Miracle-dz/UniFAR-FTUs huggingface dataset:
Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation

Aging, defined as a decrease in reproduction rate with age, is a fundamental characteristic of all living organisms down to bacteria. Yet we know little about the causal molecular mechanisms of aging within the in vivo context of a wild-type organism. One of the prominent markers of aging is protein aggregation, associated with cellular degeneracy in many age-related diseases, although its in vivo dynamics and effect are poorly understood. We followed the appearance and inheritance of spontaneous protein aggregation within lineages of Escherichia coli grown under nonstressed conditions using time-lapse microscopy and a fluorescently tagged chaperone (IbpA) involved in aggregate processing. The fluorescent marker is shown to faithfully identify in vivo the localization of aggregated proteins, revealing their accumulation upon cell division in cells with older poles. This accretion is associated with >30% of the loss of reproductive ability (aging) in these cells relative to the new-pole progeny, devoid of parental inclusion bodies, that exhibit rejuvenation. This suggests an asymmetric strategy whereby dividing cells segregate damage at the expense of aging individuals, resulting in the perpetuation of the population.
Identification of Multiphase Reaction Systems with Instantaneous Equilibria

The identification of kinetic models for multiphase reaction systems is complex due to the simultaneous effect of chemical reactions and mass transfers. The extent-based incremental approach simplifies the modeling task by transforming the reaction system into variant states called vessel extents, one for each rate process. This transformation is carried out from the measured numbers of moles (or concentrations) and requires as many measured species as there are rate processes. Then, each vessel extent can be modeled individually, that is, independently of the other dynamic effects. This paper presents a modified version of the extent-based incremental approach that can be used to identify multiphase reaction systems in the presence of instantaneous equilibria. Different routes are possible depending on the number and type of measured species. The approach is illustrated via the simulated example of the oxidation of benzyl alcohol by hypochlorite in a batch reactor.
Transcribing Lectures and Seminars ∗

This paper describes recent research carried out in the context of the FP6 Integrated Project C HIL in developing a system to automatically transcribe lectures and seminars. We made use of widely available corpora to train both the acoustic and language models, since only a small amount of C HIL data were available for system development. For acoustic model training made use of the transcribed portion of the TED corpus of Eurospeech recordings, as well as the ICSI, ISL, and NIST meeting corpora. For language model training, text materials were extracted from a variety of on-line conference proceedings. Word error rates of about 25% are obtained on test data extracted 12 seminars.
A Superoxide-Hypersusceptible Salmonella enterica Serovar Typhimurium Mutant Is Attenuated but Regains Virulence in p47phox−/− Mice

ABSTRACT Salmonella enterica serovar Typhimurium is a gram-negative, facultative intracellular pathogen that predominantly invades mononuclear phagocytes and is able to establish persistent infections. One of the innate defense mechanisms of phagocytic cells is the production of reactive oxygen species, including superoxide. S. enterica serovar Typhimurium has evolved mechanisms to resist such radicals, and these mechanisms could be decisive in its ability to survive and replicate within macrophages. Recently, we described a superoxide-hypersusceptible S. enterica serovar Typhimurium mutant strain, DLG294, that carries a transposon in sspJ, resulting in the lack of expression of SspJ, which is necessary for resistance against superoxide and replication within macrophages. Here we show that DLG294, which is a 14028s derivative, hardly induced any granulomatous lesions in the livers upon subcutaneous infection of C3H/HeN (Ityr) mice with 3 × 104 bacteria and that its bacterial counts were reduced by 3 log units compared to those of wild-type S. enterica serovar Typhimurium 14028s on day 5 after infection. In contrast, DLG294 replicated like wild-type S. enterica serovar Typhimurium 14028s and induced a phenotypically similar liver pathology in p47phox−/− mice, which are deficient in the p47phox subunit of the NADPH oxidase complex and which do not produce superoxide. Consistent with these results, DLG294 reached bacterial counts identical to those of wild-type S. enterica serovar Typhimurium 14028s in bone marrow-derived macrophages from p47phox−/− mice and in X-CGD PLB-985 cells at 24 h after challenge. These results indicate that SspJ plays a role in the bacterium's resistance to oxidative stress and in the survival and replication of S. enterica serovar Typhimurium both in vitro and in vivo.
Analysis of methylglyoxal in water and biological matrices by capillary zone electrophoresis with diode array detection

