Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Evaluation of Four Field-Scale Agricultural Drainage Denitrification Bioreactors in Iowa

Recently, interest in denitrification bioreactors to reduce the amount of nitrate in agricultural drainage has led to increased installations across the U.S. Midwest. Despite this recent attention, there are few peer-reviewed, field-scale comparative performance studies investigating the effectiveness of these denitrification bioreactors. The object of this work was to analyze nitrate removal performance from four existing bioreactors in Iowa, paying particular attention to potential performance-affecting factors including retention time, influent nitrate concentration, temperature, flow rate, age, length-to-width ratio, and cross-sectional shape. Based on a minimum of two years of water quality data from each of the four bioreactors, annual removal rates ranged from 0.38 to 7.76 g N m-3 bioreactor volume d-1. Bioreactor and total (including bypass flow) nitrate-nitrogen load reductions ranged from 12% to 76% (mean 45%) and from 12% to 57% (mean 32%), respectively, removing from 0.5 to 15.5 kg N ha-1 drainage area. Multiple regression analyses showed that temperature and influent nitrate concentration were the most important factors affecting percent bioreactor nitrate load reduction and nitrate removal rate, respectively. This analysis also indicated that load reductions within the bioreactor were significantly impacted by retention time at three of the four reactors. More field-scale performance data from bioreactors of different designs and from multiple locations around the Midwest are necessary to further enhance understanding of nitrate removal in these systems and their potential to positively impact water quality.
Improved bioinformatics tools for the analysis of mass spectrometry-based peptidomics and proteomics data

ii Declaration . iv Preface . vi Acknowledgements . viii List of Figures . xiv List of Tables . xvi List of Abbreviations . xviii Chapter 1. Background and Literature Review . 1 1.1 Biological role of peptides . 2 1.2 Mass spectrometry . 4 1.3 Sequence databases . 7 1.4 Peptide Identification . 9 1.5 Validation, FDR estimation and decoy sequence databases . 15 1.6 Aims and organisation of this thesis . 18 1.6. 1 The aims of this thesis are to: . 18 1.6. 2 This thesis is organised as follows: . 18 Chapter 2. LudwigNR: A single comprehensive, non-redundant, speciesspecific and taxonomy enabled protein sequence database for MS-based proteomics and peptidomics research . 21 2.
Highly Scaled Vertical Cylindrical SONOS Cell With Bilayer Polysilicon Channel for 3-D nand Flash Memory

A vertical cylindrical SONOS cell with a novel bilayer polysilicon channel down to 22-nm diameter for 3-D NAND Flash memory is successfully developed. We introduce a thin amorphous silicon layer along with the oxide-nitride-oxide (ONO) gate stack inside the memory hole. This silicon layer protects the tunnel oxide during opening of the gate stack at the bottom of the memory hole, after which it serves as the first layer of the bilayer polysilicon channel. This approach enables the 3-D architecture to achieve minimum cell area (4F2, with F being the feature size) without the need for the so-called pipeline connections. The smallest functional cells have the memory hole diameter F = 45 nm, resulting in 22-nm channel diameter. In case 16 cells are stacked, F = 45 nm would correspond to an equivalent 11-nm planar cell technology node. Excellent program/erase and retention obtained with the all-deposited ONO stack are demonstrated.
Image restoration in radioisotope imaging systems.

In the radioisotope image visualization, the final image must he interpreted by the human visual system. However, an inherent blurring of the image limits the amount of useful information which can he extracted from it. Attempts have been made to restore the image by compensating for the degradation. By expressing the radioisotope image as a convolution integral of a true radioisotope distribution, with the spatial resolution of the imaging system. and by using an iterative approximation method for the evaluation of the integral. a ' restored image ' is obtained. An experimental result on a profile scan demonstrates the applicability of the method to radioisotope imaging systems.
Nitroglycerin and delayed preconditioning in humans: yet another new mechanism for an old drug?

