Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease

Excess hepatic storage of triglycerides is considered a benign condition, but nonalcoholic steatohepatitis (NASH) may progress to fibrosis and promote atherosclerosis. Carriers of the TM6SF2 E167K variant have fatty liver as a result of reduced secretion of very‐low‐density lipoproteins (VLDLs). As a result, they have lower circulating lipids and reduced risk of myocardial infarction. In this study, we aimed to assess whether TM6SF2 E167K affects liver damage and cardiovascular outcomes in subjects at risk of NASH. Liver damage was evaluated in 1,201 patients who underwent liver biopsy for suspected NASH; 427 were evaluated for carotid atherosclerosis. Cardiovascular outcomes were assessed in 1,819 controls from the Swedish Obese Subjects (SOS) cohort. Presence of the inherited TM6SF2 E167K variant was determined by TaqMan assays. In the liver biopsy cohort, 188 subjects (13%) were carriers of the E167K variant. They had lower serum lipid levels than noncarriers (P < 0.05), had more‐severe steatosis, necroinflammation, ballooning, and fibrosis (P < 0.05), and were more likely to have NASH (odds ratio [OR]: 1.84; 95% confidence interval [CI]: 1.23‐2.79) and advanced fibrosis (OR, 2.08; 95% CI: 1.20‐3.55), after adjustment for age, sex, body mass index, fasting hyperglycemia, and the I148M PNPLA3 risk variant. However, E167K carriers had lower risk of developing carotid plaques (OR, 0.49; 95% CI: 0.25‐0.94). In the SOS cohort, E167K carriers had higher alanine aminotransferase ALT and lower lipid levels (P < 0.05), as well as a lower incidence of cardiovascular events (hazard ratio: 0.61; 95% CI: 0.39‐0.95). Conclusions: Carriers of the TM6SF2 E167K variant are more susceptible to progressive NASH, but are protected against cardiovascular disease. Our findings suggest that reduced ability to export VLDLs is deleterious for the liver. (Hepatology 2015;61:506‐514)
On the impact of forgetting on learning machines

People tend not to have perfect memories when it comes to learning, or to anything else for that matter. Most formal studies of learning, however, assume a perfect memory. Some approaches have restricted the number of items that could be retained. We introduce a complexity theoretic accounting of memory utilization by learning machines. In our new model, memory is measured in bits as a function of the size of the input. There is a hierarchy of learnability based on increasing memory allotment. The lower bound results are proved using an unusual combination of pumping and mutual recursion theorem arguments. For technical reasons, it was necessary to consider two types of memory : long and short term.
Modelling motion primitives and their timing in biologically executed movements

Biological movement is built up of sub-blocks or motion primitives. Such primitives provide a compact representation of movement which is also desirable in robotic control applications. We analyse handwriting data to gain a better understanding of primitives and their timings in biological movements. Inference of the shape and the timing of primitives can be done using a factorial HMM based model, allowing the handwriting to be represented in primitive timing space. This representation provides a distribution of spikes corresponding to the primitive activations, which can also be modelled using HMM architectures. We show how the coupling of the low level primitive model, and the higher level timing model during inference can produce good reconstructions of handwriting, with shared primitives for all characters modelled. This coupled model also captures the variance profile of the dataset which is accounted for by spike timing jitter. The timing code provides a compact representation of the movement while generating a movement without an explicit timing model produces a scribbling style of output.
Amborella trichopoda – Cultivation of the most ancestral angiosperm in botanic gardens

Amborella trichopoda Baill. , the most ancestral angiosperm, has been successfully cultivated in the Botanic Gardens of the University of Bonn in Germany (BG Bonn) for more than a decade. The distribution of this plant – limited to the South Pacific island of New Caledonia – and its cultivation has so far only been achieved in a few botanic gardens. This paper provides details about the cultivation and propagation of Amborella, and information on its cultivation in botanic gardens around the world. The authors propose that the collections of this plant in botanic gardens could be used to establish ex situ conservation collections.
Typical sumsets of linear codes

