Miracle-dz/UniFAR-FTUs huggingface dataset:
Red-ochre Pigment Production by Fusarium spp. on Co-cultivation with Bacillus subtilis

Bacillus strains offer several advantages over other bacteria for protection against plant pathogens because of their ability to form endospore and to produce broad spectrum antibiotics. The aim of this work was to study the interaction of Bacillus subtilis with rice pathogen, Fusarium . Eleven aerobic endospore forming bacilli were isolated from Bhitarkanika mangrove sediment, Odisha, India. Among them one strain was found to be antagonistic to the tested rice pathogens. The isolated bacterium was Gram-positive rod having sub-terminal endospore. The analysis of partial sequences containing 700 to 900 bases of the 16S ribosomal DNA gene showed 99% identity with B. subtilis. Strong inhibitory activity against Fusarium spp. was found on co-cultures with B. subtilis strain, particularly on Sabouraud dextrose agar (SDA) and Potato dextrose agar (PDA). Their interaction resulted in the secretion of red and red-ochre color pigments, probably due to melanization after seven days of co-culturing.
High Performance Messaging on Workstations: Illinois Fast Messages (FM) for Myrinet

In most computer systems, software overhead dominates the cost of messaging, reducing delivered performance, especially for short messages. Efficient software messaging layers are needed to deliver the hardware performance to the application level and to support tightly-coupled workstation clusters. Illinois Fast Messages (FM) 1.0 is a high speed messaging layer that delivers low latency and high bandwidth for short messages. For 128-byte packets, FM achieves bandwidths of 16.2MB/s and one-way latencies 32 µs on Myrinet-connected SPARCstations (user-level to user-level). For shorter packets, we have measured one-way latencies of 25 µs, and for larger packets, bandwidth as high as to 19.6MB/s — delivered bandwidth greater than OC-3. FM is also superior to the Myrinet API messaging layer, not just in terms of latency and usable bandwidth, but also in terms of the message half-power point (n_{\frac{1}{2}}), which is two orders of magnitude smaller (54 vs. 4,409 bytes). We describe the FM messaging primitives and the critical design issues in building a low-latency messaging layers for workstation clusters. Several issues are critical: the division of labor between host and network coprocessor, management of the input/output (I/O) bus, and buffer management. To achieve high performance, messaging layers should assign as much functionality as possible to the host. If the network interface has DMA capability, the I/Obus should be used asymmetrically, with the host processor moving data to the network and exploiting DMA to move data to the host. Finally, buffer management should be extremely simple in the network coprocessor and match queue structures between the network coprocessor and host memory. Detailed measurements show how each of these features contribute to high performance.
Quantiﬁcation of the unique continuation property for the nonstationary Stokes problem

The purpose of this work is to establish stability estimates for the unique continuation property of the nonstationary Stokes problem. These estimates hold without prescribing boundary conditions and are of logarithmic type. They are obtained thanks to Carleman estimates for parabolic and elliptic equations. Then, these estimates are applied to an inverse problem where we want to identify a Robin coeﬃcient deﬁned on some part of the boundary from measurements available on another part of the boundary
Reduced tubulin polyglutamylation suppresses flagellar shortness in Chlamydomonas

Tubulin polyglutamylation is a posttranslational modification known to affect ciliary/flagellar motility and assembly. Investigation of Chlamydomonas mutants deficient in axonemal polyglutamylation shows that polyglutamylation functions by increasing tubulin turnover at the flagellar tip and reducing axonemal stability.
Molecular characterization and tissue distribution of ZO-2, a tight junction protein homologous to ZO-1 and the Drosophila discs-large tumor suppressor protein

