Miracle-dz/UniFAR-FTUs huggingface dataset:
Effective Grading of Termhood in Biomedical Literature

The ever-increasing amount of textual information in biomedicine calls for effective procedures for automatic terminology extraction which assist biomedical researchers and professionals in gathering and organizing terminological knowledge encoded in text documents. In this study, we propose a new, linguistically grounded measure for automatically identifying multi-word terms from the biomedical literature. Our approach is based on the limited paradigmatic modifiability of terms and is tested on bigram, trigram and quadgram noun phrases extracted from a 104-million-word text corpus comprised of Medline abstracts. Using the UMLS Metathesaurus as a gold standard, we show that our algorithm substantially outperforms the standard term identification measures and, therefore, qualifies as a high-performing building block for any biomedical terminology mining system.
Induction of apoptosis in nutrient‐deprived cultures of hybridoma and myeloma cells

In the present study, cell death was investigated in cultures of NS/0 myelomas and SP2/0‐derived D5 hybridomas through morphological examination of cells stained with acridine orange and ethidium bromide. The relative contribution of elevated levels of lactic acid and ammonia, as well as deprivation of glutamine, cystine, and glucose on the induction of necrosis or apoptosis, was investigated. In batch culture of D5 hybridoma cells, induction of apoptotic cell death correlated with the exhaustion of glutamine, while in the case of NS/0 myelomas, it coincided with exhaustion of cystine. To determine whether limiting nutrients were the actual triggering factors for apoptosis in batch culture, exponentially growing cells were resuspended in glutamine or cystine‐free media. Within 30 to 40 h, viability decreased to 50% and the nonviable cell population displayed typical apoptotic morphology, with crescents of condensed chromatin around the periphery of the nucleus, or with the entire nucleus present as one or a group of featureless, brightly staining spherical beads. Similarly, D5 hybridomas and NS/0 myelomas cultivated in glucose‐free medium died mainly from apoptosis. Cells were also cultivated in fresh medium supplemented with elevated concentrations of ammonia (3.0 mM) and/or lactate (35 mM, 50 mM). This resulted in decreased viabilities and necrotic death in both cell lines. From these results, we conclude that D5 hybridomas and NS/0 myelomas deprived of essential nutrients die by apoptosis, whereas incubation in the presence of elevated levels of metabolic byproducts such as ammonia and lactate will induce necrotic cell death in these cells. © 1994 John Wiley & Sons, Inc.
Hybrid cell centred/vertex model for cellular nanolayers

SUMMARY Macroscopic deformations in embryonic soft tissues are due to the intra-cellular remodelling and cell intercalation. We here present a computational approach that can handle the two types of deformations, and also take into account the active cell response. The model resorts to cell centred techniques, where particles represent cell nuclei, and to vertex models, where the vertices represent cell boundaries. This hybrid approach allows to consider separately intra-cellular and inter-cellular forces, and at the same time impose cell incompressibility. The model is applied to simulate the active stretching of epithelium.
Advances in time-resolved approaches to characterize the dynamical nature of enzymatic catalysis.

While this model tends to describe the observed kinetics in many cases, the actual chemical pathway for the enzyme catalyzed conversion of “substrate” to “product” is believed to be substantially more complicated. Although the specific structures, viewed as a static collection of atomic positions, are important to understand to how enzymes work, the specific motions of these atoms also play a crucial role, a notion that can at least be traced back to Koshland’s “induced-fit” hypothesis. 1 The on-enzyme catalyzed chemistry involves considerable and specific atomic motion of both the atoms of the bound substrate and the atoms of the protein along the reaction coordinate. The types of motions involved with the chemistry are many: from the physical necessity of binding pocket atoms relaxing to accommodate the new electrostatic and steric nature of the product species compared to the substrate on one hand to conjectured “promoting vibrations” of the protein, helping to facilitate catalysis due to atomic motion within the protein along the reaction coordinate, on the other hand. Likewise, just how an enzyme binds its ligands to form the “Michaelis complex”, the specific pathway(s), the time ordering of events, and the motions of the atoms and groups of atoms involved in the binding process are all largely uncharacterized and not understood. The reason for this is that these dynamical processes cover a wide range of time scales: small scale displacements of atoms take place from picoseconds to nanoseconds; activated motions of molecular groups, such as loop motion, occur within nanoseconds to microseconds; the motions of protein domains or smaller scale group motions with high activation energies are observed on the millisecond time scale or longer. Experimental and theoretical/computational methods are just now being developed that can adequately cover this broad time range of atomic motions.
Optimum design of two-level MCML gates

