Miracle-dz/UniFAR-FTUs huggingface dataset:
In defence of an iconic ichnogenus – Oichnus Bromley, 1981

By establishing the bioerosion ichnogenus Oichnus , Richard Bromley (1981) addressed ‘small round holes in shells’ and catalysed a series of still ongoing discussions on ichnotaxonomical principles. In a recent revision by Zonneveld and Gingras (2014), Oichnus was rejected, together with Tremichnus Brett, 1985 and Fossichnus Nielsen, Nielsen and Bromley, 2003, by means of subjective synonymisation with the presumed senior synonym Sedilichnus Muller, 1977. However, Sedilichnus is nomenclaturally unavailable, because it is an atelonym (conditionally proposed). In addition, reinvestigation of the type material of ‘Sedilichnus’ shows that it probably describes variably shaped oscula and thus is a genuine morphological character of the host sponge Prokaliapsisjanus , rather than a bioerosion trace fossil. The ichnogenera Oichnus and Tremichnus are re vised, leading to the synonymisation of Balticapunctum Rozhnov, 1989 with Tremichnus, and of Fossichnus with Oichnus . The refined ichnogeneric diagnoses return Oichnus to complete or incomplete bioerosive penetrations in calcareous skeletal substrates, commonly interpreted as praedichnia with or without signs of attachment, while Tremichnus (now including O. excavatus ) exclusively refers to shallow pits passing into echinoderm skeletons that are interpreted as domichnia or fixichnia.
HYDRODYNAMIC MECHANISM OF SUSUPENDED LOAD ON RIVERBEDS VEGETATED BY WOODY PLANTS

Hydrodynamic mechanism of suspended load in open channel flows over woody plants was investigated based on the results of laboratory experiments. In the experiments, three-dimensional distributions of equilibrium sediment concentration were minutely measured in uniform flows over tree models uniformly arranged in a staggered manner. It was clarified that so-called dispersive flux plays an important role in the mass-conservation relationship of suspended load, and also that the diffusion coefficient of suspended sediment is almost proportional to the kinematic viscosity of flow. The experimental results of vertical profiles of horizontally averaged sediment concentration were accurately reproduced by a numerical model that includes an empirical model for the dispersive flux and a kE turbulent flow model for the diffusion coefficient.
Amélioration variétale de Coffea canephora. 1 : critères et méthodes de sélection

Depuis le debut de la culture de #Coffea canephora#, l'amelioration varietale a ete l'un des moyens les plus efficaces pour l'augmentation du potentiel de production de cette espece. Les varietes de #C. canephora# sont, soit des clones distribues sous forme de boutures, soit des hybrides de clones distribues sous forme de semences. L'espece #C. canephora# comprend deux groupes genetiques, les Guineens et les Congolais. Le groupe Congolais est, lui-meme, compose de deux sous-groupes (SG1 et SG2). Cette diversite est decrite au niveau genotypique et phenotypique. Pour adopter un programme de selection, il faut choisir le type de varietes recherchees (clones ou hybrides), la variabilite genetique disponible et le delai souhaite d'aboutissement du programme. Des cles d'analyses et de choix sont donnees dans ces domaines. Les varietes de demain devront produire un cafe de qualite, tout en permettant de reduire les couts en intrants et en main-d'oeuvre en respectant l'environnement. Les criteres de selection et methodes d'evaluation a mettre en oeuvre dans cette optique sont detailles. Les dispositifs statistiques couramment employes pour les parcelles d'essai sont les blocs de Fisher et la randomisation de parcelles monoarbres. Des elements de reflexion sur les methodes culturales a appliquer dans les essais de selection sont donnes. Les parametres genetiques evalues chez #C. canephora# sont rappeles. (Resume d'auteur)
Hydrothermal Breccias and Veins at the Kelian Gold Mine, Kalimantan, Indonesia: Genesis of a Large Epithermal Gold Deposit