Short episodes of ischemia and reperfusion protect the myocardium from the damage induced by episodes of sustained ischemia. Such ischemic preconditioning is apparent within minutes and lasts for 2 to 3 hours; a second phase of delayed preconditioning reappears 12 to 24 hours later and lasts for 3 to 4 days. Ischemic preconditioning, in its early and delayed form, is currently the prevailing paradigm for experimental studies aiming to reduce infarct size and other deleterious consequences of ischemia/reperfusion.1 A more detailed analysis of the underlying signal transduction is expected to provide better insight into the basic pathophysiology of myocardial ischemia/reperfusion injury and to help develop more potent and specific pharmacological treatments. The existence and significance of ischemic preconditioning in humans are less clear,2 largely because the most rigorous end point, infarct size, is not easily available in controlled, prospective studies in humans, for obvious ethical reasons. Prospective clinical studies with short episodes of fully reversible myocardial ischemia, such as that induced by percutaneous transluminal coronary angioplasty (PTCA)3 4 5 6 or by brief surgical ischemic cardiac arrest,7 8 are available. Certain parts of the experimentally established signal transduction of ischemic preconditioning have been verified using PTCA; these include preconditioning by adenosine9 10 or bradykinin11 and the prevention of ischemic preconditioning by the ATP-sensitive calcium channel (KATP) blocker glibenclamide4 or the opioid antagonist naloxone.12 Surrogate end points in such studies include ST-segment shifts in the surface or intracoronary …
Free volume of an oligomeric epoxy resin and its relation to structural relaxation: evidence from positron lifetime and pressure-volume-temperature experiments.

From positron annihilation lifetime spectroscopy analyzed with the new routine LT9.0 and pressure-volume-temperature experiments analyzed employing the equation of state (EOS) Simha-Somcynsky lattice-hole theory (SS EOS) the microstructure of the free volume and its temperature dependence of an oligomeric epoxy resin (ER6, M(n) approximately 1750 g/mol , T(g)=332 K ) of diglycidyl ether of bisphenol-A (DGEBA) have been examined and characterized by the hole free-volume fraction h, the specific free and occupied volumes V(f)=hV and V(occ)=(1-h)V, and the size distribution (mean, , and mean dispersion, sigma(h)) and the mean density N(h)'=V(f)/, of subnanometer-size holes. The results are compared with those from a previous work [G. Dlubek, Phys. Rev. E 73, 031803 (2006)] on a monomeric liquid of the same resin (ER1, M(n) approximately 380 g/mol, T(g)=255 K ). In the glassy state ER6 shows the same hole sizes as ER1 but a higher V(f) and N(h)'. In the liquid V(f), , dV(f)/dT, and dV(f)/dP are smaller for ER6. The reported dielectric alpha relaxation time tau shows certain deviations from the free-volume model which are larger for ER6 than for ER1. This behavior correlates with the SS EOS, which shows that the unit of the SS lattice is more heavy and bulky and therefore the chain is less flexible for ER6 than for ER1. The free-volume fraction h in the liquid can be described by the Schottky equation h proportional to exp(-H(h)/k(B)T) , where H(h)=7.8 - 6.4 kJ/mol is the vacancy formation enthalpy, which opens a different way for the extrapolation of the equilibrium part of the free volume. The extrapolated h decreases gradually below T(g) and becomes zero only when 0 K is reached. This behavior means that no singularity would appear in the relaxation time at temperatures above 0 K. To quantify the degree to which volume and thermal energy govern the structural dynamics, the ratio of the activation enthalpies E(i)=R[(d ln tau/dT(-1))]i, at constant volume V and constant pressure P(E(V)/E(P)), is frequently determined. We present arguments for necessity to substitute E(V) by E(Vf), the activation enthalpy at constant (hole) free volume, and show that E(Vf)/E(P) changes as expected: it increases with increasing free volume, i.e., with increasing temperature, decreasing pressure, and decreasing molecular weight. E(Vf)/E(P) exhibits smaller values than E(V)/E(P), which leads to the general inference that the free volume plays a larger role in dynamics than concluded from E(V)/E(P). The same conclusion is obtained when scaling tau to T(-1)V(f)(-gamma) instead of to T(-1)V(-gamma), where both gamma's are material constants.
Battered Women: A Medical Problem Requiring Detection

