Hierarchical growing neural gas

“The original publication is available at www.springerlink.com”. Copyright Springer.This paper describes TreeGNG, a top-down unsupervised learning method that produces hierarchical classification schemes. TreeGNG is an extension to the Growing Neural Gas algorithm that maintains a time history of the learned topological mapping. TreeGNG is able to correct poor decisions made during the early phases of the construction of the tree, and provides the novel ability to influence the general shape and form of the learned hierarchy

RNAi revised - Target mRNA-dependent enhancement of gene silencing

The discovery of RNA interference (RNAi) gave rise to the development of new nucleic acid-based technologies as powerful investigational tools and potential therapeutics. Mechanistic key details of RNAi in humans need to be deciphered yet, before such approaches take root in biomedicine and molecular therapy. We developed and validated an in silico-based model of siRNA-mediated RNAi in human cells in order to link in vitro-derived pre-steady state kinetic data with a quantitative and time-resolved understanding of RNAi on the cellular level. The observation that product release by Argonaute 2 is accelerated in the presence of an excess of target RNA in vitro inspired us to suggest an associative mechanism for the RNA slicer reaction where incoming target mRNAs actively promote dissociation of cleaved mRNA fragments. This novel associative model is compatible with highmultiple turnover rates of RNAibased gene silencing in living cells and accounts for target mRNA concentration-dependent enhancement of the RNAi machinery

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

<p>Abstract</p> <p>Background</p> <p>Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering).</p> <p>Results</p> <p>Temporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.</p> <p>Conclusion</p> <p>The new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.</p

BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection

<p>Abstract</p> <p>Background</p> <p>Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.</p> <p>Results</p> <p>In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.</p> <p>Conclusion</p> <p>BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. The BLProt software is available at <url>http://www.inb.uni-luebeck.de/tools-demos/bioluminescent%20protein/BLProt</url></p

Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model

NREM sleep is characterized by two hallmarks, namely K-complexes (KCs) during sleep stage N2 and cortical slow oscillations (SOs) during sleep stage N3. While the underlying dynamics on the neuronal level is well known and can be easily measured, the resulting behavior on the macroscopic population level remains unclear. On the basis of an extended neural mass model of the cortex, we suggest a new interpretation of the mechanisms responsible for the generation of KCs and SOs. As the cortex transitions from wake to deep sleep, in our model it approaches an oscillatory regime via a Hopf bifurcation. Importantly, there is a canard phenomenon arising from a homoclinic bifurcation, whose orbit determines the shape of large amplitude SOs. A KC corresponds to a single excursion along the homoclinic orbit, while SOs are noise-driven oscillations around a stable focus. The model generates both time series and spectra that strikingly resemble real electroencephalogram data and points out possible differences between the different stages of natural sleep

A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation

Few models exist that accurately reproduce the complex rhythms of the thalamocortical system that are apparent in measured scalp EEG and at the same time, are suitable for large-scale simulations of brain activity. Here, we present a neural mass model of the thalamocortical system during natural non-REM sleep, which is able to generate fast sleep spindles (12–15 Hz), slow oscillations (<1 Hz) and K-complexes, as well as their distinct temporal relations, and response to auditory stimuli. We show that with the inclusion of detailed calcium currents, the thalamic neural mass model is able to generate different firing modes, and validate the model with EEG-data from a recent sleep study in humans, where closed-loop auditory stimulation was applied. The model output relates directly to the EEG, which makes it a useful basis to develop new stimulation protocols

IMPLEMENTASI PEMBERIAN GANTI KERUGIAN LAYANAN PAKET DI PT TIKI JALUR NUGRAHA EKAKURIR (JNE) CABANG SURAKARTA DITINJAU DARI UNDANG-UNDANG NOMOR 38 TAHUN 2009 TENTANG POS

