Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network.

Traditional Chinese Medicine (TCM) has received increasing attention as a complementary approach or alternative to modern medicine. However, experimental methods for identifying novel targets of TCM herbs heavily relied on the current available herb-compound-target relationships. In this work, we present an Herb-Target Interaction Network (HTINet) approach, a novel network integration pipeline for herb-target prediction mainly relying on the symptom related associations. HTINet focuses on capturing the low-dimensional feature vectors for both herbs and proteins by network embedding, which incorporate the topological properties of nodes across multi-layered heterogeneous network, and then performs supervised learning based on these low-dimensional feature representations. HTINet obtains performance improvement over a well-established random walk based herb-target prediction method. Furthermore, we have manually validated several predicted herb-target interactions from independent literatures. These results indicate that HTINet can be used to integrate heterogeneous information to predict novel herb-target interactions

Effect of seed mixture composition and management on competitiveness of herbs in temporary grasslands

In multispecies grasslands the proportion of different herb species may vary considerably due to low competitiveness of some herbs. To examine the possibility for increasing the competitiveness an experiment with three factors were set up: 1) amount of herb seed in a perennial ryegrass (Lolium perenne), white clover (Trifolium repens) mixture, 2) slurry application and 3) cutting frequency. The experiment was carried out over two years. The herbs mix contained salad burnet (Sanguisorba minor), fenugreek (Trogonella foenum-gruecum), chicory (Chicorium intybus), caraway (Carum carvi), birdsfoot trefoil (Lotus corniculatus), chervil (Anthriscus cerefolium), plantain (Plantago lanceolata), Lucerne (Medicago sativa) and melilot (Melilotus officinalis). The proportion of herb seeds was 5, 25, 50 or 100 %. The herb species were most competitive in the first harvest year. In the second year the proportion of all herb species were very low in the mixtures, where white clover and perennial ryegrass were represented. The proportion of many herbs were higher at a 7-cut than at a 4-cut management, and application of cattle slurry also affected the competitiveness. In general chicory, caraway and plantain were the strongest competitors, salad burnet and birdsfoot trefoil were intermediate, and melilot, fenugreek and chervil were very weak competitors

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.

The prebiotic potential of nervine herbal medicines has been scarcely studied. We therefore used anaerobic human fecal cultivation to investigate whether medicinal herbs commonly used as treatment in neurological health and disease in Ayurveda and other traditional systems of medicine modulate gut microbiota. Profiling of fecal cultures supplemented with either Kapikacchu, Gotu Kola, Bacopa/Brahmi, Shankhapushpi, Boswellia/Frankincense, Jatamansi, Bhringaraj, Guduchi, Ashwagandha or Shatavari by 16S rRNA sequencing revealed profound changes in diverse taxa. Principal coordinate analysis highlights that each herb drives the formation of unique microbial communities predicted to display unique metabolic potential. The relative abundance of approximately one-third of the 243 enumerated species was altered by all herbs. Additional species were impacted in an herb-specific manner. In this study, we combine genome reconstruction of sugar utilization and short chain fatty acid (SCFA) pathways encoded in the genomes of 216 profiled taxa with monosaccharide composition analysis of each medicinal herb by quantitative mass spectrometry to enhance the interpretation of resulting microbial communities and discern potential drivers of microbiota restructuring. Collectively, our results indicate that gut microbiota engage in both protein and glycan catabolism, providing amino acid and sugar substrates that are consumed by fermentative species. We identified taxa that are efficient amino acid fermenters and those capable of both amino acid and sugar fermentation. Herb-induced microbial communities are predicted to alter the relative abundance of taxa encoding SCFA (butyrate and propionate) pathways. Co-occurrence network analyses identified a large number of taxa pairs in medicinal herb cultures. Some of these pairs displayed related culture growth relationships in replicate cultures highlighting potential functional interactions among medicinal herb-induced taxa

Fault tolerant hypercube computer system architecture

A fault-tolerant multiprocessor computer system of the hypercube type comprising a hierarchy of computers of like kind which can be functionally substituted for one another as necessary is disclosed. Communication between the working nodes is via one communications network while communications between the working nodes and watch dog nodes and load balancing nodes higher in the structure is via another communications network separate from the first. A typical branch of the hierarchy reporting to a master node or host computer comprises, a plurality of first computing nodes; a first network of message conducting paths for interconnecting the first computing nodes as a hypercube. The first network provides a path for message transfer between the first computing nodes; a first watch dog node; and a second network of message connecting paths for connecting the first computing nodes to the first watch dog node independent from the first network, the second network provides an independent path for test message and reconfiguration affecting transfers between the first computing nodes and the first switch watch dog node. There is additionally, a plurality of second computing nodes; a third network of message conducting paths for interconnecting the second computing nodes as a hypercube. The third network provides a path for message transfer between the second computing nodes; a fourth network of message conducting paths for connecting the second computing nodes to the first watch dog node independent from the third network. The fourth network provides an independent path for test message and reconfiguration affecting transfers between the second computing nodes and the first watch dog node; and a first multiplexer disposed between the first watch dog node and the second and fourth networks for allowing the first watch dog node to selectively communicate with individual ones of the computing nodes through the second and fourth networks; as well as, a second watch dog node operably connected to the first multiplexer whereby the second watch dog node can selectively communicate with individual ones of the computing nodes through the second and fourth networks. The branch is completed by a first load balancing node; and a second multiplexer connected between the first load balancing node and the first and second watch dog nodes, allowing the first load balancing node to selectively communicate with the first and second watch dog nodes

Root biomass and carbon storage in differently managed multispecies temporary grasslands

Species-rich grasslands may potentially increase carbon (C) storage in soil and an experiment was established to investigate C storage in highly productive temporary multi-species grasslands. Plots were established with three mixtures: 1) a herb mixture containing salad burnet (Sanguisorba minor L.), fenugreek (Trogonella foenum-gruecum), chicory (Chicorium intybus L.), caraway (Carum carvi L.), birdsfoot trefoil (Lotus corniculatus L.), chervil (Anthriscus cerefolium L.), plantain (Plantago lanceolata L.), lucerne (Medicago sativa L.) and melilot (Melilotus officinalis), 2) 50% of the herb mixture and 50% of a white clover (Trifolium repens L.)/perennial ryegrass (Lolium perenne L.) mixture, and 3) 5% of the herb mixture and 95% of the white clover/ryegrass mixture. Management factors were number of cuts per year and fertilizer application. Aboveground biomass increased considerably with increasing content of herbs and with fertilizer application in plots with a 4-cut strategy. With a 6-cut strategy without fertilizer herbs had no effect on the aboveground biomass. In the herb mixture biomass of small roots was lower than in mixtures with white clover and ryegrass. There was a tendency towards increased biomass in the large root fraction with increasing herb content. The experiment indicated increased CO2 evolution following cultivation of multispecies grasslands