Mineralized hydrothermal breccias and veins formed during and after the waning stages of maar-diatreme-related volcanic activity at Kelian, Kalimantan, Indonesia. Subsurface phreatic explosions occurred around the margins of the diatreme breccia complex, focusing high-temperature fluid flow and generating several large, mineralized hydrothermal breccia bodies. Tectonic, phreatomagmatic, and hydraulic processes also contributed to hydrothermal brecciation. Explosive phreatic brecciation was followed by in situ hydraulic brecciation, and then by minor veining as the system returned to steady-state geothermal conditions. Brecciation and mineralization mostly occurred 400 to 700 m below the paleowater table. The Kelian deposit contained more than 240 t Au prior to mining. Precious metals occur with sulfide minerals as disseminations, in sheeted and conjugate veins and as breccia cement. There is a progression from pyrite-dominated (stage 1) to base metal sulfide-dominated (stages 2 and 3) to sulfosalt-dominated hydrothermal breccias and veins (stage 4). In terms of gangue minerals, the system evolved from illite-quartz to adularia- and/or quartz- and/or illite-dominated and then carbonate-dominated. Boiling produced abundant bladed carbonate during stages 3 and 4. Overall, carbonate and base metal sulfide minerals are abundant, whereas quartz is comparatively minor. Free gold is most abundant in stages 3 and 4 but also occurs in stages 1 and 2. Native gold occurs principally as inclusions in pyrite, sphalerite, galena, arsenopyrite, quartz, bladed carbonate, and sulfosalts. Hydrothermal alteration assemblages are zoned about contacts, faults, breccias and veins, and consist of secondary quartz, illite, pyrite, chlorite, and various carbonate minerals. Kelian preserves evidence of a magmatic component to the mineralizing fluids. Fluid inclusion analyses revealed the presence of saline fluid inclusions, in particular from stage 3. Isothermal mixing of low-salinity (∼0 to 2 wt % NaCl equiv) with moderate-salinity fluids (10 to 25 wt % NaCl equiv), rather than boiling, resulted in the range of salinity and homogenization temperatures of fluid inclusions in sphalerite, carbonate and quartz deposited during stage 3. Salinities of ∼4 to 6 wt percent NaCl equiv for inclusions in adularia and quartz from stages 2 and 4 and in rhodochrosite and proustite-pyrargyrite from stage 4 may also reflect a component of mixing of low-salinity water with a moderately saline fluid. Sulfur isotope values from Kelian sulfides (δ 34S = -1.4 to 5.5 per mil) are consistent with a magmatic sulfur source. Both boiling and fluid mixing contributed to high-grade Au mineralization at Kelian. Rapid formation (hundreds of years or less) is inferred for the individual hydrothermal breccia bodies. © 2008 Society of Economic Geologists, Inc.
Measurement of Hydraulic Conductivity in Oil Sand Tailings Slurries

The authors thank the discusser for his interest in the paper. The authors agree with the discusser that the flow pump technique is an excellent method to determine hydraulic conductivity and have used this technique to measure hydraulic conductivity in conventional soils. The fine tails, however, are slurries with void ratios up to 10. At these high void ratios, the initial effective stress, at which hydraulic conductivity had to be measured, was only 0.2 kPa. Only very small head differences of approximately 0.02 kPa could be allowed to prevent consolidation during the test, and it was easier to control this with the constant head horizontal burette technique. The discusser suggests measuring the inflow and outflow to determine the volume change of the specimen. The authors did not want the specimen to change volume during flow, as this would have changed the hydraulic conductivity in these high void ratio materials. To ensure that there was no volume change, the inflow and outflow were measured and compared. Figure 1 indicates that there was no volume change during the entire hydraulic conductivity test as the inflow and outflow flow velocities are always equal. The suggestion to plot the ratio of flows with time is interesting and Fig. 2 plots the data from Fig. 1 in this manner. As the ratio is always one, it does show that no volume change was occurring. However, it fails to show an interesting property of high void ratio slurries: the almost two orders of magnitude drop in hydraulic conductivity at the beginning of the test. The reasons for this behavior are given in the paper. The authors did not have any problem distinguishing the steady state from transient state in the constant head tests. The constant head tests were performed for about 10 to 15 h, which is not dissimilar to the 26 h time for the flow pump test shown in the discussion. The authors agree that long-term tests are uneconomical, and the test results may be susceptible to physical and chemical changes in the specimen. In the flow pump test, a known quantity of flow is forced thorough the specimen and the corresponding pressure difference is measured, which is used to determine the hydraulic gradient. This is exactly the opposite of the constant head test. Aiban and Znidarcic (1989) reported that the constant head test and flow pump test yield the same hydraulic conductivity values when the specimenis tested under similar conditions. References
Glycogen synthase kinase-3β phosphorylation of MAP1B at Ser1260 and Thr1265 is spatially restricted to growing axons

