Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth strategies of four salt marsh plants on Mankyung River estuary in Korea

The emergence of seedlings, the length of roots and shoots, and the biomass of four dominant plant species and shore height were measured to investigate the growth strategy of these plants on the salt marsh of Mankyung River estuary. Four salt marsh plants showed a distinctive zonation, for example, Suaeda japonica was predominantly spread around the low salt marsh, Atriplex gmelini and Aster tripolium were in the middle, and S. asparagoides was in the upper part of the marsh. In terms of emergence of seedlings, S. japonica appeared first followed by A. gmelini, S. asparagoides, and A. tripolium. The growth strategies of halophytes were as follows: S. japonica germinated earlier than the other halophytes so that its root grew rapidly and extensively at the beginning of growth. This species adopted a continuous germination strategy, allowing growth whenever favorable conditions were provided. A. gmelini germinated later than S. japonica, as a quasi-simultaneous germination type, it showed the highest germination rate within the shortest time. Aster tripolium germinated later than any other halophyte. Since this species exhibited characteristics between the continuous germination type and the quasi-simultaneous germination type, it did not show a very high germination rate. Instead, it showed continuous germination and consistent growth of both above-ground and underground parts. Suaeda asparagoides showed an especially high emergence rate at the beginning of its growth. However, the high density retarded its growth until the middle stage. Its roots extended longer than the other halophytes, allowing it to grow well in the dry conditions of the upper marsh.
Are We Having Fun Yet? Exploring the Motivations of MPA and MPP Program Directors in the United States

Abstract The typical role of the graduate program director in higher education combines the responsibilities of both academic faculty and staff. This study uses survey data to investigate the motivations, expectations, and levels of satisfaction of Master of Public Administration and Master of Public Policy program directors in the United States. We explore the job characteristics that are primary motivators and look at what characteristics program directors expect and assign importance to. We also glean estimates of job satisfaction from the survey data. This study is preliminary, a first step in understanding the motivations, expectations, and job satisfaction of program directors.
Regulation of the Glucosyltransferase (gtfBC) Operon by CovR in Streptococcus mutans

ABSTRACT Streptococcus mutans is an important etiological agent of dental caries in humans. The extracellular polysaccharides synthesized by cell-associated glucosyltransferases (encoded by gtfBC) from sucrose have been recognized as one of the important virulence factors that promote cell aggregation and adherence to teeth, leading to dental plaque formation. In this study, we have characterized the effect of CovR, a global response regulator, on glucosyltransferase expression. Inactivation of covR in strain UA159 resulted in a marked increase in the GtfB and GtfC proteins, as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With the use of a transcriptional reporter system of a single chromosomal copy of the PgtfB-gusA and PgtfC-gusA fusions, we confirmed the transcriptional regulation of these promoters by CovR. By in vitro electrophoretic mobility shift assays with purified CovR protein, we showed that CovR regulates these promoters directly. DNase I footprinting analyses suggest that CovR binds to large regions on these promoters near the transcription start sites. Taken together, our results indicate that CovR negatively regulates the expression of the gtfB and gtfC genes by directly binding to the promoter region.
Maximizing the probability of satisfying the clinical goals in radiation therapy treatment planning under setup uncertainty.

PURPOSE This paper introduces a method that maximizes the probability of satisfying the clinical goals in intensity-modulated radiation therapy treatments subject to setup uncertainty. METHODS The authors perform robust optimization in which the clinical goals are constrained to be satisfied whenever the setup error falls within an uncertainty set. The shape of the uncertainty set is included as a variable in the optimization. The goal of the optimization is to modify the shape of the uncertainty set in order to maximize the probability that the setup error will fall within the modified set. Because the constraints enforce the clinical goals to be satisfied under all setup errors within the uncertainty set, this is equivalent to maximizing the probability of satisfying the clinical goals. This type of robust optimization is studied with respect to photon and proton therapy applied to a prostate case and compared to robust optimization using an a priori defined uncertainty set. RESULTS Slight reductions of the uncertainty sets resulted in plans that satisfied a larger number of clinical goals than optimization with respect to a priori defined uncertainty sets, both within the reduced uncertainty sets and within the a priori, nonreduced, uncertainty sets. For the prostate case, the plans taking reduced uncertainty sets into account satisfied 1.4 (photons) and 1.5 (protons) times as many clinical goals over the scenarios as the method taking a priori uncertainty sets into account. CONCLUSIONS Reducing the uncertainty sets enabled the optimization to find better solutions with respect to the errors within the reduced as well as the nonreduced uncertainty sets and thereby achieve higher probability of satisfying the clinical goals. This shows that asking for a little less in the optimization sometimes leads to better overall plan quality.
The relationship between pathology and resistance to reinfection with Schistosoma mansoni in mice: a causal mechanism of resistance in chronic infections

