Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust inference of groups in gene expression time-courses using mixtures of HMMs

MOTIVATION Genetic regulation of cellular processes is frequently investigated using large-scale gene expression experiments to observe changes in expression over time. This temporal data poses a challenge to classical distance-based clustering methods due to its horizontal dependencies along the time-axis. We propose to use hidden Markov models (HMMs) to explicitly model these time-dependencies. The HMMs are used in a mixture approach that we show to be superior over clustering. Furthermore, mixtures are a more realistic model of the biological reality, as an unambiguous partitioning of genes into clusters of unique functional assignment is impossible. Use of the mixture increases robustness with respect to noise and allows an inference of groups at varying level of assignment ambiguity. A simple approach, partially supervised learning, allows to benefit from prior biological knowledge during the training. Our method allows simultaneous analysis of cyclic and non-cyclic genes and copes well with noise and missing values. RESULTS We demonstrate biological relevance by detection of phase-specific groupings in HeLa time-course data. A benchmark using simulated data, derived using assumptions independent of those in our method, shows very favorable results compared to the baseline supplied by k-means and two prior approaches implementing model-based clustering. The results stress the benefits of incorporating prior knowledge, whenever available. AVAILABILITY A software package implementing our method is freely available under the GNU general public license (GPL) at http://ghmm.org/gql
Generalized loop-back recovery in optical mesh networks

Current means of providing loop-back recovery, which is widely used in SONET, rely on ring topologies, or on overlaying logical ring topologies upon physical meshes. Loop-back is desirable to provide rapid preplanned recovery of link or node failures in a bandwidth-efficient distributed manner. We introduce generalized loop-back, a novel scheme for performing loop-back in optical mesh networks. We present an algorithm to perform recovery for link failure and one to perform generalized loop-back recovery for node failure. We illustrate the operation of both algorithms, prove their validity, and present a network management protocol algorithm, which enables distributed operation for link or node failure. We present three different applications of generalized loop-back. First, we present heuristic algorithms for selecting recovery graphs, which maintain short maximum and average lengths of recovery paths. Second, we present WDM-based loop-back recovery for optical networks where wavelengths are used to back up other wavelengths. We compare, for WDM-based loop-back, the operation of generalized loop-back operation with known ring-based ways of providing loop-back recovery over mesh networks. Finally, we introduce the use of generalized loop-back to provide recovery in a way that allows dynamic choice of routes over preplanned directions.
Reevaluation of formulas for predicting creatinine clearance in adults and children, using compensated creatinine methods.

In clinical practice, glomerular filtration rate (GFR) is the most important marker for evaluation of renal function (1). Dosages of drugs that are eliminated by glomerular filtration are often based on GFR. At present, the most reliable methods for accurate assessment of overall GFR require intravenous administration of exogenous compounds and are both cumbersome and expensive. In clinical practice, creatinine clearance (CrCl) is widely accepted as a simple measure of GFR. However, CrCl systematically overestimates GFR because creatinine is freely filtered by the glomerulus and is also secreted by the proximal tubule. In the earliest methods, serum creatinine was assayed by the Jaffe reaction after deproteinization, eliminating the pseudo-chromogen effect of proteins (2). Similarly, the first automated methods used dialysis membranes to prevent interference from plasma proteins. Today, however, analyzers use undiluted serum and plasma, making them subject to the so-called “protein error” (3). This produces a positive difference of ∼27 μmol/L creatinine compared with HPLC methods (4)(5)(6)(7). Because urine contains relatively little or no protein, the protein error affects only creatinine determinations in serum. Therefore, CrCl is underestimated when creatinine methods affected by protein error are used. This underestimation has been stated to be compensated by the overestimation attributable to tubular secretion of creatinine. However, studies confirming this statement are lacking. In compensated Jaffe methods, the values assigned to the calibrator set point are adjusted to minimize the pseudo-creatinine contribution of proteins. The result is that compensated methods produce lower creatinine values. Alternatively, the protein error can be avoided by use of enzymatic creatinine methods. Collection of timed urine for CrCl is often a major source of error; therefore, simple formulas have been introduced to estimate GFR based on serum creatinine concentration, age, gender, body weight, and body length (8)(9) …
Evaluating the Hemodynamical Response of a Cardiovascular System under Support of a Continuous Flow Left Ventricular Assist Device via Numerical Modeling and Simulations

