Miracle-dz/UniFAR-FTUs huggingface dataset:
Photochemical syn–anti Isomerization Reactions in N2‐Hydroxyisocytosines—An Experimental Matrix Isolation and Theoretical Study ¶

N2‐hydroxyisocytosine and 1‐methyl‐N2‐hydroxyisocytosine were studied using a matrix isolation technique combined with infrared absorption spectroscopy. For N2‐hydroxyisocytosine isolated in an Ar matrix (at 10 K), two imino–oxo isomers, one with the hydroxyimino =N–OH group directed toward the N1–H group (the form called further anti) and the second with the =N–OH group directed toward N3–H (syn), were observed in the ratio 1.4:1. The syn isomer is converted totally to the anti form after UV (λ > 295 nm) irradiation of the matrix. A small amount of the N( 3 )H‐hydroxy–amino tautomer of N2‐hydroxyisocytosine was also detected in the matrix. This form did not react photochemically. For 1‐methyl‐N2‐hydroxyisocytosine, only the syn form of the imino–oxo tautomer was observed after deposition of the matrix. UV (λ > 295 nm) irradiation induced a photoreaction converting this isomer into the anti form. After 15% of the starting material had been converted into the product, a photostationary state was achieved, and no further progress of the reaction was observed. Subsequent UV irradiation (λ > 335 nm) caused a back reaction, leading to a disappearance of the anti form and to the recovery of the initial syn isomer. All isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6‐31G(d,p) level, where DFT is the density functional theory. Good agreement between the observed and predicted patterns of the spectral lines allowed for reliable identification. The experimental IR spectra were interpreted and discussed. The relative energies of the 12 isomers of N2‐hydroxyisocytosine were calculated at the MP2/6‐31G(d,p) and MP4//MP2/6‐31G(d,p) levels. For six isomers of 1‐methyl‐N2‐hydroxyisocytosine, the calculations were carried out at the MP2/6‐31G(d,p) level. The anti form of the imino–oxo tautomer of N2‐hydroxyisocytosine and the syn form of the imino–oxo tautomer of 1‐methyl‐N2‐hydroxyisocytosine were predicted to be the most stable.
Prognostic factors in non-small cell lung cancer: a decade of progress.

STUDY OBJECTIVES To provide a systematic overview of the literature investigating patient and tumor factors that are predictive of survival for patients with non-small cell lung cancer (NSCLC), and to analyze patterns in the design of these studies in order to highlight problematic aspects of their design and to advocate for appropriate directions of future studies. DESIGN A systematic search of the MEDLINE database and a synthesis of the identified literature. MEASUREMENTS AND RESULTS The database search (January 1990 to July 2001) was carried out combining the MeSH terms prognosis and carcinoma, nonsmall cell lung. Eight hundred eighty-seven articles met the search criteria. These studies identified 169 prognostic factors relating either to the tumor or the host. One hundred seventy-six studies reported multivariate analyses. Concerning 153 studies reporting a multivariate analysis of prognostic factors in patients with early-stage NSCLC, the median number of patients enrolled per study was 120 (range, 31 to 1,281 patients). The median number of factors reported to be significant in univariate analyses was 4 (range, 2 to 14 factors). The median number of factors reported to be significant in multivariate analyses per study was 2 (range, 0 to 6 factors). The median number of studies examining each prognostic factor was 1 (range, 1 to 105 studies). Only 6% of studies addressed clinical outcomes other than patient survival. CONCLUSIONS While the breadth of prognostic factors studied in the literature is extensive, the scope of factors evaluated in individual studies is inappropriately narrow. Individual studies are typically statistically underpowered and are remarkably heterogeneous with regard to their conclusions. Larger studies with clinically relevant modeling are required to address the usefulness of newly available prognostic factors in defining the management of patients with NSCLC.
Reinforcement Learning in Rich-Observation MDPs using Spectral Methods

