Evaluating the Effects of Improving Forest Road Standards on Economic Value of Forest Products

Forest roads are the key infrastructures that provide access to forest areas for sustainable management, protection, and utilization of forest resources. In order to benefit from the important functions of forest roads, they should be built in with adequate technical road standards. The road network with low technical standards require more frequent major repairs to ensure continues access to forest resources. In addition, only small trucks with low load capacity can move on the low standard roads. Furthermore, the low road standards limit the truck speed that increases vehicle travel time. These negative effects increase the transportation costs which are an important part of the timber production costs in Turkey. Thus, improving the road standards and developing forest transportation planning should be evaluated together in the most appropriate way. Large logging trucks with high load capacity are generally preferred for efficient transportation of wood-based forest products. In Turkey, large logging trucks, however, cannot operate on the most of the forest roads because insufficient technical road standards (road width, curve radius, surface materials, road structures) limit the maneuverability of large logging trucks. In this study, the objective is to determine the effects of improving forest road standards on total net profit of forest products by using the NETWORK 2000 program, a heuristic approach for solving forest transportation problems. Three Forest Enterprise Chiefs (FECs) located in Mustafakemalpaşa Forest Enterprise Directorate (FED) in Bursa Forest Regional Directorate were selected as the study area. The digital data layers for forest road network was generated by using ArcGIS 10.4 software. In the solution process, firstly, the optimum routes that minimize the transportation cost and maximize the total net profit of forest products on existing forest road networks were investigated for a truck type (15 ton) currently used in the region. In the second case, forest transportation was planned for the high load capacity truck (29 ton) moving on the forest roads with improved standards. In the first case, the transportation costs and annual major repair costs were considered in the calculation of the net profit of forest products, while one time cost of road improvement activities (i.e. road improvement construction, road structure installation, road surface construction) and annual maintenance costs were considered along with transportation costs in the second case. In both cases, the costs of other forest operations (i.e. felling, logging, etc.) were not considered since it was assumed that they do not vary with the forest transportation alternatives. As a result of the transportation plan developed for high load capacity truck, the annual transportation cost decreased by 46.85% comparing to the local logging trucks with low load capacity. Using improved road standards, the total road costs computed for the time period of 30 years (i.e. the average expected life cycle of forest roads) were reduced by 4.64%. The total net profit of forest products transported by using a high load capacity truck was 473 340 Euro more than that of using low load capacity truck on the existing forest road network. Thus, improving road standards might result in some additional costs in the road construction stage, but total net profit of forest products increase since transportation costs along with maintenance and repair costs considerably decrease in the long term

Simulating Radiating and Magnetized Flows in Multi-Dimensions with ZEUS-MP

This paper describes ZEUS-MP, a multi-physics, massively parallel, message- passing implementation of the ZEUS code. ZEUS-MP differs significantly from the ZEUS-2D code, the ZEUS-3D code, and an early "version 1" of ZEUS-MP distributed publicly in 1999. ZEUS-MP offers an MHD algorithm better suited for multidimensional flows than the ZEUS-2D module by virtue of modifications to the Method of Characteristics scheme first suggested by Hawley and Stone (1995), and is shown to compare quite favorably to the TVD scheme described by Ryu et. al (1998). ZEUS-MP is the first publicly-available ZEUS code to allow the advection of multiple chemical (or nuclear) species. Radiation hydrodynamic simulations are enabled via an implicit flux-limited radiation diffusion (FLD) module. The hydrodynamic, MHD, and FLD modules may be used in one, two, or three space dimensions. Self gravity may be included either through the assumption of a GM/r potential or a solution of Poisson's equation using one of three linear solver packages (conjugate-gradient, multigrid, and FFT) provided for that purpose. Point-mass potentials are also supported. Because ZEUS-MP is designed for simulations on parallel computing platforms, considerable attention is paid to the parallel performance characteristics of each module. Strong-scaling tests involving pure hydrodynamics (with and without self-gravity), MHD, and RHD are performed in which large problems (256^3 zones) are distributed among as many as 1024 processors of an IBM SP3. Parallel efficiency is a strong function of the amount of communication required between processors in a given algorithm, but all modules are shown to scale well on up to 1024 processors for the chosen fixed problem size.Comment: Accepted for publication in the ApJ Supplement. 42 pages with 29 inlined figures; uses emulateapj.sty. Discussions in sections 2 - 4 improved per referee comments; several figures modified to illustrate grid resolution. ZEUS-MP source code and documentation available from the Laboratory for Computational Astrophysics at http://lca.ucsd.edu/codes/currentcodes/zeusmp2

Dynamics of precipitation pattern formation at geothermal hot springs

We formulate and model the dynamics of spatial patterns arising during the precipitation of calcium carbonate from a supersaturated shallow water flow. The model describes the formation of travertine deposits at geothermal hot springs and rimstone dams of calcite in caves. We find explicit solutions for travertine domes at low flow rates, identify the linear instabilities which generate dam and pond formation on sloped substrates, and present simulations of statistical landscape evolution

Modeling recursive RNA interference.