Given two identical linear codes C with rate R over Fq of length n, we independently pick one codeword from each codebook uniformly at random. A sumset is formed by adding these two codewords entry-wise as integer vectors and a sumset is called typical, if the sum falls inside this set with high probability. In this paper we show that the asymptotic size of such typical sumsets for most codes is min{22nR, 2n(R+D)} where D depends solely on the alphabet size q. More generally, we completely characterize the asymptotic size of typical sumsets of two nested linear codes C1, C2 with different rates. We also provide two applications of the results, one on a computation problem over the general two-user multiple-access channel, and one on a communication problem over an additive two-user multiple-access channel.
Discretization of MIMO Systems with Nonuniform Input and Output Fractional Time Delays

Input and output time delays in continuous-time state-space systems are treated separately as their effects are encountered before and after the state dynamics. Existing discretization techniques for such systems usually consider the delays to be integer multiples of the sampling time. This work develops a discretization procedure for multi-variable state-space systems with nonuniform input and/or output delays, in which such delays are non-integer multiples of the sampling time. A heat exchanger process example is used to illustrate the advantage of using this technique compared to the discretization approach of rounding the delays to the closest integer multiple of the sampling time. A significant improvement towards the continuous-time response was noted when considering the fractional delays into the discretized model. This discretization improvement is expected to benefit the design and performance of model-based controllers
Learning to model relatedness for news recommendation

With the explosive growth of online news readership, recommending interesting news articles to users has become extremely important. While existing Web services such as Yahoo! and Digg attract users' initial clicks by leveraging various kinds of signals, how to engage such users algorithmically after their initial visit is largely under-explored. In this paper, we study the problem of post-click news recommendation. Given that a user has perused a current news article, our idea is to automatically identify "related" news articles which the user would like to read afterwards. Specifically, we propose to characterize relatedness between news articles across four aspects: relevance, novelty, connection clarity, and transition smoothness. Motivated by this understanding, we define a set of features to capture each of these aspects and put forward a learning approach to model relatedness. In order to quantitatively evaluate our proposed measures and learn a unified relatedness function, we construct a large test collection based on a four-month commercial news corpus with editorial judgments. The experimental results show that the proposed heuristics can indeed capture relatedness, and that the learned unified relatedness function works quite effectively.
T‐lymphoid blast crisis in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is considered to be a pleuripotential stem cell disorder with the capacity to differentiate into myeloid, erythroid, megakaryocytic, and lymphoid cell lines. Consequently, blast crisis (BC) involving each of the above lineages has been well described. Among lymphoblastic crises, differentiation frequently occurs along B‐cell lineage. We report four patients of CML who terminated in T‐cell extramedullary BC in lymph nodes after a variable duration of chronic phase. The T‐lineage was established by characteristic cytochemical staining and reactivity with a panel of anti‐T‐cell monoclonal antibodies. All four cases were Philadelphia (Ph) chromosome positive and demonstrated the Ph chromosome and associated anomalies (extra Ph, +19) in the lymph nodes. Our data adds to the growing evidence that CML is a disorder of the common stem cell from which T, B, and myeloid precursors originate.
Comparison study of image fusion based on multi-scale transforms and sparse representation

