Miracle-dz/UniFAR-FTUs huggingface dataset:
Zooplankton of turbid and hydrologically dynamic prairie rivers

SUMMARY 1. Compared with rivers in more humid, forested ecoregions of eastern and midwestern U.S.A. , rivers in semi-arid grassland of the U.S. Great Plains tend to be relatively shallow, more variable in discharge, and characterised by high suspended sediment loads. Although critical life stages of fish in prairie rivers probably depend at least partially on zooplanktonic food, data on community and distributional patterns of potamoplankton in these widespread ecosystems are almost entirely absent. 2. We examined summer zooplankton distribution in five prairie rivers (Arkansas, Kansas, Platte, Elkhorn, and Niobrara Rivers) spread over six degrees of latitude during 2003–2004. We compared our results from 126 samples with previously collected data from the Ohio and St Lawrence Rivers in forested ecoregions and correlated differences with abiotic environmental conditions. 3. The importance of hydrological retention zones to stream biota has been recently demonstrated for rivers with quasi-permanent islands and slackwater regions, but the importance of slackwaters formed by ephemeral sandbar islands in prairie rivers is unknown. We evaluated the role of hydrological retention for planktonic rotifers, cladocera, and copepods in the Kansas River during the summer of 2004. 4. Zooplankton assemblages were extremely similar among prairie rivers (Sorensen Dissimilarity Index: mean ¼ 0.07) but moderately disparate for comparisons of prairie versus forested-basin rivers (mean ¼ 0.50). 5. Total zooplankton densities in prairie rivers (approximately 81 L )1 ) were intermediate between the Ohio (approximately 92 L )1 ) and St Lawrence Rivers (approximately 43 L )1 ), but relative abundances were significantly different. Rotifers represented >99% of zooplankton individuals in grassland rivers, but only approximately 37–68% in other rivers. Rotifer species richness was lower in prairie rivers, but relative abundances of common genera were much less skewed compared with eastern rivers where Polyarthra dominated rotifer assemblages (41–73%). 6. For comparisons among rivers, rotifers were significantly more abundant in turbid rivers, while microcrustaceans were less dense. However, for comparisons within the Kansas River over time, rotifer densities were inversely related to turbidity. We hypothesise that rotifers indirectly benefit from river turbidity because their food competitors (cladocera) and predators (e.g. cyclopoid copepods and visually feeding fish) are relatively more susceptible to suspended sediments. 7. Crustacean densities were positively related to the degree of hydrological retention (negatively to current velocities) throughout the study, but rotifer densities were significantly depressed by current velocities only when river discharge was high, making
Identification and mapping of dimerization and DNA-binding domains in the C terminus of the IE2 regulatory protein of human cytomegalovirus

The 80-kDa IE2 nuclear phosphoprotein encoded by the human cytomegalovirus (HCMV) major immediate-early (MIE) gene behaves both as a nonspecific transactivator of heterologous reporter genes and as a specific repressor of its own promoter-enhancer region. To begin to examine the biochemical properties of the IE2 protein, we prepared panels of N-terminal and C-terminal truncation mutants by in vitro translation procedures. In cross-linking experiments, the C-terminal half of IE2 (which is sufficient for down-regulation) formed dimers but N-terminal segments did not do so. Cotranslated Oct2/IE2 fusion proteins containing the same IE2 C-terminal region from codons 266 to 579 also formed mixed-subunit DNA-bound oligomeric complexes in gel mobility shift assays. Furthermore, an IE2 domain bounded by codons 388 to 542 proved to immunoprecipitate as heterodimers with cotranslated subunits containing known epitopes for specific antibodies. Deletion up to codon 428 or truncation back to codon 504 prevented this interaction. In direct gel shift DNA-binding assays, a bacterial GST/IE2(346-579) fusion protein bound to a 30-mer oligonucleotide probe encompassing the major immediate-early gene negative cis-regulatory target DNA sequence but failed to bind to a single-base-pair insertion mutant probe (delta CRS). This specific DNA-binding activity was abolished by further deletion up to codon 388 on the N-terminal side or by truncation at codon 542 on the C-terminal side. Therefore, the minimal DNA-binding domain requires additional amino acid motifs on both sides of the dimerization domain. This segment of IE2 is functionally important for both transactivation and down-regulation and contains several highly conserved amino acid motifs that are shared amongst the equivalent HCMV, simian CMV, mouse CMV, rat CMV, and human herpesvirus 6 proteins from other betaherpesviruses.
Patterns of neuronal activation in the rat brain and spinal cord in response to increasing durations of restraint stress

