Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling and Analysis of Two-Way Relay Non-Orthogonal Multiple Access Systems

A two-way relay non-orthogonal multiple access (TWR-NOMA) system is investigated, where two groups of NOMA users exchange messages with the aid of one half-duplex decode-and-forward relay. Since the signal-plus-interference-to-noise ratios of NOMA signals mainly depend on effective successive interference cancellation (SIC) schemes, imperfect SIC (ipSIC), and perfect SIC (pSIC) are taken into account. In order to characterize the performance of TWR-NOMA systems, we first derive closed-form expressions for both exact and asymptotic outage probabilities of NOMA users’ signals with ipSIC/pSIC. Based on the derived results, the diversity order and throughput of the system are examined. Then, we study the ergodic rates of users’ signals by providing the asymptotic analysis in high signal-to-noise ratio (SNR) regimes. Finally, numerical simulations are provided to verify the analytical results and show that: 1) TWR-NOMA is superior to TWR-OMA in terms of outage probability in low SNR regimes; 2) due to the impact of interference signal at the relay, error floors and throughput ceilings exist in outage probabilities, and ergodic rates for TWR-NOMA, respectively; and 3) in delay-limited transmission mode, TWR-NOMA with ipSIC and pSIC have almost the same energy efficiency. However, in delay-tolerant transmission mode, TWR-NOMA with pSIC is capable of achieving larger energy efficiency compared with TWR-NOMA with ipSIC.
The Effect of TSH Suppression on Vertebral Trabecular Bone Scores in Patients With Differentiated Thyroid Carcinoma

Context The effect of thyrotropin (TSH) suppressive therapy on trabecular bone scores (TBSs) is unclear. Objective The aim of this study was to investigate the effect of TSH suppression on vertebral TBSs of postmenopausal women with differentiated thyroid carcinoma (DTC). Design, Setting, and Participants We conducted a retrospective cohort study including 273 postmenopausal women with DTC who had received TSH suppressive therapy. Bone mineral density (BMD) and TBSs at the lumbar spine were analyzed using dual-energy X-ray absorptiometry (DXA). Major Outcome Measure The association between the parameters of TSH suppressive therapy and bone parameters was investigated. Results Study subjects showed upper-normal free thyroxine levels and suppressed TSH at DXA evaluation. The mean duration of TSH suppression was 4.4 ± 2.9 years. Serum free T4 and TSH were not independently associated with lumbar spine BMD or TBS levels. Duration of TSH suppression was negatively correlated with lumbar spine TBS levels, but not with BMD. Longer duration of TSH suppression was independently associated with lower lumbar spine TBSs after adjusting for age, body mass index (BMI), and BMD. Lumbar spine TBSs were significantly lower in patients whose duration of TSH suppression was ≥5 years compared with those whose duration was <3 years after adjusting for age, BMI, and BMD. Conclusions Longer duration of TSH suppression in postmenopausal DTC patients was associated with decreased vertebral bone strength by altering TBSs rather than BMD. TBSs should be considered when estimating vertebral bone fragility in postmenopausal DTC patients receiving long-term TSH suppressive therapy.
Protein Networks Reveal Detection Bias and Species Consistency When Analysed by Information-Theoretic Methods

We apply our recently developed information-theoretic measures for the characterisation and comparison of protein–protein interaction networks. These measures are used to quantify topological network features via macroscopic statistical properties. Network differences are assessed based on these macroscopic properties as opposed to microscopic overlap, homology information or motif occurrences. We present the results of a large–scale analysis of protein–protein interaction networks. Precise null models are used in our analyses, allowing for reliable interpretation of the results. By quantifying the methodological biases of the experimental data, we can define an information threshold above which networks may be deemed to comprise consistent macroscopic topological properties, despite their small microscopic overlaps. Based on this rationale, data from yeast–two–hybrid methods are sufficiently consistent to allow for intra–species comparisons (between different experiments) and inter–species comparisons, while data from affinity–purification mass–spectrometry methods show large differences even within intra–species comparisons.
Estimating inverse probability weights using super learner when weight‐model specification is unknown in a marginal structural Cox model context