Nowadays image fusion becomes very intensive research. Multi-scale transform and sparse representation are typical tools in fusion processing. However, most of efforts are focus on the accurate registration images. A comparative study of MST and SR method over mis-registration are proposed to investigate the robust performance. Five metrics are adopted to evaluate the quality of different methods. The experimental results suggest that the kinds of transform play a crucial role for MST methods, and SR generally shows better performance. Introduction Recently many image fusion methods [1] are developed to integrate more comprehensive information from different sensors which provide complementary and redundant information. During the past two decades, multi-scale transform (MST) are the most popular tools [1] used in various image fusion scenarios. These methods assume that the underlying salient information of the source images can be extracted from the decomposed coefficients. Apparently, the selection of transform domain plays a crucial role. But those transform have fixed bases and cannot be used to form an arbitrary family of signals. Recently Yang and Li [2] introduced sparse representation (SR) into image fusion, which utilize the learning-based approach to obtain adaptive bases for source images. Although both the MSTbased and SR-based methods have achieved great success in image fusion [3], it is worthwhile to notice that the quality of fused results will be deteriorated rapidly because of the tiny difference between the pixels of the source images. Furthermore, it is practically hard to make an accurate registration between multimodal sensors. In this paper, we concern comparison of MST and SR methods on mis-registration source images to further investigated about the robust performance. Image fusion algorithms Multi-scale transforms. As shown in Fig.1, the detailed fusion scheme using multi-scale transforms contains the following steps: (1) Applying a specific multi-scale transform decomposed the source images into one low-pass and several high-pass sub-bands. (2) Merge A L and B L to obtain F L with the ‘average’ rule. (3) Merge A H and B H to obtain F H with different rules such as Burts method [4]. (4) Perform the corresponding inverse MST over F L and F H to reconstruct the final fused image F I . 4th International Conference on Advanced Materials and Information Technology Processing (AMITP 2016) © 2016. The authors Published by Atlantis Press 376
A Succinct Indexes for Strings , Binary Relations and Multi-labeled Trees

We define and design succinct indexes for several abstract data types (ADTs). The concept is to design auxiliary data structures that ideally occupy asymptotically less space than the information-theoretic lower bound on the space required to encode the given data, and support an extended set of operations using the basic operators defined in the ADT. The main advantage of succinct indexes as opposed to succinct (integrated data/index) encodings is that we make assumptions only on the ADT through which the main data is accessed, rather than the way in which the data is encoded. This allows more freedom in the encoding of the main data. In this paper, we present succinct indexes for various data types, namely strings, binary relations and multi-labeled trees. Given the support for the interface of the ADTs of these data types, we can support various useful operations efficiently by constructing succinct indexes for them. When the operators in the ADTs are supported in constant time, our results are comparable to previous results, while allowing more flexibility in the encoding of the given data. Using our techniques, we design a succinct encoding that represents a string of length n over an alphabet of size σ using nHk(S)+lg σ ·o(n)+O( n lg σ lg lg lg σ ) bits to support access/rank/select operations in o((lg lg σ) ) time, for any fixed constant > 0. We also design a succinct text index using nH0(S) +O( n lg σ lg lg σ ) bits that supports finding all the occ occurrences of a given pattern of length m in O(m lg lg σ+ occ lgn/ lg σ) time, for any fixed constant > 0. Previous results on these two problems either have a lg σ factor instead of lg lg σ in the running time, or are not compressed. Finally, we present succinct encodings of binary relations and multi-labeled trees that are more compact than previous structures.
Waiting algorithms for synchronization in large-scale multiprocessors