SUMMARY The development of resistance in mice to reinfection with Schistosoma mansoni was recorded during an early chronic infection, and compared with hepatic portal pathological and vascular changes. The latter were assessed using a microsphere injection technique. The degree of acquired resistance was directly dependent on the patent worm burden and the time post-infection. Strong correlations were noted between the development of resistance and the appearance of parasite eggs in the lungs and spleens of infected hosts. Weaker associations were present between resistance and other aspects of the disease pathology, such as portal hypertension and organ weights. The appearance of injected microspheres in the lungs and spleens correlated well with the appearance of eggs in those organs and with the development of resistance. The levels of resistance had risen and microspheres were detected in the lungs, before the development of major extra-hepatic, porta-systemic collateral vessels. It is concluded that intra-hepatic vascular alterations may be a causal factor in the development of resistance, preventing the sequestration of migrating schistosomula in the liver. It is estimated that as much as 70–75% of the recorded resistance can be attributed to this immunologically non-specific mechanism.
Early detection of spoilage moulds in bread using volatile production patterns and quantitative enzyme assays

Aims: Early detection of spoilage fungi (two Eurotium spp., a Penicilliumchrysogenum species) in bread analogues over periods of 72 h at 25°C and 0·95 water activity was evaluated using volatile production patterns, hydrolytic enzyme production, and changes in fungal populations.
Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

Designer scaffolds reveal the minimal requirements of engineered MAPK scaffolds. Designer scaffolds for kinase cascades The MAPK cascade has three sequentially acting kinases that are recruited to proteins that function as scaffolds. Ryu and Park designed synthetic scaffolds, which contained multiple copies of a PDZ domain, and kinases or phosphatases tagged with a peptide that bound the PDZ domain, to engineer a mating response circuit in yeast. Unexpectedly, when expressed with the three peptide-tagged kinases in the cascade, a scaffold with just two PDZ domains produced mating responses. The intensity or duration of the output of the synthetic circuit could be altered by expressing a phosphatase tagged with the PDZ-binding peptide that was recruited to the scaffold or by altering the affinity of the PDZ-binding peptide on a kinase. A synthetic PDZ-based MAPK circuit also functioned in mammalian cells. Thus, this synthetic biology approach of designer scaffolds revealed the minimal requirements of engineered MAPK scaffolds and provided evidence for the ability to engineer adjustable synthetic circuits in eukaryotic cells. As hubs for eukaryotic cell signaling, scaffold proteins are attractive targets for engineering and manipulating signaling circuits. We designed synthetic scaffolds with a repeated PDZ domain that interacted with engineered kinases of the mitogen-activated protein kinase (MAPK) cascade involved in yeast mating to investigate how modular interactions mediate kinase cascades. The synthetic scaffolds functioned as logic gates of signaling circuits. We replaced the endogenous yeast scaffold Ste5 with designer scaffolds with a variable numbers of a PDZ domain that bound kinases or phosphatases engineered with a PDZ-binding motif. Although association with the membrane was necessary for pathway activity, surprisingly, mating responses occurred when the circuit contained a scaffold with only two PDZ domains, which could only bind two of the three kinases simultaneously. Additionally, the three tiers of the MAPK pathway exhibited decreasing positional plasticity from the top [MAPK kinase kinase (MAPKKK)] to the bottom (MAPK) tier such that binding of a MAPKKK, but not a MAPK, from the osmoregulatory pathway or protein kinase C pathway to the synthetic scaffold activated a reporter of the mating response. We also showed that the output duration and intensity could be altered by recruiting phosphatases or varying the affinity of the recruited proteins for the scaffold and that a designer MAPK scaffold functioned in mammalian cells. Thus, this synthetic approach with designer scaffolds should enable the rational manipulation or engineering of signaling pathways and provide insight into the functional roles of scaffold proteins.
Carbon stocks and its variations with topography in an intact lowland mixed dipterocarp forest in Brunei