ZO-1 is a 210-225-kD peripheral membrane protein associated with cytoplasmic surfaces of the zonula occludens or tight junction. A 160- kD polypeptide, designated ZO-2, was found to coimmunoprecipitate with ZO-1 from MDCK cell extracts prepared under conditions which preserve protein associations (Gumbiner, B., T. Lowenkopf, and D. Apatira. 1991. Proc. Natl. Acad. Sci. USA. 88: 3460-3464). We have isolated ZO-2 from MDCK cell monolayers by bulk coimmunoprecipitation with ZO-1 followed by electroelution from preparative SDS-PAGE gel slices. Amino acid sequence information obtained from a ZO-2 tryptic fragment was used to isolate a partial cDNA clone from an MDCK library. The deduced amino acid sequence revealed that canine ZO-2 contains a region that is very similar to sequences in human and mouse ZO-1. This region includes both a 90-amino acid repeat domain of unknown function and guanylate kinase- like domains which are shared among members of the family of proteins that includes ZO-1, erythrocyte p55, the product of the lethal(1)discs- large-1 (dlg) gene of Drosophila, and a synapse-associated protein from rat brain, PSD-95/SAP90. The dlg gene product has been shown to act as a tumor suppressor in the imaginal disc of the Drosophila larva, although the functions of other family members have not yet been defined. A polyclonal antiserum was raised against a unique region of ZO-2 and found to exclusively label the cytoplasmic surfaces of tight junctions in MDCK plasma membrane preparations, indicating that ZO-2 is a tight junction-associated protein. Immunohistochemical staining of frozen sections of whole tissue demonstrated that ZO-2 localized to the region of the tight junction in a number of epithelia, including liver, intestine, kidney, testis, and arterial endothelium, suggesting that this protein is a ubiquitous component of the tight junction. Double- label immunofluorescence microscopy performed on cryosections of heart, a nonepithelial tissue, revealed the presence of ZO-1 but no ZO-2 staining at the fascia adherens, a specialized junction of cardiac myocytes which has previously been shown to contain ZO-1 (Itoh, M., S. Yonemura, A. Nagafuchi, S. Tsukita, and Sh. Tsukita. 1991. J. Cell Biol. 115:1449-1462). Thus it appears that ZO-2 is not a component of the fascia adherens, and that unlike ZO-1, this protein is restricted to the epithelial tight junction.
Reviewing and delving into the causes of the Hubble tension

: This paper explores different techniques for measuring the Hubble-Lemaˆıtre constant. After reviewing how the measurements of this important cosmological parametre have evolved through history, we present and compare the fundamental methods, both model-independent, based on standard candles/sirens and standard rulers, and model-dependent, based on the cosmic microwave background, where a discrepancy between the two groups of results has been recently named Hubble tension. Sources of systematic uncertainty as well as possible modifications to the ΛCDM model are discussed in order to mitigate this tension.
Roles and regulation of cytokinins in tomato fruit development

Cytokinins (CKs) are thought to play important roles in fruit development, especially cell division. However, the mechanisms and regulation of CK activity have not been well investigated. This study analysed CK concentrations and expression of genes involved in CK metabolism in developing tomato (Solanum lycopersicum) ovaries. The concentrations of CK ribosides and isopentenyladenine and the transcript levels of the CK biosynthetic genes SlIPT3, SlIPT4, SlLOG6, and SlLOG8 were high at anthesis and decreased immediately afterward. In contrast, trans-zeatin concentration and the transcript levels of the CK biosynthetic genes SlIPT1, SlIPT2, SlCYP735A1, SlCYP735A2, and SlLOG2 increased after anthesis. The expression of type-A response regulator genes was high in tomato ovaries from pre-anthesis to early post-anthesis stages. These results suggest that the CK signal transduction pathway is active in the cell division phase of fruit development. This study also investigated the effect of CK application on fruit set and development. Application of a synthetic CK, N-(2-chloro-pyridin-4-yl)-N’-phenylurea (CPPU), to unpollinated tomato ovaries induced parthenocarpic fruit development. The CPPU-induced parthenocarpic fruits were smaller than pollinated fruits, because of reduction of pericarp cell size rather than reduced cell number. Thus, CPPU-induced parthenocarpy was attributable to the promotion of cell division, not cell expansion. Overall, the results provide evidence that CKs are involved in cell division during development of tomato fruit.
Factors in�uencing pulmonary hemorrhage in very low-and extremely low-birth-weight infants: a meta-analysis

21-0.73, P<0.01, I 2 =25%), preterm birth (OR=1.99, 95% CI 1.34-2.97, P<0.01, I 2 =47%), and blood product transfusion (OR=6.16, 95% CI 2.15-17.69, P<0.01, I 2 =0%).
Low cost task migration initiation in a heterogeneous MP-SoC

