Miracle-dz/UniFAR-FTUs huggingface dataset:
The Tryptophanase Gene Cluster of Haemophilus influenzae Type b: Evidence for Horizontal Gene Transfer

ABSTRACT Among strains of Haemophilus influenzae, the ability to catabolize tryptophan (as detected by indole production) varies and is correlated with pathogenicity. Tryptophan catabolism is widespread (70 to 75%) among harmless respiratory isolates but is nearly universal (94 to 100%) among strains causing serious disease, including meningitis. As a first step in investigating the relationship between tryptophan catabolism and virulence, we have identified genes in pathogenic H. influenzae which are homologous to the tryptophanase (tna) operon of Escherichia coli. The tna genes are located on a 3.1-kb fragment betweennlpD and mutS in the H. influenzaetype b (Eagan) genome, are flanked by 43-bp direct repeats of an uptake signal sequence downstream from nlpD, and appear to have been inserted as a mobile unit within this sequence. The organization of this insertion is reminiscent of pathogenicity islands. Thetna cluster is found at the same map location in all indole-positive strains of H. influenzae surveyed and is absent from reference type d and e genomes. In contrast to H. influenzae, most other Haemophilus species lacktna genes. Phylogenetic comparisons suggest that thetna cluster was acquired by intergeneric lateral transfer, either by H. influenzae or a recent ancestor, and thatE. coli may have acquired its tnaA gene from a related source. Genomes of virulent H. influenzae resemble those of pathogenic enterics in having an island of laterally transferred DNA next to mutS.
Integrating 40Ar/39Ar, U-Pb, and astronomical clocks in the Cretaceous Niobrara Formation, Western Interior Basin, USA

This study revises and improves the chronostratigraphic framework for late Turonian through early Campanian time based on work in the Western Interior U.S. and introduces new methods to better quantify uncertainties associated with the development of such time scales. Building on the unique attributes of the Western Interior Basin, which contains abundant volcanic ash beds and rhythmic strata interpreted to record orbital cycles, we integrate new radioisotopic data of improved accuracy with a recently published astrochronologic framework for the Niobrara Formation. New 40Ar/39Ar laser fusion ages corresponding to eight different ammonite biozones are determined by analysis of legacy samples, as well as newly collected material. These results are complemented by new U-Pb (zircon) chemical abrasion–isotope dilution–thermal ionization mass spectrometry ages from four biozones in the study interval. When combined with published radioisotopic data from the Cenomanian-Turonian boundary, paired 206Pb/238U and 40Ar/39Ar ages spanning Cenomanian to Campanian time support an astronomically calibrated Fish Canyon sanidine standard age of 28.201 Ma. Stage boundary ages are estimated via integration of new radioisotopic data with the floating astrochronology for the Niobrara Formation. The ages are determined by anchoring the long eccentricity bandpass from spectral analysis of the Niobrara Formation to radioisotopic ages with the lowest uncertainty proximal to the boundary, and adding or subtracting time by parsing the 405 k.y. cycles. The new stage boundary age determinations are: 89.75 ± 0.38 Ma for the Turonian-Coniacian, 86.49 ± 0.44 Ma for the Coniacian-Santonian, and 84.19 ± 0.38 Ma for the Santonian-Campanian boundary. The 2σ uncertainties for these estimates include systematic contributions from the radioisotopic measurements, astrochronologic methods, and geologic uncertainties (related to stratigraphic correlation and the presence of hiatuses). The latter geologic uncertainties have not been directly addressed in prior time scale studies and their determination was made possible by critical biostratigraphic observations. Each methodological approach employed in this study—new radioisotopic analysis, stratigraphic correlation, astrochronology, and ammonite and inoceramid biostratigraphy—was critical for achieving the final result.
Prospective Comparison of Flexibility Radiographs in Adolescent Idiopathic Scoliosis