ABSTRAK Yusuf Bintang Syaifinuha, E0012414. 2016. IMPLEMENTASI PEMBERIAN GANTI KERUGIAN LAYANAN PAKET DI PT TIKI JALUR NUGRAHA EKAKURIR (JNE) CABANG SURAKARTA DITINJAU DARI UNDANG-UNDANG NOMOR 38 TAHUN 2009 TENTANG POS. Fakultas Hukum Universitas Sebelas Maret Surakarata. Penelitian ini bertujuan untuk mengetahui implementasi pemberian ganti kerugian di PT Tiki Jalur Nugraha Ekakurir (JNE) Cabang Surakarta ditinjau dari UU Pos dan untuk mengetahui cara penyelesaian sengketa yang timbul dari implementasi pemberian ganti kerugian di PT Tiki Jalur Nugraha Ekakurir (JNE) Cabang Surakarta. Metode penelitian yang digunakan dalam penelitian ini adalah deskriptif kualitatif. Jenis penelitian ini adalah penelitian empiris. Data yang digunakan terdiri dari dua data yaitu data primer dan data sekunder. Teknik pengumpulan data adalah dengan metode wawancara dan studi pustaka. Berdasarkan hasil analisis penelitian, dapat diambil kesimpulan bahwa implementasi pemberian ganti kerugian di JNE kurang sesuai dengan Pasal 28 UU Pos karena jenis ganti kerugian hanya untuk kehilangan kiriman dan kerusakan isi kiriman. Pengirim yang mengajukan klaim ganti kerugian harus memenuhi syarat administrasi yang telah ditetapkan oleh JNE. Nilai ganti kerugian yang diberikan JNE adalah 10 kali biaya pengiriman atau sesuai harga barang yang hilang dan/atau rusak jika menggunakan asuransi. JNE memilih upaya hukum diluar pengadilan (nonlitigasi) berupa negosiasi dalam menyelesaikan sengketa yang terjadi dalam implementasi pemberian ganti kerugian. Kata kunci :Perjanjian, Wanprestasi, Implementasi ganti kerugian

Inferring Market Structure from Customer Response to Competing and Complementary Products

We consider customer influences on market structure, arguing that market structure should explain the extent to which any given set of market offerings are substitutes or complements. We describe recent additions to the market structure analysis literature and identify promising directions for new research in market structure analysis. Impressive advances in data collection, statistical methodology and information technology provide unique opportunities for researchers to build market structure tools that can assist “real-time” marketing decision-making.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46981/1/11002_2004_Article_5088105.pd

Chronic oxytocin-driven alternative splicing of Crfr2α induces anxiety

The neuropeptide oxytocin (OXT) has generated considerable interest as potential treatment for psychiatric disorders, including anxiety and autism spectrum disorders. However, the behavioral and molecular consequences associated with chronic OXT treatment and chronic receptor (OXTR) activation have scarcely been studied, despite the potential therapeutic long-term use of intranasal OXT. Here, we reveal that chronic OXT treatment over two weeks increased anxiety-like behavior in rats, with higher sensitivity in females, contrasting the well-known anxiolytic effect of acute OXT. The increase in anxiety was transient and waned 5 days after the infusion has ended. The behavioral effects of chronic OXT were paralleled by activation of an intracellular signaling pathway, which ultimately led to alternative splicing of hypothalamic corticotropin-releasing factor receptor 2α (Crfr2α), an important modulator of anxiety. In detail, chronic OXT shifted the splicing ratio from the anxiolytic membrane-bound (mCRFR2α) form of CRFR2α towards the soluble CRFR2α (sCRFR2α) form. Experimental induction of alternative splicing mimicked the anxiogenic effects of chronic OXT, while sCRFR2α-knock down reduced anxiety-related behavior of male rats. Furthermore, chronic OXT treatment triggered the release of sCRFR2α into the cerebrospinal fluid with sCRFR2α levels positively correlating with anxiety-like behavior. In summary, we revealed that the shifted splicing ratio towards expression of the anxiogenic sCRFR2α underlies the adverse effects of chronic OXT treatment on anxiety

Recull de propostes per minimitzar l'impacte negatiu de gènere del sistema de teletreball a l'Ajuntament de Barcelona

Finançat amb el projecte "Impacto de GÉnero del TEletrabajo y rutinas de COnfinamiento: más allá de lo obvio" (Ref. SUPERACOVID19_2.2.IGETECO) i a través de l'Ajuntament de Barcelona pel Servei d'Estudi sobre propostes per minimitzar l'impacte negatiu de gènere del sistema de teletreball a l'Ajuntament de Barcelona (exp.20002682)El present document recull les propostes d'actuació contingues a l'estudi Propostes per minimitzar l'impacte negatiu de gènere del sistema de teletreball a l'Ajuntament de Barcelona realitzat pel Centre d'Estudis Sociològics sobre la Vida Quotidiana i el Treball (QUIT) de la Universitat Autònoma de Barcelona. L'emergència sanitària provocada per la Covid19 i el necessari confinament de la població per combatre la pandèmia ha significat, des del punt de vista de l'organització del treball, un canvi molt important cap a l'impuls de formes de treball a distància. Però aquest impuls del teletreball ha estat una resposta fruit de l'emergència, lògica davant la situació viscuda i, com a tal, no ha pogut ser planificada amb el temps i els mitjans necessaris