In this paper, we address the problem of the optimum design of two-level MOS Current Mode Logic (MCML) gates. In particular, we describe a design methodology based on the concept of crossing-point current already introduced for the optimum design of single-level MCML gates. This methodology is suited both for automated implementation and graphic estimate of the optimum design. Moreover, it clearly shows how some important design parameters affect the optimum values of delay and power consumption. Several gates were designed in an IBM 130 nm CMOS technology. The results of SPICE simulations, reported here, demonstrate the effectiveness of the proposed design methodology.
Regulation of Membrane-type-1 Matrix Metalloproteinase Activity by Its Cytoplasmic Domain*

Membrane-type-1 matrix metalloproteinase (MT1-MMP) has transmembrane and cytoplasmic domains, which target it to invasive fronts. We analyzed the role of the cytoplasmic tail by expressing wild type MT1-MMP and three mutants with progressively truncated C termini in human Bowes melanoma cells. We examined gelatinase A activation and the localization and processing of recombinant proteins in stable cell clones using gelatin zymography, immunoblotting, and immunofluorescence. Cell invasion was analyzedin vitro by Matrigel invasion assays. Gelatinase A was activated in all cell clones. However, the localization of MT1-MMP to the leading edge of migrating cells and cell invasion through Matrigel were strongly enhanced only in cells expressing either wild type or truncated MT1-MMP lacking 6 C-terminal amino acid residues (Δ577). Truncations of 10 or 16 amino acid residues in the cytoplasmic domain (Δ567 and Δ573, respectively) disturbed MT1-MMP localization. The expression of wild type and Δ577 MT1-MMPs induced also their cleavage to 43-kDa cell surface forms and the release of soluble, ∼20-kDa N-terminal fragments containing the catalytic center. A synthetic MMP inhibitor but not a gelatinase inhibitor prevented the processing, suggesting that autocatalytic cleavage occurs. Purified soluble MT1-MMP was also autoproteolytically processed to 43- and 20-kDa forms in vitro. Our results indicate that the cytoplasmic domain has an important role in cell invasion by controlling both the targeting and degradation/turnover of MT1-MMP.
An alcoholic patient who continues to drink: endoscopic treatment is preferred

EDITOR—Patients like Mr Bond in the last interactive case report are increasingly common and present difficult clinical decisions.1 Leon and McCambridge highlighted the large increase in deaths from cirrhosis in the United Kingdom between 1987-91 and 1997-2001.2 Mortality doubled (104% increase) in men in Scotland during that time, and per capita alcohol consumption also doubled in the UK between 1960 and 2002. Treatment of Mr Bond's variceal haemorrhage and associated decisions on how far to go with intervention should be based on clinical need, …
Programming design process: Providing K-12 students with a structure to attain programming goals

The Cyber Innovation Center's Cyber Science curriculum is an interdisciplinary approach to educate high school students to become better cyber-citizens. Through Cyber Science, students learn applicable fundamental concepts from political sciences, history, and law as well as science, technology, engineering, and mathematics (STEM) disciplines as they relate to cyber. In particular, the curriculum includes basic programming and structures; advanced computer science topics; and the concepts of security and privacy in relation to cyberspace. The project-driven nature of the curriculum enables students to refine their computational problem-solving abilities through challenging and engaging programming problems. Mirroring the engineering design process, the Cyber Science curriculum introduces an iterative software development process to give students a structured procedure to approach and solve programming problems. This work in progress will address the purpose for developing the Programming Design Process (PDP), define the model used to create the process, and provide an example of a programming problem guided by the PDP.
Kompetenzorientierter Informatikunterricht in der Sekundarstufe I unter Verwendung der visuellen Programmiersprache Puck

