Miracle-dz/UniFAR-FTUs huggingface dataset:
Catha edulis (khat) Induces Apoptosis in Madin-Darby Bovine Kidney Cell Line

Background: Khat (Catha edulis) is a controversial plant having a euphoretic effect, at the same time part of culture in many countries such as Africa and Arabian Peninsula. The presence of amphetamine-like substance, cathinone and cathine make this plant banned in many countries. Many neurological and other system related studies have been carried out in this plant, but the lack of toxicity studies are there especially the mechanism. Objective: In this study, Madin-Darby Bovine Kidney cell line was used as an in vitro model to study the cell death mechanism. Crude extract of fresh Khat plant leaves were prepared and exposed to cells. Materials and Methods: Trypan blue assay, phase-contrast microscopy, fluorescent microscopy, clonogenic assay, annexin-V assay, and hematoxylin and eosin (H and E) staining were employed to check the objectives. Results: Reductions in cellular viability were observed at concentrations above 1.25 mg/ml while using Trypan blue assay. The results of the clonogenic assay had shown that the untreated control with the highest number of colonies (100% survival) and the 0.1562 concentration could not prevent the colony formation significantly. The high concentrations reduced the colony formation at concentration dependent manner 27.4% and 24.9%, for 0.625 mg/ml and 1.25 mg/ml concentrations, respectively. The acridine orange/ethidium bromide experiment had observed the cells were intact with round nucleus while the apoptosis features such as blebbing and nuclear chromatin condensation were clearly observed in treatment. The shrinkage of cells was clearly observed in H and E staining. Conclusion: In addition, annexin-V binding confirmed the presence of apoptosis significantly on Khat treatment. Abbreviation used: PS: Phosphatidylserine (PS); MDBK: Madin-Darby Bovine Kidney; DMEM: Dulbecco′s modified Eagle′s medium; PI: propidium iodide; EB: ethidium bromide; PBS: Phosphate Buffer saline; FITC: fluorescein isothiocyante; TUNEL: Terminal deoxynucleotidyl transferase dUTP nick end labeling.
Conceptual framework and ecological considerations for the study of birds in oak woodlands

The distributions and abundances of birds within oak woodland communities of California are the results of geologic events leading to the formation of the Mediterranean-type ecosystem, and of more recent anthropogenic impacts that have altered the landscape. These human-wrought disturbances to oak woodlands likely are affecting population parameters and distributions of birds throughout California. Because little is known of bird-habitat relationships in oak communities, however, the actual effects of these land-use practices on birds are unknown. Here we present a framework for the study of birds in the oak woodlands of California. The principal objective of this framework is to outline aspects of bird biology, ecology and behavior that must be addressed before assessments of habitat quality can be made. Assessments of habitat quality require that population numbers, reproduction rates, and survival rates be monitored. Further, bird habitats must be studied to determine site characteristics of areas that birds actually use within oak woodlands. Determination of specific patterns of resource use entails intensive study of bird activities. Collection of all of these data requires extensive field work to determine temporal and spatial patterns of habitat and resource use. There are no shortcuts for obtaining this information. naturalists (e.g., Grinnell and Miller 1944, Leopold 1951, Miller 1951) provided valuable species accounts based on their observations. The information presented by these naturalists was generally in the form of qualitative descriptions of species' distributions and habitat associations. These data are of insufficient detail, however, to allow resource managers to assess habitat quality or to predict the effects of environmental change on bird population parameters. Further, Muick and Bartolome (1985) found few recent studies of bird-habitat relationships in oak woodlands. Consequently, a research program is required to study bird-habitat relationships in oak woodlands that provides information in sufficient detail to allow assessments of habitat quality and predictions of the effects of habitat change on birds. The purpose of this paper is to present a general framework for the study of birds in oak woodlands. Our primary objective is to outline aspects of bird biology and ecology that researchers must study to provide the baseline information required by managers to determine habitat quality for birds. We begin this framework by suggesting a scenario to describe distributional patterns of birds within oak woodlands. We use the discussion as a basis for explaining ecological and behavioral relationships of birds to their environments, and we conclude by presenting a methodology for the study of birds in oak woodlands.
Talaromyces atroroseus, a New Species Efficiently Producing Industrially Relevant Red Pigments