A one month study of the surgical and psychiatric service of a university hospital emergency room identified thirty-seven women coming for treatment as a result of physical abuse. Thirty-three of the thirty-seven women presented at the surgical services and represented 3.8 per cent of surgical admissions in the emergency room. These women came from all ages, social and ethnic groups. They usually presented with contusions or other injuries to the head and neck. The majority would not accept psychiatric treatment but were willing to discuss the problem with the emergency room physician if encouraged. The preventive implications of these findings for the nonpsychiatric physician are discussed.
Co-opted Boards

We develop two measures of board composition to investigate whether directors appointed by the CEO have allegiance to the CEO and decrease their monitoring. Co-option is the fraction of the board comprised of directors appointed after the CEO assumed office. As Co-option increases, board monitoring decreases: turnover-performance sensitivity diminishes, pay increases (without commensurate increase in pay-performance sensitivity), and investment increases. Non-Co-opted Independence—the fraction of directors who are independent and were appointed before the CEO—has more explanatory power for monitoring effectiveness than the conventional measure of board independence. Our results suggest that not all independent directors are effective monitors.
Mercury bioaccumulation, speciation, and influence on web structure in orb‐weaving spiders from a forested watershed

Atmospheric deposition is an important source of Hg in remote terrestrial ecosystems of northeastern North America. As high‐level invertebrate consumers, orb‐weaving spiders (family Araneidae) are excellent subjects for studying the impact of sublethal levels of Hg on forest animals because their webs provide snapshots of behavior and neurological function. Spiders of the diadematus group of the genus Araneus were collected from the Jeffers Brook watershed in the White Mountain National Forest, New Hampshire (USA), and analyzed for Hg content. Webs were photographed and measured to test for correlations between Hg body burden and web structure. Collected spiders contained concentrations of total Hg averaging 44.7 ± 10.0 ng/g Hg (wet mass; mean ± standard deviation), with 37 ± 6% of the total Hg present in the methylmercury form. Mercury loads were likely accumulated through diet (potential prey items contained an average of 43% of the Hg load in collected spiders) and possibly web ingestion. The present study found no direct evidence that the web structure—and thus the prey‐capture ability—of spiders in the study area was affected by their Hg body burden. Environ. Toxicol. Chem. 2011; 30:1873–1878. © 2011 SETAC
3′ processing of eukaryotic precursor tRNAs

Biogenesis of eukaryotic tRNAs requires transcription by RNA polymerase III and subsequent processing. 5′ processing of precursor tRNA occurs by a single mechanism, cleavage by RNase P, and usually occurs before 3′ processing although some conditions allow observation of the 3′‐first pathway. 3′ processing is relatively complex and is the focus of this review. Precursor RNA 3′ end formation begins with pol III termination generating a variable length 3′ oligo(U) tract that represents an underappreciated and previously unreviewed determinant of processing. Evidence that the pol III‐intrinsic 3′ exonuclease activity mediated by Rpc11p affects 3′ oligo(U) length is reviewed. In addition to multiple 3′ nucleases, precursor tRNA (pre‐tRNA) processing involves La and Lsm, distinct oligo(U)‐binding proteins with proposed chaperone activities. 3′ processing is performed by the endonuclease RNase Z or the exonuclease Rex1p (possibly others) along alternate pathways conditional on La. We review a Schizosaccharomyces pombe tRNA reporter system that has been used to distinguish two chaperone activities of La protein to its two conserved RNA binding motifs. Pre‐tRNAs with structural impairments are degraded by a nuclear surveillance system that mediates polyadenylation by the TRAMP complex followed by 3′ digestion by the nuclear exosome which appears to compete with 3′ processing. We also try to reconcile limited data on pre‐tRNA processing and Lsm proteins which largely affect precursors but not mature tRNAs. A pathway is proposed in which 3′ oligo(U) length is a primary determinant of La binding with subsequent steps distinguished by 3′ endo versus exo nucleases, chaperone activities, and nuclear surveillance. WIREs RNA 2011 2 362–375 DOI: 10.1002/wrna.64
Predicting Persistently High Primary Care Use

