Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway

Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how Mug binds DNA is of significance when considering how Mug interacts with downstream enzymes in the base-excision repair pathway. We have demonstrated differential binding modes of Mug between its substrate and abasic DNA product using both band shift and fluorescence anisotropy assays. Mug binds its product cooperatively, and a stoichiometric analysis of DNA binding, catalytic activity and salt-dependence indicates that dimer formation is of functional significance in both catalytic activity and product binding. This is the first report of cooperativity in the uracil DNA glycosylase superfamily of enzymes, and forms the basis of product inhibition in Mug. It therefore provides a new perspective on abasic site protection and the findings are discussed in the context of downstream lesion processing and enzyme communication in the base excision repair pathway.
On optimal traffic grooming in WDM rings

We consider the problem of designing a virtual topology to minimize electronic routing, that is, grooming traffic, in wavelength routed optical rings. We present a new framework consisting of a sequence of bounds, both upper and lower, in which each successive bound is at least as strong as the previous one. The successive bounds take larger amounts of computation to evaluate, and the number of bounds to be evaluated for a given problem instance is only limited by the computational power available. The bounds are based on decomposing the ring into sets of nodes arranged in a path, and adopting the locally optimal topology within each set. Our approach can be applied to many virtual topology problems on rings. The upper bounds we obtain also provide a useful series of heuristic solutions.
Changing Neuroestrogens Within the Auditory Forebrain Rapidly Transform Stimulus Selectivity in a Downstream Sensorimotor Nucleus

The activity of sensory circuits is shaped by neuromodulators, which can have downstream consequences for both sensorimotor integration and behavioral output. Recent evidence indicates that brain-derived estrogens (“neuroestrogens”) can act as local circuit modulators in the songbird auditory forebrain. Specifically, neuroestrogens fluctuate in the auditory caudomedial nidopallium (NCM) during social interactions and in response to song stimuli. Within minutes of elevation, neuroestrogens also enhance auditory response properties of NCM neurons, and acute blockade of estrogen production in NCM disrupts behavioral song preferences. Here, we test the hypothesis that fluctuating neuroestrogens within NCM influence stimulus selectivity in a downstream sensorimotor nucleus (HVC, used as a proper name) that receives indirect auditory input from NCM. Dual extracellular recordings coupled with retrodialysis delivery show that song selectivity in HVC is rapidly enhanced by increasing neuroestrogens in NCM in adult males. Conversely, inhibiting neuroestrogen production in NCM causes a rapid decline in song selectivity in HVC, demonstrating the endogenous nature of this modulatory network. In contrast, HVC selectivity is unaffected by neuroestrogen delivery to either nearby caudomedial mesopallium or into HVC itself, indicating that neuroestrogen actions are restricted to NCM. In juvenile males, identical neuroestrogen treatment in NCM also does not alter HVC selectivity, consistent with a developmental maturation of the auditory network. Lastly, the rapid actions of estrogens leading to enhanced HVC selectivity appear to be mediated by membrane-bound receptors in NCM. These findings indicate that steroid-dependent modulation of sensory processing is not locally restricted and can be transmitted transynaptically to influence downstream sensorimotor and premotor targets.
Efficient L-shape fitting of laser scanner data for vehicle pose estimation

In this paper, we propose an efficient algorithm to fit a cluster of laser scan points with an L-shape. The algorithm partitions a cluster into two disjoint sets optimally in the sense of the least square error, and then fits them with two perpendicular lines. By exploiting the characteristics of both the laser scanner sensor and the fitting problem, the algorithm can test all the possible corner points while keeping the complexity as low as 9 times that of fitting a single pair of orthogonal lines, where the 9 times scaling factor is independent of the number of points in the cluster. Specifically, we exploit the property that the scanner data points are ordered either clockwise or counterclockwise, and incrementally construct the L-shape fitting problem rather than from scratch when the corner point is different. We extend our algorithm to provide multiple hypotheses on pose estimation, which are derived from L-shape fitting, to account for the ambiguity on the corner points. The extended algorithm only requires slightly more computation, which is tested and verified with real laser scanner data. The experimental results justify the correctness and efficacy of our algorithm.
Why don't physicians follow clinical practice guidelines? A framework for improvement.

