Miracle-dz/UniFAR-FTUs huggingface dataset:
An implementation-focussed bio/algorithmic workflow for 1 synthetic biology 2

11 As synthetic biology moves away from “trial and error" and embraces more formal processes, 12 workflows have emerged that extend from the conceptualisation of a genetic device to its 13 construction and measurement. We are particularly interested in this latter aspect (i.e., 14 characterisation and measurement of synthetic genetic devices), as this is a workflow component 15 that has received relatively little attention, but is crucial to the success of such constructions. We 16 present an end-to-end use case for engineering a basic synthetic construct, which is supported by 17 information standards and computational methods, and which focuses on characterisation and 18 measurement. This workflow captures the main stages of genetic circuit design and description, 19 and offers standardised tools for both population-based measurement and single-cell analysis. 20 The main contributions of the current paper are (1) Consideration of specific vector features . 21 Although circuit design has been successfully automated, important structural information is 22 usually overlooked, as is the case of plasmid vectors. We advocate the use of the Standard 23 European Vector Architecture to select the optimal carrier for a design and a thorough description, 24 in order to unequivocally correlate digital definitions and molecular devices. We developed a 25 digital version of this plasmid format with the Synthetic Biology Open Language and a software 26
Effects of Levothyroxine on Pregnant Women With Subclinical Hypothyroidism, Negative for Thyroid Peroxidase Antibodies

Context Currently, there is no consensus on universal thyroid screening and levothyroxine (LT4) treatment of pregnant women with subclinical hypothyroidism (SCH) who are negative for thyroid peroxidase antibody (TPOAb-). Objective We aimed to evaluate the benefits of LT4 treatment on pregnancy outcomes in SCH-TPOAb- women. Design This study was conducted within the framework of the Tehran Thyroid and Pregnancy Study. A single-blind randomized clinical trial was undertaken in pregnant women who were SCH-TPOAb-. Setting Prenatal care centers of the Shahid Beheshti University of Medical Sciences. Patients Using the thyrotropin (TSH) cut point of 2.5 mIU/L, 366 SCH-TPOAb- and 1092 euthyroid TPOAb- women were recruited. Intervention SCH-TPOAb- women were randomly assigned to two groups: group A (n = 183) who were treated with LT4 and group B (n = 183) who received no treatment. A total of 1,028 euthyroid TPOAb- women served as the control group (group C). Main Outcome Measure The primary outcome was the rate of preterm delivery. Results Using the TSH cutoff of 2.5 mIU/L, no significant difference in preterm delivery was observed between groups A and B [relative risk (RR): 0.86; 95% confidence interval (CI): 0.47 to 1.55; P = 0.61]. However, log-binomial model analysis based on a cut point of 4.0 mIU/L demonstrated a significantly lower rate of preterm delivery in LT4-treated women compared with those who received no treatment (RR: 0.38; 95% CI: 0.15 to 0.98; P = 0.04). Conclusions Despite no beneficial effect of LT4 therapy in reducing preterm delivery in SCH-TPOAb- women with a TSH cut point of 2.5 to 4 mIU/L, LT4 could precisely decrease this complication using the newly recommended cutoff ≥4.0 mIU/L.
RESEARCH ON POLISHING PROCESS OF A SPECIAL POLISHING MACHINE TOOL

In this paper, a serial-parallel hybrid special polishing machine tool based on the elastic polishing theory is developed, which is used for polishing mould surface by using bound abrasives. This machine tool mostly consists of parallel mechanism of three-dimensional moving platform, series rotational mechanism of two degrees of freedom and elastic polishing tool device. The parallel mechanism controls the spatial position of the polishing tool. The series mechanism controls the pose of the polishing tool. The elastic polishing tool system can realize active control by a pneumatic servo system and passive conformity by a spring. The main process parameters that have influence on surface roughness and polishing efficiency are tool speed, feed rate, force, pose angle and polishing number of times. Optimal combination of process parameters is presented by the Taguchi and grey relational analysis, which provide a choice of parameters as a basis for free-form surface polishing in practice.
Red emission from nano-silicon nitride multilayer films prepared using hot-wire chemical vapor deposition

