Scholarometer: A Social Framework for Analyzing Impact across Disciplines

The use of quantitative metrics to gauge the impact of scholarly publications, authors, and disciplines is predicated on the availability of reliable usage and annotation data. Citation and download counts are widely available from digital libraries. However, current annotation systems rely on proprietary labels, refer to journals but not articles or authors, and are manually curated. To address these limitations, we propose a social framework based on crowdsourced annotations of scholars, designed to keep up with the rapidly evolving disciplinary and interdisciplinary landscape. We describe a system called Scholarometer, which provides a service to scholars by computing citation-based impact measures. This creates an incentive for users to provide disciplinary annotations of authors, which in turn can be used to compute disciplinary metrics. We first present the system architecture and several heuristics to deal with noisy bibliographic and annotation data. We report on data sharing and interactive visualization services enabled by Scholarometer. Usage statistics, illustrating the data collected and shared through the framework, suggest that the proposed crowdsourcing approach can be successful. Secondly, we illustrate how the disciplinary bibliometric indicators elicited by Scholarometer allow us to implement for the first time a universal impact measure proposed in the literature. Our evaluation suggests that this metric provides an effective means for comparing scholarly impact across disciplinary boundaries.     

Construction of a chimeric antigen receptor bearing a nanobody against prostate a specific membrane antigen in prostate cancer

Adoptive transfer of T cells expressing chimeric antigen receptors (CARs) is considered to be a novel anticancer therapy. To date, in most cases, single-chain variable fragments (scFvs) of murine origin have been used in CARs. However, this structure has limitations relating to the potential immunogenicity of mouse antigens in humans and the relatively large size of scFvs. For the first time, we used camelid nanobody (VHH) to construct CAR T cells against prostate specific membrane antigen (PSMA). The nanobody against PSMA (NBP) was used to show the feasibility of CAR T cells against prostate cancer cells. T cells were transfected, and then the surface expression of the CAR T cells was confirmed. Then, the functions of VHH-CAR T cell were evaluated upon coculture with prostate cancer cells. At the end, the cytotoxicity potential of NBPII-CAR in T cells was approximated by determining the cell surface expression of CD107a after encountering PSMA. Our data show the specificity of VHH-CAR T cells against PSMA⁺ cells (LNCaP), not only by increasing the interleukin 2 (IL-2) cytokine (about 400 pg/mL), but also the expression of CD69 by almost 38%. In addition, VHH-CAR T cells were proliferated by nearly 60% when cocultured with LNCaP, as compared with PSMA negative prostate cancer cell (DU-145), which led to the upregulation of CD107a in T cells upto 31%. These results clearly show the possibility of using VHH-based CAR T cells for targeted immunotherapy, which may be developed to target virtually any tumor-associated antigen for adoptive T-cell immunotherapy of solid tumors.     

An architecture for a shop-floor controller using colored Petri nets

In a dynamic and flexible manufacturing environment, a shop-floor controller must be designed so that it automatically (or with minimum human intervention) and quickly responds to the changes (e.g., in part type or part routing) in the system. Such a performance may be achieved provided that the controller is simple and sufficiently general in its scope of application. In this article, we present an architecture for such a shop-floor controller. The architecture is based on colored Petri nets with ordered colored sets and structured input and output functions.     

Large Scale Geographical Mapping of Essential Oil Volatiles in Heracleum (Apiaceae): Identification of Novel Compounds and Unraveling Cryptic Variation

Conspecific populations of plants in their native range are expected to show considerable variation due to long‐term ecological and evolutionary factors. We investigated the levels of secondary metabolites in Heracleum including H. persicum a valuable medicinal plant to depict the magnitude of cryptic variation and the potential significance of novel chemical traits. The essential oil volatiles from fruits of 34 populations from different species of Heracleum in Iranian distribution range and a native of H. sphondylium and an invasive population of H. persicum from Norway were analyzed with GC/MS. Out of 48 compounds identified, a contrasting pattern in the level of two major compounds, octyl acetate and hexyl butyrate was found among all studied species. Interestingly, a significant geographic pattern was observed; the hexyl butyrate/octyl acetate ratio was high (range 1.8 – 3.2) in the northwestern Iranian populations of H. persicum compared to that in northern and central populations (range 0.3 – 0.9). Four populations from Zagros mountains also exhibited a unique composition. Anethole was found in two populations of H. persicum from central Zagros, which has not been previously reported for essential oil of fruits of Heracleum so far. The results suggest high efficiency of large scale sampling from distribution range of species in identifying novel compounds. The unique pattern of geographic structuring also provides novel information to unravel cryptic variation in Heracleum.     