CONTEXT Despite wide promulgation, clinical practice guidelines have had limited effect on changing physician behavior. Little is known about the process and factors involved in changing physician practices in response to guidelines. OBJECTIVE To review barriers to physician adherence to clinical practice guidelines. DATA SOURCES We searched the MEDLINE, Educational Resources Information Center (ERIC), and HealthSTAR databases (January 1966 to January 1998); bibliographies; textbooks on health behavior or public health; and references supplied by experts to find English-language article titles that describe barriers to guideline adherence. STUDY SELECTION Of 5658 articles initially identified, we selected 76 published studies describing at least 1 barrier to adherence to clinical practice guidelines, practice parameters, clinical policies, or national consensus statements. One investigator screened titles to identify candidate articles, then 2 investigators independently reviewed the texts to exclude articles that did not match the criteria. Differences were resolved by consensus with a third investigator. DATA EXTRACTION Two investigators organized barriers to adherence into a framework according to their effect on physician knowledge, attitudes, or behavior. This organization was validated by 3 additional investigators. DATA SYNTHESIS The 76 articles included 120 different surveys investigating 293 potential barriers to physician guideline adherence, including awareness (n = 46), familiarity(n = 31), agreement (n = 33), self-efficacy (n = 19), outcome expectancy (n = 8), ability to overcome the inertia of previous practice (n = 14), and absence of external barriers to perform recommendations (n = 34). The majority of surveys (70 [58%] of 120) examined only 1 type of barrier. CONCLUSIONS Studies on improving physician guideline adherence may not be generalizable, since barriers in one setting may not be present in another. Our review offers a differential diagnosis for why physicians do not follow practice guidelines, as well as a rational approach toward improving guideline adherence and a framework for future research.
Comparison of the Rat Pinealocyte Ultrastructure With Melatonin Concentrations During Daytime and at Night

The aim of this study was to investigate the ultrastructure of rat pinealocyte during daytime (1600 h) and at night (0100 h) and to compare these observations with serum melatonin levels in the same animals. In addition, pineal melatonin concentrations were determined in other animals. Both serum and pineal melatonin concentrations were significantly higher at night than during daytime (34 and 21 times, respectively). Sizes of pinealocytes, their nuclei, and nucleoli, as well as cross‐sectional areas of mitochondria and granular endoplasmic reticulum were also higher at night than during daytime, whereas areas of lysosomes, Golgi apparatus, and vacuoles containing flocculent material did not differ at the time points studied. In contrast, the number of dense‐core vesicles was higher during daytime. The results of the present study show that morphological patterns of higher metabolic activity of the rat pinealocyte at night when compared to those during daytime correlate with melatonin concentrations.
HMM based semi-supervised learning for activity recognition

In this paper, we introduce a novel method for human activity recognition that benefits from the structure and sequential properties of the test data as well as the training data. In the training phase, we obtain a fraction of data labels at constant time intervals and use them in a semi-supervised graph-based method for recognizing the user's activities. We use label propagation on a k-nearest neighbor graph to calculate the probability of association of the unlabeled data to each class in this phase. Then we use these probabilities to train an HMM in a way that each of its hidden states corresponds to one class of activity. These probabilities are used to learn the transition probabilities between hidden states of the HMM which is used to predict the classes of the test data. Experimental results shows that the proposed method consistently outperforms the existing state of the art semi-supervised methods.
Integrating hidden Markov models and spectral analysis for sensory time series clustering