Through analysis and experiments, this paper investigates two-phase waiting algorithms to minimize the cost of waiting for synchronization in large-scale multiprocessors. In a two-phase algorithm, a thread first waits by polling a synchronization variable. If the cost of polling reaches a limit <italic>L<subscrpt>poll</subscrpt></italic> and further waiting is necessary, the thread is blocked, incurring an additional fixed cost, <italic>B</italic>. The choice of <italic>L<subscrpt>poll</subscrpt></italic> is a critical determinant of the performance of two-phase algorithms. We focus on methods for statically determining <italic>L<subscrpt>poll</subscrpt></italic> because the run-time overhead of dynamically determining <italic>L<subscrpt>poll</subscrpt></italic> can be comparable to the cost of blocking in large-scale multiprocessor systems with lightweight threads. Our experiments show that <italic>always-block</italic> (<italic>L<subscrpt>poll</subscrpt></italic> = 0) is a good waiting algorithm with performance that is usually close to the best of the algorithms compared. We show that even better performance can be achieved with a static choice of <italic>L<subscrpt>poll</subscrpt></italic> based on knowledge of likely wait-time distributions. Motivated by the observation that different synchronization types exhibit different wait-time distributions, we prove that a static choice of <italic>L<subscrpt>poll</subscrpt></italic> can yield close to optimal on-line performance against an adversary that is restricted to choosing wait times from a fixed family of probability distributions. This result allows us to make an optimal static choice of <italic>L<subscrpt>poll</subscrpt></italic> based on synchronization type. For exponentially distributed wait times, we prove that setting <italic>L<subscrpt>poll</subscrpt></italic> = 1n(e-1)<italic>B</italic> results in a waiting cost that is no more than <italic>e/(e-1)</italic> times the cost of an optimal off-line algorithm. For uniformly distributed wait times, we prove that setting <italic>L</italic><subscrpt>poll</subscrpt>=1/2(square root of 5 -1)<italic>B</italic> results in a waiting cost that is no more than (square root of 5 + 1)/2 (the golden ratio) times the cost of an optimal off-line algorithm. Experimental measurements of several parallel applications on the Alewife multiprocessor simulator corroborate our theoretical findings.
Taxonomy and Identification of the Burkholderia cepacia Complex

At the beginning of this review it is essential to clarify the terminology that will be used to refer to the members of the Burkholderia cepacia complex and their relatives. The name B. cepacia will relate only to B. cepacia genomovar I. Strains resembling B. cepacia may belong to the B. cepacia
Inflammatory responses to influenza vaccination at the extremes of age

Age affects the immune response to vaccination, with individuals at the extremes of age responding poorly. The initial inflammatory response to antigenic materials shapes the subsequent adaptive response and so understanding is required about the effect of age on the profile of acute inflammatory mediators. In this study we measured the local and systemic inflammatory response after influenza vaccination or infection in neonatal, young adult and aged mice. Mice were immunized intramuscularly with inactivated influenza vaccine with and without the adjuvant MF59 and then challenged with H1N1 influenza. Age was the major factor affecting the inflammatory profile after vaccination: neonatal mice had more interleukin‐1α (IL‐1α), C‐reactive protein (CRP) and granulocyte–macrophage colony‐stimulating factor (GMCSF), young adults more tumour necrosis factor‐α (TNF), and elderly mice more interleukin‐1 receptor antagonist (IL‐1RA), IL‐2RA and interferon‐γ‐induced protein 10 (IP10). Notably the addition of MF59 induced IL‐5, granulocyte colony‐stimulating factor (G‐CSF), Keratinocyte Chemotractant (KC) and monocyte chemoattractant protein 1 (MCP1) in all ages of animals and levels of these cytokines correlated with antibody responses. Age also had an impact on the efficacy of vaccination: neonatal and young adult mice were protected against challenge, but aged mice were not. There were striking differences in the localization of the cytokine response depending on the route of exposure: vaccination led to a high serum response whereas intranasal infection led to a low serum response but a high lung response. In conclusion, we demonstrate that age affects the inflammatory response to both influenza vaccination and infection. These age‐induced differences need to be considered when developing vaccination strategies for different age groups.
Evaluation in the context of natural language generation

What role should evaluation play in the development of natural language generation (nlg) techniques and systems? In this paper we describe what is involved in natural language generation, and survey how evaluation has figured in work in this area to date. We comment on the issues raised by this existing work and on how the problems of nlg evaluation are diVerent from the problems of evaluating work in natural language understanding. The paper is concluded by suggesting a way forward by looking more closely at the component problems that are addressed in natural language generation research; a particular text generation application is examined and the issues that are raised in assessing its performance on a variety of dimensions are looked at. ” 1998 Academic Press
Purification of Streptococcus group C bacteriophage lysin

A simple procedure for the purification of Streptococcus group C phage lysin to apparent homogeneity is described. The electrophoretically pure, enzymatically stable polypeptide of 98,000 molecular weight converted Streptococcus (groups A, F, and H) cells into spheroplasts within 5 min at 0 degrees C or within less than a minute at 37 degrees C.
Anatomic-landmark detection using graphical context modelling