Nitrogen fertilization raises CO2 efflux from inorganic carbon: A global assessment

Nitrogen (N) fertilization is an indispensable agricultural practice worldwide, serving the survival of half of the global population. Nitrogen transformation (e.g., nitrification) in soil as well as plant N uptake releases protons and increases soil acidification. Neutralizing this acidity in carbonate‐containing soils (7.49 × 10⁹ ha; ca. 54% of the global land surface area) leads to a CO₂ release corresponding to 0.21 kg C per kg of applied N. We here for the first time raise this problem of acidification of carbonate‐containing soils and assess the global CO₂ release from pedogenic and geogenic carbonates in the upper 1 m soil depth. Based on a global N‐fertilization map and the distribution of soils containing CaCO₃, we calculated the CO₂ amount released annually from the acidification of such soils to be 7.48 × 10¹² g C/year. This level of continuous CO₂ release will remain constant at least until soils are fertilized by N. Moreover, we estimated that about 273 × 10¹² g CO₂‐C are released annually in the same process of CaCO₃ neutralization but involving liming of acid soils. These two CO₂ sources correspond to 3% of global CO₂ emissions by fossil fuel combustion or 30% of CO₂ by land‐use changes. Importantly, the duration of CO₂ release after land‐use changes usually lasts only 1–3 decades before a new C equilibrium is reached in soil. In contrast, the CO₂ released by CaCO₃ acidification cannot reach equilibrium, as long as N fertilizer is applied until it becomes completely neutralized. As the CaCO₃ amounts in soils, if present, are nearly unlimited, their complete dissolution and CO₂ release will take centuries or even millennia. This emphasizes the necessity of preventing soil acidification in N‐fertilized soils as an effective strategy to inhibit millennia of CO₂ efflux to the atmosphere. Hence, N fertilization should be strictly calculated based on plant‐demand, and overfertilization should be avoided not only because N is a source of local and regional eutrophication, but also because of the continuous CO₂ release by global acidification.     

Phenolic compounds profiling in shake flask and bioreactor system cell cultures of <Emphasis Type="Italic">Scrophularia striata</Emphasis> Boiss

Variation in levels of phenolic acids and flavonoids in Scrophularia striata Boiss. cells cultured in both shake flask and bioreactor in vitro systems, was studied at different growth phases. Four phenolic acids (cinnamic, salicylic, coumaric, and caffeic acid), one stilbenoid (resveratrol), and seven flavonoids (diosmin, rutin, kaempferol, catechin, myricetin, quercetin, and luteolin) were analyzed by high-performance liquid chromatography with photodiode array detection. Production of phenolics in the bioreactor was higher than in shake flasks. Catechin was the most abundant flavonoid in both culture systems, while quercetin, which was detected only in the bioreactor, was the lowest amount represented (32.82 μg g^?1 DW). Resveratrol accumulation in bioreactor cultures was 59.84-fold higher than that in shake flasks. Moreover, hierarchical clustering analysis based on Pearson’s correlation coefficient confirmed a positive correlation between the growth phase and some metabolites. The flavonoid accumulation increased with the cells’ physiological age in the bioreactor. Principal component analysis showed that the time course of induction of phenolic acids, flavonoids, and a stilbenoid (resveratrol) was significantly correlated. These findings highlight the capacity of S. striata for large-scale production of desired phenolics using a bioreactor system.     

Population Dynamic of the Mudskipper <Emphasis Type="Italic">Periophthalmus waltoni</Emphasis> Koumans, 1941 from the Bay of Hormozgan Province,Persian Gulf

We studied the population structure and reproductive biology of the mudskipper Periophthalmus waltoni Koumans, 1941, living on the mudflats of bay of Hormozgan province, Persian Gulf. The specimens were haphazardly and monthly collected from August 2008 to July 2009. A total of 2060 fishes was sampled, sexed 690 of which 221 (32%) were males, and 469 (68%) females. The total length (TL) and weight relationship demonstrated growth in both sexes was isometric with the function W = 0.0078TL^3.06. The asymptotic length (L∞) and growth coefficient (K) were estimated as 16.5 cm and 0.75 yr^–1, respectively. Age of the fish at zero length (to) was calculated–0.35 and the longevity was attained 3.65 year. The estimated Von Bertalanffy function was TL_(t) = 16.5[1–exp(–0.75(t + 0.35))]. Natural mortality (M) was estimated 1.74 yr^–1. Four cohorts were distinguished annuallywith mean of TL = 7.35, 10.17, 12.74 and 13.92 cm. The maximum recruitment rate was in January at 17.5%. The overall sex ratio (F: M) (1: 0.49) was significantly different than 1: 1. The peak of the gonadosomatic index (GSI) occurred in February. The size at onset of sexual maturity (LM₅₀)wasestimated at TL = 12 cm. The mean of absolute and relative fecundity were estimated as 3558 ± 2203 and 257 ± 101 eggs, respectively.