Some species of Talaromyces secrete large amounts of red pigments. Literature has linked this character to species such as Talaromyces purpurogenus, T. albobiverticillius, T. marneffei, and T. minioluteus often under earlier Penicillium names. Isolates identified as T. purpurogenus have been reported to be interesting industrially and they can produce extracellular enzymes and red pigments, but they can also produce mycotoxins such as rubratoxin A and B and luteoskyrin. Production of mycotoxins limits the use of isolates of a particular species in biotechnology. Talaromyces atroroseus sp. nov., described in this study, produces the azaphilone biosynthetic families mitorubrins and Monascus pigments without any production of mycotoxins. Within the red pigment producing clade, T. atroroseus resolved in a distinct clade separate from all the other species in multigene phylogenies (ITS, β-tubulin and RPB1), which confirm its unique nature. Talaromyces atroroseus resembles T. purpurogenus and T. albobiverticillius in producing red diffusible pigments, but differs from the latter two species by the production of glauconic acid, purpuride and ZG–1494α and by the dull to dark green, thick walled ellipsoidal conidia produced. The type strain of Talaromyces atroroseus is CBS 133442
Electron Phase‐Space Holes in Three Dimensions: Multispacecraft Observations by Magnetospheric Multiscale

Electron phase‐space holes are kinetic plasma structures commonly observed in space plasmas on Debye length scales. Near the Earth's duskside flank at 10 Earth radii, a series of 32 electron holes (EHs) are detected within a 1‐s window on all four Magnetospheric Multiscale spacecraft. The spacecraft separation of <7 km is similar to the expected EH size in this region. Length, width, amplitude, and relative positions are determined for individual EHs using a cylindrically symmetric model fit to Magnetospheric Multiscale E field measurements. The model shows good agreement with observed E fields far from the EH center. Deviations in E⊥ from the model are present near the center, indicating observed EHs have complex, sometimes irregular, internal structure. Perturbation magnetic fields δB modeled assuming an E × B0 electron current reproduce the measured parallel perturbation in most cases, although there is a systematic variation due to geometric and finite gyroradius effects. Many EHs in this event have large amplitude for their size, reaching the theoretical lower limit in length parallel to the background magnetic field, which requires the electron phase‐space density to approach 0 in the center. It is possible that EHs of this type have recently formed, eventually weakening or becoming longer over time. This study provides the most detailed measurements of EHs to date. Their derived properties are largely in agreement with expectations from previous research. It remains unclear whether the few notable differences are due to rapid time evolution or are specific to the local environment.
THE LOVE DART OF HELIX ASPERSA MULLER

The phenomenon of dart shooting in several species of land snails has still not been explained. We were interested in whether the dart can function as a nuptial gift of calcium, as previously proposed. Donating calcium would increase the fitness of the offspring and thereby result in a higher reproductive success for the donor. We confirmed in Helix aspersa that the developing embryo takes up calcium from the egg shell for the formation of its embryonic shell. However, other results from behavioural observations and calcium measurements in various reproductive structures do not support the calcium hypothesis. We found that the dart penetrated the skin in 91.7% of the shootings, but it was internalized by the recipient in only 6.3% of the shootings. The amount of calcium in one dart is roughly equal to that of one egg, and thus it would not contribute significantly to an average clutch of 59 eggs. The spermatophore contains virtually no calcium, and therefore it is unlikely that the dart signals a donation of calcium with the sperm. The dart is also unlikely to influence egg laying since dart shooting does not predict either the latency or the productivity of egg laying in the shooter or the recipient. We conclude that the love dart of Helix aspersa is not a gift of calcium. Instead, we suggest that it is a vehicle to introduce a substance into the partner to influence the fate of the donated sperm.
Cost-effective conservation of amphibian ecology and evolution