Reinforcement learning (RL) in Markov decision processes (MDPs) with large state spaces is a challenging problem. The performance of standard RL algorithms degrades drastically with the dimensionality of state space. However, in practice, these large MDPs typically incorporate a latent or hidden low-dimensional structure. In this paper, we study the setting of rich-observation Markov decision processes (ROMDP), where there are a small number of hidden states which possess an injective mapping to the observation states. In other words, every observation state is generated through a single hidden state, and this mapping is unknown a priori. We introduce a spectral decomposition method that consistently learns this mapping, and more importantly, achieves it with low regret. The estimated mapping is integrated into an optimistic RL algorithm (UCRL), which operates on the estimated hidden space. We derive finite-time regret bounds for our algorithm with a weak dependence on the dimensionality of the observed space. In fact, our algorithm asymptotically achieves the same average regret as the oracle UCRL algorithm, which has the knowledge of the mapping from hidden to observed spaces. Thus, we derive an efficient spectral RL algorithm for ROMDPs.
Isolation and characterization of Bacillus subtilis mutants blocked in the synthesis of pantothenic acid

We have produced and characterized by physiological and enzymatic analyses pantothenate (pan) auxotrophs of Bacillus subtilis. panB auxotrophs are deficient in ketopantoate hydroxymethyltransferase, whereas panE mutants lack ketopantoic acid reductase. The pan mutations were mapped by phage PBS1-mediated two-factor crosses and found to be located in the interval purE-tre of the genetic map of B. subtilis.
Model Predictive Control for Stochastic Resource Allocation

In this paper, we consider a class of stochastic resource allocation problems where resources assigned to a task may fail probabilistically to complete assigned tasks. Failures to complete a task are observed before new resource allocations are selected. The resulting temporal resource allocation problem is a stochastic control problem, with a discrete state space and control space that grow in cardinality exponentially with the number of tasks. We modify this optimal control problem by expanding the admissible control space, and show that the resulting control problem can be solved exactly by efficient algorithms in time that grows nearly linear with the number of tasks. The approximate control problem also provides a bound on the achievable performance for the original control problem. The approximation is used as part of a model predictive control (MPC) algorithm to generate resource allocations over time in response to information on task completion status. We show in computational experiments that, for single resource class problems, the resulting MPC algorithm achieves nearly the same performance as the optimal dynamic programming algorithm while reducing computation time by over four orders of magnitude. In multiple resource class experiments involving 1000 tasks, the model predictive control performance is within 4% of the performance bound obtained by the solution of the expanded control space problem.
Fairness based admission control and beamforming design for the MISO downlink

This paper studies fairness problem concerning admission control and beamforming design in the multiple-input-and-single-output (MISO) downlink channel with various users: guaranteed users (GUs) who have the requirements on individual signal-to-interface-noise ratios (SINR) and best-effort users (BUs) who have no such requirements. The problem is modeled as maximizing the worst SINR of BUs while meeting SINR requirements of GUs and limiting total power of base station (BS). We figure out feasibility of the problem with solving the max-min-weighted-fairness (MMWF) problem. If it is feasible, we propose a heuristic removal algorithm to turn the infeasible problem into a feasible one; otherwise, we study the relation between the feasible problem and the MMWF problem by introducing auxiliary variables. Based on that relation, a fixed-point iterative algorithm converging to the optimal solution is proposed to solve the feasible problem. Besides, the algorithm can be implemented distributively. Simulation results reveal the effectiveness of the heuristic removal algorithm, and the optimality and fast convergence of the fixed-point iterative algorithm.
Calculation and experimental verification of the RBE-weighted dose for scanned ion beams in the presence of target motion