Tropical forests play a critical role in mitigating climate change, and therefore, an accurate and precise estimation of tropical forest carbon (C) is needed. However, there are many uncertainties associated with C stock estimation in a tropical forest, mainly due to its large variations in biomass. Hence, we quantified C stocks in an intact lowland mixed dipterocarp forest (MDF) in Brunei, and investigated variations in biomass and topography. Tree, deadwood, and soil C stocks were estimated by using the allometric equation method, the line intersect method, and the sampling method, respectively. Understory vegetation and litter were also sampled. We then analyzed spatial variations in tree and deadwood biomass in relation to topography. The total C stock was 321.4 Mg C ha -1 , and living biomass, dead organic matter, and soil C stocks accounted for 67%, 11%, and 23%, respectively, of the total. The results reveal that there was a relatively high C stock, even compared to other tropical forests, and that there was no significant relationship between biomass and topography. Our results provide useful reference data and a greater understanding of biomass variations in lowland MDFs, which could be used for greenhouse gas emission-reduction projects.
Student Mobility and Transnational Social Ties as Factors of Reflexivity

The article seeks to develop and apply new quantitative measurement instruments capable of significantly improving understanding of the relationship between the transnational mobility and transnational social ties of students, along with their reflexive capacities. With a focus on students building their personal networks, educational and professional activities that extend beyond the nation’s borders and organising their day-to-day routines in transnational social spaces, we analyse the role of mobility in their reflexive capacities. Applying a tool that is line with Archer’s theory and indicators to measure reflexivity, and transnational social ties as proposed by Molina et al., we analyse data collected via an on-line survey questionnaire administered to Slovenian students. In addition, students from the Middle East (Lebanon) and the USA (Hawai’i) are added for comparative purposes. The results of path analysis show the Slovenian students’ mobility as such implies higher scores for meta reflexivity, combined with lower scores for communicative and fractured reflexivity. Further, social transactions reaching beyond one’s physical localities in terms of transnational social ties implies they have higher levels of reflexivity in general.
Lamina-specific anatomic magnetic resonance imaging of the human retina.

PURPOSE Magnetic resonance imaging (MRI) of the human retina faces two major challenges: eye movement and hardware limitation that could preclude human retinal MRI with adequate spatiotemporal resolution. This study investigated eye-fixation stability and high-resolution anatomic MRI of the human retina on a 3-Tesla (T) MRI scanner. Comparison was made with optical coherence tomography (OCT) on the same subjects. METHODS Eye-fixation stability of protocols used in MRI was evaluated on four normal volunteers using an eye tracker. High-resolution MRI (100 × 200 × 2000 μm) protocol was developed on a 3-T scanner. Subjects were instructed to maintain stable eye fixation on a target with cued blinks every 8 seconds during MRI. OCT imaging of the retina was performed. Retinal layer thicknesses measured with MRI and OCT were analyzed for matching regions of the same eyes close to the optic nerve head. RESULTS The temporal SDs of the horizontal and vertical displacements were 78 ± 51 and 130 ± 51 μm (±SD, n = 4), respectively. MRI detected three layers within the human retina, consistent with MRI findings in rodent, feline, and baboon retinas. The hyperintense layer 1 closest to the vitreous likely consisted of nerve fiber, ganglion cell, and inner nuclear layer; the hypointense layer 2, the outer nuclear layer and the inner and outer segments; and the hyperintense layer 3, the choroid. The MRI retina/choroid thickness was 711 ± 37 μm, 19% (P < 0.05) thicker than OCT thickness (579 ± 34 μm). CONCLUSIONS This study reports high-resolution MRI of lamina-specific structures in the human retina. These initial results are encouraging. Further improvement in spatiotemporal resolution is warranted.
Risk of infections using anti-TNF agents in rheumatoid arthritis, psoriatic arthritis, and ankylosing spondylitis: a systematic review and meta-analysis

