Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil nitrogen cycle processes in urban riparian zones.

Riparian zones have been found to function as "sinks" for nitrate (NO3-), the most common groundwater pollutant in the U. S. , in many areas. The vast majority of riparian research, however, has focused on agricultural watersheds. There has been little analysis of riparian zones in urban watersheds, despite the fact that urban areas are important sources of NO3- to nitrogen (N)-sensitive coastal waters in many locations. In this study, we measured stream incision, water table depths, and pools, production (mineralization, nitrification), and consumption (denitrification) of NO3- in urban soils. Samples were taken from soil profiles (0-100 cm) of three forested urban and suburban zones and one forested reference riparian zone in the Baltimore, Maryland metropolitan area. Our objectives were to determine (1) if stream incision associated with urbanization results in lower riparian water tables, and (2) if pools, production, and consumption of NO3- vary systematically with stream incision and riparian water table levels. Two of the three urban and suburban streams were more incised and all three had lower water tables in their riparian zones than the forested reference stream. Urban and suburban riparian zones had higher NO3- pools and nitrification rates than the forested reference riparian zone, which was likely due to more aerobic soil profiles, lower levels of available soil carbon, and greater N enrichment in the urban and suburban sites. At all sites, denitrification potential decreased markedly with depth in the soil profile. Lower water tables in the urban and suburban riparian zones thus inhibit interaction of groundwater-borne NO3- with near surface soils that have the highest denitrification potential. These results suggest that urban hydrologic factors can increase the production and reduce the consumption of NO3- in riparian zones, reducing their ability to function as sinks for NO3- in the landscape.
Defining ventral medullary respiratory compartments with a glutamate receptor agonist in the rat

The regional organization of the ventral respiratory group (VRG) was examined with respect to generation of respiratory rhythm (breathing frequency) versus control of the respiratory motor pattern on individual nerves. In urethane‐anaesthetized, neuromuscularly blocked and vagotomized Sprague‐Dawley rats, arterial blood pressure (ABP) and respiratory motor outputs (phrenic, pharyngeal branch of the vagus, or superior laryngeal nerves) were recorded. The VRG organization was mapped systematically using injections of the excitatory amino acid dl‐homocysteic acid (DLH; 5–20 mm, 2–6 nl) from single‐ or double‐barrel pipettes at 100–200 μm intervals between the facial nucleus and the calamus scriptorius. Recording of respiratory neurons through the injection pipette ensured that the pipette was located within the VRG. At the end of each experiment, the injection pipette was used to make an electrical lesion, thereby marking the electrode position for subsequent histological reconstruction of injection sites. Four rostrocaudal regions were identified: (1) a rostral bradypnoea area, at the level of the Bötzinger complex, in which respiratory rhythm slowed and ABP increased, (2) a tachypnoea/dysrhythmia area, at the level of the preBötzinger complex, in which breathing rate either increased or became irregular, with little or no change in ABP, (3) a caudal bradypnoea area at the level of the anterior part of the rostral VRG in which ABP decreased and (4) a caudal ‘no effect’ region in the posterior part of the rostral VRG. The peak amplitude of phrenic nerve activity decreased with injections into all three rostral regions. Changes in respiratory rhythm were associated with opposite changes in inspiratory (TI) and expiratory (TE) durations after injections into either the Bötzinger complex or anterior rostral VRG, while both TI and TE decreased after injections into the preBötzinger complex. Effects on selected cranial nerves were similar to those on the phrenic nerve except that tonic activity was elicited on the superior larygneal nerve ipsilateral to injections in the Bötzinger complex and on the pharyngeal branch of the vagus ipsilateral to injections in the preBötzinger complex. These data reinforce the subdivision of the VRG into functionally distinct compartments and suggest that a further subdivision of the rostral VRG is warranted. They also suggest that region‐specific influences, especially on the pattern of cranial motor discharge, can be used to assist the identification of recording sites within the VRG. However, the postulated clear functional separation of rhythm‐ versus pattern‐generating regions was not supported.
An Exact Soultion for the Investment and Market Value of a Firm Facing Uncertainty, Adjustment Costs, and Irreversibility