Study Design. A prospective evaluation of radiographs in patients undergoing anterior spinal fusion or posterior spinal fusion for adolescent idiopathic scoliosis. Objective. To determine the most effective preoperative radiographic method for evaluating coronal plane flexibility by comparing preoperative and postoperative correction. Summary of Background Data. Curve flexibility is traditionally evaluated with side-bending radiographs. Recently, the fulcrum-bending radiograph was shown to provide better correction of thoracic curves undergoing posterior spinal fusion but was not evaluated in thoracolumbar/lumbar curves or in patients undergoing anterior spinal fusion. Methods. Preoperative coronal radiographs of 46 consecutive patients undergoing spinal fusion for adolescent idiopathic scoliosis obtained while standing, lying supine, side-bending (maximally bending while supine), push-prone (padded bolsters applied to chest wall while prone), and fulcrum-bending (curve apex suspended over a radiolucent fulcrum while lateral) were compared with standing postoperative radiographs. Cobb angles were determined and evaluated for statistical significance. Results. The fulcrum-bending radiograph demonstrated statistically better correction than other preoperative methods for main thoracic curves (P < 0.01) but fell short of demonstrating the correction obtained surgically. There was no statistical difference between side-bending, fulcrum-bending, or postoperative correction for thoracolumbar/lumbar curves (all P values > 0.07). The left side-bending was the most effective method for reducing upper thoracic curves (P < 0.001). There was no difference in the results obtained for curves corrected by anterior spinal fusion or anterior spinal fusion. Conclusion. To achieve maximal preoperative correction, thoracic fulcrum-bending radiographs should be obtained for evaluating main thoracic curves, whereas side-bending radiographs should continue to be used for evaluating both upper thoracic and thoracolumbar/lumbar curves.
Cloning and sequence analysis of czc genes in Alcaligenes sp. strain CT14.

We have isolated 14 cadmium (Cd)-resistant, soil-borne bacteria. Among those, strain CT14, which was identified as an Alcaligenes sp. , has a czc (cadmium, zinc, and cobalt divalent cation resistant determinant) system. Here we report the nucleotide sequence of 4 genes (czcCBAD) of the system. CzcCBA showed over 98% identity with those of A. eutrophus CH34, however, CzcD, the distal gene product, was 117 amino acids longer than that (199 amino acids) of A. eutrophus CH34, and had considerable similarity to the members of the CDF (cation diffusion facilitator) family proteins all over the region.
Jointly modelling the relationship between survival and pulmonary function in cystic fibrosis patients

Modelling the relationship between pulmonary function and survival in cystic fibrosis (CF) is complicated by the fact that measures of pulmonary function commonly used such as the forced expiratory volume in one second (FEV1) are measured with error, and patients with the poorest lung function are increasingly censored by death, that is, data are available only for the patients who have survived to the current age. We assume a linear random effects model for FEV1 per cent predicted, where the random intercept and slope of FEV1 per cent predicted, along with a specified transformation of the age at death follow a trivariate normal distribution. We illustrate how this model can be used to describe the relationship between age at death and parameters of the individual patient's regression of FEV1 per cent predicted versus age, such as the slope and the intercept or true value of FEV1 per cent predicted at a given age. We also illustrate how the model provides empirical Bayes estimates of these individual parameters. In particular, we explore how the predicted value of the age at death might be used as a prognostic or severity index. The model and methods are illustrated on a cohort of 188 cystic fibrosis patients with a common genotype (homozygous for the ΔF508 mutation), born on or after 1965 and followed at the CF Center at the Rainbow Babies and Children's Hospital, Cleveland, OH, U.S.A. Copyright © 2002 John Wiley & Sons, Ltd.
A Synergistically Enhanced T1–T2 Dual‐Modal Contrast Agent

Monodisperse Gd(2) O(3) -embedded iron oxide (GdIO) nanoparticles can simultaneously enhance the local magnetic field intensities of each other under an external magnetic field and result in synergistic enhancement of T(1) and T(2) effects. GdIO nanoparticles have the unique property to be both T(1) and T(2) contrast agents and can potentially lead to higher accuracy in cancer diagnosis, particularly liver tumors.
Epigenetics and child abuse: Modern‐day darwinism — The miraculous ability of the human genome to adapt, and then adapt again

