Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction and Initial Characterization of Escherichia coli Strains with Few or No Intact Chromosomal rRNA Operons

ABSTRACT The Escherichia coli genome carries seven rRNA (rrn) operons, each containing three rRNA genes. The presence of multiple operons has been an obstacle to many studies of rRNA because the effect of mutations in one operon is diluted by the six remaining wild-type copies. To create a tool useful for manipulating rRNA, we sequentially inactivated from one to all seven of these operons with deletions spanning the 16S and 23S rRNA genes. In the final strain, carrying no intact rRNA operon on the chromosome, rRNA molecules were expressed from a multicopy plasmid containing a single rRNA operon (prrn). Characterization of these rrndeletion strains revealed that deletion of two operons was required to observe a reduction in the growth rate and rRNA/protein ratio. When the number of deletions was extended from three to six, the decrease in the growth rate was slightly more than the decrease in the rRNA/protein ratio, suggesting that ribosome efficiency was reduced. This reduction was most pronounced in the Δ7 prrn strain, in which the growth rate, unlike the rRNA/protein ratio, was not completely restored to wild-type levels by a cloned rRNA operon. The decreases in growth rate and rRNA/protein ratio were surprisingly moderate in the rrndeletion strains; the presence of even a single operon on the chromosome was able to produce as much as 56% of wild-type levels of rRNA. We discuss possible applications of these strains in rRNA studies.
In Situ Sulfur Reduction and Intercalation of Graphite Oxides for Li‐S Battery Cathodes

Dr. S. Zheng, Dr. Z. Han, Prof. J. Yang School of Materials Science and Engineering University of Shanghai for Science and Technology Shanghai 200093 , China E-mail: jhyang@usst.edu. cn Dr. Y. Wen, Dr. Y. Zhu, Dr. J. Wang, Prof. C. Wang Department of Chemical and Biomolecular Engineering University of Maryland College Park , MD 20742 , USA E-mail: cswang@umd.edu Dr. J. Wang School of Materials Science and Engineering Jiamusi University Jiamusi 154007 , China
Characteristics of growth hormone secretion responsiveness to growth hormone-releasing peptide-2 (GHRP-2 or KP102) in calves.

This study was conducted to determine the effects of acute and chronic administration of GH-releasing peptide-2 (D-Ala-D-beta Nal-Ala-Trp-D-Phe-Lys-NH2, GHRP-2 or KP102) on GH responsiveness in male Holstein calves. In the dose response study of acute administration, six calves were injected iv with saline or 6.25, 12.5 and 25.0 micrograms/kg body weight (BW) of KP102. The GH AUC (area under curve, ng/ml.min, mean +/- SEM) for 60 min was significantly increased with 6.25 (676.3 +/- 125.6), 12.5 (1574.8 +/- 318.0) and 25.0 (1578.7 +/- 214.6) micrograms/kgBW of KP102 than with saline (78.6 +/- 36.1) (P < 0.01). GH responses were decreased by multiple injections of 12.5 micrograms/kgBW KP102 at every 2 h for 8 h. The GH AUC for 60 min was decreased from the first injection (1162.9 +/- 313.3) to the second injection (604.7 +/- 131.9), but the response was significantly higher for the first and second injections than the third (304.4 +/- 173.1) and fourth injections (320.7 +/- 144.2) (P < 0.05). In the chronic administration, 8 calves were implanted subcutaneously with osmotic pumps (Alzet pump). Each of the 4 calves was given with 12.5 micrograms/kgBW per hour KP102 and the other 4 calves served as the control. During the 14 day period, average daily gain was significantly increased (36.4%) over the control (P < 0.05). Food efficiency was not significant, but numerically higher (29.4%) than the control. The plasma GH concentration was not increased by chronic administration of KP102, but IGF-I appeared to increase in KP102-treated calves more than the control. These results suggest that the synthetic KP102 can be used for enhancing the growth performance in domestic animals.
Identification of a Novel Trimeric Autotransporter Adhesin in the Cryptic Genospecies of Haemophilus