This paper derives closed-form solutions for the investment and market value, under uncertainty, of competitive firms with constant returns to scale production and convex costs of adjustment. Solutions are derived for the case of irreversible investment as well as for reversible investment. Optimal investment is a non-decreasing function of q, the shadow value of capital. The conditions of optimality imply that q cannot contain a bubble; thus, optimal investment depends only on fundamentals. However, the value of the firm may contain a bubble that does not affect investment behavior. Relative to the case of reversible investment, the introduction of irreversibility does not affect q, but it reduces the fundamental market value of the firm.
Obplacental giant cells of the domestic rabbit: Development, morphology, and intermediate filament composition

Obplacental giant cells are large (210 m̈m) polyploid cells that appear in the stroma of the pregnant uterus of the rabbit following ovoimplantation. Histological examination of a complete developmental series indicates that obplacental giant cells arise from trophoblastic knobs that have traversed the uterine epithelium during early implantation. During maturation, the cells undergo a massive (approximately 6,000%) increase in volume and penetrate deeply into the uterine stroma and myometrium, where they often become associated with blood vessels and smooth muscle cells. Giant cells at mid‐gestation contain one or two large nuclei with prominent nucleoli and appear to be amitotic. They are rich in Golgi complexes, RER, SER, and cortically distributed cytoplasmic filaments, and contain intracellular canaliculi lined by microvilli. Giant cells vary with respect to the occurrence of lipid droplets, phagocytotic inclusions, lysosomal structures, and electron‐dense granules. Immunocytochemistry demonstrates that the giant cells exhibit intermediate filaments related to cytokeratin and vimentin, but are negative for desmin and for an endothelial cell marker, Factor VIII‐related antigen. The cells are positive for cytokeratin from their inception, but only become vimentin‐positive between Days 12 and 15 of pregnancy, a change seemingly related to their detachment from epithelial tissue to take on an independent existence. Our findings indicate that the giant cells originate from obplacental trophoblast and, at maturity, exhibit cytoskeletal characteristics of isolated epithelial cells, as well as a complement of organelles suggestive of synthetic activity.
Lung cancer - can autoantibodies provide an aid to diagnosis?

BACKGROUND More publications are describing autoantibodies specific to tumour-associated antigens in a range of solid tumours, including lung cancer. Importantly, these antibodies have even been described as being detectable before the tumour becomes clinically evident, making them interesting targets for use as novel biomarkers in lung cancer. OBJECTIVE This review provides an overview of the current literature regarding autoantibodies in lung cancer, and addresses the key question of whether the measurement of circulating autoantibodies can be utilised in lung cancer for diagnosis, screening, prognosis and monitoring clinical outcome. METHODS The literature used in this review was retrieved from PubMed using a combination of the following keywords: antigen array, autoantibodies, diagnosis, low-dose spiral computed tomography, lung cancer, non-small cell lung cancer, panel assay, prognosis, protein microarray, risk factors, SEREX, screening, small cell lung cancer and tumour-associated antigen. RESULTS Autoantibodies that react with autologous cellular antigens have been described in pre-diagnostic and diagnostic samples from patients with small cell, non-small cell and other forms of lung cancer, and can sometimes be correlated with clinico-pathological parameters. CONCLUSION The measurement of autoantibodies to a panel of tumour-associated antigens has the potential to provide clinicians with the opportunity to detect early amplification of the carcinogenic signal, thereby providing a sensitive, specific and simple screening tool for the early diagnosis and subsequent early clinical intervention of lung cancer.
Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in Arabidopsis1[W][OA]

Embryogenesis is central to the life cycle of most plant species. Despite its importance, because of the difficulty associated with embryo isolation, global gene expression programs involved in plant embryogenesis, especially the early events following fertilization, are largely unknown. To address this gap, we have developed methods to isolate whole live Arabidopsis (Arabidopsis thaliana) embryos as young as zygote and performed genome-wide profiling of gene expression. These studies revealed insights into patterns of gene expression relating to: maternal and paternal contributions to zygote development, chromosomal level clustering of temporal expression in embryogenesis, and embryo-specific functions. Functional analysis of some of the modulated transcription factor encoding genes from our data sets confirmed that they are critical for embryogenesis. Furthermore, we constructed stage-specific metabolic networks mapped with differentially regulated genes by combining the microarray data with the available Kyoto Encyclopedia of Genes and Genomes metabolic data sets. Comparative analysis of these networks revealed the network-associated structural and topological features, pathway interactions, and gene expression with reference to the metabolic activities during embryogenesis. Together, these studies have generated comprehensive gene expression data sets for embryo development in Arabidopsis and may serve as an important foundational resource for other seed plants.
The use of subdissociative-dose ketamine for acute pain in the emergency department.