It has long been recognized that early adversity can have life‐long consequences, and the extent to which this is true is gaining increasing attention. A growing body of literature implicates Adverse Childhood Experiences, including physical, sexual, and emotional abuse, in a broad range of negative health consequences including adult psychopathology, cardiovascular, and immune disease. Increasing evidence from animal, clinical, and epidemiological studies highlight the critical role of epigenetic programing, such as DNA methylation and histone modification, in altering gene expression, brain structure and function, and ultimately life‐course trajectories. This review outlines our developing insight into the interplay between our human biology and our changing environment, and explores the growing evidence base for how interventions may prevent and ameliorate damage inflicted by toxic stress in early life. © 2015 Wiley Periodicals, Inc.
Histologic signatures of thermal injury: Applications in transmyocardial laser revascularization and radiofrequency ablation

Cardiac treatments such as transmyocardial laser revascularization and radiofrequency ablation cause thermal injury. We sought to provide quantitative histologic methods of assessing such injury by using the inherent birefringence of cardiac muscle and collagen; specifically, to exploit the connection between thermal injury and the loss of birefringence.
Reduction of nitrosubstituted aromatic compounds by the halophilic anaerobic eubacteria Haloanaerobium praevalens and Sporohalobacter marismortui

The moderately halophilic, obligately anaerobic eubacteria Haloanaerobium praevalens DSM 2228 and Sporohalobacter marismortui ATCC 35420 are able to reduce a variety of nitrosubstituted aromatic compounds at a high rate to the corresponding amines. Compounds degraded included nitrobenzene, o-nitrophenol, m-nitrophenol, p-nitrophenol, nitroanilines, 2,4-dinitrophenol, and 2,4-dinitroaniline. Most of these compounds, when added at concentrations of 50 to 100 mg/liter, were completely transformed within 24 h, but at the highest concentrations growth rates were somewhat lowered. Growth of H. praevalens in the presence of 14C-labeled p-nitrophenol showed that the compound was not incorporated by the cells or degraded to acid-volatile compounds.
Intramodal palmprint recognition using texture feature 169

Palmprint technology is a new branch of biometrics used to identify an individual. Palmprint has rich set of features like palm lines, wrinkles, minutiae points, texture, ridges, etc. Several line and texture extraction techniques for palmprint have been extensively studied. This paper presents an intramodal authentication system based on texture information extracted from the palmprint using the Haralick features, 2D-Gabor and 2D-log Gabor filters. An individual feature vector is computed for a palmprint using the extracted texture information of each filter type. Performance of the system using three feature types is evaluated individually. Finally, we combine the three feature types using feature level fusion to develop an intramodal palmprint recognition system. The experiments are evaluated on a standard benchmark database (PolyU Database), and the results shows that significant improvement in terms of recognition accuracy and error rates with the proposed intramodal recognition system compared to individual representations.
Need for purely laboratory-based axionlike particle searches

The PVLAS signal has led to the proposal of many experiments searching for light bosons coupled to photons. The coupling strength probed by these near-future searches is, however, far from the allowed region, if astrophysical bounds apply. But the environmental conditions for the production of axionlike particles in stars are very different from those present in laboratories. We consider the case in which the coupling and the mass of an axionlike particle depend on environmental conditions such as the temperature and matter density. This can relax astrophysical bounds by several orders of magnitude, just enough to allow for the PVLAS signal. This creates exciting possibilities for a detection in near-future experiments.
High, Medium or Low? Detecting Intensity Variation Among polar synonyms in WordNet

For fine-grained sentiment analysis, we need to go beyond zero-one polarity and find a way to compare adjectives (synonyms) that share the same sense. Choice of a word from a set of synonyms, provides a way to select the exact polarity-intensity. For example, choosing to describe a person as benevolent rather than kind1 changes the intensity of the expression. In this paper, we present a sense based lexical resource, where synonyms are assigned intensity levels, viz., high, medium and low. We show that the measure P (s|w) (probability of a sense s given the word w) can derive the intensity of a word within the sense. We observe a statistically significant positive correlation between P(s|w) and intensity of synonyms for three languages, viz., English, Marathi and Hindi. The average correlation scores are 0.47 for English, 0.56 for Marathi and 0.58 for Hindi.
Advanced Control Strategy of DFIG Wind Turbines for Power System Fault Ride Through