We present an algorithm suitable for the calculation of the RBE-weighted dose for moving targets with a scanned particle beam. For verification of the algorithm, we conducted a series of cell survival measurements that were compared to the calculations. Calculation of the relative biological effectiveness (RBE) with respect to tumor motion was included in the treatment planning procedure, in order to fully assess its impact on treatment delivery with a scanned ion beam. We implemented an algorithm into our treatment planning software TRiP4D which allows determination of the RBE including its dependence on target tissue, absorbed dose, energy and particle spectra in the presence of organ motion. The calculations are based on time resolved computed tomography (4D-CT) and the corresponding deformation maps. The principal of the algorithm is illustrated in in silico simulations that provide a detailed view of the different compositions of the energy and particle spectra at different target positions and their consequence on the resulting RBE. The calculations were experimentally verified with several cell survival measurements using a dynamic phantom and a scanned carbon ion beam. The basic functionality of the new dose calculation algorithm has been successfully tested in in silico simulations. The algorithm has been verified by comparing its predictions to cell survival measurements. Four experiments showed in total a mean difference (standard deviation) of −1.7% (6.3%) relative to the target dose of 9 Gy (RBE). The treatment planning software TRiP is now capable to calculate the patient relevant RBE-weighted dose in the presence of target motion and was verified against cell survival measurements.
Forced-outage rates of generating units based on expert evaluation

The uncertainties relating to the forced outage rates (FOR) of power system generating units are important in studies such as long-term generation expansion planning. These uncertainties might be better understood by experts in the field. Expert evaluations can be modeled with fuzzy set theory, and the fuzzy-FOR so calculated reflects the conditions of operation and maintenance of the units more realistically.
Functional Characterization of an α-Factor-Like Sordaria macrospora Peptide Pheromone and Analysis of Its Interaction with Its Cognate Receptor in Saccharomyces cerevisiae

ABSTRACT The homothallic filamentous ascomycete Sordaria macrospora possesses genes which are thought to encode two pheromone precursors and two seven-transmembrane pheromone receptors. The pheromone precursor genes are termed ppg1 and ppg2. The putative products derived from the gene sequence show structural similarity to the α-factor precursors and a-factor precursors of the yeast Saccharomyces cerevisiae. Likewise, sequence similarity has been found between the putative products of the pheromone receptor genes pre2 and pre1 and the S. cerevisiae Ste2p α-factor receptor and Ste3p a-factor receptor, respectively. To investigate whether the α-factor-like pheromone-receptor pair of S. macrospora is functional, a heterologous yeast assay was used. Our results show that the S. macrospora α-factor-like pheromone precursor PPG1 is processed into an active pheromone by yeast MATα cells. The S. macrospora PRE2 protein was demonstrated to be a peptide pheromone receptor. In yeast MATa cells lacking the endogenous Ste2p receptor, the S. macrospora PRE2 receptor facilitated all aspects of the pheromone response. Using a synthetic peptide, we can now predict the sequence of one active form of the S. macrospora peptide pheromone. We proved that S. macrospora wild-type strains secrete an active pheromone into the culture medium and that disruption of the ppg1 gene in S. macrospora prevents pheromone production. However, loss of the ppg1 gene does not affect vegetative growth or fertility. Finally, we established the yeast assay as an easy and useful system for analyzing pheromone production in developmental mutants of S. macrospora.
Sperm motility patterns and metabolism in Catalonian donkey semen

The Sperm-Class Analyzer detected four subpopulations of spermatozoa with different motility characteristics in the ejaculate of the Catalonian donkey. Significant differences (P < 0.001) in the distribution of these subpopulations, as well as in total sperm number and percentage total motility, were seen in the diluted semen of four sampled donkeys. All the ejaculates evaluated showed excellent semen quality characteristics; the sperm they contained was more rapid than horse sperm. Principal components analysis showed sperm L-lactate production to be a good predictor of semen condition. This, plus the characteristics of the motility patterns of the different sperm subpopulations, provides an excellent overall indicator of semen quality. # 2004 Elsevier Inc. All rights reserved.
Coronin-1 and Calcium Signaling Governs Sympathetic Final Target Innervation