A new conservation strategy incorporates functional, phylogenetic, and taxonomic diversity for improved cost-effective outcomes. Habitat loss is the most important threat to species survival, and the efficient selection of priority areas is fundamental for good systematic conservation planning. Using amphibians as a conservation target, we designed an innovative assessment strategy, showing that prioritization models focused on functional, phylogenetic, and taxonomic diversity can include cost-effectiveness–based assessments of land values. We report new key conservation sites within the Brazilian Atlantic Forest hot spot, revealing a congruence of ecological and evolutionary patterns. We suggest payment for ecosystem services through environmental set-asides on private land, establishing potential trade-offs for ecological and evolutionary processes. Our findings introduce additional effective area-based conservation parameters that set new priorities for biodiversity assessment in the Atlantic Forest, validating the usefulness of a novel approach to cost-effectiveness–based assessments of conservation value for other species-rich regions.
Personal Characteristics Predictive of Depressive Symptoms in Hispanics with Heart Failure

Depression is a significant problem in heart failure (HF). The purposes of this study were to assess the prevalence of depressive symptoms in Hispanics with HF and to examine the personal characteristics predicting depressive symptoms at baseline and at 6-months follow-up in a telephone case management intervention. In this secondary data analysis based on 87 subjects, patient characteristics hypothesized to influence depressive symptoms included age, gender, education, living situation, co-morbidity, social support, New York Heart Association (NYHA) class, and acculturation. DSM-IV major depression was present in 39.1% (n = 35) of the participants at baseline and 1.1% (n = 1) at the 6-month follow-up. In regression analysis, factors associated with depressive symptoms at baseline were gender and NYHA class. At 6-month follow-up, acculturation, co-morbidity, and NYHA were significantly related to the presence of depressive symptoms. Depressive symptoms were highly prevalent in Hispanics with HF. Easily identifiable personal characteristics can be useful in designing interventions to reduce depression associated with HF.
New Equipment for Complementary Petrophysical Characterization of Rocks for Deep Geological Storage

The geological storage of CO2 in coal seams is an emerging option in the portfolio of mitigation actions for reduction of atmospheric greenhouse gas concentrations. A background study focused to the selection of favorable sites for CO2 geological storage are necessary steps, and in the selection of reservoirs for CO2 sequestration a complete petrophysical characterization of the sample is necessary. To complement the classical petrophysical parameters measured on the rocks of the geological formation with potential to be used to store the injected CO2, a new equipment has been designed and constructed to simulate at a laboratory scale the inter-action between the rock and the injected CO2, at different pressure conditions simulating depths of the geological formations up to 1000 m. The design and construction of this equipment allows us to investigate known physical and chemical processes that occur between the rocks store/seal and the fluid injected into geological storage. Essays focused to study the alterability of the rock in contact with CO2 either in subcritical or supercritical state, as well as essays for CO2 injectivity on the rock can be accomplished.
Results of a medication reconciliation survey from the 2006 Society of Hospital Medicine national meeting.

BACKGROUND The status of implementation of medication reconciliation across hospitals is variable to date; the degree to which hospitalists are involved is not known. METHODS To better describe the current state of medication reconciliation implementation, we conducted a survey of attendees of the 2006 Society of Hospital Medicine national meeting. RESULTS We identified a lack of uniformity across hospitals with respect to the degree of process implementation. Hospitalists were involved in design and implementation in a majority of cases, and felt that medication reconciliation would likely have a positive impact on patient safety. Tertiary care academic centers were more likely to use physicians to perform medication reconciliation, whereas community hospitals were more likely to involve nurses as well. Pharmacist participation in the medication reconciliation process was found to be quite low. Process and outcome measures were used infrequently. Patients' lack of medication knowledge and absence of preadmission medication information were cited most frequently as barriers to implementation of medication reconciliation. CONCLUSIONS Implementation of medication reconciliation is complex and challenging. Medication information is often incomplete, and elements of the medication reconciliation process result in increased time demands on providers. Current implementation efforts often have physicians and nurses "share" responsibility for compliance, and pharmacists are underutilized in medication reconciliation processes. Hospitalists have thus far played a substantial role in process design and implementation, and should continue to lead the way in advancing efforts to successfully implement medication reconciliation.
Oceanic mechanical forcing of a marine-terminating Greenland glacier

