Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers

Dairy heifers were subjected to a non-life-threatening challenge designed to induce ruminal acidosis by feeding grain and sugar. Large among animal variation in clinical signs of acidosis, rumen metabolite concentrations, and the rumen microbiome occurred. This exploratory study investigates sources of the variation by examining associations between the genome, metabolome, and microbiome, albeit with a limited population. The broader objective is to provide a rationale for a larger field study to identify markers for susceptibility to ruminal acidosis. Initially, heifers (n = 40) allocated to five feed additive groups were fed 20-days pre-challenge with a total mixed ration and additives. Fructose (0.1% of bodyweight/day) was added for the last 10 days pre-challenge. On day 21 heifers were challenged with 1.0% of bodyweight dry matter wheat + 0.2% of bodyweight fructose + additives. Rumen samples were collected via stomach tube weekly (day 0, 7, and 14) and at five times over 3.6 h after challenge and analyzed for pH and volatile fatty acid, ammonia, D-, and L-lactate concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Genotyping was undertaken using a 150K Illumina SNPchip. Genome-wide association was performed for metabolite and microbiome measures (n = 33). Few genome associations occurred with rumen pH, concentration of acetate, propionate, total volatile fatty acids, or ammonia, or the relative abundance of the Firmicutes, Bacteroidetes, and Spirochaetes phyla. Metabolites and microbial phyla that had markers associated and quantitative trait loci (QTL) were: acetate to propionate ratio (A:P), D-, L-, and total lactate, butyrate, acidosis eigenvalue, Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Planctomycetes, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Euryarchaeota, and Fibrobacteres and covered the region that codes for matrix extracellular phosphoglycoprotein (MEPE). Other overlapping regions were: (1) Chloroflexi, Tenericutes, and A:P, (2) L- and total lactate and Actinobacteria, and (3) Actinobacteria, Euryarchaeota, Fibrobacteres, and A:P. Genome-wide associations with the metabolome and microbiome occurred despite the small population, suggesting that markers for ruminal acidosis susceptibility exist. The findings may explain some of the variation in metabolomic and microbial data and provide a rationale for a larger study with a population that has variation in acidosis.
Dosimetric results in treatments of neuroblastoma and neuroendocrine tumors with (131)I-metaiodobenzylguanidine with implications for the activity to administer.

PURPOSE The aim was to investigate whole-body and red marrow absorbed doses in treatments of neuroblastoma (NB) and adult neuroendocrine tumors (NETs) with (131)I-metaiodobenzylguanidine and to propose a simple method for determining the activity to administer when dosimetric data for the individual patient are not available. METHODS Nine NB patients and six NET patients were included, giving in total 19 treatments as four patients were treated twice. Whole-body absorbed doses were determined from dose-rate measurements and planar gamma-camera imaging. For six NB and five NET treatments, red marrow absorbed doses were also determined using the blood-based method. RESULTS Dosimetric data from repeated administrations in the same patient were consistent. In groups of NB and NET patients, similar whole-body residence times were obtained, implying that whole-body absorbed dose per unit of administered activity could be reasonably well described as a power function of the patient mass. For NB, this functional form was found to be consistent with dosimetric data from previously published studies. The whole-body to red marrow absorbed dose ratio was similar among patients, with values of 1.4 ± 0.6-1.7 ± 0.7 (1 standard deviation) in NB treatments and between 1.5 ± 0.6 and 1.7 ± 0.7 (1 standard deviation) in NET treatments. CONCLUSIONS The consistency of dosimetric results between administrations for the same patient supports prescription of the activity based on dosimetry performed in pretreatment studies, or during the first administration in a fractionated schedule. The expressions obtained for whole-body absorbed doses per unit of administered activity as a function of patient mass for NB and NET treatments are believed to be a useful tool to estimate the activity to administer at the stage when the individual patient biokinetics has not yet been measured.
Microfluidic continuous separation of particles and cells by AC-dielectrophoresis