We present a novel approach for clustering sequences of multi-dimensional trajectory data obtained from a sensor network. The sensory time-series data present new challenges to data mining, including uneven sequence lengths, multi-dimensionality and high levels of noise. We adopt a principled approach, by first transforming all the data into an equal-length vector form while keeping as much temporal information as we can, and then applying dimensionality and noise reduction techniques such as spectral clustering to the transformed data. Experimental evaluation on synthetic and real data shows that our proposed approach outperforms standard model-based clustering algorithms for time series data.
Characterization of the PCMBS-dependent modification of KCa3.1 channel gating

Intermediate conductance, calcium-activated potassium channels are gated by the binding of intracellular Ca2+ to calmodulin, a Ca2+-binding protein that is constitutively associated with the C terminus of the channel. Although previous studies indicated that the pore-lining residues along the C-terminal portion of S6 contribute to the activation mechanism, little is known about whether the nonluminal face of S6 contributes to this process. Here we demonstrate that the sulfhydral reagent, parachloromercuribenze sulfonate (PCMBS), modifies an endogenous cysteine residue predicted to have a nonluminal orientation (Cys276) along the sixth transmembrane segment (S6). Modification of Cys276 manipulates the steady-state and kinetic behavior of the channel by shifting the gating equilibrium toward the open state, resulting in a left shift in apparent Ca2+ affinity and a slowing in the deactivation process. Using a six-state gating scheme, our analysis shows that PCMBS slows the transition between the open state back to the third closed state. Interpreting this result in the context of the steady-state and kinetic data suggests that PCMBS functions to shift the gating equilibrium toward the open state by disrupting channel closing. In an attempt to understand whether the nonluminal face of S6 participates in the activation mechanism, we conducted a partial tryptophan scan of this region. Substituting a tryptophan for Leu281 recapitulated the effect on the steady-state and kinetic behavior observed with PCMBS. Considering the predicted nonluminal orientation of Cys276 and Leu281, a simple physical interpretation of these results is that the nonluminal face of S6 forms a critical interaction surface mediating the transition into the closed conformation, suggesting the nonluminal C-terminal portion of S6 is allosterically coupled to the activation gate.
Beyond friendship graphs: a study of user interactions in Flickr

Most of the existing literature on empirical studies of Online Social Networks (OSNs) have focused on characterizing and modeling the structure of their inferred friendship graphs. However, the friendship graph of an OSN does not demonstrate what fraction of its users actively interact with other users, how these users interact, and how these active users and their interactions evolve over time. In this paper, we characterize indirect fan-owner interactions through photos among users in a large photo-sharing OSN, namely Flickr. Our results show that a very small fraction of users in the main component of the friendship graph is responsible for the vast majority of fan-owner interactions; moreover, these interactions involve only a small fraction of photos in Flickr. We also characterize some of the temporal properties of fan arrival. For example, we show that there is no strong correlation between age and popularity of a photo and that most photos gain a majority of their fans during the first week after their posting. Overall, our findings provide new insights into the fan-owner interactions among Flickr users.
Changes in protein and nutrient composition of milk throughout lactation in dogs.

OBJECTIVE To evaluate changes in protein and nutrient composition of milk throughout lactation in dogs. SAMPLE POPULATION Milk samples collected from 10 lactating Beagles. PROCEDURE Milk samples were collected on days 1, 3, 7, 14, 21, 28, 35, and 42 after parturition and analyzed to determine concentrations of nitrogen, nonprotein nitrogen, casein, whey proteins, amino acids, lipids, lactose, citrate, minerals, and trace elements. Optimum conditions for separating casein from whey proteins and distribution of milk proteins throughout lactation were assessed by use of polyacrylamide gel electrophoresis. RESULTS Protein concentration was high in samples collected on day 1 (143 g/L), decreased through day 21 (68.4 g/L), and increased thereafter. Concentration of nonprotein nitrogen did not change throughout lactation (5.7 to 9.9% of total nitrogen content). Casein-to-whey ratio was approximately 70:30 and remained constant throughout lactation. Lactose concentration increased from 16.6 g/L on day 1 to 34.0 to 40.2 g/L on days 7 to 42. Lipid concentration ranged from 112.5 to 1372 g/L. Citrate concentration increased from day 1 (4.8 mM) to day 7 (6.6 mM), then gradually decreased until day 42 (3.9 mM). Iron, zinc, copper, and magnesium concentrations decreased during lactation, whereas calcium and phosphorus concentrations increased. Calcium-to-phosphorus ratio remained constant throughout lactation (approx 1.6:1). Energy content of milk ranged from 1,444 to 1,831 kcal/L. CONCLUSIONS AND CLINICAL RELEVANCE Protein and nutrient composition of milk changes throughout lactation in dogs. These data can provide valuable information for use in establishing nutrient requirements of puppies during the suckling period.
Visual navigation and 3D reconstruction of underwater objects with autonomous underwater vehicle

