Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary fiber intake and head and neck cancer risk: A pooled analysis in the International Head and Neck Cancer Epidemiology consortium

The possible role of dietary fiber in the etiology of head neck cancers (HNCs) is unclear. We used individual‐level pooled data from ten case‐control studies (5959 cases and 12,248 controls) participating in the International Head and Neck Cancer Epidemiology (INHANCE) consortium, to examine the association between fiber intake and cancer of the oral cavity/pharynx and larynx. Odds Ratios (ORs) and their 95% Confidence Intervals (CIs) were estimated using unconditional multiple logistic regression applied to quintile categories of non‐alcohol energy‐adjusted fiber intake and adjusted for tobacco and alcohol use and other known or putative confounders. Fiber intake was inversely associated with oral and pharyngeal cancer combined (OR for 5th vs. 1st quintile category = 0.49, 95% CI: 0.40–0.59; p for trend <0.001) and with laryngeal cancer (OR = 0.66, 95% CI: 0.54–0.82, p for trend <0.001). There was, however, appreciable heterogeneity of the estimated effect across studies for oral and pharyngeal cancer combined. Nonetheless, inverse associations were consistently observed for the subsites of oral and pharyngeal cancers and within most strata of the considered covariates, for both cancer sites. Our findings from a multicenter large‐scale pooled analysis suggest that, although in the presence of between‐study heterogeneity, a greater intake of fiber may lower HNC risk.
Response selection codes in neurophysiological data predict conjoint effects of controlled and automatic processes during response inhibition

The inhibition of prepotent responses is a requirement for goal‐directed behavior and several factors determine corresponding successful response inhibition processes. One factor relates to the degree of automaticity of pre‐potent response tendencies and another factor relates to the degree of cognitive control that is exerted during response inhibition. However, both factors can conjointly modulate inhibitory control. Cognitive theoretical concepts suggest that codings of stimulus‐response translations may underlie such conjoint effects. Yet, it is unclear in how far such specific codes, as assumed in cognitive psychological concepts, are evident in neurophysiological processes and whether there are specific functional neuroanatomical structures associated with the processing of such codes. Applying a temporal decomposition method of EEG data in combination with source localization methods we show that there are different, intermingled codes (i.e., “stimulus codes” and “response selection codes”) at the neurophysiological level during conjoint effects of “automatic” and “controlled” processes in response inhibition. Importantly, only “response selection codes” predict behavioral performance, and are subject to conjoint modulations by “automatic” and “controlled” processes. These modulations are associated with inferior and superior parietal areas (BA40/BA7), possibly reflecting an updating of internal representations when information is complex and probably difficult to categorize, but essential for behavioral control. Codes proposed by cognitive, psychological concepts seem to have a neurophysiological analogue that fits into current views on functions of inferior and superior parietal regions.
FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects

ABSTRACT Heritability analysis of the microbiota has demonstrated the importance of host genotype in defining the human microbiota. The alpha (1,2)-fucosyltransferase 2 encoded by FUT2 is involved in the formation of the H antigen and the SNP, rs601338 is associated with ABO histo-blood group antigen secretion in the intestinal mucosa. Previous studies have provided non replicated results for the association of this polymorphism with the composition and inferred function of intestinal microbiota. We aimed to assess this relationship in a large cohort of 1,190 healthy individuals. Genotyping was performed using the HumanCoreEXOME chip, microbial composition was addressed by 16S rRNA gene sequencing. Firmicutes, Bacteroidetes, and Actinobacteria were the dominant phyla in this cohort. Although we have sufficient power to detect significant associations of FUT2 genotype/ inferred phenotype with the microbiota, our data demonstrate that FUT2 genotype and secretor status is not associated with microbial alpha diversity, microbial composition or inferred microbial function after correction for multiple testing. Thus, FUT2 genotype and inferred phenotype are not associated with human fecal microbial composition and imputed function.
Sleep Apnea and Heart Failure With a Reduced Ejection Fraction Among Persons Living With Human Immunodeficiency Virus