We describe a new method for the determination of methylglyoxal in water and biological matrices, using o‐phenylenediamine as derivatizing agent and solid‐phase extraction followed by capillary zone electrophoresis with diode array detection. 25 mM sodium phosphate running buffers at pH 2.2, 30 kV, and 25°C allowed the best instrumental conditions for the optimum separation of methylglyoxal in a suitable analytical time (< 10 min), using an uncoated fused‐silica capillary of 75 µm inner diameter and an effective length of 45.1 cm with an extended light path and the wavelength set to 200 nm. Under optimized instrumental conditions, good reproducibility of the migration time (< 1.1%), precision (< 5%), an excellent linear dynamic range from 0.1 to 3.6 mg/L (r2 = 0.9997), and low limits of detection (7.2 µg/L) were obtained for methylglyoxal measurements, using the internal standard methodology. Assays on laboratory‐spiked tap and ground water samples allowed a remarkable accuracy, presenting yields of 95.0 ± 4.3 and 94.0 ± 1.1%, respectively, and good performance to determine methylglyoxal in beer and yeast cells suspensions matrices was also obtained at trace level. The present methodology is a cost‐effective alternative for routine quality control analysis, showing to be reliable, sensitive, and with a low sample volume requirement to monitor methylglyoxal in water and biological matrices.
On the Relationship between the Macroevolutionary Trajectories of Morphological Integration and Morphological Disparity

How does the organization of phenotypes relate to their propensity to vary? How do evolutionary changes in this organization affect large-scale phenotypic evolution? Over the last decade, studies of morphological integration and modularity have renewed our understanding of the organizational and variational properties of complex phenotypes. Much effort has been made to unravel the connections among the genetic, developmental, and functional contexts leading to differential integration among morphological traits and individuation of variational modules. Yet, their macroevolutionary consequences on the dynamics of morphological disparity–the large-scale variety of organismal designs–are still largely unknown. Here, I investigate the relationship between morphological integration and morphological disparity throughout the entire evolutionary history of crinoids (echinoderms). Quantitative analyses of interspecific patterns of variation and covariation among characters describing the stem, cup, arm, and tegmen of the crinoid body do not show any significant concordance between the temporal trajectories of disparity and overall integration. Nevertheless, the results reveal marked differences in the patterns of integration for Palaeozoic and post-Palaeozoic crinoids. Post-Palaeozoic crinoids have a higher degree of integration and occupy a different region of the space of integration patterns, corresponding to more heterogeneously structured matrices of correlation among traits. Particularly, increased covariation is observed between subsets of characters from the dorsal cup and from the arms. These analyses show that morphological disparity is not dependent on the overall degree of evolutionary integration but rather on the way integration is distributed among traits. Hence, temporal changes in disparity dynamics are likely constrained by reorganizations of the modularity of the crinoid morphology and not by changes in the variability of individual traits. The differences in integration patterns explain the more stereotyped morphologies of post-Palaeozoic crinoids and, from a broader macroevolutionary perspective, call for a greater attention to the distributional heterogeneities of constraints in morphospace.
A 10Gb/s transmitter with multi-tap FIR pre-emphasis in 0.18μm CMOS technology

A 10Gb/s current mode logic (CML) transmitter with multi-tap finite impulse response (FIR) pre-emphasis has been implemented in 0. 18μm CMOS technology. A half-rate clock retiming circuit for generating symbol-spaced data is proposed to alleviate the speed requirement of the traditional full-rate clock retiming. HSPICE simulation results of a 5-tap FIR transmitter show that the closed eye over a 34" FR4 backplane can be opened to 0.72UI at 10Gb/s. The power dissipation of the transmitter is 50mW at a 1.8V supply.
Overexpression of Matrix Metalloproteinase-1 and -9 mRNA Is Associated with Progression of Oral Dysplasia to Cancer

Purpose: Although an important risk factor for oral cancer is the presence of epithelial dysplasia, many lesions will not progress to malignancy. Matrix metalloproteinases (MMPs) are zinc-dependent proteinases capable of digesting various structural components of the extracellular matrix. Because MMPs are frequently overexpressed in oral squamous cell carcinoma (SCC), we hypothesized that they are also overexpressed in oral dysplasias; we also hypothesized that those dysplasias that progress to oral cancer express higher levels of MMPs than those lesions that do not progress. Experimental Design: In this retrospective study, we examined changes in MMP-1, -2, and -9 mRNA expression using quantitative TaqMan reverse transcription-polymerase chain reaction in 34 routinely processed oral dysplasias and 15 SCCs obtained from 34 patients. After several years of close follow-up, 19 dysplasias progressed to oral SCC and 15 did not. Results: Overall, MMP-1 mRNA was overexpressed (>2-fold) in 24 of 34 (71%) dysplasias and 13 of 15 (87%) oral SCCs. MMP-2 overexpression was seen in 11 of 34 (32%) dysplasias and 7 of 15 (47%) cancers; for MMP-9, overexpression was identified in 29 of 34 (85%) dysplasias and 15 of 15 (100%) cancers. MMP-1 and -9 levels were significantly higher in the SCCs compared with all oral dysplasias (P = 0.004 and P = 0.01, respectively). MMP-1 and -9 mRNA levels were significantly higher in the oral dysplasias that progressed to oral cancer compared with those that did not (P = 0.04 and P = 0.002, respectively). Conclusions: Levels of MMP-1 and -9 mRNA may be markers of malignant transformation of oral dysplasia to oral cancer.
Hypothesis Testing in the “Gold Standard” Design for Proving the Efficacy of an Experimental Treatment Relative to Placebo and a Reference