Dilated cardiomyopathy is the most common type of the heart failure which can be characterized by impaired ventricular contractility. Mechanical circulatory support devices were introduced into practice for the heart failure patients to bridge the time between the decision to transplant and the actual transplantation which is not sufficient due to the state of donor organ supply. In this study, the hemodynamic response of a cardiovascular system that includes a dilated cardiomyopathic heart under support of a newly developed continuous flow left ventricular assist device—Heart Turcica Axial—was evaluated employing computer simulations. For the evaluation, a numerical model which describes the pressure-flow rate relations of Heart Turcica Axial, a cardiovascular system model describing the healthy and pathological hemodynamics, and a baroreflex model regulating the heart rate were used. Heart Turcica Axial was operated between 8000 rpm and 11000 rpm speeds with 1000 rpm increments for assessing the pump performance and response of the cardiovascular system. The results also give an insight about the range of the possible operating speeds of Heart Turcica Axial in a clinical application. Based on the findings, operating speed of Heart Turcica Axial should be between 10000 rpm and 11000 rpm.
Induction of Apoptosis of Metastatic Mammary Carcinoma Cells In Vivo by Disruption of Tumor Cell Surface CD44 Function

To understand how the hyaluronan receptor CD44 regulates tumor metastasis, the murine mammary carcinoma TA3/St, which constitutively expresses cell surface CD44, was transfected with cDNAs encoding soluble isoforms of CD44 and the transfectants (TA3sCD44) were compared with parental cells (transfected with expression vector only) for growth in vivo and in vitro. Local release of soluble CD44 by the transfectants inhibited the ability of endogenous cell surface CD44 to bind and internalize hyaluronan and to mediate TA3 cell invasion of hyaluronan-producing cell monolayers. Mice intravenously injected with parental TA3/St cells developed massive pulmonary metastases within 21–28 d, whereas animals injected with TA3sCD44 cells developed few or no tumors. Tracing of labeled parental and transfectant tumor cells revealed that both cell types initially adhered to pulmonary endothelium and penetrated the interstitial stroma. However, although parental cells were dividing and forming clusters within lung tissue 48 h following injection, >80% of TA3sCD44 cells underwent apoptosis. Although sCD44 transfectants displayed a marked reduction in their ability to internalize and degrade hyaluronan, they elicited abundant local hyaluronan production within invaded lung tissue, comparable to that induced by parental cells. These observations provide direct evidence that cell surface CD44 function promotes tumor cell survival in invaded tissue and that its suppression can induce apoptosis of the invading tumor cells, possibly as a result of impairing their ability to penetrate the host tissue hyaluronan barrier.
The Impact of Social Segregation on Human Mobility in Developing and Urbanized Regions

This study leverages mobile phone data to analyze human mobility patterns in developing countries, especially in comparison to more industrialized countries. Developing regions, such as the Ivory Coast, are marked by a number of factors that may influence mobility, such as less infrastructural coverage and maturity, less economic resources and stability, and in some cases, more cultural and language-based diversity. By comparing mobile phone data collected from the Ivory Coast to similar data collected in Portugal, we are able to highlight both qualitative and quantitative differences in mobility patterns - such as differences in likelihood to travel, as well as in the time required to travel - that are relevant to consideration on policy, infrastructure, and economic development. Our study illustrates how cultural and linguistic diversity in developing regions (such as Ivory Coast) can present challenges to mobility models that perform well and were conceptualized in less culturally diverse regions. Finally, we address these challenges by proposing novel techniques to assess the strength of borders in a regional partitioning scheme and to quantify the impact of border strength on mobility model accuracy.
Probing the enzyme kinetics, allosteric modulation and activation of α1- and α2-subunit-containing AMP-activated protein kinase (AMPK) heterotrimeric complexes by pharmacological and physiological activators

We have studied enzyme kinetics, nucleotide binding and allosteric modulation of six recombinant AMP-activated protein kinase (AMPK) isoforms by known allosteric activators. α1-Complexes exhibited higher specific activities and lower Km values for a peptide substrate, but α2-complexes were more readily activated by AMP.
Combined electrical and optical characterisation of recombination mechanisms and minority carrier lifetime in solar cells