By most accounts the psychological stressor restraint produces a distinct pattern of neuronal activation in the brain. However, some evidence is incongruous with this pattern, leading us to propose that the restraint-induced pattern in the central nervous system might depend on the duration of restraint used. We therefore determined the pattern of neuronal activation (as indicated by the presence of Fos protein) seen in the paraventricular nucleus (PVN), bed nucleus of the stria terminalis, amygdala, locus coeruleus, nucleus tractus solitarius (NTS), ventrolateral medulla (VLM) and thoracic spinal cord of the rat in response to 0, 15, 30 or 60 min periods of restraint. We found that although a number of cell groups displayed a linear increase in activity with increasing durations of restraint (e.g. hypothalamic corticotrophin-releasing factor (CRF) cells, medial amygdala neurons and sympathetic preganglionic neurons of the thoracic spinal cord), a number of cell groups did not. For example, in the central amygdala restraint produced both a decrease in CRF cell activity and an increase in non-CRF cell activity. In the locus coeruleus, noradrenergic neurons did not display Fos in response to 15 min of restraint, but were significantly activated by 30 or 60 min restraint. After 30 or 60 min restraint a greater degree of activation of more rostral A1 noradrenergic neurons was observed compared with the pattern of A1 noradrenergic neurons in response to 15 min restraint. The results of this study demonstrate that restraint stress duration determines the amount and the pattern of neuronal activation seen in response to this psychological stressor.
An EP4 Receptor Agonist Prevents Indomethacin-Induced Closure of Rat Ductus Arteriosus In Vivo

Indomethacin exerts a strong tocolytic effect by suppressing uterine contractions mediated by prostaglandins. However, indomethacin also induces in utero closure of fetal ductus arteriosus (DA), leading to serious neonatal consequences. Using rats, we tested the effect of an agonist for a subtype of prostaglandin E2 receptor (EP4), ONO-AE1-437 and its prodrug ONO-4819, as a DA dilator during indomethacin treatment. In vitro, ONO-AE1-437 exhibited a potent dilatory effect on DA against O2- and indomethacin-induced contractions in a concentration-dependent manner. In vivo, rat dams were given indomethacin (10 mg/kg, p.o.) alone or with ONO-4819 (0.3 μg/kg/h, s.c.) on d 21 of gestation and pups were delivered 4 h later through cesarean section to evaluate the ratio of diameter of DA to that of pulmonary artery. Pups from dams with no drug had DA/PA ratio of 0.9 ± 0.05, whereas those from dams with indomethacin alone had a decreased ratio of 0.2 ± 0.03. When ONO-4819 was co-administered to the dams, the ratio recovered significantly to 0.7 ± 0.06. The administration of ONO-4819 to the dams did not induce any increase in the uterine activity. These results suggest that administration of an EP4 agonist in addition to indomethacin might prevent adverse reactions of indomethacin on fetal DA without restricting its tocolytic effects.
Incidence and clinical significance of multiple consecutive, appropriate, high-energy discharges in patients with implanted cardioverter-defibrillators.

BACKGROUND Some patients with an automatic implantable cardioverter-defibrillator (ICD) suffer multiple appropriate, consecutive, high-energy discharges (MCDs) during follow-up. Such events might represent resistant ventricular arrhythmias and might have prognostic significance. METHODS AND RESULTS Eighty consecutive patients with an ICD were followed up for up to 82 months (mean, 21 +/- 19 months). Thirty-eight patients had survived an out-of-hospital cardiac arrest and 42 had recurrent ventricular tachycardia. During follow-up, 16 patients had MCD (group A), 26 patients had episodes of single appropriate discharges (group B), and 38 patients had no appropriate discharges (group C). Group A patients had worse functional status (P = .001), lower left ventricular ejection fractions (LVEFs) (P = .001), and lower survival rates (log rank, P = .003) than the remaining two groups of patients. Cox analysis showed LVEF (P = .001) to be an independent predictor of MCD. Independent predictors of death or heart transplant were MCD (P = .001), female sex (P = .001), age (P = .001), history of cardiac arrest (P = .003), and functional status (P = .003). The only independent predictor of total mortality was female sex (P = .002). Independent predictors of cardiac death were MCD (P = .007) and female sex (P = .018). Independent predictors of arrhythmic death were age (P = .001), female sex (P = .02), and MCD (P = .023). CONCLUSIONS In patients with an ICD, the development of MCD is an independent predictor of cardiac and arrhythmic mortality. If this finding is confirmed in larger studies, it may help to identify patients in whom other therapeutic alternatives, ie, heart transplantation, should be considered during follow-up after ICD implantation.
Role for mucosal immune responses and cell‐mediated immune functions in protection from airborne challenge with Venezuelan equine encephalitis virus *

