Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating multi-attribute similarity networks for robust representation of the protein space

MOTIVATION A global view of the protein space is essential for functional and evolutionary analysis of proteins. In order to achieve this, a similarity network can be built using pairwise relationships among proteins. However, existing similarity networks employ a single similarity measure and therefore their utility depends highly on the quality of the selected measure. A more robust representation of the protein space can be realized if multiple sources of information are used. RESULTS We propose a novel approach for analyzing multi-attribute similarity networks by combining random walks on graphs with Bayesian theory. A multi-attribute network is created by combining sequence and structure based similarity measures. For each attribute of the similarity network, one can compute a measure of affinity from a given protein to every other protein in the network using random walks. This process makes use of the implicit clustering information of the similarity network, and we show that it is superior to naive, local ranking methods. We then combine the computed affinities using a Bayesian framework. In particular, when we train a Bayesian model for automated classification of a novel protein, we achieve high classification accuracy and outperform single attribute networks. In addition, we demonstrate the effectiveness of our technique by comparison with a competing kernel-based information integration approach.
The Optimal Timing of Hepatitis C Therapy in Transplant Eligible Patients With Child B and C Cirrhosis: A Cost-Effectiveness Analysis

Background Ledipasvir (LDV)/sofosbuvir (SOF) has demonstrated high efficacy, safety, and tolerability in hepatitis C virus (HCV)-infected patients. There is limited data, however, regarding the optimal timing of therapy in the context of possible liver transplantation (LT). Methods We compared the cost-effectiveness of 12 weeks of HCV therapy before or after LT or nontreatment using a decision analytical microsimulation state-transition model for a simulated cohort of 10 000 patients with HCV Genotype 1 or 4 with Child B or C cirrhosis. All model parameters regarding the efficacy of therapy, adverse events and the effect of therapy on changes in model for end-stage liver disease (MELD) scores were derived from the SOLAR-1 and 2 trials. The simulations were repeated with 10 000 samples from the parameter distributions. The primary outcome was cost (2014 US dollars) per quality adjusted life year. Results Treatment before LT yielded more quality-adjusted life year for less money than treatment after LT or nontreatment. Treatment before LT was cost-effective in 100% of samples at a willingness-to-pay threshold of US $100 000 in the base-case and when the analysis was restricted to Child B alone, Child C, or MELD > 15. Treatment before transplant was not cost-effective when MELD was 6-10. In sensitivity analyses, the MELD after which treatment before transplant was cost-effective was 13 and the maximum cost of LDV/SOF therapy at which treatment before LT is cost-effective is US $177 381. Conclusions From a societal perspective, HCV therapy using LDV/SOF with ribavirin before LT is the most cost-effective strategy for patients with decompensated cirrhosis and MELD score greater than 13.
Stalking Part II: Victims' Problems with the Legal System and Therapeutic Considerations

Objective: This paper is the second of 2 parts reviewing the topic of stalking. It focuses on victims' difficulties with the legal system and the psychotherapeutic tasks for victims and therapists. Method: Computerized literature searches were used to identify relevant papers from psychiatric and legal journals. Publications by victims' and women's organizations provided additional information. Results: Victims suffer emotional consequences from being stalked. Additional stress is caused by the legal system's lack of understanding of the causes and consequences of stalking and inadequate and unenforced laws. The treatment of victims requires a comprehensive approach, including education, supportive psychotherapy, and discussion of practical measures. Therapists may over identify with the patient's powerlessness or hesitate to take on a case out of fear of the stalker. Female therapists may protect themselves against the realization of their own vulnerability by blaming the victim, while male therapists may feel defensive or overprotective. Conclusion: Stalking is a crime with major mental health consequences which is often poorly understood by society. Therapists need to be aware of the victim's emotional reactions, the types of legal and practical supports available, and the possible biases of society. Further education and research should be encouraged.
Prairie: A rule specification framework for query optimizers

