Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Marek’s disease virus transmission: a framework for evaluating the impact of farming practices and evolution on disease

Marek’s disease virus (MDV) is a pathogen of chickens whose control has twice been un-dermined by pathogen evolution. Disease ecology is believed to be the main driver of this evolution, yet mathematical models of MDV disease ecology have never been confronted with data to test their reliability. Here, we develop a suite of MDV models that differ in the ecological mechanisms they include. We fit these models with maximum likelihood in ‘pomp’ to data on MDV concentration in dust collected from two commercial broiler farms. Using AIC to compare the models, we find that virus dynamics are influenced by between-flock variation in host susceptibility to virus, shedding rate from infected birds, and cleanout efficiency. We also find evidence that virus is reintroduced to farms approximately once per month, but we do not find evidence that virus sanitization rates vary between flocks. Of the models that survive model selection, we find agreement between parameter estimates and previous experimental data, as well as agreement between field data and the predictions of these models, suggesting robustness of model predictions. Using the set of surviving models, we explore how changes to farming practices are predicted to influence MDV costs, should pathogen evolution undermine existing control measures. By quantitatively capturing the mechanisms of disease ecology, we have laid the groundwork to explore the future trajectory of virus evolution.
Energy saving and capacity gain of micro sites in regular LTE networks: downlink traffic layer analysis

We study the effect of deployment of low cost, low power micro base stations along with macro base stations on energy consumption and capacity of downlink LTE. [1] studied this problem, using spectral area efficiency as the performance metric. We show that the analysis proposed in [1] is inaccurate as the traffic layer specifications of LTE networks is not included in the analysis. We also investigate the effect of user association and frequency band allocation schemes on energy consumption and capacity of LTE networks. Specifically, we add the following three important elements to the analysis proposed in [1]: a traffic layer analysis that take both the physical and traffic layer specifications of LTE downlink into account; a threshold-based policy to optimally associate users to base stations; and an allocation scheme to better allocate the frequency band to macro and micro base stations. We investigate all combinations of these elements through numerical evaluation and observe that 1. there are important differences between traffic layer and physical layer analysis, 2. threshold-based user association policy improve the traffic capacity of the network by up to 33% without affecting the energy profile of the network, and 3. considerable energy saving and capacity gain can be achieved thought a careful allocation of the frequency band to macro and micro base stations. Finally, we determine the optimal network configuration and show that up to 46% saving in energy can be achieved compared to the case that no micro base stations are deployed in the network.
M31 PIXEL LENSING EVENT OAB-N2: A STUDY OF THE LENS PROPER MOTION

We present an updated analysis of the M31 pixel lensing candidate event OAB-N2 previously reported by Calchi Novati et al. Here we take advantage of new data both astrometrical and photometrical. For astrometry: using archival 4 m KPNO and Hubble Space Telescope/WFPC2 data we perform a detailed analysis of the event source whose result, although not fully conclusive on the source magnitude determination, is confirmed by the following light curve photometry analysis. For photometry: first, unpublished WeCAPP data allow us to confirm OAB-N2, previously reported only as a viable candidate, as a well-constrained pixel lensing event. Second, this photometry enables a detailed analysis in the event parameter space including the effects due to a finite source size. The combined results of these analyses allow us to put a strong lower limit on the lens proper motion. This outcome favors the MACHO lensing hypothesis over self-lensing for this individual event and points the way toward distinguishing between the MACHO and self-lensing hypotheses from larger data sets.
Deep multimodal embedding: Manipulating novel objects with point-clouds, language and trajectories

A robot operating in a real-world environment needs to perform reasoning over a variety of sensor modalities such as vision, language and motion trajectories. However, it is extremely challenging to manually design features relating such disparate modalities. In this work, we introduce an algorithm that learns to embed point-cloud, natural language, and manipulation trajectory data into a shared embedding space with a deep neural network. To learn semantically meaningful spaces throughout our network, we use a loss-based margin to bring embeddings of relevant pairs closer together while driving less-relevant cases from different modalities further apart. We use this both to pre-train its lower layers and fine-tune our final embedding space, leading to a more robust representation. We test our algorithm on the task of manipulating novel objects and appliances based on prior experience with other objects. On a large dataset, we achieve significant improvements in both accuracy and inference time over the previous state of the art. We also perform end-to-end experiments on a PR2 robot utilizing our learned embedding space.
Hazard rate of tumor recurrence over time in patients with colon cancer: implications for postoperative surveillance from three Japanese Foundation for Multidisciplinary Treatment of Cancer (JFMC) clinical trials