In dieser Arbeit wurde die aktuelle Diskussion um Bildungsstandards sowie die spezifische Situation in der Informatik dargestellt. Weiterhin wurde auf Kompetenzen, Kompetenzmodelle und zugehorige Aufgaben eingegangen. Ausgehend von diesen Analysen wurde auf Grundlage der von der GI empfohlenen „Grundsatze und Standards fur Informatik in der Schule“ ein Kompetenzmodell fur den Inhaltsbereich „Algorithmen“ der 8. bis 10. Jahrgangsstufe zusammen mit Aufgaben zum Verdeutlichen, Erwerben und Uberprufen der Kompetenzen entwickelt. Die gewonnenen Erfahrungen bei der Entwicklung des Kompetenzmodells und der Aufgaben wurden jeweils zusammengefasst. Das Erwerben von Kompetenzen zum Inhaltsbereich „Algorithmen“ ist haufig mit dem Einsatz einer konkreten Programmiersprache verbunden. Die vom Autor erstellte visuelle Programmiersprache Puck wurde im Rahmen dieser Arbeit weiterentwickelt und von verschiedenen anderen visuellen Werkzeugen abgegrenzt. Weiterhin wurden Grunde dargestellt, die fur den Einsatz solcher visueller Werkzeuge bei der Einfuhrung in die Programmierung sprechen. In einer Voruntersuchung an sechs Thuringer Schulen wurden erste Erfahrungen zu kompetenzorientiertem Informatikunterricht unter Verwendung der entwickelten Materialien und der visuellen Programmiersprache Puck zusammengetragen. Auf Grundlage dieser Ergebnisse wurden in der Hauptuntersuchung 84 Lehrerinnen und Lehrern im deutschsprachigen Raum das weiterentwickelte Kompetenzmodell, die zugehorigen Aufgaben und Puck zur Verfugung gestellt. Die Befragung von 40 Lehrpersonen, am Ende der Hauptuntersuchung ergab, dass es einem Grosteil der Lehrkrafte moglich war, anhand der bereitgestellten Materialien kompetenzorientierten Informatikunterricht zu strukturieren, vorzubereiten, durchzufuhren und auszuwerten. Es zeigte sich auserdem, dass die visuelle Programmiersprache Puck grostenteils als geeignet fur eine Einfuhrung in die Programmierung in den Jahrgangsstufen 8 bis 10 eingeschatzt wurde.
Technical Report 2016-1 — Royal Holloway , University of London Misleading Metrics : On Evaluating Machine Learning for Malware with Confidence

Malware pose a serious and challenging threat across the Internet and the need for automated learning-based approaches has become rapidly clear. Machine learning has long been acknowledged as a promising technique to identify and classify malware threats; such a powerful technique is unfortunately often seen as a black-box panacea, where little is understood and the results—especially with high accuracy—are taken without questioning their quality. For such reasons, results are often biased by the choice of empirical thresholds or dataset-specific artifacts, hindering the ability to set easy-to-understand error metrics and thus compare different approaches. This setting, calls for new metrics that look beyond quantitative measurements (e.g., precision and recall), and help in scientifically assessing the soundness of the underlying machine learning tasks. To this end, we propose conformal evaluator, a framework designed at evaluating the quality of a result in terms of statistical metrics such as credibility and confidence. Credibility tells you how much a sample is credited with one given prediction (e.g., a label), whereas confidence focuses on pointing out how much a given sample is distinguished from other predictions. Such evaluation metrics give useful insights, providing a quantifiable per-choice level of assurance and reliability. Core of conformal evaluator is a non-conformity measure, which, in essence, allows for measuring the difference between a sample and a set of samples. For this reason, our framework is general enough to be immediately applied by a large class of algorithms that rely on distances to identify and classify malware, allowing to better understand and compare machine learning results. To further support our claim, we present case studies where the outcome of three different algorithms are evaluated under conformal evaluator settings. We show how traditional metrics mislead about the performance of different algorithms. Instead, conformal evaluator’s metrics enable to understand the reasons behind the performance of a given algorithm, and reveal shortcomings of apparently highly accurate methods.
Algorithm and Architecture of Configurable Joint Detection and Decoding for MIMO Wireless Communications With Convolutional Codes