Recent experiments show that the microtubule-associated protein (MAP) 1B is a major phosphorylation substrate for the serine/threonine kinase glycogen synthase kinase-3β (GSK-3β) in differentiating neurons. GSK-3β phosphorylation of MAP1B appears to act as a molecular switch regulating the control that MAP1B exerts on microtubule dynamics in growing axons and growth cones. Maintaining a population of dynamically unstable microtubules in growth cones is important for axon growth and growth cone pathfinding. We have mapped two GSK-3β phosphorylation sites on mouse MAP1B to Ser1260 and Thr1265 using site-directed point mutagenesis of recombinant MAP1B proteins, in vitro kinase assays and phospho-specific antibodies. We raised phospho-specific polyclonal antibodies to these two sites and used them to show that MAP1B is phosphorylated by GSK-3β at Ser1260 and Thr1265 in vivo. We also showed that in the developing nervous system of rat embryos, the expression of GSK-3β phosphorylated MAP1B is spatially restricted to growing axons, in a gradient that is highest distally, despite the expression of MAP1B and GSK-3β throughout the entire neuron. This suggests that there is a mechanism that spatially regulates the GSK-3β phosphorylation of MAP1B in differentiating neurons. Heterologous cell transfection experiments with full-length MAP1B, in which either phosphorylation site was separately mutated to a valine or, in a double mutant, in which both sites were mutated, showed that these GSK-3β phosphorylation sites contribute to the regulation of microtubule dynamics by MAP1B.
Customizing the therapeutic response of signaling networks to promote antitumor responses by drug combinations

Drug resistance, de novo and acquired, pervades cellular signaling networks (SNs) from one signaling motif to another as a result of cancer progression and/or drug intervention. This resistance is one of the key determinants of efﬁcacy in targeted anti-cancer drug therapy. Although poorly understood, drug resistance is already being addressed in combination therapy by selecting drug targets where SN sensitivity increases due to combination components or as a result of de novo or acquired mutations. Additionally, successive drug combinations have shown low resistance potential.To promote a rational, systematic development of combination therapies, it is necessary to establish the underlying mechanisms that drive the advantages of combination therapies, and design methods to determine drug targets for combination regimens. Based on a joint systems analysis of cellular SN response and its sensitivity to drug action and oncogenic mutations, we describe an in silico method to analyze the targets of drug combinations. Our method explores mechanisms of sensitizing the SN through a combination of two drugs targeting vertical signaling pathways. We propose a paradigm of SN response customization by one drug to both maximize the effect of another drug in combination and promote a robust therapeutic response against oncogenic mutations. The method was applied to customize the response of the ErbB/PI3K/PTEN/AKT pathway by combination of drugs targeting HER2 receptors and proteins in the down-stream pathway. The results of a computational experiment showed that the modiﬁcation of the SN response from hyperbolic to smooth sigmoid response by manipulation of two drugs in combination leads to greater robustness in therapeutic response against oncogenic mutations determining cancer heterogeneity. The application of this method in drug combination co-development suggests a combined evaluation of inhibition effects together with the capability of drug combinations to suppress resistance mechanisms before they become clinically manifest.
efforts to translate diabetes cardiovascular outcome trials into clinical practice