Venezuelan equine encephalitis virus (VEEV) replicates in lymphoid tissues following peripheral inoculation and a high titre viraemia develops. Encephalitis develops after the virus enters the central nervous system from the blood, with the earliest neuronal involvement being via the olfactory nerve. Following aerosol challenge with virulent VEEV, the virus is thought to replicate in the nasal mucosa and there could be direct entry into the olfactory nerve via infected neuroepithelial cells. Protection from VEEV infection is believed to be primarily mediated by virus specific antibody. The correlation between protection and neutralising serum antibody titres is, however, inconsistent when the virulent virus is administered by the airborne route. This study demonstrates a link between antibody in serum and the nasal mucosa and protection by means of passive immunisation studies. Intra‐nasal administration of antibody increased protection against airborne virus in Balb/c mice. Vaccination of μMT strain mice that do not have functional B cells and cannot produce antibody revealed normal proliferation of spleen cells in vitro and robust cytokine production. Aerosol challenge of μMT mice demonstrated that complete protection was only achieved when passive immunisation with antibody was supplemented with active immunisation with the TC‐83 vaccine strain of the virus. This implies that cell‐mediated immune functions are required for protection against airborne challenge with virulent VEEV. J. Med Virol. 67:384–393, 2002. Copyright © Crown Copyright 2002. Recorded with the permission of the controller of Her Majesty's Stationery Office. Published by Wiley‐Liss, Inc.
Selective expression of CSPG receptors PTPσ and LAR in poorly regenerating reticulospinal neurons of lamprey

Disability following spinal cord injury is due to failure of axon regeneration, which has been ascribed to environmental factors in the central nervous system and a developmental loss of intrinsic growth capacity in neurons. Recently, the receptor‐like protein tyrosine phosphatases, protein tyrosine phosphatase σ (PTPσ) and leukocyte common antigen‐related phosphatase (LAR), have been identified as specific receptors for the regeneration‐inhibiting matrix molecules chondroitin sulfate proteoglycans (CSPGs). After spinal cord transection in lampreys, axons of the large, identified reticulospinal neurons have heterogeneous regenerative abilities. The bad‐regenerating neurons also undergo a delayed form of axotomy‐induced apoptosis. In the present study, a lamprey genomic database was used to identify homologs of CSPGs, clone PTPσ and LAR, and examine their mRNA expression. CSPG immunoreactivity was increased significantly near the lesion at 2 weeks post transection, and decreased thereafter. Both receptors were expressed selectively in the bad‐regenerating neurons and had overlapping cellular distributions. PTPσ was upregulated with age (LAR was not evaluated). By 2 weeks post transection, neurons expressing PTPσ also showed caspase activation, suggesting apoptosis. The probability of axon regeneration for individual identified neurons was negatively correlated with the expression level of PTPσ in both control and spinal cord–transected lampreys. In an animal 7 weeks post transection, regenerated axons were labeled retrogradely from beyond the transection. PTPσ expression and caspase labeling was seen only in neurons whose axon had not regenerated. These results are consistent with a possible role for PTPσ (and LAR) in both retrograde neuronal death and the poor intrinsic regenerative ability of bad‐regenerating neurons. J. Comp. Neurol. 522:2209–2229, 2014. © 2013 Wiley Periodicals, Inc.
Delay-dependent robust stability analysis for systems with interval delays

