Miracle-dz/UniFAR-FTUs huggingface dataset:
First-order convex feasibility algorithms for x-ray CT.

PURPOSE Iterative image reconstruction (IIR) algorithms in computed tomography (CT) are based on algorithms for solving a particular optimization problem. Design of the IIR algorithm, therefore, is aided by knowledge of the solution to the optimization problem on which it is based. Often times, however, it is impractical to achieve accurate solution to the optimization of interest, which complicates design of IIR algorithms. This issue is particularly acute for CT with a limited angular-range scan, which leads to poorly conditioned system matrices and difficult to solve optimization problems. In this paper, we develop IIR algorithms which solve a certain type of optimization called convex feasibility. The convex feasibility approach can provide alternatives to unconstrained optimization approaches and at the same time allow for rapidly convergent algorithms for their solution-thereby facilitating the IIR algorithm design process. METHODS An accelerated version of the Chambolle-Pock (CP) algorithm is adapted to various convex feasibility problems of potential interest to IIR in CT. One of the proposed problems is seen to be equivalent to least-squares minimization, and two other problems provide alternatives to penalized, least-squares minimization. RESULTS The accelerated CP algorithms are demonstrated on a simulation of circular fan-beam CT with a limited scanning arc of 144°. The CP algorithms are seen in the empirical results to converge to the solution of their respective convex feasibility problems. CONCLUSIONS Formulation of convex feasibility problems can provide a useful alternative to unconstrained optimization when designing IIR algorithms for CT. The approach is amenable to recent methods for accelerating first-order algorithms which may be particularly useful for CT with limited angular-range scanning. The present paper demonstrates the methodology, and future work will illustrate its utility in actual CT application.
Evaluation of coagulation parameters and liver enzymes among alcohol drinkers in Port Harcourt, Nigeria

Alcohol is a major contributor to the global burden of disease, disability, and death in high, middle, and low-income countries. Harmful use of alcohol is one of the main factors contributing to premature deaths and avoidable disease burden worldwide and has a major impact on public health. The aim of this present cross-sectional study was to investigate the effect of alcohol consumption on coagulation parameters and liver enzymes of subjects in Port Harcourt, Nigeria. Two hundred adults consisting of 120 alcohol dependent subjects and 80 age, gender-matched nondrinkers aged 25–65 years (mean age 45.25 ± 11.50 years) were enrolled in this study. Of the 120 chronic alcohol drinkers, 37 were dependent on local dry gin, while 83 were dependent on other alcoholic beverages. The mean values of the liver enzymes, aspartate aminotransferase and gamma glutamyl transferase, were significantly higher (P = 0.002 and P = 0.02 respectively) among the chronic alcohol consumers compared with their nondrinker counterparts. Although the value of alanine aminotransferase was higher in the chronic drinkers, it did not reveal any significant difference (P = 0.11). The coagulation parameters, prothrombin time and activated partial thromboplastin time were investigated among chronic drinkers and nondrinkers. The mean value of prothrombin time and activated partial thromboplastin time was significantly higher in the chronic alcohol drinkers compared to the nondrinkers (P = 0.04 and P = 0.02 respectively). We observed a positive and significant correlation between values of liver enzymes, serum gamma glutamyl transferase and aspartate aminotransferase, and values of prothrombin time among alcohol consumers (r = 0.72 and r = 0.68 respectively). The implementation of policies to target harm reduction strategies among alcoholics is urgently needed, alongside the building of a strong base of public awareness and community support required for the continuity and sustainability of alcohol policies. There is also the need for the Nigerian government to enforce tighter regulations and restrictions on the production and distribution of alcoholic beverages to reduce harmful use, and protect young people and other vulnerable groups.
Personalized Dynamics Models for Adaptive Assistive Navigation Interfaces

We explore the role of personalization for assistive navigational systems (e.g., service robot, wearable system or smartphone app) that guide visually impaired users through speech, sound and haptic-based instructional guidance. Based on our analysis of real-world users, we show that the dynamics of blind users cannot be accounted for by a single universal model but instead must be learned on an individual basis. To learn personalized instructional interfaces, we propose PING (Personalized INstruction Generation agent), a model-based reinforcement learning framework which aims to quickly adapt its state transition dynamics model to match the reactions of the user using a novel end-to-end learned weighted majority-based regression algorithm. In our experiments, we show that PING learns dynamics models significantly faster compared to baseline transfer learning approaches on real-world data. We find that through better reasoning over personal mobility nuances, interaction with surrounding obstacles, and the current navigation task, PING is able to improve the performance of instructional assistive navigation at the most crucial junctions such as turns or veering paths. To enable sufficient planning time over user responses, we emphasize prediction of human motion for long horizons. Specifically, the learned dynamics models are shown to consistently improve long-term position prediction by over 1 meter on average (nearly the width of a hallway) compared to baseline approaches even when considering a prediction horizon of 20 seconds into the future.
Temporal landmark validation in CML

