Miracle-dz/UniFAR-FTUs huggingface dataset:
Forest snail faunas from Transylvania (Romania) and their relationship to the faunas of Central and Northern Europe

Forty-three forest sites in seven sampling areas in mountainous parts of Transylvania were sampled to obtain inventories of their snail faunas, and to make comparisons between these and the faunas of similar sites further north along the Carpathian chain. Sampling areas ran from close to the Ukrainian border in the north to Retezat in the south-west. Altogether, 83 species were found, as well as between 19 and 40 species at individual sites. Sites within the same sampling area had more species in common than in among-area comparisons, although differences between areas did not relate to the distance between them. Such differences appear to be related more to ecological factors than to geography. Faunas of all areas were very similar to those recorded from the Polish and Ukrainian Carpathians; distance from these northern faunas had little effect on similarity. More broadly, the fauna of these forests shows a much greater affinity to those of countries to the north than to those of countries to the south. Despite the survival of forests through the last glacial period of the Pleistocene, and the greater proximity to potential Mediterranean refugia, these faunas appear to be mainly a subset of those found further north. They represent a rather small proportion of the known Romanian fauna, in which there are many endemics restricted to other habitats.
Neonatal growth and organ allometry of Northwest Atlantic harp seals (Phoca groenlandica)

Growth and organ allometry of neonatal harp seals (Phoca groenlandica) were monitored during the first 6 weeks of life from 1982 to 1984. At birth, pup mass was 9.9 ± 1.7 (1 SD) kg. After their 1st.
Characteristics of the Purple Pigment Compound in Halophytic Plant, Suaeda japonica

As one of the steps toward understanding how the plant is well adapted to strongly saline habitats, the purple pigment compound that is accumulated in Suaeda japonica was extracted and characterized. The extracted pigment compound exhibited typical characteristics of betacyanin that were represented by water solubility, pHand temperature-dependent color changes, sensitivity to light, UV-Vis spectra, and gel electrophoretic migration pattern. LC-MS of the extracted pigment compound showed the presence of two major protonated molecular ions ([M+H]) at m/z 651.1 and m/z 827.1. According to the DPPH assay, it was found to have an antioxidant activity that is linearly increased in proportion to the reaction time for up to 30 min, and the activity was comparable to that of control BHA at 9.0 mg/ml. The cytotoxic activity against several tumor cell lines was also examined following the MTT assay. The significant growth inhibitory effect was observed on two tumor cell lines, SW-156 (human kidney carcinoma) and HEC-1B (human endometrial adenocarcinoma). Probably, the pigment compound may function as an osmolyte to uphold halotolerant physiological processes in saline environment.
Natural Language Processing Techniques for Extracting and Categorizing Finding Measurements in Narrative Radiology Reports

Summary Background: Accumulating quantitative outcome parameters may contribute to constructing a healthcare organization in which outcomes of clinical procedures are reproducible and predictable. In imaging studies, measurements are the principal category of quantitative para meters. Objectives: The purpose of this work is to develop and evaluate two natural language processing engines that extract finding and organ measurements from narrative radiology reports and to categorize extracted measurements by their “temporality“. Methods: The measurement extraction engine is developed as a set of regular expressions. The engine was evaluated against a manually created ground truth. Automated categorization of measurement temporality is defined as a machine learning problem. A ground truth was manually developed based on a corpus of radiology reports. A maximum entropy model was created using features that characterize the measurement itself and its narrative context. The model was evaluated in a ten-fold cross validation protocol. Results: The measurement extraction engine has precision 0.994 and recall 0.991. Accuracy of the measurement classification engine is 0.960. Conclusions: The work contributes to machine understanding of radiology reports and may find application in software applications that process medical data. Citation: Sevenster M, Buurman J, Liu P, Peters JF, Chang PJ. Natural language processing techniques for extracting and categorizing finding measurements in narrative radiology reports. Appl Clin Inform 2015; 6: 600–610 http://dx.doi. org/10.4338/ACI-2014-11-RA-0110
Analysis, purification and quantification of extracellular DNA from aquatic environments

SUMMARY 1. The presence of extracellular DNA, but not RNA, at μg 1−1 concentrations was demonstrated in seawater, river water and in a series of eutrophic lowland ponds. 2. Extracellular DNA in natural waters invariably comprised two major components: one of high molecular weight (>20 kb) derived from viruses, and another of low molecular weight (1–500 bp) and apparently free in solution. Similar species of DNA molecules were produced within 2 weeks in simple laboratory modules. 3. A purification procedure was developed which separated extracellular DNA from other components of dissolved organic matter, and which also separated viral from soluble DNA. Both types of DNA were purified sufficiently to constitute active templates for enzymes used in DNA manipulation.
PI3K regulatory subunit p85alpha plays a tumor suppressive role in the transformation of mammary epithelial cells