Development of a functional peripheral nervous system requires axons to rapidly innervate and arborize into final target organs and then slow but not halt their growth to establish stable connections while keeping pace with organ growth. Here we examine the role of the NGF-TrkA effector protein, Coronin-1, on postganglionic sympathetic neuron final target innervation. In the absence of Coronin-1 we find that NGF-TrkA-PI3K signaling drives robust axon growth and branching in part by suppressing GSK3β. In contrast, the presence of Coronin-1 (wild-type neurons) suppresses but does not halt NGF-TrkA-dependent growth and branching. This relative suppression in axon growth behaviors is due to Coronin-1-dependent calcium release via PLC-γ1 signaling, which releases PI3K-dependent suppression of GSK3β. Finally, we demonstrate that Coro1a−/− mice display sympathetic axon overgrowth and overbranching phenotypes in the developing heart. Together with previous work demonstrating the Coronin-1 expression is NGF dependent, this work suggests that periods before and after NGF-TrkA-induced Coronin-1 expression (and likely other factors) defines two distinct axon growth states, which are critical for proper circuit formation in the sympathetic nervous system.
An Intelligent Powered Wheelchair to Enable Mobility of Cognitively Impaired Older Adults: An Anticollision System

Older adults with cognitive impairments are generally prohibited from using powered wheelchairs, because of the high risk of collisions with people and objects. This paper describes and presents the preliminary results of a system that uses an infrared sensor to provide anticollision and a prompting system for a powered wheelchair that helps guide the user safely past obstacles. Trials with the prototyped system detected collisions and stopped the chair in 95% of trials with an object and generated no false alarms
A Robust Audio Fingerprinting Algorithm in MP3 Compressed Domain

In this paper, a new robust audio fingerprinting algorithm in MP3 compressed domain is proposed with high robustness to time scale modification (TSM). Instead of simply employing short-term information of the MP3 stream, the new algorithm extracts the long-term features in MP3 compressed domain by using the modulation frequency analysis. Our experiment has demonstrated that the proposed method can achieve a hit rate of above 95% in audio retrieval and resist the attack of 20% TSM. It has lower bit error rate (BER) performance compared to the other algorithms. The proposed algorithm can also be used in other compressed domains, such as AAC. Keywords—Audio Fingerprinting, MP3, Modulation Frequency, TSM
Some HIV Antiretrovirals Increase Oxidative Stress and Alter Chemokine, Cytokine or Adiponectin Production in Human Adipocytes and Macrophages

Objectives Adipose tissue from patients with HIV-related lipodystrophy presents a state of chronic inflammation. Altered expression of cytokines/adipokines and macrophage infiltration could be involved in patients’ insulin resistance and lipoatrophy. We tested whether antiretrovirals affected adipokine release by human subcutaneous adipocytes and cytokine/chemokine production by human macrophages and examined whether reactive oxygen species (ROS) hyperproduction was related to the effect of antiretrovirals. Methods Differentiated human adipocytes and PMA-THP-1 macrophages were treated with protease inhibitors (PIs: indinavir, nelfinavir, amprenavir, lopinavir, ritonavir and atazanavir) or nucleoside reverse transcriptase inhibitors (NRTIs: stavudine, zidovudine and abacavir) for 24–48 h without or with diphenylene iodonium (DPI), an inhibitor of oxidative stress. Lipid content was assessed by Oil Red O staining and ROS production by nitroblue tetrazolium (NBT) reduction. Cytokine/chemokines, adiponectin and leptin release was evaluated by ELISA or multiplex assays. Results In human adipocytes, PIs and NRTIs (except amprenavir, atazanavir and abacavir) reduced lipid content, adiponectin and leptin release and increased in parallel ROS production and monocyte chemoattractant protein (MCP)-1 and interleukin (IL)-6 release. The effects of PIs, but not of NRTIs, were prevented by the addition of DPI. In PMA-THP-1 macrophages, all PIs, but no NRTI, increased macrophage inflammatory protein-1α and MCP-1 release. Lopinavir, nelfinavir, zidovudine and stavudine markedly increased ROS production and release of IL-1β and tumour necrosis factor-α. Conclusions Some PIs altered adipokine secretion and lipid content through ROS production in human subcutaneous adipocytes. Thymidine analogues altered adipocyte functions but their effect on adipokine secretion was not reverted by ROS production inhibition. Increased chemokine/cytokine production by adipocytes and macrophages could be involved in macrophage recruitment and participate in lipoatrophy and insulin resistance.
Multilayer Cluster Based Energy Efficient Routing Protocol for Wireless Sensor Networks