Current techniques to concurrent map building and localization (CML) have been devised for static environments, and lack robustness in more realistic situations. In this communication we provide new ideas that extend the typical stochastic estimation approach to CML, to take into account the dynamics of the environment. The basic idea consists on using the history of data association mismatches for the computation of the likelihood of future data association. The incorporation of a novel temporal landmark quality test, together with the spatial compatibility tests already available, help alleviate the difficulty of data association. We propose a pair of temporal landmark quality functions to aid in those situations in which landmark observations might not be consistent in time; and show how by incorporating these functions, the overall estimation-theoretic approach to CML is improved. Special attention is paid in that the removal of landmarks from the map does not violate the basic convergence properties of the localization and map building algorithms already described in the literature. Namely, asymptotic convergence and full correlation.
Identification and application of the concepts important for accurate and reliable protein secondary structure prediction

A protein secondary structure prediction method from multiply aligned homologous sequences is presented with an overall per residue three‐state accuracy of 70.1%. There are two aims: to obtain high accuracy by identification of a set of concepts important for prediction followed by use of linear statistics; and to provide insight into the folding process. The important concepts in secondary structure prediction are identified as; residue conformational propensities, sequence edge effects, moments of hydrophobicity, position of insertions and deletions in aligned homologous sequence, moments of conservation, auto‐correlation, residue ratios, secondary structure feedback effects, and filtering. Explicit use of edge effects, moments of conservation, and auto‐correlation are new to this paper. The relative importance of the concepts used in prediction was analyzed by stepwise addition of information and examination of weights in the discrimination function. The simple and explicit structure of the prediction allows the method to be reimplemented easily. The accuracy of a prediction is predictable a priori. This permits evaluation of the utility of the prediction: 10% of the chains predicted were identified correctly as having a mean accuracy of >80%. Existing high‐accuracy prediction methods are “black‐box” predictors based on complex nonlinear statistics (e.g., neural networks in P.HD: Rost & Sander, 1993a). For medium‐ to short‐length chains (≥90 residues and <170 residues), the prediction method is significantly more accurate (P < 0.01) than the PHD algorithm (probably the most commonly used algorithm). In combination with the PHD, an algorithm is formed that is significantly more accurate than either method, with an estimated overall three‐state accuracy of 72.4%, the highest accuracy reported for any prediction method.
easuring time preferences : A comparison of experimental ethods

Eliciting time preferences has become an important component of both laboratory and field experiments, yet there is no consensus as how to best measure discounting. We examine the predictive validity of two recent, simple, easily administered, and individually successful elicitation tools: convex time budgets (CTB) and double multiple price lists (DMPL). Using similar methods, the CTB and DMPL are compared using withinand out-of-sample predictions. While each perform equally well within sample, the CTB significantly outperforms the DMPL on out-of-sample measures. © 2015 Elsevier B.V. All rights reserved.
Genetics and Pathogenesis of Diffuse Large B‐Cell Lymphoma

Background Diffuse large B‐cell lymphomas (DLBCLs) are phenotypically and genetically heterogeneous. Gene‐expression profiling has identified subgroups of DLBCL (activated B‐cell–like [ABC], germinal‐center B‐cell–like [GCB], and unclassified) according to cell of origin that are associated with a differential response to chemotherapy and targeted agents. We sought to extend these findings by identifying genetic subtypes of DLBCL based on shared genomic abnormalities and to uncover therapeutic vulnerabilities based on tumor genetics. Methods We studied 574 DLBCL biopsy samples using exome and transcriptome sequencing, array‐based DNA copy‐number analysis, and targeted amplicon resequencing of 372 genes to identify genes with recurrent aberrations. We developed and implemented an algorithm to discover genetic subtypes based on the co‐occurrence of genetic alterations. Results We identified four prominent genetic subtypes in DLBCL, termed MCD (based on the co‐occurrence of MYD88L265P and CD79B mutations), BN2 (based on BCL6 fusions and NOTCH2 mutations), N1 (based on NOTCH1 mutations), and EZB (based on EZH2 mutations and BCL2 translocations). Genetic aberrations in multiple genes distinguished each genetic subtype from other DLBCLs. These subtypes differed phenotypically, as judged by differences in gene‐expression signatures and responses to immunochemotherapy, with favorable survival in the BN2 and EZB subtypes and inferior outcomes in the MCD and N1 subtypes. Analysis of genetic pathways suggested that MCD and BN2 DLBCLs rely on “chronic active” B‐cell receptor signaling that is amenable to therapeutic inhibition. Conclusions We uncovered genetic subtypes of DLBCL with distinct genotypic, epigenetic, and clinical characteristics, providing a potential nosology for precision‐medicine strategies in DLBCL. (Funded by the Intramural Research Program of the National Institutes of Health and others.)
Polymorphisms of nitric oxide synthase and GTP cyclohydrolase I genes in Japanese patients with medication overuse headaches