Purpose: Reliable risk estimates of recurrence are necessary to establish optimal postoperative surveillance strategies. The purpose of the present study was to clarify changes in the hazard rate (HR) for tumor recurrence over time in Japanese patients with colon cancer. Methods: Data for 3984 patients from three clinical trials evaluating the benefit of adjuvant chemotherapy for colon cancer were analyzed. Estimated HRs were plotted over time for the entire cohort, as well as for node-positive and node-negative patients separately. The changes in risk were further analyzed according to eight clinical variables, and factors predictive of early (<3 years) and late (>3 years) recurrence were explored using Cox's regression analysis. Results: In node-positive patients, there was a prominent HR peak 0.6 years after surgery, whereas HR remained at consistently low levels in node-negative patients. In node-positive patients, HR decreased steadily until 3 years, after which the decline in HR plateaued. Those with T4 tumors had a prominent HR peak around 1 year, including node-negative patients. The HR for T1/T2 Stage III colon cancers showed a similar pattern as that for T1-T3 node-negative colon cancers. Cox regression analysis revealed that a lack of adjuvant chemotherapy, positive node status, T3/T4 factors, and male gender predict early recurrence, whereas patients with lymph node metastasis, T4 tumors, and a lesser extent of lymph node removal have a higher risk of recurrence 3-4 years after surgery (P<0.05). Conclusion: The present study supports the concept of intensive surveillance during the first 3 years after curative resection. However, a reduction in surveillance intensity may be acceptable for patients with T3 Stage II and T1/T2 Stage III colon cancer.
The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.
Local Rademacher complexities

We propose new bounds on the error of learning algorithms in terms of a data-dependent notion of complexity. The estimates we establish give optimal rates and are based on a local and empirical version of Rademacher averages, in the sense that the Rademacher averages are computed from the data, on a subset of functions with small empirical error. We present some applications to classification and prediction with convex function classes, and with kernel classes in particular.
Modification of some mechanical properties of spruce by radiation induced copolymerization of acrylonitrile and methyl methacrylate with allyl glycidyl ether

In this study, spruce samples were impregnated with acrylonitrile (AN), methyl methacrylate (MMA), allyl glycidyl ether (AGE), AGE/AN or AGE/MMA monomers and monomer mixtures. In situ polymerization (copolymerization) was achieved by gamma irradiation. The relationship between the mechanical properties of the wood-polymer(copolymer) composites and the kind and quantity of polymers and copolymers, irradiation dose and artificial aging treatment of the wood was investigated. The fine structure of wood-polymer(copolymer) composites was determined by Scanning Electron Microscopy. The presence of homopolymer and copolymers increased the mechanical properties of the wood. The compressive strength and Brinell Hardness Numbers, determined for untreated and treated wood samples, indicated that the mechanical strength of wood-polymer (copolyrner) was significantly increased in the presence of P(AGE/MMA). At maximum percent conversion, the percentage increase in the compressive strength with regard to the applied force perpendicular to the fibers in spruce was 218%. After aging for 28 days, it was found that there were no significant changes in mechanical stability.
An empirical study of the perception of language rhythm

Linguists have traditionally classified languages into three rhythm classes, namely stress-timed, syllable-timed and mora-timed languages. However, this classification has remained controversial for various reasons: the search for reliable acoustic cues to the different rhythm types has long remained elusive; some languages are claimed to belong to none of the three classes; and no perceptual study has bolstered the notion. However, Ramus, Nespor & Mehler (1999), Cognition 73, 265-292, have recently proposed an acoustic/phonetic model of the different types of linguistic rhythm, and of their categorization as such by listeners. Their simulations make predictions as to which languages can be discriminated on the basis of their rhythm. Here, we present perceptual experiments that directly test the notion of rhythm classes, the simulations' predictions and the question of intermediate languages. Language discrimination experiments were run using a speech resynthesis technique to ensure that only rhythmical cues are available to the subjects. Languages investigated are English, Spanish, Catalan and Polish. Discrimination results are compatible with the rhythm class hypothesis, but Polish rhythm seems to be different from any other language studied and thus may constitute a new rhythm class. A revised version of the rhythm perception model is proposed to accommodate these findings and more simulations are run to generate new predictions.
Neurotoxicity following chronic intravenous use of “Russian Cocktail”