Abstract This article reviews the most important reasons to include a placebo and a reference treatment group in a study to investigate the efficacy of a new experimental treatment. We argue that as a general rule the regulatory requirement is the proven superiority of the experimental treatment over placebo and the proven noninferiority of the experimental treatment as compared to the reference treatment. Whether or not the reference treatment can be shown to be superior to placebo may impact the formulation of the indication but should not, per se, question the usefulness of the experimental treatment or the credibility of the principal proof of efficacy. We argue that a mandatory requirement for the reference treatment to be superior to placebo is ill founded and especially difficult to justify in the situation where the experimental treatment can also prove its superiority over the reference treatment. For this latter situation, it is shown that no adjustment for multiple hypothesis testing is needed, if at the same time superiority of the reference over placebo and superiority of the experimental treatment over the reference are investigated.
Coupled biosynthesis of cordycepin and pentostatin in Cordyceps militaris: implications for fungal biology and medicinal natural products.

Cordycepin, or 3'-deoxyadenosine, is a metabolite produced by the insect-pathogenic fungus Cordyceps militaris and is under intense investigation as a potential lead compound for cancer and inflammatory conditions. Cordycepin was originally extracted by Cunningham et al. (1) from a culture filtrate of a C. militaris culture that was grown from conidia. Subsequently, cordycepin has also been reported to be produced by Ophiocordyceps sinensis (2), a species historically used as a traditional medicine and health food, primarily in China and the wider Far East (3). Cultivated C. militaris is now widely in use as less expensive substitute. In addition, these fungi are also globally gaining a market as natural food supplements, with 30–50 products claiming to contain Cordyceps available in the UK and the USA.
Large-Margin Metric Learning for Partitioning Problems

In this paper, we consider unsupervised partitioning problems, such as clustering, image segmentation, video segmentation and other change-point detection problems. We focus on partitioning problems based explicitly or implicitly on the minimization of Euclidean distortions, which include mean-based change-point detection, K-means, spectral clustering and normalized cuts. Our main goal is to learn a Mahalanobis metric for these unsupervised problems, leading to feature weighting and/or selection. This is done in a supervised way by assuming the availability of several potentially partially labelled datasets that share the same metric. We cast the metric learning problem as a large-margin structured prediction problem, with proper definition of regularizers and losses, leading to a convex optimization problem which can be solved efficiently with iterative techniques. We provide experiments where we show how learning the metric may significantly improve the partitioning performance in synthetic examples, bioinformatics, video segmentation and image segmentation problems.
What's So Special About Working Memory?

Working memory capacity (WMC) has received attention across many areas of psychology, in part because of its relationship with intelligence. The mechanism underlying the relationship is unknown, but the nature of typical WMC tasks has led to two hypothesized mechanisms: secondary-memory processes (e.g., search and retrieval) and the maintenance of information in the face of distraction. In the present study, participants (N = 383) completed a battery of cognitive tasks assessing processing speed, primary memory, working memory, secondary memory, and fluid intelligence. Secondary memory was the strongest predictor of fluid intelligence and added unique predictive value in models that accounted for working memory. In contrast, after accounting for the variance in fluid intelligence associated with the secondary-memory construct, the working memory construct did not significantly predict variability in fluid intelligence. Therefore, the secondary-memory requirements shared by many memory tasks may be responsible for the relationship between WMC and fluid intelligence, making the relationship less unique than is often supposed.
Structure and synthesis of a simian virus 40 super T-antigen

Mouse cells transformed by simian virus 40 often contain virus-coded tumor antigens distinct from those synthesized in productively infected permissive cells. The SV3T3 C120 cell line produces no large T-antigen of apparent molecular weight 94,000 but instead a super T-antigen of apparent molecular weight 145,000. We used recombinant DNA techniques to isolate the template for this super T-antigen and determined its structure by DNA sequencing. The integrated viral early transcription unit contains an in-phase, perfect tandem duplication of 1,212 base pairs. Transfer hybridization and endonuclease S1 mapping experiments were performed to elucidate the structures of the stable, cytoplasmic mRNAs of SV3T3 C120 cells, mRNAs of 3.9 and 3.6 kilobases, containing the small t- and large T-antigen splices, respectively, were transcribed from the internally duplicated early transcription unit. We showed by in vitro translation that these mRNAs encode small t-antigen and the super T-antigen of molecular weight 145,000. Peptide mapping studies of the SV3T3 C120 super T-antigen were consistent with its being derived from an internally duplicated template, since the protein has methionine and cysteine tryptic fingerprints virtually identical to those of normal large T-antigen, with certain methionine peptides present in greater than one molar yield.
Molecular Surveillance of Rotavirus Infection in the Democratic Republic of the Congo August 2009 to June 2012