ABSTRACT Haemophilus biotype IV strains belonging to the recently recognized Haemophilus cryptic genospecies are an important cause of maternal genital tract and neonatal systemic infections and initiate infection by colonizing the genital or respiratory epithelium. To gain insight into the mechanism of Haemophilus cryptic genospecies colonization, we began by examining prototype strain 1595 and three other strains for adherence to genital and respiratory epithelial cell lines. Strain 1595 and two of the three other strains demonstrated efficient adherence to all of the cell lines tested. With a stably adherent variant of strain 1595, we generated a Mariner transposon library and identified 16 nonadherent mutants. All of these mutants lacked surface fibers and contained an insertion in the same open reading frame, which encodes a 157-kDa protein designated Cha for cryptic haemophilus adhesin. Analysis of the predicted amino acid sequence of Cha revealed the presence of an N-terminal signal peptide and a C-terminal domain bearing homology to YadA-like and Hia-like trimeric autotransporters. Examination of the C-terminal 120 amino acids of Cha demonstrated mobility as a trimer on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the capacity to present the passenger domain of the Hia trimeric autotransporter on the bacterial surface. Southern analysis revealed that the gene that encodes Cha is conserved among clinical isolates of the Haemophilus cryptic genospecies and is absent from the closely related species Haemophilus influenzae. We speculate that Cha is important in the pathogenesis of disease due to the Haemophilus cryptic genospecies and is in part responsible for the apparent tissue tropism of this organism.
Mechanistic insights into molecular evolution of species-specific differential glycosaminoglycan binding surfaces in growth-related oncogene chemokines

Chemokines are chemotactic cytokines involved in leucocyte trafficking to infected tissue. Growth-related oncogene (GRO) chemokines namely CXCL1, CXCL2 and CXCL3 are neutrophil activating chemokines sharing a conserved three-dimensional structure, but encompassing functional diversity due to gene duplication and evolutionary events. However, the evolutionary mechanisms including selection pressures involved in diversification of GRO genes have not yet been characterized. Here, we performed comprehensive evolutionary analysis of GRO genes among different mammalian species. Phylogenetic analysis illustrated a species-specific evolution pattern. Selection analysis evidenced that these genes have undergone concerted evolution. Seventeen positively selected sites were obtained, although the majority of the protein is under purifying selection. Interestingly, these positively selected sites are more concentrated on the C-terminal/glycosaminoglycan (GAG) binding and dimerization segment compared to receptor binding domain. Substitution rate analysis confirmed the C-terminal domain of GRO genes as the highest substituted segment. Further, structural analysis established that the nucleotide alterations in the GAG binding domain are the source of surface charge modulation, thus generating the differential GAG binding surfaces and multiple binding sites as per evolutionary pressure, although the helical surface is primordial for GAG binding. Indeed, such variable electrostatic surfaces are crucial to regulate chemokine gradient formation during a host's defence against pathogens and also explain the significance of chemokine promiscuity.
Voice source features for forensic voice comparison - an evaluation of the GLOTTEX software package

GLOTTEX R ⃝ is a software package which extracts information about voice source properties, including estimates of properties related to physical structures of the vocal folds. It has been proposed that the output of GLOTTEX R ⃝ can be used as part of a forensic-voice-comparison system. We test this using manually labeled segments from a database of voice recordings of 60 female Chinese speakers. Performance was assessed relative to a baseline MFCC GMM-UBM system. GMM-UBM systems based on features extracted by GLOTTEX R ⃝ were combined with the baseline system using logistic-regression fusion. System performance was assessed in three channel conditions: high-quality v high-quality, mobile-to-landline v mobileto-landline, and mobile-to-landline v high-quality. Substantial improvements over the baseline system were not observed.
Association of 25-Hydroxyvitamin D with Liver Cancer Incidence and Chronic Liver Disease Mortality in Finnish Male Smokers of the ATBC Study

Background: Although circulating 25-hydroxyvitamin D [25(OH)D] concentrations were linked to liver cancer and chronic liver disease (CLD) in laboratory studies, few epidemiologic studies have addressed the associations. Methods: Within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study, we measured 25(OH)D in baseline serum of 202 incident liver cancer cases and 225 CLD deaths that occurred during nearly 25 years of follow-up, and 427 controls. ORs and 95% confidence intervals (CIs) were estimated using unconditional logistic regression. We examined predetermined clinically defined cut-points, and season-specific and season-standardized quartiles. Results: Low serum 25(OH)D concentrations were associated with higher risk of liver cancer (<25 nmol/L vs. ≥50 nmol/L: 1.98; 95% CI, 1.22–3.20; Ptrend across categories = 0.003) and CLD mortality (1.93; 95% CI, 1.23–3.03; Ptrend = 0.006) in models adjusted for age and date of blood draw. After additional adjustment for body mass index, diabetes, smoking, and other potential confounders, the association remained statistically significant for liver cancer (1.91; 95% CI, 1.16–3.15; Ptrend = 0.008), but was somewhat attenuated for CLD mortality (1.67; 95% CI, 1.02–2.75; Ptrend = 0.05). Associations were similar for analyses using season-specific and season-standardized quartiles, and after excluding participants with diabetes, or hepatitis B or C. Conclusions: Our results suggest a possible preventive role for vitamin D against liver cancer and CLD, although the importance of the liver for vitamin D metabolism and the lack of information about underlying liver disease makes reverse causality a concern. Impact: Future studies are needed to evaluate associations of vitamin D with liver cancer and liver disease in other populations, particularly those with a different constellation of risk factors. Cancer Epidemiol Biomarkers Prev; 27(9); 1075–82. ©2018 AACR.
Effects of Integrated Use of Prilled Urea, Urea Super Granule and Poultry Manure on Yield of Transplant Aus Rice and Field Water Quality