This paper is concerned with the stability analysis for uncertain systems with interval time-varying delays. An appropriate class of Lyapunov-Krasovskii functionals is proposed and, splitting the known bounds of the delay interval in two subintervals, a new delay-dependent criterion is derived. In addition, we resort to the use of a polytope to introduce a novel treatment of the time-varying delays. A number of different examples are given to demonstrate the reduced conservatism of this method.
The Pharmacology of the Cytochrome P450 Epoxygenase/Soluble Epoxide Hydrolase Axis in the Vasculature and Cardiovascular Disease

Over the last 20 years, it has become clear that cytochrome P450 (P450) enzymes generate a spectrum of bioactive lipid mediators from endogenous substrates. However, studies focused on the determining biologic activity of the P450 system have focused largely on the metabolites generated by one substrate (i.e., arachidonic acid). However, epoxides and diols derived from other endogenous substrates, such as linoleic acid, eicosapentaenoic acid, and docosahexaenoic acid, may be generated in higher concentrations and may potentially be of more physiologic relevance. Recent studies that used a combination of phenotyping and lipid array analyses revealed that rather than being inactive products, fatty acid diols play important roles in a number of biologic processes including inflammation, angiogenesis, and metabolic regulation. Moreover, inhibitors of the soluble epoxide hydrolase that increase epoxide but decrease diol levels have potential for the treatment of the metabolic syndrome.
Does PTH have a direct effect on intestine?

Dogma for the past three decades has dictated that parathyroid hormone (PTH) has no direct effect on intestine with regard to calcium or phosphate absorption, but rather that PTH acts to promote the synthesis of a hormonally active form of vitamin D, namely 1,25‐dihydroxyvitamin D3 [1,25(OH)2D3]. However, diverse laboratories have each provided some evidence to suggest PTH does indeed have a direct effect on intestine. We will briefly review the evidence for biological effects, biochemical effects, and the presence of intestinal receptors for PTH, and conclude with the implications for biomedical research. J. Cell. Biochem. 86: 29–34, 2002. © 2002 Wiley‐Liss, Inc.
Further comparison of faecal egg count reduction test procedures: Sensitivity and specificity

Extract In a recent communication (McKenna2006), a comparison was made between four different methods for calculating results from faecal egg count reduction (FECR) tests (FECRTs). The first and most complex of these, referred to as FECRT1, involved the use of the formula: FECR = 100 × (1−[T2/T1][C1/C2]), where T1 and T2 represented the mean pre- and post-treatment faecal nematode egg counts (FECs) of a treated group, and C1 and C2 represented the mean pre- and post-treatment FECs of an untreated control group, respectively. The other three formulae consisted of more simplified versions of this procedure. In one of them (FECRT2), only post-treatment samples were considered, whereas the other two were based on comparisons between the FECs of groups of animals sampled at the time of anthelmintic treatment (pre-treatment) with those sampled several days later (post-treatment). Thus, FECRT2 was determined according to the formula: FECR = 100 × (1−[T2/C2]), while FECRT3 was calculated from FECR = 100 × (1−[T2/T1]). The fourth procedure (FECRT4) was based on a further simplification of FECRT3 where pre-treatment FECs from only one treatment group were used for comparison with all post-treatment results. This base-line pre-treatment group thus effectively functioned as an untreated control group and hence the formula for FECRT4 was FECR = 100 × (1−[T2/C1]).
Administration of Two Antagonists of the Cholecystokinin B /Gastrin Receptor Does Not Totally Inhibit the Pancreatic Response to a Meal in the Pig

Introduction and Aims The role of the cholecystokinin B (CCK B )/gastrin receptor in the pancreatic response to a standard meal was investigated in the pig. Methodology Twenty-four pigs were prepared surgically for the collection of the pancreatic juice and an intravenous perfusion. On experimental days, the pigs were perfused with one of two CCK B antagonists (L-365,260 or PD 135156) or the vehicle for 2 hours. We offered them a standard meal 30 minutes after the beginning of the perfusion. The pancreatic secretion was collected for 4 hours starting 30 minutes before the perfusion. Its volume was recorded, and the protein concentrations were assayed. Results Neither antagonist totally abolished the postprandial peak of the pancreatic protein. Conclusions We suggest that the stimulation of pancreatic protein secretion by a meal is not mediated by CCK B /gastrin receptors. Because we previously showed that the CCK A receptor antagonist MK329 was no more able to abolish this response, CCK is probably not responsible for this response.
Unit Test Case Selection to Evaluate Changes in Critical Time