Introduction. Recently, neurological abnormalities in methcathinone users have been attributed to manganese. We report similar toxicity in three patients following the use of a mixture similar to methcathinone: potassium permanganate, ephedrine, and aspirin. Case Reports. Three teenagers (15 to 19 years old) presented with extrapyramidal abnormalities and movement disorders following chronic intravenous use of a mixture known as “Russian Cocktail”. All three patients had multiple movement disorders. One patient had normal blood manganese concentration (<19 μg/L) and MRI. The other two had elevated blood manganese (2100 μg/L and 3176 μg/L) and MRIs showing bilateral symmetric hyper-intensities on T1-weighted-images in the dentate nucleus, subcortical white substance of cerebellar hemisphere, globus pallidus, and putamen. Abstinence and treatment with EDTA, levodopa, and para-aminosalicylic acid was associated with decreasing blood manganese concentrations and subjective improvement, but no change in objective findings. Discussion. The “Russian Cocktail” likely contains manganese as a result of the oxidation of ephedrine by potassium permanganate in water acidified by acetylsalicylic acid. We believe that manganese with the possible contribution of methcathinone caused the neurological impairments. Conclusions. Three toxic substances have been made into a mixture administered intravenously, similar to methcathinone. Our patients learned of this mixture, called “Russian Cocktail”, from their friends. The toxicity from repeated use of this mixture is one of extrapyramidal abnormalities and movement disorders. Standard therapies were unsuccessful in reversing the clinical toxicity.
Optimizing the management of acute ischaemic stroke: a review of the utilization of intravenous recombinant tissue plasminogen activator (tPA)

What is known and Objective: Thrombolysis using intravenous tissue plasminogen activator (tPA) is the only available evidence‐based treatment for acute ischaemic stroke; however, its current utilization is very low. Therefore, the aim of this article is to review the literature regarding the use of intravenous tPA for the treatment of acute ischaemic stroke. The review will also compare utilization rates of thrombolysis in different centres across the world and identify key reasons for the underutilization of thrombolysis in stroke.
Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein

Human XPG nuclease makes the 3′ incision during nucleotide excision repair of DNA. The enzyme cleaves model DNA bubble structures specifically near the junction of unpaired DNA with a duplex region. It is not yet known, however, whether an unpaired structure is an intermediate during actual DNA repair. We find here that XPG requires opening of >5 bp for efficient cleavage. To seek direct evidence for formation of an open structure around a lesion in DNA during a nucleotide excision repair reaction in vitro, KMnO4 footprinting experiments were performed on a damaged DNA molecule bearing a uniquely placed cisplatin adduct. An unwound open complex spanning ∼25 nucleotides was observed that extended to the positions of 5′ and 3′ incision sites and was dependent on XPA protein and on ATP. Opening during repair occurred prior to strand incision by XPG.
An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

Computational methods have now become a valuable tool to understand the way in which enzymes catalyse chemical reactions and to aid the interpretation of a diverse set of experimental data. This study focuses on the influence of the condensed-phase environment structure on proton transfer mechanisms, with an aim to understand how C–H bond cleavage is mediated in enzymatic reactions. We shall use a combination of molecular simulation, ab initio or semi-empirical quantum chemistry and semi-classical multidimensional tunnelling methods to consider the primary kinetic isotope effects of the enzyme methylamine dehydrogenase (MADH), with reference to an analogous application to triosephosphate isomerase. Analysis of potentially reactive conformations of the system, and correlation with experimental isotope effects, have highlighted that a quantum tunnelling mechanism in MADH may be modulated by specific amino acid residues, such as Asp428, Thr474 and Asp384.
First trimester fetal growth restriction and cardiovascular risk factors in school age children: population based cohort study