An important application of the RNA interference (RNAi) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo. In several published experiments, RNAi has been used to inactivate components of the RNAi pathway itself, a procedure termed recursive RNAi in this report. The theoretical basis of recursive RNAi is unclear since the procedure could potentially be self-defeating, and in practice the effectiveness of recursive RNAi in published experiments is highly variable. A mathematical model for recursive RNAi was developed and used to investigate the range of conditions under which the procedure should be effective. The model predicts that the effectiveness of recursive RNAi is strongly dependent on the efficacy of RNAi at knocking down target gene expression. This efficacy is known to vary highly between different cell types, and comparison of the model predictions to published experimental data suggests that variation in RNAi efficacy may be the main cause of discrepancies between published recursive RNAi experiments in different organisms. The model suggests potential ways to optimize the effectiveness of recursive RNAi both for screening of RNAi components as well as for improved temporal control of gene expression in switch off-switch on experiments

Whole genome linkage scan of recurrent depressive disorder from the depression network study

Genome-wide linkage analysis was carried out in a sample of 497 sib pairs concordant for recurrent major depressive disorder (MDD). There was suggestive evidence for linkage on chromosome 1p36 where the LOD score for female-female pairs exceeded 3 (but reduced to 2.73 when corrected for multiple testing). The region includes a gene, MTHFR, that in previous studies has been associated with depressive symptoms. Two other regions, on chromosomes 12q23.3-q24.11 and 13q31.1-q31.3, showed evidence for linkage with a nominal P<0.01. The 12q peak overlaps with a region previously implicated by linkage studies of unipolar and bipolar disorders and contains a gene, DAO, that has been associated with both bipolar disorder and schizophrenia. The 13q peak lies within a region previously linked strongly to panic disorder. A fourth modest peak with an LOD of greater than 1 on chromosome 15q lies within a region that showed genome-wide significant evidence of a recurrent depression locus in a previous sib-pair study. Both the 12q and the 15q findings remained significant at genome-wide level when the data from the present study and the previous reports were combine

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

Genomic and serologic characterization of enterovirus A71 brainstem encephalitis

OBJECTIVE: In 2016, Catalonia experienced a pediatric brainstem encephalitis outbreak caused by enterovirus A71 (EV-A71). Conventional testing identified EV in the periphery but rarely in CSF. Metagenomic next-generation sequencing (mNGS) and CSF pan-viral serology (VirScan) were deployed to enhance viral detection and characterization. METHODS: RNA was extracted from the CSF (n = 20), plasma (n = 9), stool (n = 15), and nasopharyngeal samples (n = 16) from 10 children with brainstem encephalitis and 10 children with meningitis or encephalitis. Pathogens were identified using mNGS. Available CSF from cases (n = 12) and pediatric other neurologic disease controls (n = 54) were analyzed with VirScan with a subset (n = 9 and n = 50) validated by ELISA. RESULTS: mNGS detected EV in all samples positive by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (n = 25). In qRT-PCR-negative samples (n = 35), mNGS found virus in 23% (n = 8, 3 CSF samples). Overall, mNGS enhanced EV detection from 42% (25/60) to 57% (33/60) (p-value = 0.013). VirScan and ELISA increased detection to 92% (11/12) compared with 46% (4/12) for CSF mNGS and qRT-PCR (p-value = 0.023). Phylogenetic analysis confirmed the EV-A71 strain clustered with a neurovirulent German EV-A71. A single amino acid substitution (S241P) in the EVA71 VP1 protein was exclusive to the CNS in one subject. CONCLUSION: mNGS with VirScan significantly increased the CNS detection of EVs relative to qRT-PCR, and the latter generated an antigenic profile of the acute EV-A71 immune response. Genomic analysis confirmed the close relation of the outbreak EV-A71 and neuroinvasive German EV-A71. A S241P substitution in VP1 was found exclusively in the CSF.Grants supporting this project include the National Multiple Sclerosis Society and the American Academy of Neurology award FAN-1608-25607 (R.D.S.), Clinical Research Training Scholarship P0534134 (P.S.R.), Sandler and William K. Bowes Jr Foundations (M.R.W., J.L.D., L.M.K., H.A.S., K.C.Z.), Rachleff Family Foundation (M.R.W.), and NINDS of the NIH under award K08NS096117 (M.R.W.) and F31NS113432 (K.E.L.). This study was partially supported by a grant from the Spanish National Health Institute [grant number PI15CIII-00020] and the European Regional Development Fund (FEDER funds). UCSF Biomedical Sciences Program (I.A.H., K.E.L.), UCSF Medical Scientist Training Program (K.E.L.), and the Chan Zuckerberg Biohub (J.E.P., W.W., C.K.C., J.L.D., E.D.C.) also supported this project.S