Hyperactivation of the phosphatidylinositol 3-kinase (PI3K) pathway is one of the most common events in human cancers. Class IA PI3Ks are heterodimers of a p110 catalytic and a p85 regulatory subunit that coordinate the cellular response to extracellular stimuli. Activating mutations in class IA PIγK catalytic isoform p110g are well established as causative in a number of cancer types. More recently, mutation or loss of the class IA regulatory isoform p85g (encoded by PIK3R1) has emerged as contributing to oncogenesis. In this dissertation, we use both in vitro and in vivo approaches to examine the role of p85g as a tumor suppressor in the transformation of mammary epithelial cells. Using publically available online databases, we find heterozygous deletion of PIK3R1 occurs in 19-26% of breast tumors. Moreover, PIK3R1 expression is significantly decreased in breast tumors compared to normal breast tissue. In human mammary epithelial cells expressing dominant negative p53 (DDp53-HMECs), RNAi-mediated knockdown of PIK3R1 increases PI3K/AKT activation in response to growth factor stimulation and leads to transformation as assessed by anchorage-independent growth. PIK3R1 knockdown also augments transformation of DDp53-HMECs by oncogenes, including activated HER2/neu. In a mouse model of HER2/neu-driven breast cancer, genetic ablation of Pik3r1 accelerates mammary tumor development. Transformation driven by p85g loss is largely mediated by signaling through catalytic isoform p110g, as
Datability of Pecan Tree Rings

Analyses of stem cross sections of 97 pecan (Carya illinoinensis (Wangenh.) K. Koch) and 22 post oak (Quercus stellata Wangenh.) trees from seven sites showed tree rings were sensitive to the environment and were datable by tree, among trees within a site, among sites, and between species. Pecan had well-defined annual growth rings averaging from 1.25 to 3.36 mm in width and that varied synchronously among trees. Pecan had a mean sensitivity of about 0.3 compared to 0.4 for post oak, indicating a smaller but adequate response of pecan to reflect climatic variations and to use pecan tree rings in other dendrological studies.
Massive Growth of the Invasive Algae Didymosphenia Geminata Associated with Discharges from a Mountain Reservoir Alters the Taxonomic and Functional Structure of Macroinvertebrate Community

The objective of this paper is to determine the alteration of the taxonomic composition and functional structure of macroinvertebrate community associated with a massive growth of the invasive algae Didymosphenia geminata downstream of a mountain reservoir (Pajares Reservoir, La Rioja, Northern Spain). As the massive growth of the alga disappears a few kilometres downstream of the reservoir associated with the input of nutrients from a nearby village sewage, we may compare the community composition between nine stations in three different conditions: three stations heavily affected by the presence of D. geminata, three further downstream stations without the algal massive growth but affected by river regulation and three control stations (unregulated and without the algae). Results show a significant disturbance of the composition and structure of macroinvertebrate community in sites affected by the stream flow regulation downstream of the dam compared with unregulated streams, but the alterations are more dramatic in the area where the growth of D. geminata is massive because of the total substrate occupation by the algal filaments. Scrapers and others invertebrates living on the coarse substrate are especially affected at such sites. Moreover, an important increase in the relative abundance of chironomids is associated with the algal massive growth, especially in case of Eukiefferiella devonica and Cricotopus spp. , reducing the assemblage diversity and leading to the taxonomic and functional homogenization of the community. Changes in the reservoir management (such as releasing the water from surface rather than from the hypolimnion) may be useful to control the massive growth of D. geminata and thus reducing the effects of river regulation on macroinvertebrate assemblage composition. Copyright © 2014 John Wiley & Sons, Ltd.
Preliminary investigation of chemical fractionation and heavy metal accumulation in plant maize ( Zea mays ) grown on chromated copper arsenate (CCA) contaminated soil amended with poultry droppings

Poultry droppings used as soil amendments and a sequential chemical speciation (six steps) procedure were used to predict the uptake of Cr, Cu and As by maize (Zea mays) plant in chromated copper arsenate (CCA) contaminated soil. A pot experiment containing contaminated soil samples to different percentage levels of amendments and control (no amendment) was set up. The initial concentration of Cr, Cu and As in the contaminated soil sample were established. The six fractions based on sequential extractions were also established. The distribution patterns of the metals based on their mobility factor Mf showed values high enough to predict high lability and bioavailability for arsenic, moderate for chromium and low for copper. The amendment, an energy-rich source substance enhanced mobility and bioavailability of the metals and their subsequent uptake and accumulation in the maize plant. This led to a cleanup at 20% amendment of As (20.6%), Cr (2%), and Cu (17.1%) after a period of twenty days. These figures are impressive considering the fact that the increase in pH occasioned by the poultry dropping amendment must have bound the metals.
Epigallocatechin gallate from Camellia sinensis L. (Kuntze) is a potential quorum sensing inhibitor in Chromobacterium violaceum

