Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodegradation of Atrazine by Agrobacterium radiobacter J14a and Use of This Strain in Bioremediation of Contaminated Soil

ABSTRACT We examined the ability of a soil bacterium, Agrobacterium radiobacter J14a, to degrade the herbicide atrazine under a variety of cultural conditions, and we used this bacterium to increase the biodegradation of atrazine in soils from agricultural chemical distribution sites. J14a cells grown in nitrogen-free medium with citrate and sucrose as carbon sources mineralized 94% of 50 μg of [14C-U-ring]atrazine ml−1 in 72 h with a concurrent increase in the population size from 7.9 × 105 to 5.0 × 107 cells ml−1. Under these conditions cells mineralized the [ethyl-14C]atrazine and incorporated approximately 30% of the 14C into the J14a biomass. Cells grown in medium without additional carbon and nitrogen sources degraded atrazine, but the cell numbers did not increase. Metabolites produced by J14a during atrazine degradation include hydroxyatrazine, deethylatrazine, and deethyl-hydroxyatrazine. The addition of 105 J14a cells g−1 into soil with a low indigenous population of atrazine degraders treated with 50 and 200 μg of atrazine g−1soil resulted in two to five times higher mineralization than in the noninoculated soil. Sucrose addition did not result in significantly faster mineralization rates or shorten degradation lag times. However, J14a introduction (105 cells g−1) into another soil with a larger indigenous atrazine-mineralizing population reduced the atrazine degradation lag times below those in noninoculated treatments but did not generally increase total atrazine mineralization.
The Natural Language of Playlists

We propose a simple, scalable, and objective evaluation procedure for playlist generation algorithms. Drawing on standard techniques for statistical natural language processing, we characterize playlist algorithms as generative models of strings of songs belonging to some unknown language. To demonstrate the procedure, we compare several playlist algorithms derived from content, semantics, and meta-data. We then develop an efficient algorithm to learn an optimal combination of simple playlist algorithms. Experiments on a large collection of naturally occurring playlists demonstrate the efficacy of the evaluation procedure and learning algorithm.
Reliability of self-reported blood pressure measurements.

BACKGROUND Home blood pressure (BP) monitoring improves BP control, but it is unknown whether patients accurately report home BP readings to their physician. This study compared self-reported with electronically stored home BP and heart rate (HR) readings and evaluated this agreement in patients with controlled vs. uncontrolled hypertension. METHODS A single-blind, randomized clinical trial was conducted in an ambulatory managed care population. Subjects were identified by hypertension-related codes from the International Classification of Diseases, Ninth Revision (401.0, 401.1, and 401.9). Subjects recorded systolic BP (SBP), diastolic BP (DBP), and HR 3 times daily for 1 week by means of a digital BP monitor. Subjects were unaware that the monitor electronically stored results. RESULTS Thirty subjects were enrolled (29 complete data sets); their mean age (+/-SD) was 56+/-9 years, and 15 (52%) were women. Sixty-eight percent of subject-recorded SBP, DBP, and HR measurements were identical to electronically stored results. Twenty percent of recorded SBPs and 17% of recorded DBPs differed from stored SBP and DBP by more than 10 mm Hg. Erroneous reporting was evident in 9% of uncontrolled vs 4% of controlled SBPs (P<.001). Similarly, 21% of uncontrolled and 4% of controlled DBPs were erroneously reported (P<.001). In cases where the stored HR exceeded 100 beats/min, 43% of HR readings were recorded as 100 beats/min or less (P<.001). CONCLUSIONS Most self-reported BP and HR readings were identical to electronically stored measurements. However, erroneous reporting occurred significantly more often in cases of uncontrolled BP and HR, which may misguide physicians in the optimal treatment of their patients with hypertension.
Detecting unsafe BGP policies in a flexible world