Wireless sensor networks (WSNs) are one of the most promising technologies and have immense potential in both the military and civil field. WSNs offer a range of challenges for scientists and engineers of today. The biggest challenge among all is the energy constraint of these networks. In this context, various schemes have been presented in order to improve the life time of these networks and to overcome the energy constraint. One of the effective schemes is based on clustering of sensor nodes within a network in order to improve the network life time and decrease communication latency. Clustering algorithms are believed to be the best for wireless sensor networks because they work on the principle of divide and conquer. This paper includes a brief survey of various existing clustering algorithms and present a new clustering algorithm based on nondetermistic finite automata which further divides the communication between cluster heads into multihop by using a few nodes from each cluster. Performance studies indicate that the proposed algorithm is more efficient in terms of energy consumption and network connectivity.
Syndesmotic Fixation in Supination-External Rotation Ankle Fractures

Background: This study compared mid-term functional and radiologic results of syndesmotic transfixation with no fixation in supination external rotation (SER) ankle fractures with intraoperatively confirmed syndesmosis disruption. Our hypothesis was that early-stage good functional results would remain and unfixed syndesmosis disruption in SER IV ankle fractures would not lead to an increased incidence of osteoarthritis. Methods: A prospective study of 140 operatively treated patients with Lauge-Hansen SER IV (Weber B) ankle fractures was performed. After bony fixation, the 7.5-Nm standardized external rotation stress test for both ankles was performed under fluoroscopy. A positive stress examination was defined as a difference of more than 2 mm side-to-side in the tibiotalar or tibiofibular clear spaces on mortise radiographs. The patients were randomized to either syndesmotic screw fixation (13 patients) or no syndesmotic fixation (11 patients). After a minimum of 4 years of follow-up (mean, 58 months), ankle function and pain (Olerud-Molander, a 100-mm visual analogue scale [VAS] for ankle function and pain) and quality of life (RAND-36) of all 24 patients were assessed. Ankle joint congruity and osteoarthritis were assessed using mortise and lateral projection plain weight-bearing radiographs and magnetic resonance imaging (MRI; 3T) scans. Results: Improvement in Olerud-Molander score, VAS, and RAND-36 showed no significant difference between groups during the follow-up. In the syndesmotic transfixation group, improvements in all functional parameters and pain measurements were not significant, whereas in the group without syndesmotic fixation, the Olerud-Molander score improved from 84 to 93 (P = .007) and the pain (VAS) score improved from 11 to 4 (P = .038) from 1 year to last follow-up. X-ray or MRI imaging showed no difference between groups at the last follow-up visit. Conclusion: With the numbers available, no significant difference in functional outcome or radiologic findings could be detected between syndesmosis transfixation and no-fixation patients with SER IV ankle fracture after a minimum of 4 years of follow-up. Level of Evidence: Level II, prospective comparative study.
First isolation of leptospires from dairy goats in Brazil

Leptospires have never been recovered from goats in Brazil. Serum samples were obtained from 248 goats from Rio de Janeiro and from the seroreactive animals, urine samples were collected and processed for Leptospira isolation. A total of 52 positive reactions were observed, corresponding to 20.9% of the samples. The most prevalent reactions were to serovars Hardjo (36.5%), Shermani (30.8%), Icterohaemorrhagiae (9.6%), Grippotyphosa (9.6%), Autumnalis (5.8%), Castellonis (3.8%) and Bratislava (3.8%). Two strains of Leptospira sp. were isolated, both in the same region, but from different flocks. Presumptive identification based on serologic methods suggests those strains to be from Grippotyphosa serogroup.