From our experience, current rule-based query optimizers do not provide a very intuitive and well-defined framework to define rules and actions. To remedy this situation, we propose an extensible and structured algebraic framework called Prairie for specifying rules. Prairie facilitates rule-writing by enabling a user to write rules and actions more quickly, correctly and in an easy-to-understand and easy-to-debug manner. Query optimizers consist of three major parts: a search space, a cost model and a search strategy. The approach we take is only to develop the algebra which defines the search space and the cost model and use the Volcano optimizer-generator as our search engine. Using Prairie as a front-end we translate Prairie rules to Volcano to validate our claim that Prairie makes it easier to write rules. We describe our algebra and present experimental results which show that using a high-level framework like Prairie to design large-scale optimizers does not sacrifice efficiency. <<ETX>>
Transmission dynamics of parasitic sea lice from farm to wild salmon

Marine salmon farming has been correlated with parasitic sea lice infestations and concurrent declines of wild salmonids. Here, we report a quantitative analysis of how a single salmon farm altered the natural transmission dynamics of sea lice to juvenile Pacific salmon. We studied infections of sea lice (Lepeophtheirus salmonis and Caligus clemensi ) on juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) as they passed an isolated salmon farm during their seaward migration down two long and narrow corridors. Our calculations suggest the infection pressure imposed by the farm was four orders of magnitude greater than ambient levels, resulting in a maximum infection pressure near the farm that was 73 times greater than ambient levels and exceeded ambient levels for 30 km along the two wild salmon migration corridors. The farm-produced cohort of lice parasitizing the wild juvenile hosts reached reproductive maturity and produced a second generation of lice that re-infected the juvenile salmon. This raises the infection pressure from the farm by an additional order of magnitude, with a composite infection pressure that exceeds ambient levels for 75 km of the two migration routes. Amplified sea lice infestations due to salmon farms are a potential limiting factor to wild salmonid conservation.
Lowering of tumoral interstitial fluid pressure by prostaglandin E1 is paralleled by an increased uptake of 51Cr‐EDTA

High intra‐tumoral fluid pressure (TPIF) may impair uptake of anticancer drugs into tumors, contributing to poor efficiency in treatment of carcinomas. Here, we demonstrate that lowering of TPIF parallels increased transport of 51Cr‐EDTA (m.w. 341) into tumor interstitium. Introduction of 15 μg prostaglandin E1 (PGE1) ‐methyl ester into the s.c. tissue surrounding transplanted rat colonic (PROb) carcinomas or chemically‐induced rat mammary carcinomas, lowered TPIF by 30%. Transcapillary transport into the interstitium of PROb tumors quantified by microdialysis increased by 39.6% after PGE1 treatment 40 min prior to administration of 51Cr‐EDTA (n=6; p<0.05) compared to vehicle (n=10). In mammary tumors, PGE1 increased transport into the tumors by 86.9% over controls (n=16; p<0.05). Both tumors had well developed stroma containing collagen and hyaluronan. Our data demonstrate that adjuvant treatment with PGE1 lowers TPIF, and enhances transport into the tumors. This principle may be of value as adjuvant therapy in treatment of solid malignancies with currently used anticancer drugs. Int. J. Cancer 86:636–643, 2000. © 2000 Wiley‐Liss, Inc.
On the Strength of Connections Between Localist Mental Modules as a Source of Frequency-of-Occurrence Effects

Frequency-of-occurrence effects (e.g., effects of word frequency or familiarity) are widely thought to arise through differences in resting levels of activation in localist input-output modules. A different account posits that these effects at least partially reflect the strength of connections between various localist modules. Given that Arabic numerals appear more frequently than their alphabetic counterparts, we contrasted reaction times to stimuli in both formats in a naming/reading-aloud task and a parity-judgment task. The script effect (the difference between reaction times to Arabic and to alphabetic formats) was large in the parity-judgment task but absent in the naming/reading-aloud task. This script-by-task interaction follows naturally from the idea that at least part of the effect of frequency of occurrence of a printed word or digit (and other instances of familiarity) resides in the strength of connections between specialized localist input-output modules and a localist semantic module. This conclusion is likely applicable across a variety of domains.
Delay-Dependent Stability for Time-Delay Systems with Nonlinear Perturbations

We study the stability of a class of time-delay systems with nonlinear perturbations. A new delay-dependent stability condition which can deal with arbitrarily time-varying delays is formulated by constituting a Lyapunov-Krasovskii functional, the result has less conservatism than those presented before. Numerical examples are presented to indicate significant improvements over some existing results
Early-Life Social Isolation Impairs the Gonadotropin-Inhibitory Hormone Neuronal Activity and Serotonergic System in Male Rats