Correct specification of the inverse probability weighting (IPW) model is necessary for consistent inference from a marginal structural Cox model (MSCM). In practical applications, researchers are typically unaware of the true specification of the weight model. Nonetheless, IPWs are commonly estimated using parametric models, such as the main‐effects logistic regression model. In practice, assumptions underlying such models may not hold and data‐adaptive statistical learning methods may provide an alternative. Many candidate statistical learning approaches are available in the literature. However, the optimal approach for a given dataset is impossible to predict. Super learner (SL) has been proposed as a tool for selecting an optimal learner from a set of candidates using cross‐validation. In this study, we evaluate the usefulness of a SL in estimating IPW in four different MSCM simulation scenarios, in which we varied the specification of the true weight model specification (linear and/or additive). Our simulations show that, in the presence of weight model misspecification, with a rich and diverse set of candidate algorithms, SL can generally offer a better alternative to the commonly used statistical learning approaches in terms of MSE as well as the coverage probabilities of the estimated effect in an MSCM. The findings from the simulation studies guided the application of the MSCM in a multiple sclerosis cohort from British Columbia, Canada (1995–2008), to estimate the impact of beta‐interferon treatment in delaying disability progression. Copyright © 2017 John Wiley & Sons, Ltd.
Adipose Stem Cell Function Maintained with Age: An Intra-Subject Study of Long-Term Cryopreserved Cells

Background The progressive decline in tissue mechanical strength that occurs with aging is hypothesized to be due to a loss of resident stem cell number and function. As such, there is concern regarding use of autologous adult stem cell therapy in older patients. To abrogate this, many patients elect to cryopreserve the adipose stromal-vascular fraction (SVF) of lipoaspirate, which contains resident adipose stem cells (ASC). However, it is not clear yet if there is any clinical benefit from banking cells at a younger age. Objectives We performed a comparative analysis of SVF composition and ASC function from cells obtained under GMP conditions from the same three patients with time gap of 7 to 12 years. Methods SVF, cryobanked under good manufacturing practice (GMP) conditions, was thawed and cell yield, viability, and cellular composition were assessed. In parallel, ASC proliferation and efficiency of tri-lineage differentiation were evaluated. Results The results showed no significant differences existed in cell yield and SVF subpopulation composition within the same patient between harvest procedures 7 to 12 years apart. Further, no change in proliferation rates of cultured ASCs was found, and expanded cells from all patients were capable of tri-lineage differentiation. Conclusions By harvesting fat from the same patient at two time points, we have shown that despite the natural human aging process, the prevalence and functional activity of ASCs in an adult mesenchymal stem cell, is highly preserved. Level of Evidence 5.
Concurrent emergence of Hume-Rothery phases in Cu-8.6% Sn alloy annealed at 573 K

Precipitating phases in a supersaturated Cu-8.6 at. % Sn alloy annealed at 573 K have been studied by using transmission electron microscopy. Three Hume-Rothery (HR) phases, δ, ζ and ϵ were identified in the α matrix, each with distinct morphologies. The δ phase emerges in the form of rhombic precipitates inside grains with an orientation relationship (OR): . The ζ phase emerges both inside grains and at grain boundaries. Frequently observed OR is . Intragranular ζ particles consistently satisfy this OR; while it is proposed that a cellular morphology, whose details have been reported separately, develops only when this condition is satisfied for ζ precipitates at grain boundaries. The ϵ phase emerges along {111}α planes inside grains with a planar morphology. These plates exhibit two types of ORs: . and . The latter is the OR, reported for the same alloy annealed at 593 K. These findings are discussed from the viewpoints of the layer structures of the respective HR phases. It was shown that both the atomic configuration and interlayer spacing of the δ and ζ phases match well with {111}α, while the ϵ phase cannot satisfy these two conditions simultaneously, resulting in one of the two ORs.
Polo-like kinase inhibitor volasertib marginally enhances the efficacy of the novel Fc-engineered anti-CD33 antibody BI 836858 in acute myeloid leukemia

Acute myeloid leukemia (AML) is the second most common type of leukemia in adults. Incidence of AML increases with age with a peak incidence at 67 years. Patients older than 60 years have an unfavorable prognosis due to resistance to conventional chemotherapy. Volasertib (BI 6727) is a cell-cycle regulator targeting polo-like kinase which has been evaluated in clinical trials in AML. We evaluated effects of volasertib in primary patient samples and NK cells. At equivalent doses, volasertib is cytotoxic to AML blasts but largely spares healthy NK cells. We then evaluated the effect of volasertib treatment in combination with BI 836858 on primary AML blast samples using antibody-dependent cellular cytotoxicity (ADCC) assays. Volasertib treatment of NK cells did not impair NK function as evidenced by comparable levels of BI 836858 mediated ADCC in both volasertib-treated and control-treated NK cells. In summary, volasertib is cytotoxic to AML blasts while sparing NK cell viability and function. Higher BI 836858 mediated ADCC was observed in patient samples pretreated with volasertib. These findings provide a strong rationale to test combination of BI 836858 and volasertib in AML.
Peer effects and academics ' industry involvement : The moderating role of age on professional imprinting