Run-time task migration in a heterogeneous multiprocessor system-on-chip (MP-SoC) is a challenge that requires cooperation between the task and the operating system. In task migration, minimization of the overhead during normal task execution (i.e., when not migrating) and the minimization of the migration reaction time are important. We introduce a novel technique that reuses the processor's debug registers in order to minimize the overhead during normal execution. This paper explains our task migration proof-of-concept setup and compares it to the state-of-the art. By reusing existing hardware and software functionality our approach reduces the run time overhead.
A Visualized Review of Ecological Planning and Design based on Bibliometrics from 1992 to 2017

: To rapidly and clearly define the knowledge structure, research focus, and research trends in the field of ecological planning and design, the bibliometric method was combined with visualization tools to conduct a classified statistical study of 712 articles on ecological planning and design in the core database of Web of Science (WoS) from 1992 to 2017, making a contrastive analysis of information like the author, journal, research institution, country, keywords of those articles from three perspectives, namely co-authorship analysis, co-citation analysis, and co-words analysis. Three conclusions were drawn. First, academic exchanges and cooperation in the field of ecological planning and design should be strengthened between countries and scientific research institutions, especially China and its research institutions should actively participate in such exchanges and cooperation, and scholars are expected to seize the opportunities to cooperate with each other in research and practice in this field. Second, as developed European and American countries outweigh Asian countries in terms of research results and overall influence in the field of ecological planning and design, the popularity and influence of journals from Asian countries need to be improved, particularly as they study and report on ecosystem services. Third, as research on ecological planning and design become increasingly systematic, comprehensive, and humanistic, resilience has become a research hotspot in this field in recent years, thus enough attention should be paid to this aspect. Finally, the author hopes that the combination of visualization tools and the bibliometric method can foster enlightenment and research ideas among researchers and practitioners in this field.
smyRNA: A Novel Ab Initio ncRNA Gene Finder

Background Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. Methodology/Principal Findings We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. Conclusions/Significance Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability: http://compbio.cs. sfu.ca/taverna/smyrna
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such ‘DNA looping’ interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (‘diffusive’) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern.
Context-Independent Scatter and Tabu Search for Permutation Problems

In this paper, we develop a general-purpose heuristic for permutations problems. The procedure is based on the scatter-search and tabu-search methodologies and treats the objective-function evaluation as a black box, making the search algorithm context-independent. Therefore, our main contribution consists of the development and testing of a procedure that uses no knowledge from the problem context to search for the optimal solution. We perform computational experiments with four well-known permutation problems to study the efficiency and effectiveness of the proposed method. These experiments include a comparison with two commercially available software packages that are also based on meta-heuristic optimization technology and allow solutions to be represented as permutations.
Autophagy facilitates TLR4- and TLR3-triggered migration and invasion of lung cancer cells through the promotion of TRAF6 ubiquitination

Autophagy contributes to the pathogenesis of cancer, whereas toll-like receptors (TLRs) also play an important role in cancer development and immune escape. However, little is known about the potential interaction between TLR signaling and autophagy in cancer cells. Here we show that autophagy induced by TLR4 or TLR3 activation enhances various cytokine productions through promoting TRAF6 (TNF receptor-associated factor 6, E3 ubiquitin protein ligase) ubiquitination and thus facilitates migration and invasion of lung cancer cells. Stimulation of TLR4 and TLR3 with lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid [poly(I:C)] respectively triggered autophagy in lung cancer cells. This was mediated by the adaptor protein, toll-like receptor adaptor molecule 1 (TICAM1/TRIF), and was required for TLR4- and TLR3-induced increases in the production of IL6, CCL2/MCP-1 [chemokine (C-C motif) ligand 2], CCL20/MIP-3α [chemokine (C-C motif) ligand 20], VEGFA (vascular endothelial growth factor A), and MMP2 [matrix metallopeptidase 2 (gelatinase A, 72 kDa gelatinase, 72 kDa type IV collagenase)]. These cytokines appeared to be necessary for enhanced migration and invasion of lung cancer cells upon TLR activation. Remarkably, inhibition of autophagy by chemical or genetic approaches blocked TLR4- or TLR3-induced Lys63 (K63)-linked ubiquitination of TRAF6 that was essential for activation of MAPK and NFKB (nuclear factor of kappa light polypeptide gene enhancer in B-cells) pathways, both of which were involved in the increased production of the cytokines. Collectively, these results identify induction of autophagy by TLR4 and TLR3 as an important mechanism that drives lung cancer progression, and indicate that inhibition of autophagy may be a useful strategy in the treatment of lung cancer.
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder

Obsessive-compulsive disorder (OCD) is a psychiatric condition characterized by intrusive and unwilling thoughts (obsessions) giving rise to anxiety. The patients feel obliged to perform a behavior (compulsions) induced by the obsessions. The World Health Organization ranks OCD as one of the 10 most disabling medical conditions. In the class of Anxiety Disorders, OCD is a pathology that shows an hereditary component. Consequently, an online resource collecting and integrating scientific discoveries and genetic evidence about OCD would be helpful to improve the current knowledge on this disorder. We have developed a manually curated database, OCD Database (OCDB), collecting the relations between candidate genes in OCD, microRNAs (miRNAs) involved in the pathophysiology of OCD and drugs used in its treatments. We have screened articles from PubMed and MEDLINE. For each gene, the bibliographic references with a brief description of the gene and the experimental conditions are shown. The database also lists the polymorphisms within genes and its chromosomal regions. OCDB data is enriched with both validated and predicted miRNA-target and drug-target information. The transcription factors regulations, which are also included, are taken from David and TransmiR. Moreover, a scoring function ranks the relevance of data in the OCDB context. The database is also integrated with the main online resources (PubMed, Entrez-gene, HGNC, dbSNP, DrugBank, miRBase, PubChem, Kegg, Disease-ontology and ChEBI). The web interface has been developed using phpMyAdmin and Bootstrap software. This allows (i) to browse data by category and (ii) to navigate in the database by searching genes, miRNAs, drugs, SNPs, regions, drug targets and articles. The data can be exported in textual format as well as the whole database in.sql or tabular format. OCDB is an essential resource to support genome-wide analysis, genetic and pharmacological studies. It also facilitates the evaluation of genetic data in OCD and the detection of alternative treatments. Database URL: http://alpha.dmi. unict.it/ocdb/
Spectral style transfer for human motion between independent actions

Human motion is complex and difficult to synthesize realistically. Automatic style transfer to transform the mood or identity of a character's motion is a key technology for increasing the value of already synthesized or captured motion data. Typically, state-of-the-art methods require all independent actions observed in the input to be present in a given style database to perform realistic style transfer. We introduce a spectral style transfer method for human motion between independent actions, thereby greatly reducing the required effort and cost of creating such databases. We leverage a spectral domain representation of the human motion to formulate a spatial correspondence free approach. We extract spectral intensity representations of reference and source styles for an arbitrary action, and transfer their difference to a novel motion which may contain previously unseen actions. Building on this core method, we introduce a temporally sliding window filter to perform the same analysis locally in time for heterogeneous motion processing. This immediately allows our approach to serve as a style database enhancement technique to fill-in non-existent actions in order to increase previous style transfer method's performance. We evaluate our method both via quantitative experiments, and through administering controlled user studies with respect to previous work, where significant improvement is observed with our approach.
aCGHViewer: A Generic Visualization Tool For aCGH data

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark. org/aCGHview/.
Node Aggregation for Distributed Inference in Bayesian Networks

This study describes a general framework and several algorithms for reducing Bayesian networks with loops (i.e., undirected cycles) into equivalent networks which are singly connected. The purpose of this conversion is to take advantage of a distributed inference algorithm (6). The framework and algorithms center around one basic operation, node aggregation. In this operation, a cluster of nodes in a network is replaced with a single node without changing the underlying joint distribution of the network. The framework for us ing this operation includes a node aggregation theorem which describes whether a cluster of nodes can be combined, and a complexity analysis which estimates the computational require ments for the resulting networks. The algorithms described include a heuristic search algorithm which finds the set of node aggregations that makes a network singly connected and allows inference to execute in minimum time, and a "graph-directed" algorithm which is guaranteed to find a feasible but not necessary optimal solution and with less computation than the search algorithm.