The problem on the widespread occurrence of antibiotic resistant strains of bacteria calls for novel methods of control of bacterial activity. One of the new viable alternatives to antibiotics is the use of substances that inhibit quorum sensing (QS) – a bacterial communication system that has been known to regulate the expression of virulence genes during infection. In this study, epigallocatechin gallate (EGCG) from green tea, Camellia sinensis L. (Kuntze) was tested for its ability to inhibit QS in a test organism, Chromobacterium violaceum . This microorganism produces a violet-colored substance, violacein, through QS. This study aimed to detect inhibition of QS-regulated violacein production in C. violaceum by EGCG and to determine the dynamics of QS inhibition relative to the concentration of EGCG. The effect of increasing concentration of EGCG on both violacein production and cell density of treated and untreated C. violaceum was determined in a 96-well-microplate format and read at 570nm and 620nm for violacein production and growth, respectively. The results show that addition of EGCG increased the growth of the organism while there is concentration-dependent decrease in the QS-controlled production of violacein. This study thus establishes that EGCG is a potential QS inhibitor and can be further studied and developed for its use as an anti-pathogenic but non-toxic drug.
Preference of two populations of Propylea quatuordecimpunctata (coleoptera: coccinellidae) for Aphis fabae and Aphis gossypii (homoptera: aphididae)

Prey preference of natural enemies is an important parameter used in studies on their efficiency. Feeding preferences of individuals from two populations of Propylea quatuordecimpunctata (L.) (Coleoptera: Coccinellidae) for the essential prey items, Aphis fabae Scopoli, 1763 and Aphis gossypii Glover, 1877 (Homoptera: Aphididae) were evaluated in the laboratory using Manly's β preference index (β). For the predator preference experiment, equal numbers of A. fabae and A. gossypii were offered to the predator. The experiment was conducted on a broad bean leaf disc with 20 replicates. After 24 h, the unconsumed aphids were counted. Individuals of P. quatuordecimpunctata from both populations consumed more A. gossypii [Karaj population (mean ± SE): 28.15 ± 1.04 and Sari population 34.35 ± 0.51] than A. fabae (Karaj population: 17.95 ± 0.64 and Sari population: 17.7 ± 1.01). The values of Manly's β preference index (β) for A. gossypii were 0.73 ± 0.01 and 0.77 ± 0.01 for the Karaj and Sari populations, respectively and for A. fabae were 0.26 ± 0.01 and 0.22 ± 0.01 for the Karaj and Sari populations, respectively. Comparison of the preference indices using a t-test revealed significant differences between the prey preferences of those from the Sari population (t = 22.53, df = 38, P < 0.0001) and the Karaj population (t = 26, df = 38, P < 0.0001). These results reveal that P. quatuordecimpunctata from the two populations prefer A. gossypii over A. fabae.
Vernalization and Photoperiod Response in Annual Wild Cicer Species and Cultivated Chickpea

Wild Cicer species possess high levels of resistance to many stresses and can contribute to enhance levels of resistances besides broadening the genetic base of cultivated chickpea (Cicer arietinum L.). However, longer duration of wild Cicer species and nonsynchronization of flowering with cultigen remains a major deterrence for their use in chickpea improvement. In this study, the response to vernalization (V), photoperiod (P), and combination of both (V + P) was studied in terms of rate of progress toward flowering in cultivated and wild Cicer species belonging to primary, secondary, and tertiary gene pools. Both V and P treatments, alone and in combination, significantly increased the rate of progress toward flowering in wild Cicer species compared with control. Effect of P in increasing the rate of progress toward flowering was significantly higher than V in C. reticulatum Ladiz. , C. echinospermum P. H. Davis, C. judaicum Boiss. , C. pinnatifidum Jaub. & Spach, C. bijugum Rech. f. , and C. yamashitae Kitam. and vice versa in C. chorassanicum (Bunge) Popov and C. cuneatum Hochst. ex A. Rich. Synergistic effects of V and P were observed in C. bijugum, C. yamashitae, C. chorassanicum, and C. cuneatum. However, both V and P treatments had minimal effect on the rate of progress toward flowering in early-maturing and greater effects on medium- and late-maturing chickpea varieties. These results would contribute significantly to enhance use of wild Cicer species for chickpea improvement through synchronization of flowering facilitating hybridization. Also, it would improve the regeneration efficiency of wild Cicer species by genebanks and offer convenient alternate methods for rapid generation turnover.
Diet history of ice seals using stable isotope ratios in claw growth bands