Abstract Dynamics of marine-terminating major outlet glaciers are of high interest because of their potential for drawing down large areas of the Greenland ice sheet. We quantify short-term changes in ice flow speed and calving at a major West Greenland glacier and examine their relationship to the presence of the sea-ice melange and tidal stage. A field campaign at the terminus of Store Gletscher (70.40˚N, 50.55˚W) spanning the spring and summer of 2008 included four broadband seismometers, three time-lapse cameras, a tide gauge, an automatic weather station and an on-ice continuous GPS station. Sub-daily fluctuations in speed coincide with two modes of oceanic forcing: (1) the removal of the ice melange from the terminus front and (2) tidal fluctuations contributing to speed increases following ice melange removal. Tidal fluctuations in ice flow speed were observed 16km from the terminus and possibly extend further. Seismic records suggest that periods of intensive calving activity coincide with ice-flow acceleration following breakup of the melange in spring. A synchronous increase in speed at the front and clearing of the melange suggests that the melange directly resists ice flow. We estimate a buttressing stress (~30–60 kPa) due to the presence of the ice melange that is greater than expected from the range of observed tides, though an order of magnitude less than the driving stress.
On the Annealed Large Deviation Rate Function for a Multi-Dimensional Random Walk in Random Environment

We derive properties of the rate function in Varadhan's (annealed) large deviation principle for multi-dimensional, ballistic random walk in random environ- ment, in a certain neighborhood of the zero set of the rate function. Our approach relates the LDP to that of regeneration times and distances. The analysis of the latter is possible due to the i.i. d. structure of regenerations.
Androgens and penile erection: evidence for a direct relationship between free testosterone and cavernous vasodilation in men with erectile dysfunction

Androgens are essential in the maintenance of nitric oxide‐mediated erectile activity in the rat. The objective of the present study was to investigate the role of androgens in regulating trabecular smooth muscle relaxation in the corpus cavernosum in response to vasoactive challenge in men with erectile dysfunction (ED).
Impact of Cold Ischemia Time in Kidney Transplants From Donation After Circulatory Death Donors

Background Deceased-donor kidneys are exposed to ischemic events from donor instability during the process of donation after circulatory death (DCD). Clinicians may be reluctant to transplant DCD kidneys with prolonged cold ischemia time (CIT) for fear of an additional deleterious effect. Methods We performed a retrospective cohort study examining US registry data between 1998 and 2013 of adult first-time kidney-only recipients of paired kidneys (derived from the same donor transplanted into different recipients) from DCD donors. Results On multivariable analysis, death-censored graft survival (DCGS) was comparable between recipients of kidneys with higher CIT relative to paired donor recipients with lower CIT when the CIT difference was 1 hour or longer (adjusted hazard ratio, [aHR], 1.02; 95% confidence interval [CI], 0.88-1.17; n = 6276), 5 hours or longer (aHR, 0.98; 95% CI, 0.80-1.19; n = 3130), 10 hours or longer (aHR, 1.15; 95% CI, 0.82-1.60; n = 1124) or 15 hours (aHR, 1.15; 95% CI, 0.66-1.99; n = 498). There was a higher rate of primary non function in the long CIT groups for delta 1 hour or longer (0.89% vs 1.63%; P = 0.006), 5 hours (1.09% vs 1.67%, P = 0.13); 10 hours (0.53% vs 1.78%; P = 0.03), and 15 hours (0.40% vs 1.61%; P = 0.18), respectively. Between each of the 4 delta CIT levels of shorter and longer CIT, there was a significantly and incrementally higher rate of delayed graft function in the long CIT groups for delta 1 hour or longer (37.3% vs 41.7%; P < 0.001), 5 hours (35.9% vs 42.7%; P < 0.001), 10 hours (29.4% vs 44.2%, P < 0.001), and 15 hours (29.6% vs 46.1%, P < 0.001), respectively. Overall patient survival was comparable with delta CITs of 1 hour or longer (aHR, 0.96; 95% CI, 0.84-1.08), 5 hours (aHR, 1.01; 95% CI, 0.85-1.20), and 15 hours (aHR, 1.27; 95% CI, 0.79-2.06) but not 10 hours (aHR, 1.47; 95% CI, 1.09-1.98). Conclusions These results suggest that in the setting of a prior ischemic donor event, prolonged CIT has limited bearing on long-term outcomes.
Insight into the Interaction of Metal Ions with TroA from Streptococcus suis