This work presents the development of a measurement system which combines optical and electrical characterisation of carrier lifetime and recombination mechanisms of thin film solar cells. It combines spectrally-resolved photoluminescence (PL), time-resolved photoluminescence (TRPL), and transient photocurrent (TPCD), which are measured using a single excitation laser source at the same spot of the solar cell. Initial PL, TRPL and TPCD measurements have been conducted on CdS/CdTe and MZO/CdTe samples. The resulting PL spectra show emission peaks corresponding to the material bandgap. Under the same excitation conditions and same measurement spot, initial TRPL and TPCD measurements were successfully conducted, yielding effective carrier lifetime values (τ1=1.39ns, τ2=3.91ns) and (τ=40.5ns), respectively for the CdS/CdTe sample and (τ1=0.98ns, τ2=3.3ns) and (τ=36.8ns), respectively for the MZO/CdTe sample. These values are affected by different recombination processes in solar cells. Therefore, as well as characterising solar cell material quality, the electronic properties of the finished PV device can also be characterised.
An improved method for preparing thick sections for immuno/histochemistry and confocal microscopy and its use to identify rare events

Detection of rare events within solid tissues by immunocytochemistry is aided by imaging thick sections. Sections of 40–100 µm thickness of paraformaldehyde‐fixed solid tissue can be prepared by use of a vibrating microtome and when immunolabelled these sections can be imaged in a confocal microscope. This approach provides excellent preservation of the structure of the sample and imposes minimal antigenic damage. In studies of the invasion of the bovine intestinal epithelium by Salmonella, this method has allowed detection of individual invading bacteria within large samples. The thick vibrating microtome sections were also used for the detection of rare apoptotic cell nuclei identified by TUNEL staining.
Local Optimization for Global Alignment of Protein Interaction Networks

We propose a novel algorithm, PISwap, for computing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other NP-hard problems, such as the Traveling Salesman Problem. Our algorithm begins with a sequence-based network alignment and then iteratively adjusts the alignment by incorporating network structure information. It has a worst-case pseudo-polynomial running-time bound and is very efficient in practice. It is shown to produce improved alignments in several well-studied cases. In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignments. Finally, this algorithm can yield interesting insights into the evolutionary history of the compared species.
Unsupervised wrapper induction using linked data

This work explores the usage of Linked Data for Web scale Information Extraction and shows encouraging results on the task of Wrapper Induction. We propose a simple knowledge based method which is (i) highly flexible with respect to different domains and (ii) does not require any training material, but exploits Linked Data as background knowledge source to build essential learning resources. The major contribution of this work is a study of how Linked Data - an imprecise, redundant and large-scale knowledge resource - can be used to support Web scale Information Extraction in an effective and efficient way and identify the challenges involved. We show that, for domains that are covered, Linked Data serve as a powerful knowledge resource for Information Extraction. Experiments on a publicly available dataset demonstrate that, under certain conditions, this simple unsupervised approach can achieve competitive results against some complex state of the art that always depends on training data.
Royalty-Free Video Coding Standards in MPEG [Standards in a Nutshell]

On 7 March 2013, the Moving Picture Experts Group Licensing Association (MPEG LA) and Google announced that they have entered into an agreement granting Google a license to techniques, if the patents in MPEG LA might be essential to VP8. Under this agreement, hardware and software companies are free to use the VP8 technology when developing their own products. Considering that it is now common to find patent disputes in headline news, the patent issues related to video coding standards are no exception. In this article, we report on the recent developments in royalty-free codec standardization in MPEG, particularly Internet video coding (IVC), Web video coding (WVC), and video coding for browser, by reviewing the history of royalty-free standards in MPEG and the relationship between standards and patents.
Process-oriented risk assessment in integrated logistics networks: an AHP approach

As the importance of integrated logistics networks increases together with the advancements in information technology, the proper evaluation and selection of third-party logistics services becomes a core issue for the participants of these networks. The paper describes a proposed risk assessment approach that can help the customers in the proper evaluation of the mentioned services. The concept employs the analytic hierarchy process (AHP), a well known and widely applied multi-criteria decision making method, for the structured evaluation of the primary operational risk factors which are relevant to the customers. In the proposed approach, the quantification of these risk factors at the side of the service providers is realized through the utilization of process capability indices, the latter are well known and widely applied in the fields of quality management and statistical process control. The aim is to provide a relatively straight-forward and easily applicable way for the risk-based evaluation of third-party logistics services in integrated logistics networks. Another advantage of the concept is that it could be utilized in different fields of the logistics industry, regardless of the concrete field of application.
Issues in Informing Science and Information Technology Impact of Motivation on Intentions in Online Learning: Canada Vs China