Abstract Defects blocking major business transactions may be found while a software system is in production. Due to the urgency of returning the system to proper operation, these defects are frequently resolved in the production environment itself, under such a restricted deadline that there is not enough time to run the complete set of unit test cases upon the patched version of the software. Declining to run the test case suite allows quicker deployment to production, but also allows for other defects to be introduced into the system. This paper evaluates whether a heuristic search approach can help a decision-maker selecting a subset of a unit test case suite to validate a set of changes made in the production environment. The selected test cases should maximize the coverage of changed features and must be executed under a strict time constraint. We designed and executed an experiment which compared different algorithms and found that heuristic search can provide better solutions to this test case selection problem (though at higher cost) than local or random search when the time restriction is a small fraction of the time required to run the full suite.
Choroidal Thickness, Age, and Refractive Error in Healthy Korean Subjects

Purpose To investigate choroidal thickness (CT) in healthy Korean subjects measured by enhanced depth imaging optical coherence tomography and its association with age, axial length, and refractive error. Methods Choroidal scans using enhanced depth imaging optical coherence tomography in each eye of 286 healthy eyes were obtained at the macula. Choroidal thickness was measured at the fovea. Two separate line scans were obtained (one horizontal and one vertical). Results The mean (±SD) age was 40.18 (±17.89) years (range, 13 to 75 years). The mean (±SD) subfoveal CT was 307.26 (±95.18) &mgr;m. Multivariable linear regression suggested that age and refractive error were the most significant factors associated with subfoveal CT (all p < 0.0001) with an adjusted R2 = 0.181. In subjects younger than 60 years, refractive error or axial length and age retained statistically significant correlation with subfoveal CT, whereas such a relationship was lost in subjects older than 60 years. Conclusions The mean subfoveal CT measurement showed the most significant positive correlation with refractive error and the most significant negative correlation with age. For patients younger than 60 years, there was a significant correlation of subfoveal CT with age and refractive error or axial length, whereas such significant association was not observed in subjects older than 60 years.
The Capacity of the Noncoherent Rician Fading Channel∗

Transmission of information over a discrete-time memoryless Rician fading channel is considered where neither the receiver nor the transmitter knows the fading coefficients. First the structure of the capacity-achieving input signals is investigated when the input is constrained to have limited peakedness. It is shown that uniform phase is optimal if there is a line of sight component and the capacity-achieving input amplitude distribution is discrete in the lowpower regime. Then, the Rician fading with phase noise channel model, where there is phase uncertainty in the specular component, is analyzed. For this model it is shown that, with only an average power constraint, the capacity-achieving input amplitude is discrete with a finite number of levels. For the noncoherent Rician fading channel, the spectral-efficiency/bit-energy tradeoff in the power-limited regime is examined when the input has limited peakedness. It is shown that, in contrast to the behavior observed in average power limited channels, the minimum bit energy is not always achieved at zero spectral efficiency. In this case, it is argued that one should avoid operating in the region where the spectral efficiency is lower than the spectral efficiency of the minimum bit energy point. Finally, we propose a quinary signaling scheme, On-Off Quadrature Phase Shift Keying (OOQPSK), which is shown to be optimally efficient in the low-power limit.
C O ] 5 S ep 2 01 3 Eigenvalues and Linear Quasirandom Hypergraphs

Let p(k) denote the partition function of k. For each k ≥ 2, we describe a list of p(k) − 1 quasirandom properties that a k-uniform hypergraph can have. Our work connects previous notions on linear hypergraph quasirandomness of KohayakawaRödl-Skokan and Conlon-Hàn-Person-Schacht and the spectral approach of FriedmanWigderson. For each of the quasirandom properties that are described, we define a largest and second largest eigenvalue. We show that a hypergraph satisfies these quasirandom properties if and only if it has a large spectral gap. This answers a question of Conlon-Hàn-Person-Schacht. Our work can be viewed as a partial extension to hypergraphs of the seminal spectral results of Chung-Graham-Wilson for graphs.