Background The scavenging ability of sufficient divalent metal ions is pivotal for pathogenic bacteria to survive in the host. ATP-binding cassette (ABC)-type metal transporters provide a considerable amount of different transition metals for bacterial growth. TroA is a substrate binding protein for uptake of multiple metal ions. However, the function and structure of the TroA homologue from the epidemic Streptococcus suis isolates (SsTroA) have not been characterized. Methodology/Principal Findings Here we determined the crystal structure of SsTroA from a highly pathogenic streptococcal toxic shock syndrome (STSS)-causing Streptococcus suis in complex with zinc. Inductively coupled plasma mass spectrometry (ICP-MS) analysis revealed that apo-SsTroA binds Zn2+ and Mn2+. Both metals bind to SsTroA with nanomolar affinity and stabilize the protein against thermal unfolding. Zn2+ and Mn2+ induce distinct conformational changes in SsTroA compared with the apo form as confirmed by both circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra. NMR data also revealed that Zn2+/Mn2+ bind to SsTroA in either the same site or an adjacent region. Finally, we found that the folding of the metal-bound protein is more compact than the corresponding apoprotein. Conclusions/Significance Our findings reveal a mechanism for uptake of metal ions in S. suis and this mechanism provides a reasonable explanation as to how SsTroA operates in metal transport.
RNIE: genome-wide prediction of bacterial intrinsic terminators

Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.
A Genetic Programming Approach to Estimate Vegetation Cover in the Context of Soil Erosion Assessment

This work describes a genetic programming (GP) approach that creates vegetation indices (VI’s) to automatically detect the sum of healthy, dry, and dead vegetation. Nowadays, it is acknowledged that VI’s are the most popular method for extracting vegetation information from satellite imagery. In particular, erosion models like the “Revised Universal Soil Loss Equation” (RUSLE) can use VI’s as input to measure the effects of the RUSLE soil cover factor (C). However, the results are generally incomplete, because most indices recognize only healthy vegetation. The aim of this study is to devise a novel approach for designing new VI’s that are better - correlated with C, using field and satellite information. Our approach consists on stating the problem in terms of optimization through GP learning, building novel indices by iteratively recombining a set of numerical operators and spectral channels until the best composite operator is found. Experimental results illustrate the efficiency and reliability of our approach in contrast with traditional indices like those of the NDVI and SAVI family. This study provides evidence that similar problems related to soil erosion assessment could be analyzed with our proposed methodology.
A general formula for the stabilization of event-based controlled systems

In this paper, a universal formula is proposed for event-based stabilization of general nonlinear systems affine in the control. The feedback is derived from the original one proposed by Sontag. Under the assumption of the existence of a smooth Control Lyapunov Function, it enables smooth (except at the origin) global asymptotic stabilization of the origin while ensuring that the sampling interval do not contract to zero. Indeed, for any initial condition within any given closed set the minimal sampling interval is proved to be strictly positive. Under homogeneity assumptions the control can be proved to be smooth anywhere and the sampling intervals bounded below for any initial condition.