram of the additive mass renormalisation encountered in chiral-symmetry breaking Wilson-type fermion actions is seen to narrow upon introducing fat links in the irrelevant operators. The exceptional configuration problem of quenched QCD is reduced, enabling access to the light quark mass regime of mπ/mρ≃1/3. In particular, quenched chiral nonanalytic behaviour is revealed in the light quark mass dependence of the Δ-baryon mass. FLIC fermions offer a promising approach to revealing the properties of full QCD at light quark masses.

Physics issues in simulations with dynamical overlap fermions

We discuss the impact of various improvements on simulations of dynamical overlap fermions using the Hybrid Monte Carlo algorithm. We focus on the usage of fat links and multiple pseudo-fermion fields.

Penguin diagrams for improved staggered fermions

We calculate, at the one-loop level, penguin diagrams for improved staggered fermion operators constructed using various fat links. The main result is that diagonal mixing coefficients with penguin operators are identical between the unimproved operators and the improved operators using such fat links as Fat7, $\mathrm{F}\mathrm{a}\mathrm{t}7+\mathrm{L}\mathrm{e}\mathrm{p}\mathrm{a}\mathrm{g}\mathrm{e}$, $\overline{\mathrm{F}\mathrm{a}\mathrm{t}7}$, HYP (I) and HYP (II). In addition, it turns out that the off-diagonal mixing vanishes for those constructed using fat links of Fat7, $\overline{\mathrm{F}\mathrm{a}\mathrm{t}7}$ and HYP (II). This is a consequence of the fact that the improvement by various fat links changes only the mixing with higher dimension operators and off-diagonal operators. The results of this paper, combined with those for current-current diagrams, provide complete matching at the one-loop level with all corrections of $\mathcal{O}({g}^{2})$ included.

Properties of the FLIC overlap quark propagator

FLIC overlap fermions are a type of smeared link action in which the FLIC (Fat Link Irrelevant Clover) fermion action is used as the overlap kernel instead of the standard Wilson fermion action. We study the (quenched) quark propagator in momentum space using the FLIC overlap fermion action, and compare it to that of the Wilson overlap. We find that the two actions have different discretization errors which decrease with the quark mass. We also examine the FLIC overlap quark propagator within the dynamical kernel approximation, where the FLIC Overlap action is used for the valence quarks and the FLIC fermion action is used for the quark sea. Our results indicate that the quark propagator is relatively insensitive to the fermion sea.

Hybrid Monte Carlo algorithm with fat link fermion actions

The use of APE smearing or other blocking techniques in lattice fermion actions can provide many advantages. There are many variants of these fat link actions in lattice QCD currently, such as FLIC fermions. The FLIC fermion formalism makes use of the APE blocking technique in combination with a projection of the blocked links back into the special unitary group. This reunitarisation is often performed using an iterative maximisation of a gauge invariant measure. This technique is not differentiable with respect to the gauge field and thus prevents the use of standard Hybrid Monte Carlo simulation algorithms. The use of an alternative projection technique circumvents this difficulty and allows the simulation of dynamical fat link fermions with standard HMC and its variants. The necessary equations of motion for FLIC fermions are derived, and some initial simulation results are presented. The technique is more general however, and is straightforwardly applicable to other smearing techniques or fat link actions.

Comparison of and HYP fat links

We study various methods of constructing fat links based upon the HYP (by Hasenfratz & Knechtli) and Fat7-bar (by W. Lee) algorithms. We present the minimum plaquette distribution for these fat links. This enables us to determine which algorithm is most effective at reducing the spread of plaquette values.