Internet Service Providers (ISPs) need to balance multiple opposing objectives. On one hand, they strive to offer innovative services to obtain competitive advantages; on the other, they have to interconnect with potentially competing ISPs to achieve reachability, and coordinate with them for certain services. The complexity of balancing these objectives is reflected in the diversity of policies of the Border Gateway Protocol (BGP), the standard inter-domain routing protocol. Unforeseen interactions among the BGP policies of different ISPs can cause routing anomalies. In this work, we propose a methodology to allow ISPs to check their BGP policy configurations for guaranteed convergence to a single stable state. This requires that a set of ISPs share their configurations with each other, or with a trusted third party. Compared to previous approaches to BGP safety, we (1) allow ISPs to use a richer set of policies, (2) do not modify the BGP protocol itself, and (3) detect not only instability, but also multiple stable states. Our methodology is based on the extension of current theoretical frameworks to relax their constraints and use incomplete data. We believe that this provides a rigorous foundation for the design and implementation of safety checking tools.
Presence of Helicobacter pylori in subgingival plaque of periodontitis patients with and without dyspepsia, detected by polymerase chain reaction and culture

Background: Helicobacter pylori is an important gastrointestinal pathogen that is strongly associated with gastritis as well as peptic ulcer disease. Antimicrobial therapy frequently fails to cure H. pylori infection, which suggests there may be sanctuary sites where the organism resides. This study was aimed to assess the role of oral cavity as a reservoir of H. pylori by evaluating the occurrence of the organism in subgingival plaque of dyspeptic patients by polymerase chain reaction as well as culture. Materials and Methods: Thirty chronic periodontitis patients whose biopsy specimens were found to be H. pylori positive with rapid urease test and histopathologic examination were considered as cases and 20 chronic periodontitis patients who never had any symptoms of gastritis or peptic ulcer were taken as controls. Subgingival plaque samples were collected and sent to microbiological laboratory for detection of H. pylori by 16S rRNA based polymerase chain reaction as well as culture. Results: 60% of the samples were found to be positive with polymerase chain reaction in the case group when compared to 15% in the controls. Also, 30% of the cases were found to be positive with culture compared to none in controls. Conclusion: A higher frequency of detection of H. pylori in those patients with positive antral biopsy report was seen. Also, polymerase chain reaction was found to be more sensitive than culture for detection. Thus, we conclude that detection of H. pylori in dental plaque of dyspeptic patients cannot be neglected and might represent a risk factor for recolonization of stomach after systemic eradication therapy.
Why are GPs treating subclinical hypothyroidism? Case note review and GP survey

Background Subclinical hypothyroidism (SCHo) is a common biochemical diagnosis in older age. Evidence of impact is inconclusive and guidelines are inconsistent. With increasing numbers of thyroid function tests (TFTs) performed, GPs frequently have to make management decisions regarding this diagnosis. However, little is known about how SCHo is currently being managed in primary care. Aim To explore management of SCHo in primary care and GP reported rationale for treatment of SCHo in older individuals. Design Descriptive study using retrospective case note review and GP survey. Setting Nineteen General Practices, Central England, UK. Methods Follow-up of a large cohort with subsequent detailed review of individuals for whom therapy had been initiated following diagnosis of SCHo. Data on practice policies, and rationale behind treatment were collected via GP questionnaire. Results Forty-two individuals were treated following identification of SCHo. Factors regarded as supporting instigation of therapy recorded by practitioners included symptoms, a positive antithyroid antibody test and history of radioiodine therapy. In all, 55% were registered at 3/19 practices suggesting significant between practice variation. Reasons for testing included chronic disease check-up (n = 14), presenting ‘thyroid symptoms’ (n = 5) and presenting other symptoms (n = 9). Reasons for therapy initiation were only recorded in 26 cases and included presence of symptoms, persistently high or increasing serum thyroid stimulating hormone concentration and patient request. Only 2/15 GPs reported having practice guidelines on management. Conclusion Results suggest that GPs are uncertain how to interpret symptoms and TFT results in older individuals. There is considerable variation in management of SCHo between GPs with some GPs treating patients outside of all guideline recommendations.
Effect of mouse antisera targeting the Phlebotomus papatasi midgut chitinase PpChit1 on sandfly physiology and fitness