Background Sleep apnea (SA) is common and has prognostic significance among broad groups of patients with heart failure (HF). There are no data characterizing the presence, associations, and prognostic significance of SA among persons living with human immunodeficiency virus (PLHIV) with HF. Methods We conducted a single-center study of PLHIV with HF with reduced ejection fraction (HFrEF; left ventricular ejection fraction [LVEF] <50%) and analyzed the relationship of SA with 30-day HF hospital readmission rate. Results Our cohort included 1124 individuals admitted with HFrEF; 15% were PLHIV, and 92% were on antiretroviral therapy. SA was noted in 28% of PLHIV and 26% of uninfected controls. Compared to uninfected controls with HFrEF and SA, PLHIV with HFrEF and SA had a lower body mass index, lower LVEF, a higher pulmonary artery systolic pressure (PASP), were more likely to have obstructive rather than central SA (P < .05 for all). In a multivariable model, PASP, low CD4 count, high viral load (VL), and SA parameters (apnea-hypopnea index, CPAP use and duration) were predictors of 30-day HF readmission rate. Each 1-hour increase in CPAP use was associated with a 14% decreased risk of 30-day HF readmission among PLHIV. Conclusions Compared to uninfected controls, PLHIV were more likely to have obstructive SA than central SA. Apnea severity, low CD4 count, high VL, and cocaine use were positively associated with 30-day HF hospital readmission rate, whereas CPAP use and increased duration of CPAP use conferred protection.
On Topology Reconfiguration for Defect-Tolerant NoC-Based Homogeneous Manycore Systems

Homogeneous manycore systems are emerging for tera-scale computation and typically utilize Network-on-Chip (NoC) as the communication scheme between embedded cores. Effective defect tolerance techniques are essential to improve the yield of such complex integrated circuits. We propose to achieve fault tolerance by employing redundancy at the core-level instead of at the microarchitecture level. When faulty cores exist on-chip in this architecture, however, the physical topologies of various manufactured chips can be significantly different. How to reconfigure the system with the most effective NoC topology is a relevant research problem. In this paper, we first show that this problem is an instance of a well known NP-complete problem. We then present novel solutions for the above problem, which not only maximize the performance of the on-chip communication scheme, but also provide a unified topology to Operating System and application software running on the processor. Experimental results show the effectiveness of the proposed techniques.
Influence of surface layer on mechanical and corrosion properties of nickel-titanium orthodontic wires.

OBJECTIVE To analyze the effect of various coating formulations on the mechanical and corrosion properties of nickel-titanium (NiTi) orthodontic wires. MATERIALS AND METHODS Uncoated, rhodium-coated, and nitrified NiTi wires were observed with a three-point-bend test, surface roughness (Ra) measurement, scanning electron microscopy, energy dispersive spectroscopy, and electrochemical testing (open circuit potential, electrochemical impedance spectroscopy, and cyclic polarization scan). Differences in the properties of tested wire types were analyzed with analysis of variance and Tukey post hoc test. RESULTS Uncoated and nitrified NiTi wires showed similar mechanical and anticorrosive properties, while rhodium-coated NiTi wires showed the highest Ra and significantly higher modulus of elasticity, yield strength, and delivery of forces during loading but not in unloading. Rhodium-coated NiTi wires also had the highest corrosion current density and corrosion potential, lowest impedance modulus, and two time constants on Bode plot, one related to the Rh/Au coating and the other to underlying NiTi. CONCLUSION Working properties of NiTi wires were unaffected by various coatings in unloading. Nitrification improved corrosion resistance. Rhodium coating reduced corrosion resistance and pronounced susceptibility to pitting corrosion in artificial saliva because of galvanic coupling between the noble coating and the base alloy.
Differential effects of coffee on the risk of type 2 diabetes according to meal consumption in a French cohort of women: the E3N/EPIC cohort study.