Social isolation in early life deregulates the serotonergic system of the brain, compromising reproductive function. Gonadotropin-inhibitory hormone (GnIH) neurons in the dorsomedial hypothalamic nucleus are critical to the inhibitory regulation of gonadotropin-releasing hormone neuronal activity in the brain and release of luteinizing hormone by the pituitary gland. Although GnIH responds to stress, the role of GnIH in social isolation-induced deregulation of the serotonin system and reproductive function remains unclear. We investigated the effect of social isolation in early life on the serotonergic–GnIH neuronal system using enhanced green fluorescent protein (EGFP)-tagged GnIH transgenic rats. Socially isolated rats were observed for anxious and depressive behaviors. Using immunohistochemistry, we examined c-Fos protein expression in EGFP–GnIH neurons in 9-week-old adult male rats after 6 weeks post-weaning isolation or group housing. We also inspected serotonergic fiber juxtapositions in EGFP–GnIH neurons in control and socially isolated male rats. Socially isolated rats exhibited anxious and depressive behaviors. The total number of EGFP–GnIH neurons was the same in control and socially isolated rats, but c-Fos expression in GnIH neurons was significantly reduced in socially isolated rats. Serotonin fiber juxtapositions on EGFP–GnIH neurons were also lower in socially isolated rats. In addition, levels of tryptophan hydroxylase mRNA expression in the dorsal raphe nucleus were significantly attenuated in these rats. These results suggest that social isolation in early-life results in lower serotonin levels, which reduce GnIH neuronal activity and may lead to reproductive failure.
Western and Dot Blotting Analyses of Ehrlichia chaffeensis Indirect Fluorescent-Antibody Assay-Positive and -Negative Human Sera by Using Native and Recombinant E. chaffeensis and E. canis Antigens

ABSTRACT Human monocytic ehrlichiosis is an emerging infectious disease caused by Ehrlichia chaffeensis, a gram-negative obligatory intracellular bacterium closely related to E. canis. The immunoreactive recombinant fusion proteins rP28 and rP30 have become available after cloning and expressing of the 28- and 30-kDa major outer membrane protein genes of E. chaffeensis and E. canis, respectively. Western immunoblotting was performed to analyze the antibody responses of the 37 E. chaffeensisindirect fluorescent-antibody assay (IFA)-positive and 20 IFA-negative serum specimens with purified whole organisms, rP28, and rP30. All IFA-negative sera were negative with purified whole organisms, rP28, or rP30 by Western immunoblot analysis (100% relative diagnostic specificity). Of 37 IFA-positive sera, 34 sera reacted with any native proteins of E. chaffeensis ranging from 44 to 110 kDa, and 30 sera reacted with 44- to 110-kDa native E. canisantigens. The 28-kDa E. chaffeensis and 30-kDa E. canis native proteins were recognized by 25 IFA-positive sera. Fifteen IFA-positive sera reacted with rP28 by Western blot analysis, whereas 34 IFA-positive sera reacted with rP30 (92% relative diagnostic specificity), indicating that rP30 is more sensitive than rP28 for detecting the antibodies in IFA-positive sera. These 34 IFA-positive sera were positive by the dot blot assay with rP30, distinguishing them from IFA-negative sera. Except for three rP30-negative but IFA-positive specimens that instead showed anE. ewingii infection-like profile by Western immunoblotting, the results of Western and dot blot assays with rP30 matched 100% with the IFA test results. Densitometric analysis of dot blot reactions showed a positive correlation between the dot density and the IFA titer. These results suggest that rP30 antigen would provide a simple, consistent, and rapid serodiagnosis for human monocytic ehrlichiosis.
Wirelessly Powered Backscatter Communication Networks: Modeling, Coverage and Capacity