Ultrathin silicon nitride multilayer films were prepared by varying silane/ammonia flow ratios 1/10 and 1/20 alternately in a silicon nitride hot-wire chemical vapor deposition chamber. Some films were annealed at 1000 °C for 1 h in an argon environment. Cross-sectional transmission electron microscopy shows ~6 nm silicon clusters formed in the annealed film. Strong visible red emission in the wavelength range 810–820 nm was detected from the films when excited with the 325 nm He–Cd laser excitation. A blueshift in the photoluminescence of the annealed film with respect to the as-deposited film is attributed to the silicon quantum confinement due to the presence of silicon clusters. Disappearance of the photoluminescence peak at 521 nm related to silicon dangling bonds in the annealed film in comparison with the as-deposited film was confirmed by the photoluminescence measurements.
Automated detection of lung tumors in PET/CT images using active contour filter

In a previous study, we developed a hybrid tumor detection method that used both computed tomography (CT) and positron emission tomography (PET) images. However, similar to existing computer-aided detection (CAD) schemes, it was difficult to detect low-contrast lesions that touch to the normal organs such as the chest wall or blood vessels in the lung. In the current study, we proposed a novel lung tumor detection method that uses active contour filters to detect the nodules deemed "difficult" in previous CAD schemes. The proposed scheme detects lung tumors using both CT and PET images. As for the detection in CT images, the massive region was first enhanced using an active contour filter (ACF), which is a type of contrast enhancement filter that has a deformable kernel shape. The kernel shape involves closed curves that are connected by several nodes that move iteratively in order to enclose the massive region. The final output of ACF is the difference between the maximum pixel value on the deformable kernel, and pixel value on the center of the filter kernel. Subsequently, the PET images were binarized to detect the regions of increased uptake. The results were integrated, followed by the false positive reduction using 21 characteristic features and three support vector machines. In the experiment, we evaluated the proposed method using 100 PET/CT images. More than half of nodules missed using previous methods were accurately detected. The results indicate that our method may be useful for the detection of lung tumors using PET/CT images.
Repeat-Specific Functions for the C-Terminal Domain of RNA Polymerase II in Budding Yeast

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII) is required to regulate transcription and to integrate it with other essential cellular processes. In the budding yeast Saccharomyces cerevisiae, the CTD of Rpb1p consists of 26 conserved heptad repeats that are post-translationally modified to orchestrate protein factor binding at different stages of the transcription cycle. A long-standing question in the study of the CTD is if there are any functional differences between the 26 repeats. In this study, we present evidence that repeats of identical sequence have different functions based on their position within the CTD. We assembled plasmids expressing Rpb1p with serine to alanine substitutions in three defined regions of the CTD and measured a range of phenotypes for yeast expressing these constructs. Mutations in the beginning and middle regions of the CTD had drastic, and region-specific effects, while mutating the distal region had no observable phenotype. Further mutational analysis determined that Ser5 within the first region of repeats was solely responsible for the observed growth differences and sequencing fast-growing suppressors allowed us to further define the functional regions of the CTD. This mutational analysis is consistent with current structural models for how the RNAPII holoenzyme and the CTD specifically would reside in complex with Mediator and establishes a foundation for studying regioselective binding along the repetitive RNAPII CTD.
Reflection-mode Optical Injection Locking