BACKGROUND Coffee consumption has been associated with a lower risk of diabetes, but little is known about the mechanisms responsible for this association, especially related to the time when coffee is consumed. OBJECTIVE We examined the long-term effect of coffee, globally and according to the accompanying meal, and of tea, chicory, and caffeine on type 2 diabetes risk. DESIGN This was a prospective cohort study including 69,532 French women, aged 41-72 y from the E3N/EPIC (Etude Epidémiologique auprès de Femmes de la Mutuelle Générale de l'Education Nationale/European Prospective Investigation into Cancer and Nutrition) cohort study, without diabetes at baseline. Food and drink intakes per meal were assessed by using a validated diet-history questionnaire in 1993-1995. RESULTS During a mean follow-up of 11 y, 1415 new cases of diabetes were identified. In multivariable Cox regression models, the hazard ratio in the highest category of coffee consumption [> or =3 cups (375 mL)/d] was 0.73 (95% CI: 0.61, 0.87; P for trend < 0.001), in comparison with no coffee consumption. This inverse association was restricted to coffee consumed at lunchtime (hazard ratio: 0.66; 95% CI: 0.57, 0.76) when comparing >1.1 cup (125 mL)/meal with no intake. At lunchtime, this inverse association was observed for both regular and decaffeinated coffee and for filtered and black coffee, with no effect of sweetening. Total caffeine intake was also associated with a statistically significantly lower risk of diabetes. Neither tea nor chicory consumption was associated with diabetes risk. CONCLUSIONS Our data support an inverse association between coffee consumption and diabetes and suggest that the time of drinking coffee plays a distinct role in glucose metabolism.
Favored and less favored codon–anticodon duplexes arising from the GC codon family box encoding for alanine: some computational perspectives

Alanine is encoded by the four codons of the GC box (GCA, GCG, GCU, and GCC). Known alanine anticodons include the UGC, IGC, and VGC triplets (I = inosine; V = uridine-5-oxyacetic acid). The energy-minimized structures of all possible codon–anticodon combinations involving all the alanine codons GCA, GCG, GCU, and GCC with the alanine anticodons UGC, IGC, and VGC are studied using the AMBER software. Fifteen H-bonded duplex structures arising out of these combinations are studied here, all having Watson–Crick-type base pairs at the first and second codon positions, and a variety of base pairing possibilities at the third (or wobble) position. Structural and stability considerations suggest that some codon–anticodon duplexes would be more favored than others for accommodation during the translation process. The UGC anticodon is predicted to favor the GCA codon for reading, while the GCC codon is least favored. The IGC anticodon would prefer to read the GCC codon, the GCG codon being least favored, while a syn conformer for A in the GCA codon could allow for it to be read. For the VGC anticodon, the GCA codon is predicted to be read most favorably, and the GCC codon least favorably, while a syn conformer for V in the anticodon would allow for the codon GCU to be read through a wobble pair which involves the exocyclic 5-oxyacetate group of V in H-bonding.
Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells

Tumor endothelial cells (TEC) play an indispensible role in tumor growth and metastasis although much of the detailed mechanism still remains elusive. In this study we characterized and compared the global gene expression profiles of TECs and control ECs isolated from human breast cancerous tissues and reduction mammoplasty tissues respectively by single cell RNA sequencing (scRNA-seq). Based on the qualified scRNA-seq libraries that we made, we found that 1302 genes were differentially expressed between these two EC phenotypes. Both principal component analysis (PCA) and heat map-based hierarchical clustering separated the cancerous versus control ECs as two distinctive clusters, and MetaCore disease biomarker analysis indicated that these differentially expressed genes are highly correlated with breast neoplasm diseases. Gene Set Enrichment Analysis software (GSEA) enriched these genes to extracellular matrix (ECM) signal pathways and highlighted 127 ECM-associated genes. External validation verified some of these ECM-associated genes are not only generally overexpressed in various cancer tissues but also specifically overexpressed in colorectal cancer ECs and lymphoma ECs. In conclusion, our data demonstrated that ECM-associated genes play pivotal roles in breast cancer EC biology and some of them could serve as potential TEC biomarkers for various cancers.
Time and length scales of polymer melts studied by coarse-grained molecular dynamics simulations