AC-dielelectrophoresis is utilized inside a lab-on-a-chip device to separate particles and cells. Dielectrophoresis is the movement of particles in a non-uniform electric field due to the interaction of the particle's dipole and spatial gradient of the electric field. Dielectrophoresis is a subtle solution to manipulate particles and cells at microscale due to its favorable scaling for reduced size of the system. Dielectrophoresis is applicable with both DC and AC fields. DC-dielectrophoresis only depends on the electrical conductivities of the particle and the medium. AC-dielectrohoresis depends on the permittivities of the particle and the medium, and the field frequency. AC-dielectrophoresis is richer in the sense that both positive and negative dielectrophoretic force can be generated for biological particles by tuning the field frequency. The dielectrophoretic force depends on the size and the electrical properties of the particles and the suspending medium which makes the separation of particles and cells based on their size and based on their electrical properties possible. In this dissertation, the continuous separation of particles and cells based on their size and based on their electrical properties is achieved inside a lab-on-a-chip device. PDMS (polydimethylsiloxane) microchannels are fabricated using soft lithography technique. The flow is induced by pressure gradient. Simple, 3D electrodes which are fabricated by a simple and inexpensive technique extended from soft-lithographic fabrication are used to achieve a localized, non-uniform electric field. Dielectrophoretic force is generated in the transverse direction to the flow by inserting 3D electrodes along the channel side walls. The localized electric field is important to reduce the Joule heating and any adverse effects on biological particles due to the interaction of particles with the electric field. Latex particles of different size and mixture of white blood cells (which have a typical size of 8-12 micron) and yeast cells (which have a typical size of 3-5 micron) is separated based on their size difference. The separation based on electrical properties is demonstrated by means of the separation of 10 micron latex particles and white blood cells. A numerical simulation based on Lagrangian tracking method is used to simulate the particle trajectories. The present designs have the feature of using simple electrodes like DC-dielectrohoretic devices and of using low electrical potential like AC-dielectrophoretic devices; they are unique in a sense that the effect of the electric field is confined in a small area which means a very short time for the interaction of the particles with the electric field.
Genotypic and phenotypic spectrum of pyridoxine-dependent epilepsy ( ALDH 7 A 1 deficiency )

Genotypic and phenotypic spectrum of pyridoxine-dependent epilepsy (ALDH7A1 deficiency) Philippa B. Mills, Emma J. Footitt, Kevin A. Mills, Karin Tuschl, Sarah Aylett, Sophia Varadkar, Cheryl Hemingway, Neil Marlow, Janet Rennie, Peter Baxter, Olivier Dulac, Rima Nabbout, William J. Craigen, Bernhard Schmitt, François Feillet, Ernst Christensen, Pascale De Lonlay, Mike G. Pike, M. Imelda Hughes, Eduard A. Struys, Cornelis Jakobs, Sameer M. Zuberi and Peter T. Clayton
Impact Response Comparison Between Parametric Human Models and Postmortem Human Subjects with a Wide Range of Obesity Levels

Field data analyses have shown that obesity significantly increases the occupant injury risks in motor vehicle crashes, but the injury assessment tools for people with obesity are largely lacking. The objectives of this study were to use a mesh morphing method to rapidly generate parametric finite element models with a wide range of obesity levels and to evaluate their biofidelity against impact tests using postmortem human subjects (PMHS).
Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals.
Hepatic rupture associated with preeclampsia, report of three cases and literature review

Abstract Background: Hepatic rupture is a complication during pregnancy that, although rare, accounts for high morbidity and mortality rates. It is mainly associated with severe preeclampsia and HELLP syndrome. Incidence is estimated to be at one per 67,000 births or one per 2000 patients with preeclampsia/eclampsia/HELLP, mainly in multiparous women; women in their 40s; after 32 weeks of gestation; and during the first 15 h postpartum. Cases: This article exposes the institutional experience at Fundación Valle del Lili in Cali, Colombia, in managing and treating hepatic rupture associated with severe preeclampsia and HELLP syndrome in three patients in the 30th, the 26th, and the 27th week of gestation, not resulting in maternal death. Discussion: A search in Pubmed, Embase, and Ovid from 2000 to 2017 resulted in 35 cases reported in either pregnant or puerperal women. Hepatic rupture is a rare complication in pregnancy associated with preeclampsia and HELLP syndrome. Its pathophysiology is attributed to the presence of vasospasm due to an increase in concentration and sensitivity to circulating vasopressors during pregnancy. There is no standard management, but surgery reduces mortality significantly. It includes endovascular management, partial hepatectomy, or transplant (only one patient required a liver transplant in our search). The most used techniques have been ligation of the hepatic artery, embolization of the hepatic artery, and examination, packing, and drainage of hepatic lesion for bleeding control (27 cases were treated with laparotomy with evacuation of hematoma and hemostasis and four cases were treated with embolization of the hepatic artery). Hepatic artery occlusion both by surgery ligation and by embolization through interventional radiology has reported successful and failing results during pregnancy Conclusion: Management of pathologies as hepatic rupture associated with severe preeclampsia and HELLP syndrome has to be clearly protocolized for prompt diagnosis and early management. Furthermore, it has to be carried out through multidisciplinary teams in high-complexity obstetrics scenarios.
Utility and Validation of Day and Night Snorkel Counts for Estimating Bull Trout Abundance in First‐ to Third‐Order Streams