Future Internet-of-Things (IoT) will connect billions of small computing devices embedded in the environment and support their device-to-device (D2D) communication. Powering this massive number of embedded devices is a key challenge of designing IoT since batteries increase the devices' form factors and their recharging/replacement is difficult. To tackle this challenge, we propose a novel network architecture that integrates wireless power transfer and backscatter communication, called wirelessly powered backscatter communication (WP-BC) networks. In this architecture, power beacons (PBs) are deployed for wirelessly powering devices; their ad-hoc communication relies on backscattering and modulating incident continuous waves from PBs, which consumes orders-of-magnitude less power than traditional radios. Thereby, the dense deployment of lowcomplexity PBs with high transmission power can power a largescale IoT. In this paper, a WP-BC network is modeled as a random Poisson cluster process in the horizontal plane where PBs are Poisson distributed and active ad-hoc pairs of backscatter communication nodes with fixed separation distances form random clusters centered at PBs. Furthermore, by harvesting energy from and backscattering radio frequency (RF) waves transmitted by PBs, the transmission power of each node depends on the distance from the associated PB. Applying stochastic geometry, the network coverage probability and transmission capacity are derived and optimized as functions of the backscatter reflection coefficient and duty cycle as well as the PB density. The effects of the parameters on network performance are characterized.
Estimation of Time-Dependent Input from Neuronal Membrane Potential

The set of firing rates of the presynaptic excitatory and inhibitory neurons constitutes the input signal to the postsynaptic neuron. Estimation of the time-varying input rates from intracellularly recorded membrane potential is investigated here. For that purpose, the membrane potential dynamics must be specified. We consider the Ornstein-Uhlenbeck stochastic process, one of the most common single-neuron models, with time-dependent mean and variance. Assuming the slow variation of these two moments, it is possible to formulate the estimation problem by using a state-space model. We develop an algorithm that estimates the paths of the mean and variance of the input current by using the empirical Bayes approach. Then the input firing rates are directly available from the moments. The proposed method is applied to three simulated data examples: constant signal, sinusoidally modulated signal, and constant signal with a jump. For the constant signal, the estimation performance of the method is comparable to that of the traditionally applied maximum likelihood method. Further, the proposed method accurately estimates both continuous and discontinuous time-variable signals. In the case of the signal with a jump, which does not satisfy the assumption of slow variability, the robustness of the method is verified. It can be concluded that the method provides reliable estimates of the total input firing rates, which are not experimentally measurable.
Efficacy of florfenicol for treatment of naturally occurring infectious bovine keratoconjunctivitis.

OBJECTIVE To determine the efficacy of florfenicol for treatment of calves with naturally occurring infectious bovine keratoconjunctivitis (IBK). DESIGN Randomized controlled field trial. ANIMALS 63 beef calves and 80 dairy calves between 4 and 12 months of age. PROCEDURE Calves were randomly assigned to 1 of 3 treatment groups. Calves in the SC treatment group received a single dose of florfenicol (40 mg/kg [18.2 mg/lb of body weight), SC, on day 0. Calves in the IM treatment group received florfenicol (20 mg/kg [9.1 mg/lb]), IM, on days 0 and 2. Calves in the control group received injections of saline solution (0.9% NaCl), IM, on days 0 and 2. Calves were reevaluated every other day for 20 days after treatment. RESULTS Corneal ulcers healed by day 20 in 48 of 49 (98%) calves treated with florfenicol IM, 39 of 42 (93%) calves treated with florfenicol SC, and 33 of 52 (63%) control calves. CONCLUSIONS AND CLINICAL RELEVANCE Florfenicol administered SC (1 dose) or IM (2 doses 48 hours apart) was effective for treatment of calves with naturally occurring IBK.
Two-stage induction of the soxRS (superoxide response) regulon of Escherichia coli

soxR and soxS are adjacent genes that govern a superoxide response regulon. Previous studies revealed that induction of the regulon is accompanied by increased transcription of soxS, which can activate the target genes. Therefore, induction may occur in two stages: the soxR-dependent activation of soxS, followed by the soxS-dependent induction of other genes. However, the requirement for soxR was unproven because the only existing soxR mutations either were of the regulon-constitutive type or also involved soxS. Therefore, we produced an insertion mutation that was shown by complementation to inactivate only soxR. In confirmation of the two-stage model, soxR was required for the induction by paraquat of the target genes studied (nfo, zwf, and sodA), for paraquat resistance, and for the 47- to 76-fold induction of soxS-lacZ gene fusions. Paraquat did not affect the expression of soxR-lacZ gene fusions. In a soxRS deletion mutant, the regulon was constitutively activated by a runaway soxS+ plasmid. However, a lower-copy-number plasmid failed to activate nfo, zwf, or sodA but did increase the paraquat resistance of a soxRS mutant. Therefore, there is a differential response of the regulon genes to soxS overproduction. A soxR regulon-constitutive mutation was suppressed by a soxR+ plasmid, suggesting a competition between native and activated forms of SoxR. It is proposed that to enhance the sensitivity of the response, the cell minimizes such potential competition by manufacturing only a small amount of this sensor protein, thereby necessitating signal amplification via induction of soxS.
Probe Oscillation Shear Elastography (PROSE): A High Frame-Rate Method for Two-Dimensional Ultrasound Shear Wave Elastography