A novel model including the interference effect of master laser reflection is established for reflection-mode optical injection locking. This model sheds insight on the physical origin of some rather distinct but unexplained modulation characteristics of optical injection-locked vertical-cavity surface-emitting lasers (VCSELs), including data pattern inversion in on-off keying modulation, a large RF gain at low frequency, and an anomalous DC-suppression under small signal modulation, in specific locking conditions. Excellent agreement is obtained between the simulation and experiment results. Strong optical injection-locked semiconductor lasers demonstrating > 100-GHz resonance frequencies and 80-GHz intrinsic bandwidths, " Opt. Greatly increased fiber transmission distance with an optically injection-locked vertical-cavity surface-emitting laser, " Opt. " 90-km single-mode fiber transmission of 10-Gb/s multimode VCSELs under optical injection locking, " in A new amplifier model for resonance enhancement of optically injection-locked lasers, " IEEE Photon. Frequency response enhancement of optical injection-locked lasers, " IEEE Cavity resonance shift and bandwidth enhancement in semiconductor lasers with strong light injection, " IEEE J. enhancement and broadband noise reduction in injection-locked semiconductor lasers, " IEEE Photon. Locking conditions and stability properties for a semiconductor laser with external light injection, " IEEE J. Physical origin of data pattern inversion in optical injection-locked VCSELs, " in Locking range and stability of injection locked 1.54 µm InGaAsP semiconductor lasers, " IEEE J.
Qualitative and Quantitative Analysis of Interviewer Help Answering the Time Tradeoff

Objectives. The time tradeoff (TTO) is an important method to directly obtain health utilities. Challenges of the TTO are, among others, “nontraders” and illogical answers. In TTO interviews, these challenges are resolved by the interviewer. In web-based TTOs, training procedures and logical checks are used based on the views of the researchers. As web-based TTOs will be used more often in the future, we investigated how respondents arrive at their ratings to determine the help they require. Methods. In 2 earlier studies performed by this research group, respondents valued 6 EQ-5D states on a TTO. Respondents were asked to think out loud, and all interviews were audiotaped. A random selection of these interviews were transcribed and double-coded by two independent raters, using a priori and inductive coding until saturation was reached. Based on the retrieved mistakes and comments, a list of frequently asked questions (FAQ) was developed. Results. In total, 91 interviews were coded. In all, 85% made at least 1 mistake, 41% made a misreading/miscalculation, 70% misunderstood the tradeoff, 27% misunderstood the EQ-5D dimensions, 29% misunderstood the scenario, 45% made a comment about the TTO, and 43% expressed frustration. More misunderstandings were reported in the Peeters study, which was performed in a realistic setting, whereas the van Osch study was conducted in a more ideal setting. Misunderstandings of the scenario were mosly reported by patients. Conclusions. Almost all respondents need interviewer help. This may have implications for the validity of interviewer-based TTO elicitations when social acceptability bias is an issue or with explicit hypothesis and the interviewer is not blinded. The FAQ list can be used to standardize interviewer help or as a help function in a web-based TTO.
Strand Invasion of DNA Quadruplexes by PNA: Comparison of Homologous and Complementary Hybridization

Molecular recognition of DNA quadruplex structures is envisioned to be a strategy for regulating gene expression at the transcriptional level and for in situ analysis of telomere structure and function. The recognition of DNA quadruplexes by peptide nucleic acid (PNA) oligomers is presented here, with a focus on comparing complementary, heteroduplex‐forming and homologous, heteroquadruplex‐forming PNAs. Surface plasmon resonance and optical spectroscopy experiments demonstrated that the efficacy of a recognition mode depended strongly on the target. Homologous PNA readily invades a quadruplex derived from the promoter regulatory region found upstream of the MYC proto‐oncogene to form a heteroquadruplex at high potassium concentration mimicking the intracellular environment, whereas complementary PNA exhibits virtually no hybridization. In contrast, complementary PNA is superior to the homologous in hybridizing to a quadruplex modeled on the human telomere sequence. The results are discussed in terms of the different structural morphologies of the quadruplex targets and the implications for in vivo recognition of quadruplexes by PNAs.
Dysfunction of different cellular degradation pathways contributes to specific β‐amyloid42‐induced pathologies