This paper presents an advanced control strategy for the rotor and grid side converters of the doubly fed induction generator (DFIG) based wind turbine (WT) to enhance the low-voltage ride-through (LVRT) capability according to the grid connection requirement. Within the new control strategy, the rotor side controller can convert the imbalanced power into the kinetic energy of the WT by increasing its rotor speed, when a low voltage due to a grid fault occurs at, e.g., the point of common coupling (PCC). The proposed grid side control scheme introduces a compensation term reflecting the instantaneous DC-link current of the rotor side converter in order to smooth the DC-link voltage fluctuations during the grid fault. A major difference from other methods is that the proposed control strategy can absorb the additional kinetic energy during the fault conditions, and significantly reduce the oscillations in the stator and rotor currents and the DC bus voltage. The effectiveness of the proposed control strategy has been demonstrated through various simulation cases. Compared with conventional crowbar protection, the proposed control method can not only improve the LVRT capability of the DFIG WT, but also help maintaining continuous active and reactive power control of the DFIG during the grid faults.
Electro-Optically Tunable ${\rm As}_{2}{\rm S}_{3}$ Mach–Zehnder Interferometer on ${\rm LiNbO}_{3}$  Substrate

An electro-optically tunable vertically integrated As<sub>2</sub>S<sub>3</sub> Mach-Zehnder interferometer side coupled to a Ti-diffused waveguide on LiNbO<sub>3</sub> substrate was designed and fabricated. Asymmetric coplanar strip electrodes were placed along the As<sub>2</sub>S<sub>3</sub> path, which show strong electro-optic tuning capability, shifting the FSR of the interferometer. The tuning of the TM polarization with 7-mm-long electrodes having a 7-μm gap was observed with V<sub>π</sub>L = 15.9 V-cm, giving a tuning rate of 0.028 nm/V at 1530 nm. To our knowledge, this is the first demonstration of electro-optic tuning of an As<sub>2</sub>S<sub>3</sub> guided mode on LiNbO<sub>3</sub> substrate.
Hamstring Fatigue and Muscle Activation Changes During Six Sets of Nordic Hamstring Exercise in Amateur Soccer Players

Abstract Marshall, PWM, Lovell, R, Knox, MF, Brennan, SL, and Siegler, JC. Hamstring fatigue and muscle activation changes during six sets of Nordic hamstring exercise in amateur soccer players. J Strength Cond Res 29(11): 3124–3133, 2015—The Nordic hamstring exercise (NHE) is a bodyweight movement commonly prescribed to increase eccentric hamstring strength and reduce the incidence of strain injury in sport. This study examined hamstring fatigue and muscle activation responses throughout 6 sets of 5 repetitions of the NHE. Ten amateur-level soccer players performed a single session of 6 sets of 5 repetitions of NHE. Maximal eccentric and concentric torque output (in newton meters) was measured after every set. Hamstrings electromyograms (EMG) were measured during all maximal contractions and exercise repetitions. Hamstring maximal eccentric torque was reduced throughout the range of motion after only a single set of NHE between 7.9 and 17.1% (p ⩽ 0.05), with further reductions in subsequent sets. Similarly, maximal concentric torque reductions between 7.8 and 17.2% were observed throughout the range of motion after 1 set of NHE (p ⩽ 0.05). During the descent phase of the NHE repetitions, hamstring muscle activity progressively increased as the number of sets performed increased. These increases were observed in the first half of the range of motion. During the ascent phase, biceps femoris muscle activity but not medial hamstrings was reduced from the start of exercise during latter sets of repetitions. These data provide unique insight into the extent of fatigue induced from a bodyweight only exercise after a single set of 5 repetitions. Strength and conditioning coaches need to be aware of the speed and extent of fatigue induced from NHE, particularly in practical settings in which this exercise is now prescribed before sport-specific training sessions (i.e., the FIFA-11 before soccer training).
Percutaneous endoscopic gastrostomy (PEG): the role and perspective of nurses.