Anatomical landmarks in images play an important role in medical practice. This paper presents a graphical model that fully automatically detects such landmarks. The model includes a unary potential using a random forest classifier based on local appearance and binary and ternary potentials encoding geometrical context among different landmarks. The weightings of different potentials are learned in a maximum likelihood manner. The final detection result is formulated as the maximum-a-posteriori estimation jointly over the whole set of landmarks in one image. For validation, the model is applied to detect right-ventricle insert points in cardiac MR images. The result shows that the context modelling is able to substantially improve the overall accuracy.
The Mesorhizobium loti purB Gene Is Involved in Infection Thread Formation and Nodule Development in Lotus japonicus

ABSTRACT The purB and purH mutants of Mesorhizobium loti exhibited purine auxotrophy and nodulation deficiency on Lotus japonicus. In the presence of adenine, only the purH mutant induced nodule formation and the purB mutant produced few infection threads, suggesting that 5-aminoimidazole-4-carboxamide ribonucleotide biosynthesis catalyzed by PurB is required for the establishment of symbiosis.
Performance of the deliberate clipping with adaptive symbol selection for strictly band-limited OFDM systems

The performance of the strictly band-limited OFDM systems with deliberate clipping is examined in terms of the peak-to-average power ratio (PAPR) and the resultant bit error performance. The clipping is performed on the OFDM signals sampled at the Nyquist rate, followed by the ideal low-pass filter, Since the low-pass filter considerably enlarges the PAPR, there is a severe limitation in PAPR reduction capability. Thus, in order to achieve further reduction of the PAPR, the application of the adaptive symbol selection scheme is also considered. It is shown that the significant PAPR reduction with moderate complexity can be achieved by the combination of the clipping and the adaptive symbol selection. The price to be paid for PAPR reduction by this scheme is its performance degradation. The paper theoretically analyzes the bit error rate performance of the OFDM system with the Nyquist-rate clipping combined with the adaptive symbol selection, and considers the use of the forward error correction for compensation of the degradation. It is shown that even though the clipping scheme causes severe loss in required signal-to-noise ratio, the use of a powerful channel coding scheme such as turbo codes significantly alleviates the bit error rate performance degradation.
Hepatocellular Carcinoma: Reasons for Phase III Failure and Novel Perspectives on Trial Design

Hepatocellular carcinoma (HCC) is a major health problem. Most patients with HCC experience a recurrence after resection/ablation or are diagnosed at advanced stages. Sorafenib remains the only approved systemic drug for these patients. Molecular therapies targeting signaling cascades involved in hepatocarcinogenesis have been explored in phase III clinical trials. However, none of the drugs tested have shown positive results in the first-line (brivanib, sunitinib, erlotinib, and linifanib) or second-line (brivanib, everolimus) setting after sorafenib progression. Reasons for failure are heterogeneous and include lack of understanding of critical drivers of tumor progression/dissemination, liver toxicity, flaws in trial design, or marginal antitumoral potency. These trials are also challenging time to progression as a surrogate endpoint of survival. Trials ongoing testing drugs head-to-head versus sorafenib in “all comers” might have difficulties in achieving superior results in the first line. Novel trials are also designed testing drugs in biomarker-based subpopulations of patients with HCC. Most common mutations, however, are undruggable, such as p53 and CTNNB1. Two types of studies are proposed: (i) phase II pivotal proof-of-concept studies testing drugs blocking potential oncogenic addiction loops, such as the one testing MEK inhibitors in RAS+ patients or amplification of FGF19 as a target; and (ii) phase II to III studies using biomarker-based trial enrichment for defining HCC subpopulations, such as the case of enriching for MET-positive tumors. These strategies have been deemed successful in breast, melanoma, and lung cancers, and are expected to change the landscape of trial design of HCC. Clin Cancer Res; 20(8); 2072–9. ©2014 AACR.