A PARTAN-Accelerated Frank-Wolfe Algorithm for Large-Scale SVM Classification

Frank-Wolfe algorithms have recently regained the attention of the Machine Learning community. Their solid theoretical properties and sparsity guarantees make them a suitable choice for a wide range of problems in this field. In addition, several variants of the basic procedure exist that improve its theoretical properties and practical performance. In this paper, we investigate the application of some of these techniques to Machine Learning, focusing in particular on a Parallel Tangent (PARTAN) variant of the FW algorithm that has not been previously suggested or studied for this type of problems. We provide experiments both in a standard setting and using a stochastic speed-up technique, showing that the considered algorithms obtain promising results on several medium and large-scale benchmark datasets for SVM classification

Disassembly of a Medial Transenvelope Structure by Antibiotics during Intracellular Division.

Chlamydiales possess a minimal but functional peptidoglycan precursor biosynthetic and remodeling pathway involved in the assembly of the division septum by an atypical cytokinetic machine and cryptic or modified peptidoglycan-like structure (PGLS). How this reduced cytokinetic machine collectively coordinates the invagination of the envelope has not yet been explored in Chlamydiales. In other Gram-negative bacteria, peptidoglycan provides anchor points that connect the outer membrane to the peptidoglycan during constriction using the Pal-Tol complex. Purifying PGLS and associated proteins from the chlamydial pathogen Waddlia chondrophila, we unearthed the Pal protein as a peptidoglycan-binding protein that localizes to the chlamydial division septum along with other components of the Pal-Tol complex. Together, our PGLS characterization and peptidoglycan-binding assays support the notion that diaminopimelic acid is an important determinant recruiting Pal to the division plane to coordinate the invagination of all envelope layers with the conserved Pal-Tol complex, even during osmotically protected intracellular growth

Rancang Bangun Sistem Sensor pada Model Fuze Proximity untuk Mendukung Rudal Nasional

Fuze proximity berfungsi sebagai pemicu awal berlangsungnya peledakan, pada jarak tertentu dari objek-objek yang bergerak dengan semakin cepat, seperti pesawat tempur, kapal perang, peluru kendali. Fuze ini merupakan komponen utama dari sebuah munisi yang saat ini 100% masih diimpor dari negara lain, sehingga rawan diembargo dan tidak lagi memiliki aspek kerahasiaan karena jumlahnya selalu dapat diketahui oleh negara pembuat atau pengirimnya. Selain itu, fuze juga tidak boleh mudah rusak dan harus tahan lama disimpan, tahan terhadap cuaca dan lingkungan sekeliling, serta tahan diperlakukan kasar (rugged) saat dipindahkan, sebelum munisi diluncurkan. Dengan persyaratan yang sedemikian ketat, maka tidak semua pabrik senjata dan pabrik munisi mampu membuat sendiri fuzenya. Dengan kondisi tersebut, ancaman embargo dari negara-negara produsen fuze setiap saat dapat dikenakan kepada negara pengimpornya, bila ada perselisihan. Untuk itu, fuze pada munisi kaliber besar (MKB), maupun rudal perlu dikembangkan sehingga mampu mendukung industri pertahanan nasional untuk lebih mandiri. Pada tulisan ini dibahas mengenai hasil-hasil pengembangan sistem sensor pada model fuze proximity di BPP Teknologi

FtsZ-independent septal recruitment and function of cell wall remodelling enzymes in chlamydial pathogens.

The nature and assembly of the chlamydial division septum is poorly defined due to the paucity of a detectable peptidoglycan (PG)-based cell wall, the inhibition of constriction by penicillin and the presence of coding sequences for cell wall precursor and remodelling enzymes in the reduced chlamydial (pan-)genome. Here we show that the chlamydial amidase (AmiA) is active and remodels PG in Escherichia coli. Moreover, forward genetics using an E. coli amidase mutant as entry point reveals that the chlamydial LysM-domain protein NlpD is active in an E. coli reporter strain for PG endopeptidase activity (ΔnlpI). Immunolocalization unveils NlpD as the first septal (cell-wall-binding) protein in Chlamydiae and we show that its septal sequestration depends on prior cell wall synthesis. Since AmiA assembles into peripheral clusters, trimming of a PG-like polymer or precursors occurs throughout the chlamydial envelope, while NlpD targets PG-like peptide crosslinks at the chlamydial septum during constriction

Multilayered control of chromosome replication in Caulobacter crescentus.