Abstract Despite the widespread use of underwater observation to census stream-dwelling fishes, the accuracy of snorkeling methods has rarely been validated. We evaluated the efficiency of day and night snorkel counts for estimating the abundance of bull trout Salvelinus confluentus in 215 sites within first- to third-order streams. We used a dual-gear approach that applied multiple-pass electrofishing catch data adjusted for capture efficiency to estimate true or baseline fish abundance. Our multiple-pass electrofishing capture efficiency models were based on a prior study and used recapture data for known numbers of individually marked fish. Snorkeling efficiency was estimated by comparing day and night snorkel counts with the baseline. We also evaluated the influence of fish size and stream habitat features on snorkeling efficiency. Bull trout snorkeling efficiency was higher at night (mean = 33.2%) than during the day (mean = 12.5%). Beta-binomial regression indicated that bull trout day and night sno.
The one-out-of-k retrieval problem and linear network coding

In this paper we show how linear network coding can reduce the number of queries needed to retrieve one specific message among k distinct ones replicated across a large number of randomly accessed nodes storing one message each. Without network coding, this would require k queries on average. After proving that no scheme can perform better than a straightforward lower bound of 0. 5k average queries, we propose and asymptotically evaluate, using mean field arguments, a few example practical schemes, the best of which attains 0. 82k queries on average. The paper opens two complementary challenges: a systematic analysis of practical schemes so as to identify the best performing ones and design guideline strategies, as well as the need to identify tighter, nontrivial, lower bounds.
De Novo Assembly, Functional Annotation and Comparative Analysis of Withania somnifera Leaf and Root Transcriptomes to Identify Putative Genes Involved in the Withanolides Biosynthesis

Withania somnifera is one of the most valuable medicinal plants used in Ayurvedic and other indigenous medicine systems due to bioactive molecules known as withanolides. As genomic information regarding this plant is very limited, little information is available about biosynthesis of withanolides. To facilitate the basic understanding about the withanolide biosynthesis pathways, we performed transcriptome sequencing for Withania leaf (101L) and root (101R) which specifically synthesize withaferin A and withanolide A, respectively. Pyrosequencing yielded 8,34,068 and 7,21,755 reads which got assembled into 89,548 and 1,14,814 unique sequences from 101L and 101R, respectively. A total of 47,885 (101L) and 54,123 (101R) could be annotated using TAIR10, NR, tomato and potato databases. Gene Ontology and KEGG analyses provided a detailed view of all the enzymes involved in withanolide backbone synthesis. Our analysis identified members of cytochrome P450, glycosyltransferase and methyltransferase gene families with unique presence or differential expression in leaf and root and might be involved in synthesis of tissue-specific withanolides. We also detected simple sequence repeats (SSRs) in transcriptome data for use in future genetic studies. Comprehensive sequence resource developed for Withania, in this study, will help to elucidate biosynthetic pathway for tissue-specific synthesis of secondary plant products in non-model plant organisms as well as will be helpful in developing strategies for enhanced biosynthesis of withanolides through biotechnological approaches.
Identifying abnormal nodes in complex networks by using random walk measure

Identifying outlier nodes is an important task in complex network mining. In this paper, we analyze the problem of identifying outliers in a network structure and propose an outlier measure by using the random walk distance measure and the dissimilarity index between pairs of vertices. Our method determines a “view” to the whole network for each node and infers that outliers are those nodes whose views differ significantly from majority of the nodes. Usually, outlier is detected by applying a specific criteria, for example, the farthest ones from the central node. Consequently, only one type of outliers satisfying the predefined criteria can be determined. On the other hand, our method incorporates both local and global information of the network due to random walk feature and can give more general outlier detection results. We have applied the method to artificial and real networks and some interesting results have been obtained.
Spatio-Temporal Matching for Urban Transportation Applications