PURPOSE We wanted to identify risk factors for persistently high use of primary care. METHODS We analyzed outpatient office visits to practitioners in family medicine, general internal medicine, general pediatrics, and obstetrics for 1997–1999 among patients in a small Midwestern city covered by a fee-for-service insurance plan with no co-payments for physician visits and no requirement for referral to specialty care. Logistic regression was used to predict which patients with 10 or more primary care visits in 1997 would repeat high use in 1998 based on demographic and diagnostic categories (adjusted clinical groups [ACGs]). A confirmatory data set (high primary care use in 1998 persistent into 1999) was used to evaluate the model. RESULTS Two percent of the 54,074 patients had 10 or more primary care visits in 1997, and of these, almost 19% had 10 or more visits in the next year. Among adults, 4 ambulatory diagnosis groups (ADGs) were simultaneously positive predictors of repeated high primary care visits: unstable chronic medical conditions, see and reassure conditions, minor time-limited psychosocial conditions, and minor signs and symptoms. Meanwhile, pregnancy was negatively associated. The area under the receiver operating characteristic (ROC) curve was 0.794 for adults in the developmental data set and 0.752 in the confirmatory data set, indicating a moderately accurate assessment. A satisfactory model was not developed for pediatric patients. CONCLUSIONS Many persistently high primary care users appear to be overserviced but underserved, with underlying problems not addressed by a medical approach. Some may benefit from psychosocial support, whereas others may be good candidates for disease management interventions.
Interactive visual categorization of spinel-group minerals

Spinel-group minerals are excellent indicators of geological environments and are of invaluable help in the search for mineral deposits of economic interest. The geologists analyze them by means of Barnes and Roeder's contours. In this paper, we present a collection of novel, interactive methods, which assist geologists in the categorization of spinel-group minerals. We fully integrate Barnes and Roeder's contours using a polygonal representation. This makes it possible to efficiently superimpose user-provided point data over the contours, and to automatically rank the contours based on the number of enclosed points. We also allow the expert to create contours for the user-provided point data. Once user contours are created, they can be compared with Barnes and Roeder's contours. During the analysis, the user can drill-down by means of brushing. As we deal with specific data, we apply two novel brushing techniques, i.e., the percentile brush and the contour brush. The novel brushing mechanisms along with the interactive comparison speed-up the analysis significantly. We evaluate the newly introduced approach and the resulting novel workflow using real-word data from different locations in Argentina. According to the domain experts, the classification of spinel minerals needs several minutes now, while it took a few days with the current state of the art approach in the domain.
Biosynthetic pathways in chemical phylogeny

An approach to chemical phylogeny is discussed, based on an emphasis on alterations of biosynthetic pathways rather than on isolations of individual compounds. Some offshoots of biosynthetic pathways to target molecules such as gibberellic acid are considered. Attempts are made to assess the significance of alterations of pathways in terms of the chemical probabilities of their occurrences. Attempts have been made to assist that essentially artificial dassification, taxonomy, by considering the structures of plant constituents as markers on a level with morphological characteristics. This is quite legitimate, but both taxonomy and its much more fundamental relative phylogeny may weil be illuminated much more by considerations of biosynthetic pathways than of individual structures. Some tentative attempts have been made but there appears tobe required a more systematic analysis of the whole situation. The constituents of plants and microorganisms can be divided roughly into two categories; molecules which are of primary metabolic and structural importance, and molecules of secondary, or no known, functions. The first dass contains small molecules which appear to be ubiquitous, such as sugars, amino acids, citric acid, etc., which are the universal building blocks and energy sources. It also contains proteins, nucleic acids, polysaccharides, etc., which may differ in structural details from one organism to another but which appear to have universal types of function as enzymes, structural materials and carriers of hereditary mechanisms. More arguable as to category are rather specialized structural materials characteristic of dasses of whole organisms rather than of individual cells, such as Iignin. The secondary category indudes a great diversity of chemical types, usually in fairly small molecules, with a sporadic occurrence. Although the first dass is a more fundamental one, and undoubtedly will be examined in structural terms to define relations between organisms in a way which has already been done, for example, with the globin portion of haemoglobins, the task is much more difficult because of the great molecular complexity · involved and because of the universal distribution of types in which alterations may be small, for example, the replacement of one amino acid by another in a molecule containing many such units.
Enhanced exercise‐induced plasma cytokine response and oxidative stress in COPD patients depend on blood oxygenation