Objective To examine whether first trimester fetal growth restriction correlates with cardiovascular outcomes in childhood. Design Population based prospective cohort study. Setting City of Rotterdam, the Netherlands. Participants 1184 children with first trimester fetal crown to rump length measurements, whose mothers had a reliable first day of their last menstrual period and a regular menstrual cycle. Main outcomes measures Body mass index, total and abdominal fat distribution, blood pressure, and blood concentrations of cholesterol, triglycerides, insulin, and C peptide at the median age of 6.0 (90% range 5.7-6.8) years. Clustering of cardiovascular risk factors was defined as having three or more of: high android fat mass; high systolic or diastolic blood pressure; low high density lipoprotein cholesterol or high triglycerides concentrations; and high insulin concentrations. Results One standard deviation score greater first trimester fetal crown to rump length was associated with a lower total fat mass (−0.30%, 95% confidence interval −0.57% to −0.03%), android fat mass (−0.07%, −0.12% to −0.02%), android/gynoid fat mass ratio (−0.53, −0.89 to −0.17), diastolic blood pressure (−0.43, −0.84 to −0.01, mm Hg), total cholesterol (−0.05, −0.10 to 0, mmol/L), low density lipoprotein cholesterol (−0.04, −0.09 to 0, mmol/L), and risk of clustering of cardiovascular risk factors (relative risk 0.81, 0.66 to 1.00) in childhood. Additional adjustment for gestational age and weight at birth changed these effect estimates only slightly. Childhood body mass index fully explained the associations of first trimester fetal crown to rump length with childhood total fat mass. First trimester fetal growth was not associated with other cardiovascular outcomes. Longitudinal growth analyses showed that compared with school age children without clustering of cardiovascular risk factors, those with clustering had a smaller first trimester fetal crown to rump length and lower second and third trimester estimated fetal weight but higher weight growth from the age of 6 months onwards. Conclusions Impaired first trimester fetal growth is associated with an adverse cardiovascular risk profile in school age children. Early fetal life might be a critical period for cardiovascular health in later life.
Usability and Design Guidelines of Smart Canes for Users with Visual Impairments

A white cane is one of the most common mobility aids for the visually impaired. However, it does not help users with visual impairments find obstacles at head- or knee-level, or at distances greater than 1 m. To overcome these difficulties, smart canes with vibration alerts and an extended obstacle detection range have been introduced. However, several usability problems mean that users with visual impairments rarely adopt a smart cane. The goal of this study was to understand the potential for using a smart cane, along with the existing usability problems and then to develop design guidelines for improved smart canes. Both quantitative and qualitative methods were used to address these goals. A quantitative evaluation was performed of users with visual impairments using a prototype smart cane. Then, in-depth interviews of cane users were conducted. The results showed that a smart cane was more effective in avoiding obstacles than a white cane, but there were several potential usability problems. On the basis of the results, design guidelines for a smart cane prototype were devised.
A new approach to prediction of short-range conformational propensities in proteins

MOTIVATION Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data. RESULTS A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.
A quantitative comparison of the influence of individual versus population‐derived vascular input functions on dynamic contrast enhanced‐MRI in small animals

For quantitative analysis of dynamic contrast enhanced magnetic resonance imaging data, the time course of the concentration of the contrast agent in the blood plasma, or vascular input function (VIF), is required. We compared pharmacokinetic parameters derived using individual and population‐based VIFs in mice for two different contrast agents, gadopentetate dimeglumine and P846. Eleven mice with subcutaneous 4T1 breast cancer xenografts were imaged at 7 T. A precontrast T1 map was acquired along with dynamic T1‐weighted gradient echo images before, during, and after a bolus injection of contrast agent delivered via a syringe pump. Each animal's individual VIF and derived population‐averaged VIF were used to extract parameters from the signal‐time curves of tumor tissue at both the region of interest and voxel level. The results indicate that for both contrast agents, Ktrans values estimated using population‐averaged VIF have a high correlation (concordance correlation coefficient > 0.85) with Ktrans values estimated using individual VIF on both a region of interest and voxel level. This work supports the validity of using of a population‐based VIF with a stringent injection protocol in preclinical dynamic contrast enhanced magnetic resonance imaging studies. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.