In sandflies, the absence of the peritrophic matrix (PM) affects the rate of blood digestion. Also, the kinetics of PM secretion varies according to species. We previously characterised PpChit1, a midgut-specific chitinase secreted in Phlebotomus papatasi (PPIS) that is involved in the maturation of the PM and showed that antibodies against PpChit1 reduce the chitinolytic activity in the midgut of several sandfly species. Here, sandflies were fed on red blood cells reconstituted with naïve or anti-PpChit1 sera and assessed for fitness parameters that included blood digestion, oviposition onset, number of eggs laid, egg bouts, average number of eggs per bout and survival. In PPIS, anti-PpChit1 led to a one-day delay in the onset of egg laying, with flies surviving three days longer compared to the control group. Anti-PpChit1 also had a negative effect on overall ability of flies to lay eggs, as several gravid females from all three species were unable to lay any eggs despite having lived longer than control flies. Whereas the longer survival might be associated with improved haeme scavenging ability by the PM, the inability of females to lay eggs is possibly linked to changes in PM permeability affecting nutrient absorption.
Natural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock

Natural selection of variants within the Arabidopsis thaliana circadian clock can be attributed to adaptation to varying environments. To define a basis for such variation, we examined clock speed in a reporter-modified Bay-0 x Shakdara recombinant inbred line and localized heritable variation. Extensive variation led us to identify EARLY FLOWERING3 (ELF3) as a major quantitative trait locus (QTL). The causal nucleotide polymorphism caused a short-period phenotype under light and severely dampened rhythm generation in darkness, and entrainment alterations resulted. We found that ELF3-Sha protein failed to properly localize to the nucleus, and its ability to accumulate in darkness was compromised. Evidence was provided that the ELF3-Sha allele originated in Central Asia. Collectively, we showed that ELF3 protein plays a vital role in defining its light-repressor action in the circadian clock and that its functional abilities are largely dependent on its cellular localization. DOI: http://dx.doi. org/10.7554/eLife.02206. 001
Knowing What Others Know: Coordination Motives in Information Acquisition

We explore how optimal information choices change the predictions of strategic models. When a large number of agents play a game with strategic complementarity, information choices exhibit complementarity as well: If an agent wants to do what others do, they want to know what others know. This makes heterogeneous beliefs difficult to sustain and may generate multiple equilibria. In models with substitutability, agents prefer to differentiate their information choices. We use these theoretical results to determine the role of information choice in recent price-setting models and to propose modeling techniques that ensure equilibrium uniqueness.
RSSI is Under Appreciated

There is a general belief in the Wireless Sensor Network (WSN) community that the received signal strength indicator (RSSI) is a bad estimator of the link quality. This belief is due to the existence of many asymmetry links in older radios such as CC1000 and TR1000. Newer radios that are based on IEEE 802.15. 4 standard such as CC2420 implement another parameter called link quality indicator (LQI) which is believed to be a better indicator than RSSI. There is so far no extensive evaluation of CC2420 to validate this claim. We have conducted such an evaluation and our preliminary results indicate that RSSI for a given link has very small variation over time for a link. Our results also indicate that when the RSSI is above the sensitivity threshold (about -87 dBm), the packet reception rate (PRR) is atleast 85%. Around this sensitivity threshold, however, the PRR is not correlated possibly due to variations in local phenomena such as noise. LQI, on the other hand, varies over a wider range over time for a given link. However, the mean LQI computed over many packets has a better correlation with PRR.
Antidiabetic effect of chitosan oligosaccharide (GO2KA1) is mediated via inhibition of intestinal alpha‐glucosidase and glucose transporters and PPAR&ggr; expression

We have previously reported that administration of low molecular weight chitosan oligosaccharide (GO2KA1) significantly suppressed postprandial blood glucose rise with increased plasma adiponectin and HbA1c levels in animals and humans. However, the cellular mechanisms whereby GO2KA1 exerts antihyperglycemic effects still remain to be determined. Using intestinal Caco-2 cells and 3T3-L1 cells, here we show that GO2KA1 has dual modes of antidiabetic action by (1) inhibiting intestinal α-glucosidase as well as glucose transporters SGLT1 and GLUT2 that were distinct from the acarbose effect; (2) enhancing adipocyte differentiation, PPARγ expression and its target genes, such as FABP4, adiponectin, and GLUT4, whereas the effects were abolished by co-treatment with BADGE, a PPARγ antagonist. Moreover, GO2KA1 significantly increased glucose uptake, which was reduced in the presence of BADGE. Our data show that GO2KA1 may prevent hyperglycemia by inhibiting intestinal glucose digestion and transport and also enhance glucose uptake, at least in part, by upregulating adiponectin expression through PPARγ in adipocytes. These findings may provide potential molecular modes of action for the antidiabetic effects of chitosan oligosaccharide observed in clinical and animal studies. © 2016 BioFactors, 43(1):90-99, 2017.
New Hubble Space Telescope Discoveries of Type Ia Supernovae at z ≥ 1: Narrowing Constraints on the Early Behavior of Dark Energy