ABSTRACT Introduction: Five anti-tumor necrosis factor (anti-TNF) agents have received regulatory approval for use in rheumatology: adalimumab, golimumab, infliximab, certolizumab, and etanercept. Apart from their well-documented therapeutic value, it is still uncertain to what extent they are associated with an increased risk of infectious adverse events. Areas covered: We conducted a systematic review and meta-analysis of published randomized studies to determine the effect of anti-TNF drugs on the occurrence of infectious adverse events (serious infections; tuberculosis; opportunistic infections; any infection). We searched Medline, Embase, and the Cochrane Library up to May 2014 to identify eligible studies in adult patients with rheumatoid arthritis, psoriatic arthritis, or ankylosing spondylitis that evaluated anti-TNF drugs compared with placebo or no treatment. Expert opinion: Our study encompassed data from 71 randomized controlled trials involving 22,760 participants (range of follow-up: 1–36 months) and seven open label extension studies with 2,236 participants (range of follow-up: 6–48 months). Quantitative synthesis of the available data found statistically significant increases in the occurrence of any infections (20%), serious infections (40%), and tuberculosis (250%) associated with anti-TNF drug use, while the data for opportunistic infections were scarce. The quality of synthesized evidence was judged as moderate. Further evidence from registries and long-term epidemiological studies are needed to better define the relationship between anti-TNF agents and infection complications.
Duration of antibiotic therapy for penetrating abdominal trauma: a prospective trial.

BACKGROUND The optimal duration of antibiotic use in penetrating abdominal trauma is incompletely defined. It is generally accepted that short-term antibiotics are appropriate for low-risk wounds. However, with colon injury and significant degree of injury, abdominal trauma index (ATI) more than 25, concern exists that short-term treatment is not adequate. METHODS The study was a prospective double-blind trial of 24-hour treatment (cefoxitin or cefotetan) compared with 5-day treatment in 515 patients. Major abdominal infections (MAI) included abscess, necrotizing fasciitis, and diffuse peritonitis. RESULTS MAI occurred in 8% of those patients with 1-day therapy and 10% with 5-day therapy. Subgroup analysis of high-risk groups (colon wounds and ATI of more than 25) showed the following MAI rates: colon, 1-day therapy, 14%; 5-day therapy, 15%; ATI of more than 25, 1-day therapy, 17%; 5-day therapy, 30%. CONCLUSIONS Regardless of contamination and degree of injury, 24-hour antibiotic therapy is satisfactory for all penetrating abdominal trauma.
Fever and survival

The significance of fever in response to a bacterial infection has been investigated using the lizard Dipsosaurus dorsalis as an animal model. These lizards develop a fever of about 2 degrees C after injection with the bacterium Aeromonas hydrophila. To determine whether this elevation in body temperature increases the resistance of the host to this infection, as measured by survival, lizards were infected with the live bacteria and placed in a neutral (38 degrees C), low (34 degrees or 36 degrees C), or high (40 degrees or 42 degrees C) ambient temperature. An elevation in temperature following experimental bacterial infection results in a significant increase in host survival.
European rural entrepreneur and tourism‐based diversification: Does national culture matter?

Integrated rural tourism assumes a pivotal role in the regeneration of rural areas. The farmer's transition towards rural tourism is influenced by diverse macroeconomic and microeconomic factors. This paper contributes to the debate on tourism-based farm diversification by cross-fertilizing 3 theoretical domains-integrated rural tourism, cultural contexts, and rural entrepreneurship-in order to investigate how national cultural dimensions can influence European rural entrepreneur diversification into the tourism sector. To address our research question, we analyse the tourism-based diversification of farmers in 17 European countries that have instituted the European Rural Development Policy of 2007-2013.
GFAP‐positive hippocampal astrocytes in situ respond to glutamatergic neuroligands with increases in [Ca2+]i