This paper presents an algorithm and a VLSI architecture of a configurable joint detection and decoding (CJDD) scheme for multi-input multioutput (MIMO) wireless communication systems with convolutional codes. A novel tree-enumeration strategy is proposed such that the MIMO detection and decoding of convolutional codes can be conducted in single stage using a tree-searching engine. Moreover, this design can be configured to support different combinations of quadrature amplitude modulation (QAM) schemes as well as encoder code rates, and thus can be more practically deployed to real-world MIMO wireless systems. A formal outline of the proposed algorithm will be given and simulation results for 16-QAM and 64-QAM with rate-1/2 and rate-1/3 codes will be presented showing that, compared with the conventional separate scheme, the CJDD algorithm can greatly improve bit error rate (BER) performance with different system settings. In addition, the VLSI architecture and implementation of the CJDD approach will be illustrated. The architectures and circuits are designed to support configurability and flexibility while maintaining high efficiency and low complexity. The postlayout experimental results for 16-QAM and 64-QAM with rate-1/2 and rate-1/3 codes show that, compared with the previous configurable design, this architecture can achieve reduced or comparable complexity with improved BER performance.
Ultra low power active-RC filter in 180 nm CMOS technology

This paper presents the design of a low voltage, ultra low power fifth order Chebyshev low pass filter operating at a power supply voltage of 0.5 V in 180 nm CMOS technology. A CMOS inverter based transconductor is used as the building block. A sub-threshold model is developed for the transconductor as the transistors are operating in sub-threshold region. A feedforward compensated OTA is designed using this transconductor and is used to realize the filter. Designed filter has a cutoff frequency of 150 kHz and offers a dynamic range of 54.16 dB with a figure of merit of 0.02 fJ. Power consumed by the filter is 21.79 microwatt.
Mixed-signal CMOS wavelet compression imager architecture

The CMOS imager architecture implements DeltaSigma-modulated block matrix transforms, such as Haar wavelet transform, on the focal plane, for real-time video compression. The active pixel array is integrated with a bank of column-parallel first-order incremental oversampling analog-to-digital converters (ADCs). Each ADC performs column-wise distributed focal-plane sampling and concurrent signed weighted average quantization, realizing a one-dimensional spatial filter. A digital delay and adder loop performs spatial accumulation over multiple adjacent ADC outputs. This amounts to computing a two-dimensional block matrix transform, with no overhead in time and negligent overhead in area compared to a baseline digital imager system. The architecture is experimentally validated on a 0.35 micron CMOS prototype with a bank of first-order incremental oversampling ADCs computing Haar wavelet transform of an emulated pixel array output. The architecture yields simulated computational throughput of 1.4 GMACS with SVGA imager resolution at 30 frames per second
RNAi Approaches for Neuroprotection and Regeneration after Brain and Spinal Cord Injury

Copyright: © 2013 Yu CG. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This special issue for Brain & Spinal Cord Injury focuses on the development of RNA interference (RNAi) as a therapeutic modality for traumatic brain injury (TBI) and spinal cord injury (SCI). TBI is a leading cause of mortality and morbidity and often causes long-term disabling changes in cognition, sensorimotor function, and personality. SCI is also a devastating clinical disorder that often results in chronic pain, permanent motor disability, and other neurological dysfunctions. Although numerous molecular targets of secondary injury after TBI and SCI have been identified and validated during the past decade, no individual target has been readily druggable and no effective therapy for CNS injury has been established [1-3]. Therefore, there remain important unmet medical needs in the treatments of TBI and SCI.
Ral signaling pathway in health and cancer

The Ral (Ras‐Like) signaling pathway plays an important role in the biology of cells. A plethora of effects is regulated by this signaling pathway and its prooncogenic effectors. Our team has demonstrated the overactivation of the RalA signaling pathway in a number of human malignancies including cancers of the liver, ovary, lung, brain, and malignant peripheral nerve sheath tumors. Additionally, we have shown that the activation of RalA in cancer stem cells is higher in comparison with differentiated cancer cells. In this article, we review the role of Ral signaling in health and disease with a focus on the role of this multifunctional protein in the generation of therapies for cancer. An improved understanding of this pathway can lead to development of a novel class of anticancer therapies that functions on the basis of intervention with RalA or its downstream effectors.
Etude des protéines de la famille H-NS : régulation différentielle des opérons LEE par les protéines H-NS et Ler chez les EPEC