Diabetic patients suffer from a high rate of cardiovascular events and such risk increases with HbA1c. However, lowering HbA1c does not appear to yield the same benefit on macrovascular endpoints, as observed for microvascular endpoints. As the number of glucose-lowering medications increases, clinicians have to consider several open questions in the management of type 2 diabetes, one of which is the cardiovascular risk profile of each regimen. Recent placebo-controlled cardiovascular outcome trials (CVOTs) have responded to some of these questions, but careful interpretation is needed. After general disappointment around CVOTs assessing safety of DPP-4 inhibitors (SAVOR, TECOS, EXAMINE) and the GLP-1 receptor agonist lixisenatide (ELIXA), the EMPA-REG Outcome trial and the LEADER trial have shown superiority of the SGLT2-I empagliflozin and the GLP-1RA liraglutide, respectively, on the 3-point MACE outcome (cardiovascular death, non-fatal myocardial infarction or stroke) and cardiovascular, as well as all-cause mortality. While available mechanistic studies largely support a cardioprotective effect of GLP-1, the ability of SGLT2 inhibitor(s) to prevent cardiovascular death was unexpected and deserves future investigation. We herein review the results of completed CVOTs of glucose-lowering medications and suggest a possible treatment algorithm based on cardiac and renal co-morbidities to translate CVOT findings into clinical practice.
Cretaceous to Neogene structural evolution of the Lampedusa Shelf (Pelagian Sea, Central Mediterranean)

Studies of multichannel seismic reflection profiles, calibrated with borehole data, have been carried out in the Tunisian shelf surrounding the islands of Lampione and Lampedusa, in order to define the Mesozoic-Cenozoic stratigraphie and structural evolution of this sector of the Pelagian foreland. The stratigraphy and subsidence history show a subsiding Upper Jurassic carbonate platform buried, by syn- and post-rift neritic to deep marine siliciclastics, marls and limestones of Neocomian-early Eocene age. Thick Middle-Upper Eocene shallow-water carbonates (Halk el Menzel Fm.), lie unconformably over the deep-water sediments and exhibit progradational geometries. Messinian evaporites are confined to the deepest parts of the Neogene basins and Plio-Quaternary sediments are widespread over the area. Several unconformities affect the stratigraphic column and have been interpreted as related to compressive events during Late Cretaceous-early Tertiary times. These compressive events produced uplift, folding and reverse faulting, trending about NW-SE and partly reactivating Lower Cretaceous extensional structures. The uppermost regional unconformity indicates widespread emergence and erosion during Oligocene and Miocene tintes and was probably related to a younger compressional phase. A strong Upper Miocene-Quaternary extension event also affected the area, characterized by WNW-ESE trending normal faults, parallel to faults flanking the main grabens of the Sicily Strait rift zone. Since the Messinian, the structural evolution of the area has been controlled by rift-related processes which triggered crustal extension in the Pelagian foreland.
Long-term effects of applied organic manures and inorganic fertilizers on yield and soil fertility in a wheat-rice cropping pattern.

An 11 years study was conducted to investigate the effects of nine treatments of organic manures (PM: Poultry manure and FYM: Farmyard manure) in combination with chemical fertilizers (NPKSZn) on crop productivity and soil fertility in a wheat-rice experiment in Bangladesh. Organic manures had direct and residual effects on rice and wheat yields, but the effect of PM was dominant. Plots with FYM plus 75% NPKSZn produced equivalent or higher yields as 100% NPKSZn. The PM direct to wheat produced 12 % higher yield than 100% NPKSZn. After 3 crop cycles, soil pH was increased in plots with PM and unchanged in inorganic fertilizers and FYM. Percent OM (organic matter) was reduced (13 to 19%) with inorganic fertilizers and increased (7 to39%) with organic manures. Percent total N (Nitrogen) was unchanged in OM plots, but reduced in others. Available P (Phosphorus) increased dramatically in PM plots and was reduced in control plots. Exchangeable K (Potassium) was reduced in control and inorganic fertilizer treatments, but was sustained for others. After 9 years, %OM, % total N and exchangeable K were reduced further in inorganic treatment and increased in OM treatments. The soil pH increased in PM receiving treatments.
Extractable soil phosphorus, correlation with P forms in soil runoff, and relationships with the Texas p index as a nutrient management tool for cafos