It is becoming increasingly clear that astrocytes play very dynamic and interactive roles that are important for the normal functioning of the central nervous system. In culture, astrocytes express many receptors coupled to increases in intracellular calcium ([Ca2+]i). In vivo, it is likely that these receptors are important for the modulation of astrocytic functions such as the uptake of neurotransmitters and ions. Currently, however, very little is known about the expression or stimulation of such astrocytic receptors in vivo. To address this issue, confocal microscopy and calcium sensitive fluorescent dyes were used to examine the dynamic changes in astrocytic [Ca2+]i, within acutely isolated hippocampal slices. Astrocytes were subsequently identified by immunocytochemistry for glial fibrillary acidic protein. In this paper, we present data indicating that hippocampal astrocytes in situ respond to glutamate, kainate, α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA), 1‐aminocyclopentane‐trans‐1,3‐dicarboxylic acid (t‐ACPD), N‐methyl‐D‐aspartate (NMDA), and depolarization with increases in [Ca2+]i. The increases in [Ca2+]i occurred in both the astrocytic cell bodies and the processes. Temporally the changes in [Ca2+]i were very dynamic, and various patterns ranging from sustained elevations to oscillations of [Ca2+]i were observed. Individual astrocytes responded to neuroligands selective for both ionotropic and metabotropic glutamate receptors with increases in [Ca2+]i. These findings indicate that astrocytes in vivo contain glutamatergic receptors coupled to increases in [C2+]i and are able to respond to neuronally released neurotransmitters. (c) 1995 Wiley‐Liss, Inc.
Phenotypic rescue of Chlamydia trachomatis growth in IFN‐γ treated mouse cells by irradiated Chlamydia muridarum

Chlamydia trachomatis and C. muridarum, human and mouse pathogens, respectively, share more than 99% of open reading frames (ORFs) but differ in a cytotoxin locus. Presence or absence of cytotoxin gene(s) in these strains correlates with their ability to grow in IFN‐γ treated mouse cells. Growth of toxin‐positive C. muridarum is not affected in IFN‐γ treated cells, whereas growth of toxin‐negative C. trachomatis is inhibited. We previously reported that this difference in IFN‐γ sensitivity is important to the in vivo infection tropism of these pathogens. Here we describe a phenotypic rescue assay that utilizes C. muridarum gamma irradiated killed elementary bodies (iEB) to rescue C. trachomatis infectivity in IFN‐γ treated mouse cells. Rescue by iEB was temporal, maximal early post infection, directly related to multiplicity of iEB infection, and was independent of de novo chlamydial transcription. Lastly, C. muridarum iEB vacuoles and C. trachomatis inclusions were not fusogenic, suggesting the factor(s) responsible for rescue was secreted or exposed to the cytosol where it inactivated IFN‐γ induced effectors. Chlamydial phenotypic rescue may have broader utility for the study of other EB associated virulence factors that function early in the interaction of chlamydiae with host cells.
Dermojet delivery of bleomycin for the treatment of recalcitrant plantar warts

Background: Plantar warts may cause significant morbidity. Intralesional bleomycin is effective. When bleomycin is injected with a needle and syringe, it is difficult to prevent the bleomycin from infiltrating the dermis adjacent to the wart, producing unnecessary acute pain, persistent pain, and potential sloughing of normal adjacent skin. Efficacy of delivery by dermojet is not yet established. Objectives: To assess the response of recalcitrant plantar warts to bleomycin delivered by dermojet. Methods: A total of 47 patients with 138 plantar warts present for more than 2 years and resistant to 10 cycles of cryosurgery, were recruited. Bleomycin (1 U/ml) was delivered intralesionally by dermojet at 5‐week intervals for 25 weeks. Results: Out of 138, 124 (89.9%) plantar warts showed complete or partial clearance after one to five sets of bleomycin injections. The recurrence rate was 6/138 (4.4%), and 8/138 (5.8%) warts failed to clear. The reduction in mean surface area of the plantar warts after each set of bleomycin injections compared to baseline surface area was statistically significant. Local side effects were similar to other methods of delivery. No systemic side effects were reported. Conclusions: This study assesses therapeutic efficacy of bleomycin delivered by dermojet in solely recalcitrant plantar warts. It provides preliminary evidence that this method of delivery may benefit a group of patients with particularly recalcitrant plantar warts and is safe and easy to use in routine dermatology practice.