This study explores the interaction between professional imprinting and age in the context of industry-science collaboration. Specifically, we examine the impact of localized and personal peer effects on academics’ involvement with industry and how these effects are moderated by the career age of the scientist. We suggest that both localized and personal peer effects drive industry involvement but that the effects from such imprinting are more pronounced for younger researchers, suggesting that professional imprinting takes place in the early stages of a scientist’s academic career. Based on a sample of 330 German academics in the field of biotechnology and publication data from the Science Citation Index Expanded (SCIE), we find that scientists with industry-oriented co-authors are more likely to be involved with industry (personal peer effect). Moreover, we find that the scientist’s involvement increases with the orientation of the scientist’s department towards industry (localized peer effect). Only the latter effect turns out to be moderated by scientist’s age. While personal peer effects are independent of the scientist’s age, localized peer effects emerge for younger researchers.
Detecting Rumors Through Modeling Information Propagation Networks in a Social Media Environment

In the midst of today's pervasive influence of social media content and activities, information credibility has increasingly become a major issue. Accordingly, identifying false information, e.g., rumors circulated in social media environments, attracts expanding research attention and growing interests. Many previous studies have exploited user-independent features for rumor detection. These prior investigations uniformly treat all users relevant to the propagation of a social media message as instances of a generic entity. Such a modeling approach usually adopts a homogeneous network to represent all users, the practice of which ignores the variety across an entire user population in a social media environment. Recognizing this limitation in modeling methodologies, this paper explores user-specific features in a social media environment for rumor detection. The new approach hypothesizes whether a user tending to spread a rumor message is dependent on specific attributes of the user in addition to content characteristics of the message itself. Under this hypothesis, the information propagation patterns of rumors versus those of credible messages in a social media environment are differentiable. To explore and exploit this hypothesis, we develop a new information propagation model based on a heterogeneous user representation and modeling approach. By applying the new approach, we are able to differentiate rumors from credible messages through observing distinctions in their respective propagation patterns in social media. The experimental results show that the new information propagation model based on heterogeneous user representation can effectively distinguish rumors from credible social media content. Our experimental findings further show that rumors are more likely to spread among certain user groups.
Rapid Clearance and Frequent Reinfection With Enteric Pathogens Among Children With Acute Diarrhea in Zanzibar

Background Acute infectious gastroenteritis is an important cause of illness and death among children in low-income countries. In addition to rotavirus vaccination, actions to improve nutrition status, sanitation, and water quality are important to reduce enteric infections, which are frequent also among asymptomatic children. The aim of this study was to investigate if the high prevalence of these infections reflects that they often are not cleared properly by the immune response or rather is due to frequent pathogen exposure. Methods Rectal swabs were collected at time of acute diarrhea and 14 days later from 127 children, aged 2-59 months and living in rural Zanzibar, and were analyzed by real-time polymerase chain reaction targeting multiple pathogens. Results At baseline, detection rates >20% were found for each of enterotoxigenic Escherichia coli, Shigella, Campylobacter, Cryptosporidium, norovirus GII, and adenovirus. At follow-up, a large proportion of the infections had become cleared (34-100%), or the pathogen load reduced, and this was observed also for agents that were presumably unrelated to diarrhea. Still, the detection frequencies at follow-up were for most agents as high as at baseline, because new infections had been acquired. Neither clearance nor reinfection was associated with moderate malnutrition, which was present in 21% of the children. Conclusions Children residing in poor socioeconomic conditions, as in Zanzibar, are heavily exposed to enteric pathogens, but capable of rapidly clearing causative and coinfecting pathogens.
Maximum Sum Rate of Slotted Aloha With Successive Interference Cancellation

This is a sequel of our previous work on characterization of maximum sum rate of slotted Aloha networks. By extending the analysis to incorporate the capacity-achieving receiver structure, successive interference cancellation (SIC), this paper aims to identify the rate loss due to random access. Specifically, two representative SIC receivers are considered, i.e., ordered SIC, where packets are decoded in a descending order of their received power, and unordered SIC, where packets are decoded in a random order. The maximum sum rate and the corresponding optimal parameter setting including the transmission probability and the information encoding rate in both cases are obtained as the functions of the mean received signal-to-noise ratio (SNR). The comparison to the capture model shows that the gains are significant only with the ordered SIC at moderate values of the mean received SNR <inline-formula> <tex-math notation="LaTeX">$\rho $ </tex-math></inline-formula>. With a large <inline-formula> <tex-math notation="LaTeX">$\rho $ </tex-math></inline-formula>, the rate gap diminishes, and they all have the same high-SNR slope of <inline-formula> <tex-math notation="LaTeX">$e^{-1}$ </tex-math></inline-formula>, which is far below that of the ergodic sum capacity of fading channels. The effect of multipacket reception (MPR) on the sum rate performance is also studied by comparing the MPR receivers including SIC and the capture model to the classical collision model.
Nasal high‐flow oxygen delivery in children with abnormal airways