A field experiment was carried out to investigate the effects of prilled urea (PU) and urea super granule (USG) alone and their combinations with poultry manure (PM) on growth and yield of transplant Aus rice (cv. BR 21) and field water quality. The experiment was laid out in a Randomized Complete Block Design (RCBD) with three replications. The treatments were T1: Control (no fertilizer), T2: (165 kg N ha-1 from prilled urea), T3: (119 kg N ha-1 from USG), T4: (82 kg N ha-1 from prilled urea + 3 t ha-1 poultry manure) and T5: (56 kg N ha-1 from USG + 3 t ha-1 poultry manure). The highest grain (3.19 tha-1) and straw yields (4.51tha-1) were obtained from treatment T5 (56 kg N ha-1 USG + 3.0 t ha-1 poultry manure) while the lowest grain (1.99 tha-1) and straw yield (3.38 tha-1) were recorded for T1 (control). Treatment T3 (119 kg N ha-1 from USG) performed better than T2 and T4 indicating the superior effect of USG over prilled urea. The N, P, K and S contents in the grain and straw and their total uptake were influenced profoundly due to application of PU, USG alone or in combination with poultry manure. In case of rice field water quality, the USG generated available NH4-N slowly but spontaneously over the entire growth period compared to prilled urea indicating a beneficial role of USG. The other properties of field water like pH, EC were also influenced by the application of prilled urea, USG and poultry manure. The overall results indicate that application of USG in combination with poultry manure was more effective in producing higher rice yield and at the same time reduce water pollution. (Nusrat Jahan, Md. Rafiqul Islam, A. B. Siddique, M. Rafiqul Islam, M. M. Hasan, S. M. Shamsuzzaman and A. W. Samsuri. Effects of Integrated Use of Prilled Urea, Urea Super Granule and Poultry Manure on Yield of Transplant Aus Rice and Field Water Quality. Life Sci J 2014;11(8):101-108). (ISSN:1097-8135). http://www.lifesciencesite. com. 14
Design principles for phase-splitting behaviour of coupled cellular oscillators: clues from hamsters with ‘split’ circadian rhythms

Nonlinear interactions among coupled cellular oscillators are likely to underlie a variety of complex rhythmic behaviours. Here we consider the case of one such behaviour, a doubling of rhythm frequency caused by the spontaneous splitting of a population of synchronized oscillators into two subgroups each oscillating in anti-phase (phase-splitting). An example of biological phase-splitting is the frequency doubling of the circadian locomotor rhythm in hamsters housed in constant light, in which the pacemaker in the suprachiasmatic nucleus (SCN) is reconfigured with its left and right halves oscillating in anti-phase. We apply the theory of coupled phase oscillators to show that stable phase-splitting requires the presence of negative coupling terms, through delayed and/or inhibitory interactions. We also find that the inclusion of real biological constraints (that the SCN contains a finite number of non-identical noisy oscillators) implies the existence of an underlying non-uniform network architecture, in which the population of oscillators must interact through at least two types of connections. We propose that a key design principle for the frequency doubling of a population of biological oscillators is inhomogeneity of oscillator coupling.
AI safety via debate

To make AI systems broadly useful for challenging real-world tasks, we need them to learn complex human goals and preferences. One approach to specifying complex goals asks humans to judge during training which agent behaviors are safe and useful, but this approach can fail if the task is too complicated for a human to directly judge. To help address this concern, we propose training agents via self play on a zero sum debate game. Given a question or proposed action, two agents take turns making short statements up to a limit, then a human judges which of the agents gave the most true, useful information. In an analogy to complexity theory, debate with optimal play can answer any question in PSPACE given polynomial time judges (direct judging answers only NP questions). In practice, whether debate works involves empirical questions about humans and the tasks we want AIs to perform, plus theoretical questions about the meaning of AI alignment. We report results on an initial MNIST experiment where agents compete to convince a sparse classifier, boosting the classifier's accuracy from 59.4% to 88.9% given 6 pixels and from 48.2% to 85.2% given 4 pixels. Finally, we discuss theoretical and practical aspects of the debate model, focusing on potential weaknesses as the model scales up, and we propose future human and computer experiments to test these properties.
Impact of Fault-Prone Components on Effective Software Testing: An Industrial Survey

In a real-time software system, often a small portion of the components holds the major operations of the system. Thus, the rate of failure of those portions is high, which leads to major loss to the system. In order to develop cost-effective and high-quality software systems, those fault-prone components must be identified and tested rigorously. This paper analyzes the industrial questionnaire survey with a focus on the significance of early identification of fault-prone components within a system and importance of the fault-prone components-based testing. From the survey results, it has been inferred that, fault-prone components can be identified using software models, formal specifications and appropriate metrics and measures; which would, in turn, reduce the cost of defect and testing. Furthermore, the present study endeavours to investigate as to how far research efforts are essential in providing guidelines in the adoption of fault-prone components-based development, thus improving the quality of software development.
Endocrine outcomes with proton and photon radiotherapy for standard risk medulloblastoma.