We present coarse-grained molecular dynamics simulations of linear polyethylene (PE) melts, ranging in chain length from C80 to C1000. The employed effective potentials, frictions, and random forces are all derived from detailed molecular dynamics simulations, leaving no adjustable parameters. Uncrossability constraints are introduced in the coarse-grained model to prevent unphysical bond crossings. The dynamic and zero-shear rate rheological properties are investigated and compared with experiment and other simulation work. In the analysis of the internal relaxations we identify a new length scale, called the slowing down length Ns, which is smaller than the entanglement length Ne. The effective segmental friction rapidly increases around Ns leading, at constant density, to a transition in the scaling of the diffusion coefficient from D~N–1 to D~N–2, a transition in the scaling of the viscosity from ~N to ~N1.8, and conspicuous nonexponential relaxation behavior. These effects are attributed to strong local kinetic constraints caused by both chain stiffness and interchain interactions. The onset of nonlocal (entanglement) effects occurs at a chain length of C120. Full entanglement effects are observed only above C400, where the shear relaxation modulus displays a plateau and the single chain coherent dynamic structure factor agrees with the reptation model.
Thyroid hormone fluctuations indicate a thermoregulatory function in both a tropical (Alouatta palliata) and seasonally cold‐habitat (Macaca fuscata) primate

Thyroid hormones boost animals’ basal metabolic rate and represent an important thermoregulatory pathway for mammals that face cold temperatures. Whereas the cold thermal pressures experienced by primates in seasonal habitats at high latitudes and elevations are often apparent, tropical habitats also display distinct wet and dry seasons with modest changes in thermal environment. We assessed seasonal and temperature‐related changes in thyroid hormone levels for two primate species in disparate thermal environments, tropical mantled howlers (Alouatta palliata), and seasonally cold‐habitat Japanese macaques (Macaca fuscata). We collected urine and feces from animals and used ELISA to quantify levels of the thyroid hormone triiodothyronine (fT3). For both species, fT3 levels were significantly higher during the cooler season (wet/winter), consistent with a thermoregulatory role. Likewise, both species displayed greater temperature deficits (i.e., the degree to which animals warm their body temperature relative to ambient) during the cooler season, indicating greater thermoregulatory pressures during this time. Independently of season, Japanese macaques displayed increasing fT3 levels with decreasing recently experienced maximum temperatures, but no relationship between fT3 and recently experienced minimum temperatures. Howlers increased fT3 levels as recently experienced minimum temperatures decreased, although demonstrated the opposite relationship with maximum temperatures. This may reflect natural thermal variation in howlers’ habitat: wet seasons had cooler minimum and mean temperatures than the dry season, but similar maximum temperatures. Overall, our findings support the hypothesis that both tropical howlers and seasonally cold‐habitat Japanese macaques utilize thyroid hormones as a mechanism to boost metabolism in response to thermoregulatory pressures. This implies that cool thermal pressures faced by tropical primates are sufficient to invoke an energetically costly and relatively longer‐term thermoregulatory pathway. The well‐established relationship between thyroid hormones and energetics suggests that the seasonal hormonal changes we observed could influence many commonly studied behaviors including food choice, range use, and activity patterns.
Fermionic Statistics in the Strongly Correlated Limit of Density Functional Theory

Exact pieces of information on the adiabatic connection integrand, Wλ[ρ], which allows evaluation of the exchange-correlation energy of Kohn–Sham density functional theory, can be extracted from the leading terms in the strong coupling limit (λ → ∞, where λ is the strength of the electron–electron interaction). In this work, we first compare the theoretical prediction for the two leading terms in the strong coupling limit with data obtained via numerical implementation of the exact Levy functional in the simple case of two electrons confined in one dimension, confirming the asymptotic exactness of these two terms. We then carry out a first study on the incorporation of the Fermionic statistics at large coupling λ, both numerical and theoretical, confirming that spin effects enter at orders ∼e–√λ.
Biomarkers of Myocardial Fibrosis: Revealing the Natural History of Fibrogenesis in Fabry Disease Cardiomyopathy