Le genome des bacteries vivantes n’est pas une entite statique mais au contraire c’est quelque chose tres dynamique evoluant avec le temps. Les bacteries evoluent en acquerant par transfert horizontal des genes du materiel genetique. C’est le cas des EPEC qui ont acquis l’ilot LEE via ce mecanisme. La proteine H-NS joue un role important dans la reconnaissance de cet ADN etranger, dans la liaison a cet ADN et dans la repression de son expression quand ce n’est pas en profit du « fitness » de la bacterie. Comme resultat H-NS regule la majorite des genes associes a la virulence chez les enterobacteries Salmonella, Yersinia et les EPEC. Les EPEC possedent une proteine paralogue a H-NS et codee dans le premier operon de leur ilot LEE, il s’agit de la proteine Ler. Une fois exprimee Ler induit l’expression des 4 operons restant de la region parmi lesquels LEE5. Ler partage une grande homologie avec H-NS surtout au niveau de leurs domaines de reconnaissance de l’ADN. Malgre cette homologie H-NS reprime LEE5 tandis que Ler l’active. De plus si H-NS est un regulateur global agissant sur plus de 500 genes chez E. coli Ler est une proteine specifique qui ne va agir que sur un petit nombre de promoteurs tous impliques dans la virulence L’etude qualitative et quantitative de l’interaction de H-NS et de Ler avec la region promotrice de LEE5 montre qu’elles partagent globalement les memes sites de fixation sur des regions etendues en amont et en aval du +1 de la transcription. Ces sites de fixation sont bien definis d’une dizaine de paires de bases. L’affinite de ces sites pour H-NS est variable. Trois sites de haute affinite pour H-NS ont ete identifies. La sequence de ces sites est similaire a celle du site consensus elabore en etudiant le promoteur proU(Bouffartigues et al - 2007). Des differences dans l’interaction de ces deux proteines avec le promoteur LEE5 resident surtout autour du +1 et des boites -10 et -35. Il s’agit de la premiere etude comparant la fixation de H-NS et de Ler sur des regions etendues de ce promoteur dans le but d’expliquer la regulation differentielle de ces deux proteines paralogues. L’etude de l’expression de LEE5 in vivo nous a permis de proposer que le mecanisme essentiel d’action de Ler est dirige contre la repression induite par H-NS et que le taux maximum d’expression du promoteur LEE5 wtobserve dans la souche mutante pour hnsen presence de Ler (en comparaison avec la souche double mutante ou Ler est absente) n’est pas du a une activation directe par Ler mais plutot a une repression par StpA, sensible a la mutation des sites de haute affinite de H-NS.
GRADUAL CHANGE IN HUMAN TOOTH SIZE IN THE LATE PLEISTOCENE AND POST‐PLEISTOCENE

Starting with the onset of the last glaciation approximately 100,000 years ago and continuing to the end of the Late Pleistocene approximately 10,000 years ago, human tooth size began to reduce at a rate of 1% every 2,000 years. Both the mesial‐distal and the buccal‐lingual dimensions of mandibular and maxillary teeth were undergoing the same rate of reduction. From the beginning of the Post‐Pleistocene until the present, the overall rate of dental reduction doubled, becoming approximately 1% per thousand years. Buccal‐lingual dimensions are now reducing twice as fast as mesial‐distal dimensions, and maxillary teeth are reducing at an even more rapid rate than mandibular teeth. Late Pleistocene rates are comparable in Europe and the Middle East. The Post‐Pleistocene rates are also the same for Europe, the Middle East, China, Japan, and Southeast Asia. It is suggested that the cookery at the beginning of the Late Pleistocene allowed the earlier changes to occur. The use of pottery within the last 10,000 years further reduced the amount of selection that had previously maintained usable tooth substance. Reduction then occurred as a consequence of the Probable Mutation Effect (Brace, 1963; McKee, 1984).