An approach to the solution of a problem for autonomous underwater vehicle navigation and 3D reconstruction of locality by stereo images is described. The basis for navigation by stereo images is the method of visual odometry. Several modifications of the method directed to increase in accuracy of vehicle localization and decrease in computing expenses were suggested. It includes an adaptive procedure of trajectory calculation, an algorithm for the features processing on the trajectory fragments increasing an accuracy of calculation for local motion of vehicle as well as the method of visual navigation for underwater vehicle in the conditions of local maneuvering based on using of virtual network for coordinate referencing. Besides, the method of problem solution for 3D objects reconstruction based on images processing needed for survey underwater operations execution is described.
Enhanced Antitumor Efficacy of a Vascular Disrupting Agent Combined with an Antiangiogenic in a Rat Liver Tumor Model Evaluated by Multiparametric MRI

A key problem in solid tumor therapy is tumor regrowth from a residual viable rim after treatment with a vascular disrupting agent (VDA). As a potential solution, we studied a combined treatment of a VDA and antiangiogenic. This study was approved by the institutional ethical committee for the use and care of laboratory animals. Rats with implanted liver tumors were randomized into four treatment groups: 1) Zd6126 (Zd); 2) Thalidomide (Tha); 3) Zd in combination with Tha (ZdTha); and 4) controls. Multiparametric MRIs were performed and quantified before and after treatment. Circulating endothelial progenitor cells (EPCs) and plasma stromal cell-derived factor-1α (SDF-1α) were monitored. Tumor apoptosis, necrosis, and microvessels were verified by histopathology. A single use of Zd or Tha did not significantly delay tumor growth. The combined ZdTha showed enhanced antitumor efficacy due to synergistic effects; it induced a cumulative tumor apoptosis or necrosis, which resulted in significant delay in tumor growth and reduction in the viable tumor rim; it also reduced tumor vessel permeability; and it improved tumor hemodynamic indexes, most likely via a transient normalization of tumor vasculature induced by Tha. A stepwise linear regression analysis showed that the apparent diffusion coefficient was an independent predictor of tumor growth. We found no significant increases in Zd-induced circulating EPCs or plasma SDF-1α. ZdTha showed improved therapeutic efficacy in solid tumors compared to either agent alone. The therapeutic effects were successfully tracked in vivo with multiparametric MRI.
Geometric Upper Bounds on Rates of Variable-Basis Approximation

In this paper, approximation by linear combinations of an increasing number n of computational units with adjustable parameters (such as perceptrons and radial basis functions) is investigated. Geometric upper bounds on rates of convergence of approximation errors are derived. The bounds depend on certain parameters specific for each function to be approximated. The results are illustrated by examples of values of such parameters in the case of approximation by linear combinations of orthonormal functions.
The Prevalence of Previously Undiagnosed Leprosy in the General Population of Northwest Bangladesh