Background Cardiomyopathy is a major determinant of overall Fabry disease (FD) prognosis, with the worst outcomes in patients with myocardial fibrosis. Late gadolinium enhancement is currently the gold standard for evaluation of replacement myocardial fibrosis; however, this event is irreversible, thus identification of biomarkers of earlier diffuse fibrosis is paramount. Methods and Results Type I collagen synthesis and degradation biomarkers (PICP [carboxyterminal propeptide of procollagen type I], ICTP [carboxyterminal telopeptide of type I collagen], and MMP1 [matrix metalloproteinase 1] and MMP2) and markers of bone synthesis and degradation were evaluated (to adjust type I collagen metabolism to bone turnover) in FD patients and controls. FD patients were grouped by cardiomyopathy severity, according to echocardiogram: (1) normal, (2) tissue Doppler abnormalities, (3) left ventricular hypertrophy. A significant increase in PICP and a significant decrease in matrix metalloproteinases were observed in FD patients; even the group with normal echocardiogram had a significant increase in PICP. We also found a significant correlation between left ventricular mass and PICP (ρ=0.378, P=0.003) and MMP1 (ρ=−0.484, P<0.001). PICP (adjusted for bone turnover) was the better predictor of left ventricular mass in multivariable regression, and its diagnostic accuracy to predict late gadolinium enhancement was also significant. Conclusions Collagen type I synthesis is increased in FD cardiomyopathy, even in the earlier stages of the disease, and this profibrotic state has good predictive value for and is likely to be critical to the development of overt left ventricular hypertrophy. Moreover, inhibition of enzymes involved in collagen type I cleavage also seems crucial to myocardial collagen deposition.
A subset of sweet-sensing neurons identified by IR56d are necessary and sufficient for fatty acid taste

Fat represents a calorically potent food source that yields approximately twice the amount of energy as carbohydrates or proteins per unit of mass. The highly palatable taste of free fatty acids (FAs), one of the building blocks of fat, promotes food consumption, activates reward circuitry, and is thought to contribute to hedonic feeding underlying many metabolism-related disorders. Despite a role in the etiology of metabolic diseases, little is known about how dietary fats are detected by the gustatory system to promote feeding. Previously, we showed that a broad population of sugar-sensing taste neurons expressing Gustatory Receptor 64f (Gr64f) is required for reflexive feeding responses to both FAs and sugars. Here, we report a genetic silencing screen to identify specific populations of taste neurons that mediate fatty acid (FA) taste. We find neurons identified by expression of Ionotropic Receptor 56d (IR56d) are necessary and sufficient for reflexive feeding response to FAs. Functional imaging reveals that IR56d-expressing neurons are responsive to short- and medium-chain FAs. Silencing IR56d neurons selectively abolishes FA taste, and their activation is sufficient to drive feeding responses. Analysis of co-expression with Gr64f identifies two subpopulations of IR56d-expressing neurons. While physiological imaging reveals that both populations are responsive to FAs, IR56d/Gr64f neurons are activated by medium-chain FAs and are sufficient for reflexive feeding response to FAs. Moreover, flies can discriminate between sugar and FAs in an aversive taste memory assay, indicating that FA taste is a unique modality in Drosophila. Taken together, these findings localize FA taste within the Drosophila gustatory center and provide an opportunity to investigate discrimination between different categories of appetitive tastants.
Selective spectroscopic imaging of hyperpolarized pyruvate and its metabolites using a single‐echo variable phase advance method in balanced SSFP

In balanced steady state free precession (bSSFP), the signal intensity has a well‐known dependence on the off‐resonance frequency, or, equivalently, the phase advance between successive radiofrequency (RF) pulses. The signal profile can be used to resolve the contributions from the spectrally separated metabolites. This work describes a method based on use of a variable RF phase advance to acquire spatial and spectral data in a time‐efficient manner for hyperpolarized 13C MRI.