We investigated whether polymorphisms of the endothelial nitric oxide synthase (eNOS), neuronal NOS (nNOS), and GTP cyclohydrolase I (GTPCH) genes are involved in the aggravation of migraine induced by overuse of medications. We studied 47 patients with migraine (six males and 41 females; 36.4 ± 10.3 years of age) and 22 patients with migraine exhibiting medication overuse headache (MOH, one male and 21 females; 39.6 ± 9.9 years of age). The genotypes of polymorphisms of the eNOS (rs1799983), nNOS (rs2682826), and GTPCH (rs841) genes were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The genotypic distributions of rs2682826 (T/T plus T/C vs. C/C, P = 0.254), rs1799983 (G/G vs. G/T plus T/T, P = 1.000), and rs841 (T/T plus T/C vs. C/C, P = 0.149) were not significantly different between patients with migraine and patients with MOH. The results of this study showed an absence of association between the polymorphisms of eNOS, nNOS, and GTPCH genes and the complication of MOH in patients with migraine.
A comparison of voids in stone skeleton mixtures and voids in aggregate fractions

The voids in the stone skeleton play an important role in the properties of stone mastic asphalt mixtures. The voids in these types of asphalt mixtures are to a large extent a product of the proportions of the different aggregate fractions that form the stone skeleton. However, the relationship between the voids in the asphalt mixture and the voids in the individual aggregate fractions that form the skeleton is not clearly understood. The aim of this study was to investigate and if possible quantify this relationship. The voids in the stone mastic asphalt mixtures were determined from gyratory compacted specimens while the voids in the aggregate fractions were determined from rodded aggregate fractions specimens. The aggregate fractions were compacted using the rodding method that is used in the determination of the rodded unit weight in the Bailey mix design method. The study showed that the voids in the stone mastic asphalt mixtures can be related to the voids in the aggregate fractions that form the skeleton in a logical manner.
In vitro and in vivo evaluation of kenaf (Hibiscus cannabinus L.) as a roughage source for beef cattle

Objective The goal of this study was to evaluate kenaf as a roughage source in vitro and its effects on meat quality of Hanwoo (Korean native) cattle. Methods Three roughage materials, rice straw silage, ryegrass silage, and kenaf silage, were tested in a batch culture and feeding trial. Rumen fermentation parameters, including gas, pH, volatile fatty acid (VFA), and ammonia were analyzed. In the feeding trial, Hanwoo steers (373.5±5.1 kg, n = 36, 11 month of age) were divided into three feeding groups (n = 12 each). Animals were fed with each silage and concentrate until the fattening stage. Results Crude protein, ether extract, and non-structural carbohydrates were greater in kenaf silage. Total gas production was higher in ryegrass silage, followed by kenaf silage and rice straw silage (p<0.05). Total VFA and individual VFA (acetate, propionate, and n-butyrate) were greater in kenaf silage than rice straw silage (p<0.05). In vitro dry matter digestibility showed a similar trend to that of total gas and VFA production; it was higher in ryegrass silage and lower in rice straw (p<0.05). Throughout the feeding trial, the rice straw silage group showed significantly greater average daily gain than did the others (p<0.05). The feed conversion ratio in the group fed kenaf silage was significantly greater than that of others (p<0.05). No significant differences were observed in yield or quality traits, including carcass weight, ribeye area, backfat thickness, and scores for marbling, meat color, and fat color (p>0.05). Conclusion The results indicated that no negative effects on growth performance and carcass characteristics occurred across treatments. Therefore, kenaf could be substituted for rice straw, which is most widely used as a roughage source in Korea.
Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network