Transnasal Humidified Rapid‐Insufflation Ventilatory Exchange has been shown to safely prolong the safe apnea time in well children post induction of anesthesia and is rapidly becoming a new standard for apneic oxygenation in adults. The same oxygenation technique is described as nasal high flow and can be used in infants and children at risk of apnea during anesthesia.
Health effects of vegetarian and vegan diets

Vegetarian diets do not contain meat, poultry or fish; vegan diets further exclude dairy products and eggs. Vegetarian and vegan diets can vary widely, but the empirical evidence largely relates to the nutritional content and health effects of the average diet of well-educated vegetarians living in Western countries, together with some information on vegetarians in non-Western countries. In general, vegetarian diets provide relatively large amounts of cereals, pulses, nuts, fruits and vegetables. In terms of nutrients, vegetarian diets are usually rich in carbohydrates, n−6 fatty acids, dietary fibre, carotenoids, folic acid, vitamin C, vitamin E and Mg, and relatively low in protein, saturated fat, long-chain n−3 fatty acids, retinol, vitamin B12 and Zn; vegans may have particularly low intakes of vitamin B12 and low intakes of Ca. Cross-sectional studies of vegetarians and vegans have shown that on average they have a relatively low BMI and a low plasma cholesterol concentration; recent studies have also shown higher plasma homocysteine concentrations than in non-vegetarians. Cohort studies of vegetarians have shown a moderate reduction in mortality from IHD but little difference in other major causes of death or all-cause mortality in comparison with health-conscious non-vegetarians from the same population. Studies of cancer have not shown clear differences in cancer rates between vegetarians and non-vegetarians. More data are needed, particularly on the health of vegans and on the possible impacts on health of low intakes of long-chain n−3 fatty acids and vitamin B12. Overall, the data suggest that the health of Western vegetarians is good and similar to that of comparable non-vegetarians.
Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. Our package takes as input the sequencing reads of 3C-based experiments and performs the following main tasks: (i) pre-process the reads, (ii) map the reads to a reference genome, (iii) filter and normalize the interaction data, (iv) analyze the resulting interaction matrices, (v) build 3D models of selected genomic domains, and (vi) analyze the resulting models to characterize their structural properties. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition. TADbit provides three-dimensional models built from 3C-based experiments, which are ready for visualization and for characterizing their relation to gene expression and epigenetic states. TADbit is an open-source Python library available for download from https://github.com/3DGenomes/tadbit.
Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1

ABSTRACT Recent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation. However, such explorations have rarely been conducted on marine organisms, and it is unclear how marine habitats have influenced genome stability. This report resolves the mutation rate and spectrum of the coral reef pathogen Vibrio shilonii, which causes coral bleaching and endangers the biodiversity maintained by coral reefs. We found that its mutation rate and spectrum are highly similar to those of other studied bacteria from various habitats, despite the saline environment. The mutational properties of this marine bacterium are thus controlled by other general evolutionary forces such as natural selection and genetic drift. We also found that as pH drops, the mutation rate decreases and the mutation spectrum is biased in the direction of generating G/C nucleotides. This implies that evolutionary features of this organism and perhaps other marine microbes might be altered by the increasingly acidic ocean water caused by excess CO2 emission. Nonetheless, further exploration is needed as the pH range tested in this study was rather narrow and many other possible mutation determinants, such as carbonate increase, are associated with ocean acidification. IMPORTANCE This study explored the pH dependence of a bacterial genome-wide mutation rate. We discovered that the genome-wide rates of appearance of most mutation types decrease linearly and that the mutation spectrum is biased in generating more G/C nucleotides with pH drop in the coral reef pathogen V. shilonii. This study explored the pH dependence of a bacterial genome-wide mutation rate. We discovered that the genome-wide rates of appearance of most mutation types decrease linearly and that the mutation spectrum is biased in generating more G/C nucleotides with pH drop in the coral reef pathogen V. shilonii.