Dynamical FLIC fermions

The use of APE smearing or other blocking techniques in fermion actions can provide many advantages. There are many variants of these fat link actions in lattice QCD currently, such as FLIC fermions. The FLIC fermion formalism makes use of the APE blocking technique in combination with a projection of the blocked links back into the special unitary group. This reunitarisation is often performed using an iterative maximisation of a gauge invariant measure. This technique is not differentiable with respect to the gauge field and thus prevents the use of standard Hybrid Monte Carlo simulation algorithms. The use of an alternative projection technique circumvents this difficulty and allows the simulation of dynamical fat link fermions with standard HMC and its variants.

Penguin diagrams for the HYP staggered fermions

We present results of the one-loop corrections originating from the penguin diagrams for the improved staggered fermion operators constructed using various fat links such as Fat7, Fat7+Lepage, $\bar{\rm Fat7}$, HYP (I) and HYP (II). The main results include the diagonal/off-diagonal mixing coefficients and the matching formula between the continuum and lattice operators.

Description and comparison of and HYP fat links

We study various methods of constructing fat links based upon the HYP (by Hasenfratz & Knechtli) and Fat7 (by W. Lee) algorithms. We present the minimum plaquette distribution for these fat links. This enables us to determine which algorithm is most effective at reducing the spread of plaquette values — a strong indicator of improved statistics for spectrum and static potential measurements, among other quantities.

Dynamical fat link fermions

The use of APE smearing or other blocking techniques in fermion actions can provide many advantages. There are many variants of these fat link actions in lattice QCD currently, such as FLIC fermions. Frequently, fat link actions make use of the APE blocking technique in combination with a projection of the blocked links back into the special unitary group. This reunitarisation is often performed using an iterative maximisation of a gauge invariant measure. This technique is not differentiable with respect to the gauge field and thus prevents the use of standard Hybrid Monte Carlo simulation algorithms. The use of an alternative projection technique circumvents this difficulty and allows the simulation of dynamical fat link fermions with standard HMC and its variants.

Perturbative matching of staggered four-fermion operators with hypercubic fat links

We calculate the one-loop matching coefficients between continuum and lattice four-fermion operators for lattice operators constructed using staggered fermions and improved by the use of fattened links. In particular, we consider hypercubic fat links and SU(3) projected Fat-7 links, and their mean-field improved versions. We calculate only current-current diagrams, so that our results apply for operators whose flavor structure does not allow ``eye-diagrams''. We present general formulae, based on two independent approaches, and give numerical results for the cases in which the operators have the taste (staggered flavor) of the pseudo-Goldstone pion. We find that the one-loop corrections are reduced down to the 10-20% level, resolving the problem of large perturbative corrections for staggered fermion calculations of matrix elements.

Locality and topology with fat link overlap actions

We study the locality and topological properties of fat link clover overlap (FCO) actions. We find that a small amount of fattening (2-4 steps of APE or 1 step of HYP) already results in greatly improved properties compared to the Wilson overlap (WO). We present a detailed study of the localisation of the FCO and its connection to the density of low modes of $A^\dagger A$. In contrast to the Wilson overlap, on quenched gauge backgrounds we do not find any dependence of the localization of the FCO on the gauge coupling. This suggests that the FCO remains local in the continuum limit. The FCO also faithfully reproduces the zero mode wave functions of typical lattice instantons, not like the Wilson overlap. After a general discussion of different lattice definitions of the topological charge we also show that the FCO together with the Boulder charge are likely to satisfy the index theorem in the continuum limit. Finally, we present a high statistics computation of the quenched topological susceptibility with the FCO action.

Spin-3/2 baryons in lattice QCD

We present first results for masses ofspin-3/2 baryons in lattice QCD, using a novel fat-link clover fermion action in which only the irrelevant operators are constructed using fat links. In theisospin-1/2 sector; we observe, after appropriate spin and parity projection, a strong signal for the J P =3/2 − state, and find good agreement between the½ + mass and earlier nucleon mass simulations with aspin-½ interpolating field. For theisospin-3/2 Δ states, clear mass splittings are observed between the various½ ±and3/2 ± channels, with the calculated level orderings in good agreement with those observed empirically.