OBJECTIVES Ketamine is a well-known anesthetic with its use trailing back to the 1960s. It has antagonistic effects at the N-methyl-d-aspartate receptor. There is emerging literature to suggest the use of subdissociative-dose ketamine (SDDK) for pain reduction. This evidence-based review evaluates the evidence regarding the use of SDDK for acute pain control in the emergency department (ED). METHODS The MEDLINE and EMBASE databases were searched. Randomized controlled trials (RCTs) that described or evaluated the use of SDDK for acute pain in the ED were included. Literature was excluded if it was not published in English. Duplicate articles, unpublished reports, abstracts, and review articles were also excluded. Quality assessment and evaluation of literature were evaluated based on the GRADE criteria. The primary outcome of interest in this review was the difference in pain score from baseline to cutoff time as specified in the studies. Secondary outcome measures were the incidence of adverse events and reduction in the amount of adjuvant opioids consumed by patients who received SDDK. RESULTS Four RCTs met the inclusion criteria, which enrolled a total of 428 patients. Three adult trials and one pediatric trial were identified. The level of evidence for the individual trials ranged from low to moderate. A significant reduction in pain scores was only found in two of the four trials. One trial found a significant reduction in mean pain scores when ketamine was compared to morphine (p < 0.05). Another trial reported a significant decrease in mean distress scores, favoring SDDK over fentanyl (1.0 vs. 2.7, p < 0.05). One trial found a significant reduction in the amount of morphine consumed, favoring ketamine over placebo (0.14 mg/kg, 95% confidence interval [CI] = 0.13 to 0.16 mg/kg vs. 0.2 mg/kg, 95% CI = 0.18 to 0.22 mg/kg; p < 0.001). An emergence phenomenon was reported in one trial. CONCLUSIONS Four RCTs with methodologic limitations failed to provide convincing evidence to either support or refute the use of SDDK for acute pain control in the ED.
COMPILE—A Generic Benchmark Case for Predictions of Marine Pile-Driving Noise

The prediction of underwater noise emissions from impact pile driving during near-shore and offshore construction activities and its potential effect on the marine environment has been a major field of research for several years. A number of different modeling approaches have been suggested recently to predict the radiated sound pressure at different distances and depths from a driven pile. As there are no closed-form analytical solutions for this complex class of problems and for a lack of publicly available measurement data, the need for a benchmark case arises to compare the different approaches. Such a benchmark case was set up by the Institute of Modelling and Computation, Hamburg University of Technology (Hamburg, Germany) and the Organisation for Applied Scientific Research (TNO, The Hague, The Netherlands). Research groups from all over the world, who are involved in modeling sound emissions from offshore pile driving, were invited to contribute to the first so-called COMPILE (a portmanteau combining computation, comparison, and pile) workshop in Hamburg in June 2014. In this paper, the benchmark case is presented, alongside an overview of the seven models and the associated results contributed by the research groups from six different countries. The modeling results from the workshop are discussed, exhibiting a remarkable consistency in the provided levels out to several tens of kilometers. Additionally, possible future benchmark case extensions are proposed.
Dynamic Conservation of Forest Genetic Resources in 33 European Countries

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan‐European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species‐oriented strategy in which national conservation networks are specifically designed for key target species and a site‐oriented strategy in which multiple‐target units include so‐called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however, <2% of the conserved populations seem to be at risk of extinction. On the basis of our results, we recommend combining species‐oriented and site‐oriented strategies.
Drinking Like a Guy: Frequent Binge Drinking Among Undergraduate Women