This study is one of the few empirical studies to examine students' acceptance of a web-based learning system (WLS). By incorporating intrinsic motivator into the technology acceptance model, our model attempts to explain students' behavioral intention in using the system from a motivational perspective. Unlike most studies using subjects from developed countries, this study aims to extend knowledge by examining WLS adoption and usage behavior in a developing country (China) and then compares with findings of the same examination using Canadian subjects. The results show that both perceived usefulness and enjoyment have significant impact on stu-dents' intention to use WLS in two groups. However, in contrast to Chinese subjects, Canadian subjects do not think ease of use has impact on their intention to use WLS. Implications of this study are important for both researchers and practitioners, especially for institutions of higher education, planning to adopt WLS in the two countries.
Deriving MoS2 nanoribbons from their flakes by chemical vapor deposition

Two-dimensional (2D) materials have attracted great interest due to their unique structures and exotic properties related to promising applications and fundamental research. Reducing the dimensionality of 2D materials into their 1D nanostructure is also highly desirable for the exploitation of novel properties and offers new research opportunities. In this work, we demonstrate a bottom-up synthesis of molybdenum disulfides (MoS2) nanoribbons on graphene substrate via chemical vapor deposition (CVD) by precisely tuning the growth parameters into a sulfur-enriched condition. MoS2 nanoribbons are mainly formed from the CVD grown MoS2 flakes along the armchair (AC) direction. Atomic resolution ADF-STEM imaging characterizations show an alternating presence of molybdenum and sulfur zigzag edge terminations at the edges of MoS2 nanoribbons. While at the apex of the nanoribbon, sulfur terminated zigzag edges become dominant. Taking these results together, we revealed the underlying growth mechanism of MoS2 nanoribbons. Electronic transport properties of the MoS2 nanoribbons were also measured by fabricating back-gate-effect transistors (FETs). The nanoribbon FETs present n-type behavior with a current on/off ratio higher than 104 at VDS = 1 and a carrier mobility of 1.39 cm2 V−1 s−1. This work offers a new route to synthesize 1D MoS2 nanoribbons, which has great potential in fabricating other 2D materials-derived 1D nanostructures.
Single wall carbon nanotube growth from bimetallic nanoparticles : a parametric study of the synthesis up to potential application in nano-electronics.

This manuscript presents an experimental study around the single wall carbon nanotubes (SWCNT) synthesis and their possible integration in nanodevices. The unique electronic and optical properties of carbon nanotubes make them a choice material for various applications, particularly in nano-electronics.Nevertheless, their integration in effective devices is still a challenge. This is mainly due to the difficulty to obtain large quantity of SWCNT with uniform properties, defined by their structure (i.e. chiral angle and diameter). Therefore, structure controlled growth of SWCNTs is a key point for progress in this field.Here, we established a new synthesis approach based on coordination chemistry and hot-filament chemical vapor deposition. This approach allows the design of various bimetallic catalyst nanoparticles for the SWCNT growth. As the synthesis process is generic, parametric study can be performed in order to better understand the influence of the various parameters on the structure of the as-grown SWCNTs. In particular, we will discuss the role of the growth temperature and the chemical composition of the catalyst on the final SWCNTs structure. The obtained SWCNTs are mainly characterized by Raman spectroscopy and electronic microscopy.In order to validate the observations performed by Raman measurement, the synthesized SWCNTs have been also integrated in field effect transistors (FET) devices. An analysis of the performance of the FET-device as a function of the SWCNTs used in its channel will be presented.Finally, SWCNTs integrated in these transistors have been functionalized with an inorganic chromophore of ruthenium.We demonstrate that the functionalization of the SWCNTs leads to a three order of magnitude reversible switch of the device conductivity triggered by visible light.
Comparative Genomic Analysis Reveals 2-Oxoacid Dehydrogenase Complex Lipoylation Correlation with Aerobiosis in Archaea

Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.