The environmental Alphaproteobacterium Caulobacter crescentus is a classical model to study the regulation of the bacterial cell cycle. It divides asymmetrically, giving a stalked cell that immediately enters S phase and a swarmer cell that stays in the G1 phase until it differentiates into a stalked cell. Its genome consists in a single circular chromosome whose replication is tightly regulated so that it happens only in stalked cells and only once per cell cycle. Imbalances in chromosomal copy numbers are the most often highly deleterious, if not lethal. This review highlights recent discoveries on pathways that control chromosome replication when Caulobacter is exposed to optimal or less optimal growth conditions. Most of these pathways target two proteins that bind directly onto the chromosomal origin: the highly conserved DnaA initiator of DNA replication and the CtrA response regulator that is found in most Alphaproteobacteria The concerted inactivation and proteolysis of CtrA during the swarmer-to-stalked cell transition license cells to enter S phase, while a replisome-associated Regulated Inactivation and proteolysis of DnaA (RIDA) process ensures that initiation starts only once per cell cycle. When Caulobacter is stressed, it turns on control systems that delay the G1-to-S phase transition or the elongation of DNA replication, most probably increasing its fitness and adaptation capacities

Bacillus subtilis fadB (ysiB) gene encodes an enoyl-CoA hydratase

Fatty acids are essential components of membranes and are an important source of metabolic energy. In bacteria, the β-oxidation pathway is well known in Escherichia coli. Bacillus subtilis possesses a considerable number of genes, organized in five operons, that are most likely involved in the β-oxidation of fatty acids. Among these genes, only one product, FadRBs (YsiA), has been recently characterized as a transcriptional regulatory protein which negatively regulates the expression of β-oxidation genes including those belong- ing to the lcfA operon, including fadRBs (ysiA). The probable involvement of the FadRBs (YsiA) regulon members in β- oxidation is inferred from data based on BLASTP similarity of their gene products. In this work, we report the cloning and the expression of B. subtilis fadBBs(ysiB), belonging to the lcfA operon, and the functional characterization of its product as an enoyl-CoA hydratase, demonstrating the actual involvement of these genes in fatty acid β-oxidation

Black microcolonial fungi as deteriogens of two famous marble statues in Florence, Italy

Blackened areas on outdoor marble statues are a significant esthetic problem due to the presence of deteriorating agents. Microcolonial black fungi, which have their natural ecological niche on rocks, play an important role in deterioration of stones used in monuments, such as marble and limestone. Black fungi were isolated from two very valuable statues exposed to the outdoor environment in Florence, Italy, the "Ratto delle Sabineâ" and the "Copia del David", and these fungi were demonstrated to be responsible for the blackening areas on the statues. The black strains showed many features common to members of rock-inhabitants dematiaceous fungi. Morphological and molecular characterization, including phylogenetic analysis, indicated that the strains isolated from both statues and in different times belong to the same species and can be assigned to the rock-inhabitant genera Sarcinomyces and Phaeococcomyces. Red yeasts growing in close proximity to the black ones, with no visible effect on the statues, were also characterized on the morphological and molecular level and identified as Sporobolomyces yunnanensis

Cell wall precursors are required to organize the chlamydial division septum.

Members of the Chlamydiales order are major bacterial pathogens that divide at mid-cell, without a sequence homologue of the FtsZ cytokinetic tubulin and without a classical peptidoglycan cell wall. Moreover, the spatiotemporal mechanisms directing constriction in Chlamydia are not known. Here we show that the MreB actin homologue and its conserved regulator RodZ localize to the division furrow in Waddlia chondrophila, a member of the Chlamydiales order implicated in human miscarriage. RodZ is recruited to the septal site earlier than MreB and in a manner that depends on biosynthesis of the peptidoglycan precursor lipid II by the MurA enzyme. By contrast, crosslinking of lipid II peptides by the Pbp3 transpeptidase disperses RodZ from the septum. Altogether, these findings provide a cytological framework for understanding chlamydial cytokinesis driven by septal cell wall synthesis

Control of proline utilization by the Lrp-like regulator PutR in Caulobacter crescentus.

Cellular metabolism recently emerged as a central player modulating the bacterial cell cycle. The Alphaproteobacterium Caulobacter crescentus appears as one of the best models to study these connections, but its metabolism is still poorly characterized. Considering that it lives in oligotrophic environments, its capacity to use amino-acids is often critical for its growth. Here, we characterized the C. crescentus PutA bi-functional enzyme and showed that it is required for the utilization of proline as a carbon source. We also found that putA transcription and proline utilization by PutA are strictly dependent on the Lrp-like PutR activator. The activation of putA by PutR needs proline, which most likely acts as an effector molecule for PutR. Surprisingly, we also observed that an over-production of PutR leads to cell elongation in liquid medium containing proline, while it inhibits colony formation even in the absence of proline on solid medium. These cell division and growth defects were equally pronounced in a ΔputA mutant background, indicating that PutR can play other roles beyond the control of proline catabolism. Altogether, these findings suggest that PutR might connect central metabolism with cell cycle processes