We have discovered 21 new Type Ia supernovae (SNe Ia) with the Hubble Space Telescope (HST) and have used them to trace the history of cosmic expansion over the last 10 billion yr. These objects, which include 13 spectroscopically confirmed SNe Ia at z ≥ 1, were discovered during 14 epochs of reimaging of the GOODS fields North and South over 2 yr with the Advanced Camera for Surveys on HST. Together with a recalibration of our previous HST-discovered SNe Ia, the full sample of 23 SNe Ia at z ≥ 1 provides the highest redshift sample known. Combining these data with previous SN Ia data sets, we measured H(z) at discrete, uncorrelated epochs, reducing the uncertainty of H(z > 1) from 50% to under 20%, strengthening the evidence for a cosmic jerk—the transition from deceleration in the past to acceleration in the present. The unique leverage of the HST high-redshift SNe Ia provides the first meaningful constraint on the dark energy equation-of-state parameter at z ≥ 1. The result remains consistent with a cosmological constant [w(z) = −1] and rules out rapidly evolving dark energy (dw/dz ≫ 1). The defining property of dark energy, its negative pressure, appears to be present at z > 1, in the epoch preceding acceleration, with ~98% confidence in our primary fit. Moreover, the z > 1 sample-averaged spectral energy distribution is consistent with that of the typical SN Ia over the last 10 Gyr, indicating that any spectral evolution of the properties of SNe Ia with redshift is still below our detection threshold.
At the Elbow of Another: Learning to Teach by Coteaching

At the Elbow of Another is about teaching and learning to teach, written from the perspectives and experiences of two educators who teach and, in so doing, learn to teach. Teaching and learning to teach at the elbows of other teachers (including ourselves) provide us with new and different understandings and allow us to describe a different epistemology of teaching. We adopt a first-person perspective on teaching, sometimes our own and at other times that of peers but through the eyes of coparticipants engaged in an activity with the same primary intention of assisting students to learn. Throughout this book, we focus on teaching and learning to teach at different stages of the career ladder and explore different ways of conceiving the roles of researchers, supervisors, evaluators, cooperating teachers, and "new teachers. "
Roflumilast: the new orally active, selective phophodiesterase-4 inhibitor, for the treatment of COPD

Introduction: Chronic obstructive pulmonary disease (COPD) is a progressive disease, the clinical course of which is punctuated by acute exacerbations. While long-acting bronchodilators and inhaled corticosteroids can reduce exacerbations, some patients do not respond adequately to these agents. Roflumilast, a novel orally active, once-daily phophodiesterase-4-selective inhibitor with anti-inflammatory properties, has been shown to reduce exacerbations and has been approved for the treatment of the subset of COPD patients with symptoms of chronic cough and sputum who have a history of exacerbations. Areas covered: This article describes the pre-clinical and clinical pharmacology of roflumilast and analytically reviews the published data from the most relevant Phase-II and -III clinical trials evaluating its efficacy and safety. Expert opinion: Roflumilast is the first drug specifically targeted to a particular subset of the heterogeneous population of COPD patients, namely those with chronic bronchitis in addition to severe airflow obstruction and an exacerbation history. Its efficacy in reducing exacerbations in patients already receiving a LABA or anticholinergic bronchodilator underscores its potential utility as an add-on agent in patients who continue to experience exacerbations despite treatment with other agents. Adverse events include gastrointestinal side effects, most commonly, as well as unexplained weight loss.
Some psychological concomitants of chronic bronchitis