BACKGROUND Endocrine dysfunction is a common sequela of craniospinal irradiation (CSI). Dosimetric data suggest that proton radiotherapy (PRT) may reduce radiation-associated endocrine dysfunction but clinical data are limited. METHODS Seventy-seven children were treated with chemotherapy and proton (n = 40) or photon (n = 37) radiation between 2000 and 2009 with ≥3 years of endocrine screening. The incidence of multiple endocrinopathies among the proton and photon cohorts is compared. Multivariable analysis and propensity score adjusted analysis are performed to estimate the effect of radiotherapy type while adjusting for other variables. RESULTS The median age at diagnosis was 6.2 and 8.3 years for the proton and photon cohorts, respectively (P = .010). Cohorts were similar with respect to gender, histology, CSI dose, and total radiotherapy dose and whether the radiotherapy boost was delivered to the posterior fossa or tumor bed. The median follow-up time was 5.8 years for proton patients and 7.0 years for photon patients (P = .010). PRT was associated with a reduced risk of hypothyroidism (23% vs 69%, P < .001), sex hormone deficiency (3% vs 19%, P = .025), requirement for any endocrine replacement therapy (55% vs 78%, P = .030), and a greater height standard deviation score (mean (± SD) -1.19 (± 1.22) vs -2 (± 1.35), P = . 020) on both univariate and multivariate and propensity score adjusted analysis. There was no significant difference in the incidence of growth hormone deficiency (53% vs 57%), adrenal insufficiency (5% vs 8%), or precocious puberty (18% vs 16%). CONCLUSIONS Proton radiotherapy may reduce the risk of some, but not all, radiation-associated late endocrine abnormalities.
Self-Selected Training Load and RPE During Resistance and Aerobic Training Among Recreational Exercisers

This study compared training load and ratings of perceived exertion (RPE) during resistance training (RT) and aerobic training (AT) sessions at self-selected intensity. Participants were 54 recreationally trained subjects assigned to either RT or AT groups. During RT, participants performed three sets of 10 repetitions of each exercise at a self-selected intensity (load). After RT completion, participants performed one repetition maximum (1RM) and 10RM tests. During AT, participants performed a treadmill exercise at a self-selected intensity and duration (velocity and time). After AT completion, participants performed a treadmill maximal exercise test using a ramp protocol. During RT, subjects chose an intensity (43.6%–60.2% 1RM) below typical training recommendations, and RPE increased in successive exercise sets. During AT, participants chose an intensity (83.9% Heart Ratepeak) in line with typical training recommendations, and RPE increased from the first to second quartile of the session (from a mean of 3.9, standard deviation [SD] = 1.7 to a mean of 5.4, SD = 1.7; p < .05) and remained stable thereafter. These recreationally trained participants self-selected lower RT intensities than are typically recommended for strength and hypertrophy increases (>67% 1RM) and AT intensities in line with typically recommended intensity (64%–95% HRmax) for cardiovascular fitness increases. Thus, for recreational trained individuals to perform RT at recommended intensities, specific instruction will be required.
Arc-length-based axial deformation and length preserved animation

In real life, some objects may deform along axial curves and the lengths of their skeletons usually remain constant during the axial deformation, such as a swimming fish, a swaying tree, etc. This paper presents a practical approach of arc-length-based axial deformation and axial-length-preserved animation. The space spanned by the arc-length parameter and the rotation-minimizing frame on the axis is taken as the embedding space. During animation, the keyframe axial curves are consistently approximated by polylines after sufficient subdivisions and both the edge lengths and the directional vertex angles of the keyframe polylines (or unit edge vectors) are then interpolated to generate the intermediate polylines which are regarded as the discrete expressions of the intermediate axes. Experiments show that our method is very useful, intuitive and easy to control.
beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types

Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R. These alternative representations are not easily compatible with high-performance C++ code used for computationally intensive tasks in existing R/Bioconductor packages. Here, we describe a C++ interface named beachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with dense, sparse and file-backed matrices, amongst others. We evaluated the performance of beachmat for accessing data from each matrix representation using both simulated and real scRNA-seq data, and defined a clear memory/speed trade-off to motivate the choice of an appropriate representation. We also demonstrate how beachmat can be incorporated into the code of other packages to drive analyses of a very large scRNA-seq data set.