In healthy subjects, hypoxemia and exercise represent independent stressors promoting the exercise‐induced cytokine response and oxidative stress. We hypothesized that hypoxemia in patients with chronic obstructive pulmonary disease (COPD) may affect the cytokine production and/or the changes in oxidant–antioxidant status in response to maximal exercise. Exercise‐induced changes in PaO2 allowed to transiently increase or decrease baseline hypoxemia and to point out its specific action on muscle metabolism. COPD patients with severe to moderate hypoxemia (56 < PaO2 < 72 mmHg) performed an incremental cycling exercise until volitional exhaustion. Two cytokines [interleukin (IL)‐6 and tumour necrosis factor (TNF)‐α] and three blood indices of oxidative stress [plasma thiobarbituric acid reactive substances (TBARS) and two antioxidants, reduced erythrocyte glutathione (GSH), and reduced plasma ascorbic acid, RAA] were measured at rest, then during and after exercise. The changes in the cytokine levels and oxidant–antioxidant status were analysed in relation with the baseline PaO2 and its exercise‐induced variations. Data were compared with those obtained in an age‐ and body mass index‐matched group of healthy subjects. Compared with healthy subjects, COPD patients presented a marked accentuation of exercise‐induced increase in IL‐6 level and earlier changes in their oxidant–antioxidant status. Resting levels of IL‐6 and TNF‐α and exercise‐induced peak variations of TBARS, IL‐6 and TNF‐α were negatively correlated with the baseline PaO2. In COPD patients, the peak increases in IL‐6 and TBARS were attenuated when exercise hyperventilation reduced the baseline hypoxemia. Our study indicates that the PaO2 level affects both the exercise‐induced oxidative stress and cytokine response in hypoxemic COPD patients.
Comparison of the spinal neuropathic pain induced by intraspinal injection of N-methyl-d-aspartate and quisquate in rats.

OBJECTIVE Excitatory amino acids play important roles in the development of secondary pathology following spinal cord injury (SCI). This study was designed to evaluate morphological changes in the dorsal horn of the spinal cord and assess profiles of pain behaviors following intraspinal injection of N-methyl-D-aspartate (NMDA) or quisqualate (QUIS) in rats. METHODS Forty male Sprague-Dawley rats were randomized into three groups : a sham, and two experimental groups receiving injections of 125 mM NMDA or QUIS into their spinal dorsal horn. Following injection, hypersensitivity to cold and mechanical stimuli, and excessive grooming behaviors were assessed serially for four weeks. At the end of survival periods, morphological changes in the spinal cord were evaluated. RESULTS Cold allodynia was developed in both the NMDA and QUIS groups, which was significantly higher in the QUIS group than in the NMDA group. The mechanical threshold for the ipsilateral hind paw in both QUIS and NMDA groups was significantly lower than that in the control group. The number of groomers was significantly higher in the NMDA group than in the QUIS group. The size of the neck region of the spinal dorsal horn, but not the superficial layer, was significantly smaller in the NMDA and QUIS groups than in the control group. CONCLUSION Intraspinal injection of NMDA or QUIS can be used as an excitotoxic model of SCI for further research on spinal neuropathic pain.
Effect of KMD‐3213, an α1A‐adrenoceptor antagonist, on the prostatic urethral pressure and blood pressure in male decerebrate dogs

Background: KMD‐3213 is an α1A‐adrenoceptor‐selective antagonist currently being developed for the treatment of urinary outlet obstruction in patients with benign prostatic hyperplasia. In the present study, the uroselectivity of KMD‐3213 was evaluated and compared with that of prazosin and tamsulosin in a decerebrate dog model.