The endosomal‐lysosomal system (ELS), autophagy, and ubiquitin‐proteasome system (UPS) are cel‐ lular degradation pathways that each play a critical role in the removal of misfolded proteins and the prevention of the accumulation of abnormal proteins. Recent studies on Alzheimer's disease (AD) pathogenesis have suggested that accumulation of aggregated β‐amyloid (Aβ) peptides in the AD brain results from a dysfunction in these cellular clearance systems. However, the specific roles of these pathways in the removal of Aß peptides and the pathogenesis underlying AD are unclear. Our in vitro and in vivo genetic approaches revealed that ELS mainly removed monomeric β‐amyloid42 (Aβ42), while autophagy and UPS clear oligomeric Aβ42. Although over‐ production of phosphatidylinositol 4‐phosphate‐5 increased Aβ42 clearance, it reduced the life span of Aβ42 transgenic flies. Our behavioral studies further demonstrated impaired autophagy and UPS‐enhanced Aβ42‐ induced learning and memory deficits, but there was no effect on Aβ42‐induced reduction in life span. Results from genetic fluorescence imaging showed that these pathways were damaged in the following order: UPS, autophagy, and finally ELS. The results of our study demonstrate that different degradation pathways play distinct roles in the removal of Aβ42 aggregates and in disease progression. These findings also suggest that pharmacologic treatments that are designed to stimulate cellular degradation pathways in patients with AD should be used with caution. —Ji, X. ‐R. , Cheng, K. ‐C. , Chen, Y. ‐R. , Lin, T. ‐Y. , Cheung, C. H. A. , Wu, C. ‐L. , Chiang, H. ‐C. Dysfunction of different cellular degradation pathways contributes to specific β‐amyloid42‐induced pathologies. FASEB J. 32,1375‐1387 (2018). www.fasebj. org
Tumor Necrosis Factor α and Regulatory T Cells in Oncoimmunology

Tumor necrosis factor α (TNF) is a potent pro-inflammatory cytokine that has deleterious effect in some autoimmune diseases, which led to the use of anti-TNF drugs in some of these diseases. However, some rare patients treated with these drugs paradoxically develop an aggravation of their disease or new onset autoimmunity, revealing an immunosuppressive facet of TNF. A possible mechanism of this observation is the direct and positive effect of TNF on regulatory T cells (Tregs) through its binding to the TNF receptor type 2 (TNFR2). Indeed, TNF is able to increase expansion, stability, and possibly function of Tregs via TNFR2. In this review, we discuss the role of TNF in graft-versus-host disease as an example of the ambivalence of this cytokine in the pathophysiology of an immunopathology, highlighting the therapeutic potential of triggering TNFR2 to boost Treg expansion. We also describe new targets in immunotherapy of cancer, emphasizing on the putative suppressive effect of TNF in antitumor immunity and of the interest of blocking TNFR2 to regulate the Treg compartment.
Sources of Dietary Protein in Relation to Blood Pressure in a General Dutch Population

Background Little is known about the relation of different dietary protein types with blood pressure (BP). We examined whether intake of total, plant, animal, dairy, meat, and grain protein was related to BP in a cross sectional cohort of 20,820 Dutch adults, aged 20–65 y and not using antihypertensive medication. Design Mean BP levels were calculated in quintiles of energy-adjusted protein with adjustment for age, sex, BMI, education, smoking, and intake of energy, alcohol, and other nutrients including protein from other sources. In addition, mean BP difference after substitution of 3 en% carbohydrates or MUFA with protein was calculated. Results Total protein and animal protein were not associated with BP (ptrend = 0.62 and 0.71 respectively), both at the expense of carbohydrates and MUFA. Systolic BP was 1.8 mmHg lower (ptrend<0.01) in the highest (>36 g/d) than in the lowest (<27 g/d) quintile of plant protein. This inverse association was present both at the expense of carbohydrates and MUFA and more pronounced in individuals with untreated hypertension (−3.6 mmHg) than in those with normal (+0.1 mmHg) or prehypertensive BP (−0.3 mmHg; pinteraction<0.01). Meat and grain protein were not related to BP. Dairy protein was directly associated with systolic BP (+1.6 mmHg, ptrend<0.01), but not with diastolic BP (ptrend = 0.24). Conclusions Total protein and animal protein were not associated with BP in this general untreated Dutch population. Plant protein may be beneficial to BP, especially in people with elevated BP. However, because high intake of plant protein may be a marker of a healthy diet and lifestyle in general, confirmation from randomized controlled trials is warranted.
Computational Nanophotonics: Model Optical Interactions and Transport in Tailored Nanosystem Architectures