Background The prevalence of previously undiagnosed leprosy (PPUL) in the general population was determined to estimate the background level of leprosy in the population and to compare this with registered prevalence and the known PPUL in different levels of contacts of leprosy patients. Methodology and Principal Findings Multistage cluster sampling including 20 clusters of 1,000 persons each in two districts with over 4 million population. Physical examination was performed on all individuals. The number of newly found leprosy cases among 17,862 people above 5 years of age from the cluster sample was 27 (19 SLPB, 8 PB2-5), giving a PPUL rate of 15.1 per 10,000. Conclusions and Significance PPUL in the general population is six times higher than the registered prevalence, but three times lower than that in the most distant subgroup of contacts (neighbour of neighbour and social contacts) of leprosy patients in the same area. Full village or neighbourhood surveys may be preferable to contact surveys where leprosy is highly endemic.
Urodilatin is involved in sodium homeostasis and exerts sodium-state-dependent natriuretic and diuretic effects.

Urodilatin is involved in sodium homeostasis exerts sodium-state-dependent natriuretic and diuretic cts. Eight male volunteers participated in a study consisting of three consecutive phases of 7 days each. The volunteers a sodium diet with 52, 172.6, and 347.8 mmol um/day. Sodium excretion increased from 57.4 +/- 3.7 via . 8 +/- 4.6 (P < 0.001) to 322.5 +/- 10.2 mmol/24 h (P < 0.001) at the end of each sodium diet. Urinary urodilatin excretion increased from 24.8 +/- 3.0 via 35.5 +/- 9.0 (P = 0.07) to 49.0 = mol/min (P < 0.01). At the end of each diet, urodilatin was infused for 2 h at 20 ng.kg body wt-1.min-1. Natriuresis increased after low- (4.1 to 52.9 mmol/h, P < 0.001), normal (6.9 to 44.9 mmol/h, P < 0.05), and high-sodium diet (20.1 to 102.9 mmol/h, P < 0.001). Diuresis increased from 174 to 709 (P < 0.001), 395 to 1,026 (P < 0.05), and 266 to 1,339 ml/h < 0.001). The present results indicate that endogenous urodilatin plays an important role in sodium homeostasis and that renal response to exogenous urodilatin is modulated by sodium balance.
Interactions between the diatom Thallasiosira pseudonanna and an associated pseudomonad in a mariculture system

The marine diatom Thallasiosira pseudonanna (3H) and several bacteria associated with it were isolated from batch cultures at the University of Delaware mariculture facility. The interaction between the algae and each of the bacteria was investigated. One of the isolates, T827/2B (Pseudomonas sp.), was incapable of surviving in f/2 culture medium unless the algae were present. When the algae and T827/2B were grown together in the f/2 medium, the bacterial growth was stimulated and the algal growth was inhibited. Bacterial filtrate had a similar effect on the algae, indicating that the bacterial effect is an indirect one most likely resulting from the excretion of a harmful compound into the medium. Preliminary characterization of the material excreted by the bacteria indicates that it s proteinaceous in nature. The interactions observed does not fit into any single category of interactions but can be explained as a combination of competition and indirect parasitism.
Malicious Shellcode Detection with Virtual Memory Snapshots

Malicious shellcodes are segments of binary code disguised as normal input data. Such shellcodes can be injected into a target process's virtual memory. They overwrite the process's return addresses and hijack control flow. Detecting and filtering out such shellcodes is vital to prevent damage. In this paper, we propose a new malicious shellcode detection methodology in which we take snapshots of the process's virtual memory before input data are consumed, and feed the snapshots to a malicious shellcode detector. These snapshots are used to instantiate a runtime environment that emulates the target process's input data consumption to monitor shellcodes' behaviors. The snapshots can also be used to examine the system calls that shellcodes invoke, these system call parameters, and the process's execution flow. We implement a prototype system in Debian Linux with kernel version 2.6. 26. Our extensive experiments with real traces and thousands of malicious shellcodes illustrate our system's performance with low overhead and few false negatives and few false positives.