Ultrasound shear wave elastography (SWE) utilizes the propagation of induced shear waves to characterize the shear modulus of soft tissue. Many methods rely on an acoustic radiation force (ARF) “push beam” to generate shear waves. However, specialized hardware is required to generate the push beams, and the thermal stress that is placed upon the ultrasound system, transducer, and tissue by the push beams currently limits the frame-rate to about 1 Hz. These constraints have limited the implementation of ARF to high-end clinical systems. This paper presents Probe Oscillation Shear Elastography (PROSE) as an alternative method to measure tissue elasticity. PROSE generates shear waves using a harmonic mechanical vibration of an ultrasound transducer, while simultaneously detecting motion with the same transducer under pulse-echo mode. Motion of the transducer during detection produces a “strain-like” compression artifact that is coupled with the observed shear waves. A novel symmetric sampling scheme is proposed such that pulse-echo detection events are acquired when the ultrasound transducer returns to the same physical position, allowing the shear waves to be decoupled from the compression artifact. Full field-of-view (FOV) two-dimensional (2D) shear wave speed images were obtained by applying a local frequency estimation (LFE) technique, capable of generating a 2D map from a single frame of shear wave motion. The shear wave imaging frame rate of PROSE is comparable to the vibration frequency, which can be an order of magnitude higher than ARF based techniques. PROSE was able to produce smooth and accurate shear wave images from three homogeneous phantoms with different moduli, with an effective frame rate of 300 Hz. An inclusion phantom study showed that increased vibration frequencies improved the accuracy of inclusion imaging, and allowed targets as small as 6.5 mm to be resolved with good contrast (contrast-to-noise ratio ≥ 19 dB) between the target and background.
Expression of the Irisin Precursor FNDC5 in Skeletal Muscle Correlates With Aerobic Exercise Performance in Patients With Heart Failure

Background—Exercise-induced increase in peroxisome proliferator-activated receptor-&ggr; coactivator-1&agr; (PGC-1&agr;) expression has been shown to increase the expression of the fibronectin type III domain containing 5 (FNDC5) gene and thereby its product, irisin, in mice. Given that exercise intolerance is a hallmark characteristic of heart failure (HF), and because PGC-1&agr; and irisin promote exercise benefits in animals, we hypothesized that expression of these genes relates to aerobic performance in patients with HF. Methods and Results—Systolic HF (left ventricular ejection fraction ⩽40%) patients underwent cardiopulmonary exercise testing to evaluate aerobic performance. High versus low aerobic performance was assessed using oxygen consumption (peak VO2 [>14 versus ⩽14 mL O2·kg−1·min−1]) and ventilatory efficiency (VE/VCO2 slope [<34 versus ≥34]). Muscle biopsies of the vastus lateralis and real-time polymerase chain reaction were used to quantify muscle gene expression. Twenty-four patients were studied. FNDC5 (5.7±3.5 versus 3.1±1.2, P<0.05) and PGC-1&agr; (9.9±5.9 versus 4.5±1.9, P<0.01) gene expressions were greater in the high-peak VO2 group; correlation between FNDC5 and PGC-1&agr; was significant (r=0.56, P<0.05) only in the high-peak VO2 group. Similarly, FNDC5 and PGC-1&agr; gene expression was greater in the high-performance group based on lower VE/VCO2 slopes (5.8±3.6 versus 3.3±1.4, P<0.05 and 9.7±6 versus 5.3±3.4, P<0.05); FNDC5 also correlated with PGC-1&agr; (r=0.55, P<0.05) only in the low VE/VCO2 slope group. Conclusions—This is the first study to show that FNDC5 expression relates to functional capacity in a human HF population. Lower FNDC5 expression may underlie reduced aerobic performance in HF patients.