Climate change and sea-ice reduction may lead to modifications of food-web structure in the Arctic, and this may impact foraging of ice-associated predators. We examined the dietary history recorded in cornified claw sheaths of ringed seals (Pusa hispida (Schreber, 1775)) and bearded seals (Erignathus barbatus (Erxleben, 1777)) to describe potential seasonal and interannual changes in their foraging. Seasonal layers of cornified cells deposited in claws can document trophic history up to about 10 years; thereafter, the claws start to wear at the distal end. A total of 38 claws were collected during Alaska Native subsistence harvests in 2008–2010 and seasonal growth bands were examined for stable nitrogen and carbon isotope ratios to assess long-term diet patterns. During 2007 (record ice minimum), proportionally more ringed seals fed at a lower trophic level. Bearded seals may have been foraging more pelagically from 2008 to 2010. Interannual variations and high variability between the two ice seal specie.
Referees’ Attitudes toward Open Peer Review and Electronic Transmission of Papers

A survey was mailed to 293 referees from the review board of Food Science and Technology International with the following personal characteristics: ages: 35–45 (35%), 45–55 (37%), and 55–65 (27%); 93% PhD graduates; 69% male, 98% researchers, 82% teachers too, 85% review for other journals as well to assess reviewers’ attitudes or preferences in favor of or against masking their identity, and toward the electronic transmission of papers for review. The reviewers were mainly from Europe, North America, and South America. The questionnaire was anonymous and asked if respondents were in favor of an open review or masking of the reviewers, and if they agreed with the electronic transmission of the papers for their review (both from the point of view of author and reviewer). The response rate was 35% (103 respondents). The consistency between the answers as being authors or reviewers when asked by the peer review process was significant (P<0.001) without significant differences in terms of gender or age. Seventy-five percent were in favor of masking reviewers, and 17% completely favored unblinded review. The consistency between the answers for paper transmission was significant (P<0.001) without significant differences in terms of gender or age. Seventy-five percent were in favor of electronic transmission, 25% were against it. There was a significant association between the answers in favor of or against e-transmission and the age either as reviewers (P=0.009) or as authors (P= 0.031). The other associations between the system of review and gender or age were not significant. There was a preference among the participants for masking the reviewers, and a tendency to use the Web as the transmission medium because it is considered faster, easier, simpler, and more economic.
Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?

ABSTRACT Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. We document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multilocus phylogenetic analyses unequivocally place D. galeatus within Celeus, indicating that the former has subsequently converged in appearance upon the distantly related and syntopic Dryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpecker's ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game-theory models and the hypothesis of interspecific social-dominance mimicry (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant to Celeus and Dryocopus foraging behavior. In light of our results, we recommend taxonomic transfer of D. galeatus to Celeus and emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimic's acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.
Screening sunflower seedlings for resistance to toxic metabolites produced by Sclerotinia sclerotiorum.

Culture filtrates of Sclerotinia sclerotiorum (Lib.) de Bary were toxic to sunflower seedlings, causing wilt symptoms similar to those developed on naturally infected plants. Seedlings of nine inbred lines, six F1 hybrids and one open-pollinated cultivar were assayed for response to culture filtrates. The reaction varied from moderately resistant to highly susceptible. The screening technique was reproducible, effective, rapid and simple; thus it could be useful in studying the resistance of sunflower plants to the wilt phase of the disease syndrome.
Elevated UV‐B radiation has no effect on litter quality and decomposition of two dune grassland species: evidence from a long‐term field experiment

From studies on living plant tissues it has been inferred that elevated UV‐B radiation could negatively affect litter quality and subsequent decomposition. However, in general, the effects of UV‐B radiation on litter chemistry and decomposition reported in the literature are variable and are often only marginally (if at all) significant. This might be due to the ecologically unrealistic conditions under which these experiments were performed.
Protein Digestibility of Selected Legumes Treated with Ultrasound and High Hydrostatic Pressure During Soaking

ABSTRACT In vitro protein digestibility (IVPD) of lentils, chickpeas, peas, and soybeans treated with ultrasound or high hydrostatic pressure (HHP) during soaking and then heated for 30 min at 98°C was determined using the three-enzyme method (trypsin, chymotrypsin, and peptidase). The IVPD of raw legumes ranged from 72% for soybeans to 83% for dry green peas. The increase in the IVPD after soaking was observed in lentils but not in other legumes. Heating increased the IVPD of the tested legumes by 2–13%. While the effects of applying ultrasound or HHP on IVPD of legumes were mostly inconsistent or insignificant, soaking under HHP for 1 hr and subsequent heating at 98°C for 30 min increased IVPD of legumes. Compared with raw legumes, the soluble protein concentrates exhibited 2–4% higher IVPD, while insoluble proteins exhibited 0.2–1.5% lower IVPD. SDS-PAGE of legume proteins before enzyme digestion exhibited 8–18 protein bands from 20 kDa to 100 kDa representing isolated soluble proteins and from 20 kDa .