Extractable Soil Phosphorus, Correlation with P Forms in Soil Runoff, and Relationships with the Texas P Index as a Nutrient Management Tool for CAFOs. (May 2005) Freddy J. Jacoby, B.S., California State University, Los Angeles; M.S., Clemson University Chair of Advisory Committee: Dr. Sam E. Feagley Phosphorus (P) inputs into water reservoirs are the primary cause for accelerated eutrophication affecting water quality. Attempts are underway to regulate inputs originating from concentrated animal feeding operations (CAFOs). The purpose of this research was to relate runoff dissolved (DP) and total P (TP) losses to site-specific characteristics from plots in CAFOs and compare them to their corresponding risk assessment using the Texas Phosphorus Index (PI). Initial studies showed that soil test P (STP) methods used in Texas by inductively coupled plasma were highly reproducible regardless of manure source or application rate. However, NH4OAc-EDTA extraction efficiency was increased with respect to other methods as soil conditions became less acidic, probably due to dissolution of the greater portion of Ca-bound P resulting in STP values that could be three times greater than those of Mehlich III for the same soil. Surface application of dairy manure to high pH soils were positively correlated to STP at various soil-sampling depths down to 15 cm. First order linear relationships between STP values and DP concentrations in runoff were statistically significant for extraction methods and sampling depths but were different among different soils under neutral to calcareous conditions. Attempts to reproduce this relationship on fields that received
Relationship between Trace Elements and Premature Hair Graying

Context: Hair is said to gray prematurely when a minimum of five gray hairs occurs before the age of 20 in fair skinned, 25 in Asians, and 30 in Africans. It may be genetically associated with autoimmune syndromes or certain environmental factors. Aims: The aim of this study was to evaluate the serum level of iron, copper, and calcium and to assess their role in premature hair graying. Subjects and Methods: This study was carried out on 60 patients with premature hair graying (PHG) and 30 age- and sex-matched healthy individuals served as a control group. The severity of PHG was assessed by the hair whitening scoring system. Serum iron, copper, and calcium concentrations were measured using Beckman Coulter instrument and spectrophotometric method. Results: There was a reduction in serum levels of iron, copper, and calcium in patients with PHG in comparison with controls. There was a statistically negative significant correlation between the severity of PHG and serum iron and calcium levels. There was a negative nonsignificant correlation between body mass index and serum iron, copper, and calcium levels. Conclusions: Serum iron, copper, and calcium levels were reduced in association with PHG and correlated with its severity. Premature graying may be an indicator that hair is not getting enough nutrients and minerals, and supplementation with these trace elements might reverse and is expected to prevent progression of canities; however, further studies are needed to find the underlying mechanism of this relationship.
Rehabilitating the floodplain of the lower River Dyje for fish

The lower reaches of the River Dyje were heavily modified between 1975 and 1985. The river was straightened, isolating its meanders and reducing its length by 22%. As a consequence, the river bed showed a markedly lower diversity in both hydrological and morphological characteristics. Because the River Dyje forms the state boundary between the Czech Republic and Austria, fluvial activity of the lower reaches is excluded. Along the River Dyje an active alluvium has been preserved, with approximately 1300 hectares in the Czech Republic and somewhat less in Austria. The flow regime in the lower reaches is regulated by 19 water reservoirs and a number of fishponds, with a total capacity of approximately 45% of the annual drainage. These modifications have distinctly impacted the living conditions of the indigenous ichthyofauna. Based on the results of our ichthyological investigations from 1994 to 2000, we have recommended a number of modifications that could improve the environmental conditions for fishes: (i) controlled flooding of the alluvial meadows, aimed at creating conditions for the spawning of phytophilous fish species; (ii) restoration of permanent connections between separated river meanders and the River Dyje to increase the hydrological and morphological diversity in the river bed; (iii) creation of artificial pools in the floodplain to provide more suitable habitats for fishes. Copyright © 2003 John Wiley & Sons, Ltd.