Background: Rotavirus is a major cause of severe diarrhea worldwide. It causes 453,000 deaths in children annually. In the Democratic Republic of the Congo, sentinel site surveillance of rotavirus gastroenteritis started in 2009 and aimed to document burden of rotavirus diarrhea and identify circulating rotavirus genotypes. Methods: Between August 2009 to June 2012, stool samples were collected in Kinshasa and Lubumbashi, from children <5 years of age who met the WHO case definition for rotavirus gastroenteritis. Rotavirus antigen detection was performed using an enzyme immunoassay technique and rotavirus strains were characterized using a multiplex reverse transcription polymerase chain reaction assay. Results: During the study period, 1614 stool samples were screened for rotavirus by enzyme immunoassay and 990 (61%) were positive. Of these, the genotype was determined in 330 (33%) samples. The most common genotypes found in the samples analyzed were G1P[8] in 2009 (28%) and 2012 (33%), G2P[4] (33%) in 2010 and G2P[6] (28%) in 2011. Uncommon strains like G8P[6] (5%), G6P[6] (5%), G12P[6] (3%), G12P[8] (3%) and G8P[8] (2%) were also detected. Conclusions: In Democratic Republic of the Congo, 61% of the diarrhea in children in <5 years of age was caused by rotavirus infection and a variety of rotavirus genotypes were detected. Implementation of rotavirus genotyping at the national level has improved the timely identification of rotavirus strains. These results will help decision makers in Democratic Republic of the Congo plan the implementation of a rotavirus vaccination program.
A method to select a good setting for the kNN algorithm when using it for breast cancer prognosis

Breast cancer is the world's second most frequent type of cancer and in Japan it is the third most frequent one. The prognosis of its recurrence, after a first treatment, is very important to increase the survival rate of a patient. This work shows the application of the k-Nearest Neighbors (kNN) method to prognosis breast cancer and also proposes a method to select a good setting with the parameters that can be changed when using this classification method. Using our method with the Wisconsin's breast cancer prognosis data, the kNN method has an average accuracy of 76%, a small standard deviation, and a small difference between its maximum and minimum values.
Dynamic test selection for reconfigurable diagnosis

Detecting and isolating multiple faults is a computationally intense task which typically consists of computing a set of tests, and then computing the diagnoses based on the test results. This paper proposes a method to reduce the computational burden by only running the tests that are currently needed, and dynamically starting new tests when the need changes. A main contribution is a method to select tests such that the computational burden is reduced while maintaining the isolation performance of the diagnostic system. Key components in the approach are the test selection algorithm, the test initialization procedures, and a knowledge processing framework that supports the functionality needed. The approach is exemplified on a relatively small dynamical system, which still illustrates the complexity and possible computational gain with the proposed approach.
Video based Activity Recognition in a Trauma Center

We present a feasibility study of automated, vision-based detection and recognition of trauma procedures in a medical emergency room. Given a ceiling-mounted camera view of the trauma room, our goal is to track and transcribe the activities performed during resuscitation of a patient, the time instances of their initiation and their temporal durations. We represent activities through complex spatiotemporal relationships between image features based on scene dynamics, patient localization, clinicians’ hand motions and medical devices. We design an activity grammar based on trauma specific domain-knowledge and model the resulting logic as a Markov Logic Network. Probabilistic inference of activity posterior is computed efficiently in the presence of observed features. To this end, we demonstrate our approach on videos of realistic trauma simulations in challenging, multi-agent. multi-task settings. This study primarily aims at exploring the overall problem of visual recognition of trauma procedures. The accuracy of the results we obtained from our recognition scheme confirms the suitability of our framework.
IBM Power Systems built with the POWER8 architecture and processors

This paper describes architectures and significant implementation features of two systems in the IBM POWER8™ processor-based family of servers. Specifically, the scale-out 2-socket rack server and the enterprise scale-up 16-socket rack server are detailed. The description of these systems highlights the increase in memory bandwidth from previous POWER® systems, the enablement of coherent accelerators, the highly-extensible I/O subsystem, and the high-performance directly attached storage subsystem. In addition, reliability, availability, and serviceability features are described. These systems deliver significant increases in core count, memory, and input/output bandwidth over previous POWER systems—with reliability and availability enhancements commensurate with the performance improvements.