The purpose of this exploratory study was to examine why there has been an increase in frequent binge drinking among the most recent generation of female undergraduate students. Specifically, we examined whether female undergraduate women associated being able to “drink like a guy” (e.g., drink large amounts of alcohol, drinking competitively) with gender equality. Focus groups were conducted in March of 2003 with 42 female undergraduate women who consumed alcohol. Participants were recruited from respondents of a random sample survey of undergraduate students attending a large, public university and reflected the demographic characteristics of this population: traditional-age college students (i.e., attending college between 18 and 22 years of age), who were primarily white from middle or upper middle class families and living on or near the college campus. Focus groups were based on drinking trajectories during college (Stable High, Stable Low, Decreasers, Increasers) and sorority status. While women of all drinking levels reported feeling pressure to drink “heavily” because of the favorable impression they could make on their male peers, primarily women who were frequent binge drinkers throughout college felt that “drinking like a guy” described their own drinking behaviors. While women reported that being able to “drink like a guy” provided them with a sense of equality with their male peers, analysis of the transcripts suggests that “drinking like a guy” had less to do with gender equality and more to do with emphasizing women's (hetero)sexuality. Findings are discussed in terms of how “heavy alcohol consumption” affords college women positive attention from their male peers, but likely increases their vulnerability to sexual assault and alcohol use related health problems.
Partial compliance with antipsychotics increases mental health hospitalizations in schizophrenic patients: analysis of a national managed care database.

OBJECTIVE To investigate the relationship between partial compliance with antipsychotic medication and mental health hospitalization in managed care patients with schizophrenia. STUDY DESIGN We performed a retrospective evaluation of 1499 outpatients with ≥1 antipsychotic claims and a diagnosis of schizophrenia in a managed care database (PHARMetrics). METHODS Patients were followed for 12 months after their initial oral antipsychotic prescribing event. Compliance was estimated by gaps in medication therapy, medication consistency and persistence, and medication possession ratio. Categorical and logistic regression analyses modeled effects of compliance, age, and gender on hospitalization risk. RESULTS The managed care cohort had an overall hospitalization risk of 5.9% during follow-up. Increased hospitalization risk was associated with lower partial compliance, as measured by 3 of the 4 definitions. Patients with a maximum gap of >30 days were 4.7 times more likely to be hospitalized than those with a maximum gap of 0 to 10 days (P <.001). Low medication consistency of <70% and a medication possession ratio of <70% were significantly associated with increased risk of hospitalization (P <.001). Logistic regression analyses indicated that hospitalization odds decreased 16.9% (P <.001) and 18.8% (P <.001) for every 10% increase in medication possession ratio and medication consistency, respectively. CONCLUSION Small decreases in compliance with antipsychotics are associated with increased hospitalization risk among patients with schizophrenia in a managed care population.
Saddled with Attention: Overreaction to Bankruptcy Filings

We analyze the effect of investor attention on stock prices around Chapter 11 bankruptcy filings. We measure investor attention as abnormal search volume from Google, and find that attention&#8208;grabbing companies have more negative abnormal stock returns in the days before and during bankruptcy filings and more positive abnormal returns immediately thereafter. That is, for companies receiving high attention, investors overreact to a bankruptcy filing; for companies receiving low attention, they underreact. This pattern is more pronounced for companies with low institutional ownership and holds after controlling for standard predictors of stock performance during bankruptcy.
Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.
A systematic approach to the amplified expression, functional characterization and purification of inositol transporters from Bacillus subtilis

Abstract A systematic approach was used for the cloning and amplified expression in Escherichia coli of the genes for each of three inositol transport proteins (IolF, IolT, YfiG) from Bacillus subtilis that are evolutionarily-related to human transporters. Inducible amplified expression of each was achieved to levels of ∼ 10–15% of total protein in E. coli inner membrane preparations. The functional integrity of each heterologously-expressed protein was demonstrated by measuring the kinetics of 3H-myo-inositol transport into energized whole cells; this confirmed that IolT is the major inositol transporter, IolF is an inefficient transporter of this substrate and demonstrated that YfiG is an inositol transport protein for the first time. Competition for 3H-myo-inositol transport by 17 unlabelled compounds revealed all three proteins to be highly specific in recognizing inositols over sugars. IolT was confirmed to be highly specific for both myo- and D-chiro-inositol and IolF was confirmed to prefer D-chiro-inositol over myo-inositol. YfiG selectively recognized myo-inositol, D-chiro-inositol and, uniquely, L-chiro-inositol. All three proteins were successfully solubilized and purified in milligram quantities from inner membrane preparations and their suitability for inclusion in crystallization trials was assessed by analysis of structural integrity and thermal stability using circular dichroism spectroscopy followed by examination for monodispersity using gel filtration chromatography.