In this article, we present a search problem in which mobile agents are searching for static resources. Each agent wants to obtain exactly one resource. Both agents and resources are spatially located on a road network and the movement of the agents is constrained to the road network. This problem applies to various transportation applications including: vehicles (agents) searching for parking (resources) and taxicabs (agents) searching for clients to pick up (resources). In this work, we design search algorithms for such scenarios. We model the problem in different scenarios that vary based on the level of information that is available to the agents. These scenarios vary from scenarios in which agents have complete information about other agents and resources, to scenarios in which agents only have access to a fraction of the data about the availability of resources (uncertain data). We also propose pricing schemes that incentivize vehicles to search for resources in a way that benefits the system and the environment. Our proposed algorithms were tested in a simulation environment that uses real-world data. We were able to attain up to 40% improvements over other approaches that were tested against our algorithms.
Patterns of chondrification and ossification in the skull of Graptemys pseudogeographica, the false map turtle (Emydidae)

Patterns of ossification and chondrification are well‐described for several species of turtles, but details of the chondrocranial anatomy are known for only a handful of species. Cleared and double‐stained embryos of Graptemys pseudogeographica were used to examine the fully formed chondrocranium and the formation, chondrification, and ossification of the cranium. The chondrocranium of G. pseudogeographica possesses an unusually large, irregularly shaped foramen epiphaniale that is joined with the fenestra olfactoria. As in other emydids, and many turtles generally, the taenia marginalis is present only as a small projection and the taenia medialis is lacking in mature stages of embryonic development. Ossification data for G. pseudogeographica are consistent with those of other Testudines in that the dentary and maxilla (dermal elements of the upper and lower jaws) ossify early, whereas the articular (an endochondral bone of the lower jaw) ossifies relatively late. Additionally, comparative ossification shows that the vomer is quite variable in its relative timing of ossification across Testudines.
Influence of a Combination of Chemical Enhancers and Iontophoresis on In Vitro Transungual Permeation of Nystatin

To promote transungual permeation of nystatin (NYST), molecule with high molecular weight, no water-soluble, amphoteric by iontophoresis. The synergic effect of the combination of cetylpyridinium chloride, CPC, or polyoxyethylene (20) sorbitan monooleate, TW80, and iontophoresis was investigated. In vitro permeation experiments were carried out through bovine hoof slices using vertical diffusion cells. A low current density (0.2 mA/cm2) was applied by introducing Ag/AgCl electrodes in the donor (anode) and receptor (cathode) chambers. The donor phase consisted of a solution, a suspension, or gel-type vehicles containing NYST and surfactants in pH 5.6 HEPES buffer. The addition of CPC to NYST suspension (SOSP) produced a fivefold increase on the permeability of the bovine hoof membrane to the drug. The application of anodal iontophoresis further improved NYST flux. Conversely, NYST transungual permeation was not influenced by TW80 either in the passive diffusion or iontophoretic flux. Furthermore, the iontophoretic treatment does not appear to induce irreversible alterations to the hoof bovine membranes. The present work demonstrated the efficacy of iontophoresis as a treatment for different nail pathologies with large molecules very slightly soluble in water without irreversibly affecting the nail structure. A synergistic effect between CPC and iontophoresis was observed.
Effect of micro-silica on mechanical and durability properties of high volume fly ash recycled aggregate concretes (HVFA-RAC)

This paper presents the effect of different micro-silica (MS) contents of 5, 10 and 15 wt. % as partial replacement of cement on mechanical and durability properties of high volume fly ash recycled aggregate concretes (HVFA-RAC) containing 50% class F fly ash (FA) and 35% recycled coarse aggregate (RCA) as partial replacement of cement and natural coarse aggregate (NCA), respectively. The measured mechanical and durability properties are compressive strength, indirect tensile strength, elastic modulus, drying shrinkage, water sorptivity and chloride permeability. The effects of different curing ages of 7, 28, 56 and 91 days on above properties are also considered in this study. The results show that the addition of MS up to 10% improved the early age (7 days) strength properties of HVFA-RAC, however, at later ages (e.g. 28-91 days) the above mechanical properties are improved for all MS contents. The 5% MS exhibited the best performance among all MS contents for all mechanical properties of HVFA-RAC. In the case of measured durability properties, mix results are obtained, where 10% and 5% MS exhibited the lowest sorptivity and drying shrinkage, respectively at all ages. However, in the case of chloride ion permeability a decreasing trend is observed with increase in MS contents and curing ages. Strong correlations of indirect tensile strength and modulus of elasticity with square root of compressive strength are also observed in HVFA-RAC. Nevertheless, it is established in this study that MS contributes to the sustainability of HVFA-RAC significantly by improving the mechanical and durability properties of concrete containing 50% less cement and 35% less natural coarse aggregates.