Synopsis Thirty chronic bronchitic patients with severe airways obstruction were individually matched with non-bronchitic controls from the general population. The 2 groups were compared using the Zung Self-Rating Depression Scale (SDS) and the General Health Questionnaire (GHQ) to assess non-psychotic psychiatric disturbance, the Eysenck Personality Inventory (EPI) to assess personality traits, and the Marlowe–Crowne (M–C) scale plus the L (Lie) scale of the EPI to assess social-desirability response set. Chronic bronchitic patients were both more psychiatrically disturbed and more neurotic in personality than were their matched controls; but there were no differences between the 2 groups on the personality trait of extraversion or on measure of social desirability response set. The results are discussed in the context of both chronic bronchitis specifically and chronic illness in general, and future investigations are proposed.
Susceptibility to primary angle closure glaucoma in Saudi Arabia: the possible role of mitochondrial DNA ancestry informative haplogroups

Purpose In a previous preliminary analysis we reported that mitochondrial DNA (mtDNA) haplogroup R0a was significantly more frequent in primary angle closure glaucoma (PACG) Saudi patients than in healthy Saudi controls. This result prompted us to extend our work using a significant larger Saudi PACG cohort and more healthy controls. Methods We sequenced the mtDNA regulatory hypervariable region-I (HVS-I) and coding regions, comprising haplogroup diagnostic polymorphisms, in 227 PACG Saudi patients and compared their haplogroup frequencies with those obtained from 186 matched healthy controls (free of PACG by examination) and from a large sample of 810 healthy Saudi Arabs representing the general Saudi population. Results MtDNA Haplogroups R0a and J, the most abundant lineages in Saudi Arabia, were in significant higher frequencies in the PACG patients than in controls, while the widespread western Eurasian haplogroup U was associated with reduced risk to developing PACG. Conclusions Haplogroups R0a and J could be ancestry informative markers for PACG in the Saudi Arabian population. In addition, the western Eurasian haplogroup U may play a mild protective effect to this illness.
Phoneme recognition using spectral envelope and modulation frequency features

We present a new feature extraction technique for phoneme recognition that uses short-term spectral envelope and modulation frequency features. These features are derived from sub-band temporal envelopes of speech estimated using Frequency Domain Linear Prediction (FDLP). While spectral envelope features are obtained by the short-term integration of the sub-band envelopes, the modulation frequency components are derived from the long-term evolution of the sub-band envelopes. These features are combined at the phoneme posterior level and used as features for a hybrid HMM-ANN phoneme recognizer. For the phoneme recognition task on the TIMIT database, the proposed features show an improvement of 4.7% over the other feature extraction techniques.
Motoneurons of the Lateral and Medial Rectus Extraocular Muscles in Squirrel Monkey and Cat

The goal of this study was to examine and compare the number and size of motoneurons in the cat and squirrel monkey abducens nucleus. We also examined medial rectus muscle motoneuron compartmentalization in the squirrel monkey oculomotor nucleus and compared those cells to abducens nucleus motoneurons. Retrograde labeling of the motoneurons, using cholera toxin conjugate of horseradish peroxidase (CTHRP) injected into cat and monkey lateral or medial rectus muscles, was observed after 24 h. The CTHRP was histochemically localized with tetramethylbenzidine. The slide-mounted sections were analyzed using a computerized imaging system. Cat abducens nucleus motoneurons showed a wide range of cell sizes (26.0–66.0 µm, mean = 37.2 ± 6.2 µm), four or more dendrites per cell and an average of 1,418 cells within a relatively loosely packed nucleus. Squirrel monkey abducens nucleus motoneurons were significantly smaller than those in the cat with a narrower range of cell sizes (20.0–44.0 µm, mean = 31.7 ± 3.8 µm), four or more dendrites per cell and an average of 2,473 cells densely packed within the nucleus. Squirrel monkey medial rectus muscle motoneurons were organized into MRa, MRb and MRc subgroups. MRa motoneurons comprise the primary innervation for the medial rectus muscle and were similar in size to abducens nucleus motoneurons while the MRc subgroup cells were significantly smaller in size. Similar relationships among medial rectus motoneurons have been seen in rhesus monkeys. The relationship of these anatomical findings to previous physiological results regarding the generation of extraocular muscle force in the squirrel monkey is discussed.