ABSTRACT The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, yet the components and structure of the STM gene regulatory network (GRN) are largely unknown. Here, we show that transcriptional regulators are overrepresented among STM-regulated genes and, using these as GRN components in Bayesian network analysis, we infer STM GRN associations and reveal regulatory relationships between STM and factors involved in multiple aspects of SAM function. These include hormone regulation, TCP-mediated control of cell differentiation, AIL/PLT-mediated regulation of pluripotency and phyllotaxis, and specification of meristem-organ boundary zones via CUC1. We demonstrate a direct positive transcriptional feedback loop between STM and CUC1, despite their distinct expression patterns in the meristem and organ boundary, respectively. Our further finding that STM activates expression of the CUC1-targeting microRNA miR164c combined with mathematical modelling provides a potential solution for this apparent contradiction, demonstrating that these proposed regulatory interactions coupled with STM mobility could be sufficient to provide a mechanism for CUC1 localisation at the meristem-organ boundary. Our findings highlight the central role for the STM GRN in coordinating SAM functions. Highlighted Article: The Arabidopsis transcription factor SHOOT MERISTEMLESS coordinates multiple aspects of meristem function by regulating the expression of other transcription factors with key roles in pluripotency and pattern formation.
Pathways of association between maternal haemoglobin and stillbirth: path-analysis of maternity data from two hospitals in England

Objective To investigate the mechanisms that link maternal haemoglobin concentration with stillbirth. Design A retrospective cohort analysis using anonymised maternity data from two hospitals in England. Setting The Royal Wolverhampton NHS Trust and Guy’s and St Thomas’ NHS Foundation Trust. Study population 12 636 women with singleton pregnancies ≥24 weeks of gestation giving birth in the two hospitals during 2013–2015. Method A conceptual framework of hypothesised pathways through birth weight-for-gestational age and maternal infection including potential confounders and other risk factors was developed and examined using path-analysis. Path-analysis was performed by fitting a set of regression equations using weighted least squares adjusted for mean and variance. Goodness-of-fit indices were estimated. Main outcome measures Coefficient of association (β) for relationship between each parameter, and direct, indirect and total effects via the postulated pathways. Results The path-model showed a significant adjusted indirect negative effect of maternal haemoglobin on stillbirth mediated via birth weight-for-gestational age (standardised estimate (SE)=−0.01; 95% CI=−0.01 to −0.001; P=0.028). The effect through maternal infection was not significant at P<0.05 (SE=0.001; 95% CI=−0.004 to 0.01; P=0.610). There was a residual direct negative effect of maternal haemoglobin on stillbirth (SE=−0.12; 95% CI −0.23 to −0.02; P=0.020) after accounting for the two pathways. Total indirect SE=−0.004; 95% CI −0.01 to 0.003; P=0.267; total direct and indirect SE=−0.13; 95% CI −0.23 to −0.02; P=0.016. The goodness-of-fit indices showed a good fit between the model and the data. Conclusion While some of the influence on risk of stillbirth acts through low birth weight-for-gestational age, the majority does not. Several new mechanisms have been suggested for how haemoglobin may be exerting its influence on the risk of stillbirth possibly involving genetic, epigenetic and/or alternative obstetric and nutritional pathologies, but much more research is needed.
Codes With Local Regeneration and Erasure Correction

Regenerating codes and codes with locality are two coding schemes that have recently been proposed, which in addition to ensuring data collection and reliability, also enable efficient node repair. In a situation where one is attempting to repair a failed node, regenerating codes seek to minimize the amount of data downloaded for node repair, while codes with locality attempt to minimize the number of helper nodes accessed. This paper presents results in two directions. In one, this paper extends the notion of codes with locality so as to permit local recovery of an erased code symbol even in the presence of multiple erasures, by employing local codes having minimum distance >2. An upper bound on the minimum distance of such codes is presented and codes that are optimal with respect to this bound are constructed. The second direction seeks to build codes that combine the advantages of both codes with locality as well as regenerating codes. These codes, termed here as codes with local regeneration, are codes with locality over a vector alphabet, in which the local codes themselves are regenerating codes. We derive an upper bound on the minimum distance of vector-alphabet codes with locality for the case when their constituent local codes have a certain uniform rank accumulation property. This property is possessed by both minimum storage regeneration (MSR) and minimum bandwidth regeneration (MBR) codes. We provide several constructions of codes with local regeneration which achieve this bound, where the local codes are either MSR or MBR codes. Also included in this paper, is an upper bound on the minimum distance of a general vector code with locality as well as the performance comparison of various code constructions of fixed block length and minimum distance.
Sarinfacetamides A and B, Nitrogenous Diterpenoids with Tricyclo[6.3.1.01,5]dodecane Scaffold from the South China Sea Soft Coral Sarcophyton infundibuliforme.

Two novel nitrogenous diterpenoids, sarinfacetamides A (1) and B (2), featuring an uncommon tricyclo[6.3. 1.01,5]dodecane scaffold, and a known related diterpene (3) were isolated from the South China Sea soft coral Sarcophyton infundibuliforme. Their structures, including the absolute configuration of 1, were established by extensive spectroscopic analysis and TDDFT-ECD calculation. Compounds 1 and 3 exhibited interesting promotion effects on the ConA-induced T lymphocyte proliferation. A plausible biosynthetic pathway for 1 and 2 was also proposed.