The program is directed toward development of new computational approaches to photoprocesses in nanostructures whose geometry and composition are tailored to obtain desirable optical responses. The emphasis of this specific program is on the development of computational methods and prediction and computational theory of new phenomena of optical energy transfer and transformation on the extreme nanoscale (down to a few nanometers).
Novel stability criteria of Cohen–Grossberg neural networks with time‐varying delays

In this paper, a class of Cohen–Grossberg neural networks with time‐varying delays is investigated. Based on several new Lyapunov–Krasovskii functionals, by employing the homeomorphism mapping principle, the Halanay inequality, a nonlinear measure approach and linear matrix inequality techniques, several delay‐independent sufficient criteria are obtained for the existence, uniqueness and globally exponential stability of considered neural networks. Without assuming the boundedness and monotonicity of activation functions, the obtained conditions generalize some previous results in the literature. Two examples are also given to show the less conservativeness of the obtained conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Noninvasive Localization of IGBT Faults by High-Sensitivity Magnetic Probe With RF Stimulation

This paper presents a new and simple method to noninvasively localize failure sites in an insulated-gate bipolar transistor (IGBT) module by using a magnetic probe. The method detects the magnetic field generated by leakage currents occurring at the broken gates of an IGBT module. In this method, not only an RF stimulus signal but also a dc bias voltage is applied to the IGBT module under test, because the resistance of the failure site’s change depends upon the dc bias condition. A high-sensitivity magnetic probe is used to detect the magnetic field to locate the corresponding fault positions. The magnetic probe is fully integrated onto a chip by a 180-nm CMOS process and includes a magnetic pickup coil, a low-noise amplifier, a downconversion mixer, and a low-pass filter. Magnetic scanning experiments are implemented for two kinds of IGBT module samples to demonstrate the detection of the broken gate positions. In addition, a visual confirmation of the broken gate positions is performed. Several postprocessing steps in a clean room are applied to these samples in order to visually confirm the scanning results of the proposed method. Experimental results successfully demonstrate that our method can be used for noninvasive localization of small intrinsic faults, on two kinds of SiC and Si substrates, of IGBT modules.
Typology and Dynamics of Heavier Drinking Styles in Great Britain: 1978–2010

Abstract Aims To identify a typology of heavier drinking styles in Great Britain and to identify socio-demographic trends in the typology over the period 1978–2010. Methods We applied multiple correspondence analysis and agglomerative hierarchical clustering to beverage-specific quantity–frequency measures of alcohol consumption in the repeated cross-sectional General Lifestyle Survey of Great Britain, 1978–2010. The cluster analysis focuses on the 60,043 adult respondents over this period reporting average drinking levels above the UK Government guidelines. We projected sex, age, income, education, socio-economic status and tobacco consumption variables onto the clusters to inspect socio-demographic trends in heavier drinking. Results We identified four stable clusters of heavier drinking: (a) high volume beer; (b) beer and spirit combination; (c) all beverage and (d) wine and spirit only. The socio-demographic characteristics of the clusters were distinct from both each other and the general population. However, all clusters had higher median incomes and higher smoking rates than the population. Increases in the prevalence of heavier drinking were driven by a 5-fold increase in the contribution of the female-dominated, wine and spirit only cluster. Conclusions Recent changes in per capita alcohol consumption in Great Britain occurred within the context of a stable typology of heavier drinking styles and shifting socio-demographics. Identifying these trends is essential to better understand how drinking cultures develop over time and where potentially problematic drinking styles may emerge. Our findings suggest that careful attention to patterns and cultures of consumption is more important than relying on headline consumption data, for both understanding drinking behaviours and targeting interventions. Short Summary This analysis of alcohol consumption survey data identifies four styles of heavier drinking in Great Britain, which remain unchanged over the period 1978–2010. The socio-demographic characteristics of the drinking styles are distinct from both each other and the general population, with increased participation of female and older drinkers over time.