AIMS AND OBJECTIVES To study the perspectives of nurses on (i) the process of decision-making regarding the placement of feeding gastrostomies, (ii) their role in the process, (iii) the impact this participation has on them personally and (iv) gastrostomy placement in general. BACKGROUND The decision to commit patients to long-term feeding using a gastrostomy tube can be very difficult, particularly when the anticipated benefits are uncertain. Strategies to improve such decision-making are required. Nurses are in an excellent position to provide valuable insights regarding this decision-making and their increased participation in this process might substantially improve it. DESIGN A cross-sectional, exploratory design using in-depth semi-structured interviews and a self-administered questionnaire. METHODS In-depth semi-structured interviews with 17 nurses experienced in percutaneous endoscopic gastrostomy decision-making were undertaken and analysed. RESULTS Individuals making decisions regarding feeding gastrostomy placement were observed to be insufficiently informed regarding the device and the ramifications of its placement. Nurses were perceived to play an important, although underused, role in decisions to commit patients to long-term feeding. Participation in the making of these decisions may be stressful to nurses, particularly when the only result anticipated is the sustaining of a life of poor quality. Sixteen nurses reported that they would not want to have a gastrostomy for themselves if they were unable to maintain some quality of life. Strategies that could improve decision-making were suggested. CONCLUSIONS Decision-making could be improved by providing better information to decision makers. A team-orientated approach and more active dialogue with regard to care planning among health professionals, especially between doctors and nurses is needed. Effective decisions regarding feeding gastrostomy placement require adequate resources, especially sufficient time for caregivers to communicate effectively with those who must make these decisions. RELEVANCE TO CLINICAL PRACTICE The role of nurses in decision-making regarding commitments to long-term feeding using gastrostomy tubes could be effectively augmented.
Depressive psychopathology in male sleep apneics.

Depression has been reported to be frequent in sleep apnea syndromes. In a sample of 25 consecutive male sleep apneics, 40% met Research Diagnostic Criteria for an affective disorder or for alcohol abuse. A multiple regression analysis indicated that 61% of the variance in depression ratings could be explained by four variables: age, REM activity, REM latency (square root), and presence or absence of antihypertensive medications (multiple R = 0.78). The use of these variables in a discriminant function analysis correctly predicted the membership of 68% of the sample in either a low or high depression group (kappa = 0.44; p less than .01). These findings are reviewed in relation to other research on age-related sleep changes and vulnerability to depression.
SOME STUDIES ON THE EFFECT OF ANGIOTENSIN II ON ADRENOCORTICAL HORMONE SECRETION IN HYPOPHYSECTOMIZED RATS WITH RENAL PEDICLE LIGATION.

Infusion of angiotensin II into the jugular vein of hypophysectomized rats with ligated renal blood vessels generally resulted in an increase in aldosterone production, as measured by the secretion rate into adrenal vein blood. Hypophysectomy was performed one week before study. Measurements were done on the pooled blood of several animals by the soda fluorescence reaction and also on the blood of single animals by the double isotope derivative method. The change in aldosterone production was not clearly related to the dose of angiotensin or the change in blood pressure resulting from the infusion. Possible explanations for the variable results are discussed. Angiotensin II infusion either resulted in a small increase in corticosterone secretion which is not considered physiologically significant, or it had no effect. (Endocrinology 74: 325, 1964)
Data mining for simulation algorithm selection

While simulationists devise ever more efficient simulation algorithms for specific applications and infrastructures, the problem of automatically selecting the most appropriate one for a given problem has received little attention so far. One reason for this is the overwhelming amount of performance data that has to be analyzed for deriving suitable selection mechanisms. We address this problem with a framework for data mining on simulation performance data, which enables the evaluation of various data mining methods in this context. Such an evaluation is essential, as there is no best data mining algorithm for all kinds of simulation performance data. Once an effective data mining approach has been identified for a specific class of problems, its results can be used to select efficient algorithms for future simulation problems. This paper covers the components of the framework, the integration of external tools, and the re-formulation of the algorithm selection problem from a data mining perspective. Basic data mining strategies for algorithm selection are outlined, and a sample algorithm selection problem from Computational Biology is presented.