LLukas22/scidocs huggingface dataset:
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model

A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly controlled transcriptional program. An important and yet challenging task in systems biology is to reconstruct cellular signaling system in a data-driven manner. In this study, we investigate the utility of deep hierarchical neural networks in learning and representing the hierarchical organization of yeast transcriptomic machinery. We have designed a sparse autoencoder model consisting of a layer of observed variables and four layers of hidden variables. We applied the model to over a thousand of yeast microarrays to learn the encoding system of yeast transcriptomic machinery. After model selection, we evaluated whether the trained models captured biologically sensible information. We show that the latent variables in the first hidden layer correctly captured the signals of yeast transcription factors (TFs), obtaining a close to one-to-one mapping between latent variables and TFs. We further show that genes regulated by latent variables at higher hidden layers are often involved in a common biological process, and the hierarchical relationships between latent variables conform to existing knowledge. Finally, we show that information captured by the latent variables provide more abstract and concise representations of each microarray, enabling the identification of better separated clusters in comparison to gene-based representation. Contemporary deep hierarchical latent variable models, such as the autoencoder, can be used to partially recover the organization of transcriptomic machinery.
Triple therapy: Phaco-vitrectomy with ILM peeling, retinal endophotocoagulation, and intraoperative use of Bevacizumab for diffuse diabetic macular edema

BACKGROUND
The aim of this study was to evaluate the visual acuity and structural outcomes of combined phacovitrectomy with ILM peeling, retinal endophotocoagulation and use of bevacizumab in patients with diffuse diabetic macular edema (DDME).


MATERIAL/METHODS
In this prospective, nonrandomized, interventional study we included 29 eyes of 26 patients with DDME. The best-corrected visual acuity (BCVA) and central retinal thickness and volume (CRT and CRV) were recorded at 4, 8, 12, and 16 months after surgery.


RESULTS
The mean preoperative BCVA was 0.74±0.36 logMAR (0.3-1.5) and improved finally to 0.4±0.24 logMAR (-0.1-1.0) p=0.000006. The mean preoperative CRT in the 1mm zone was 516±184 microm (256-950) and decreased postoperatively at the last control to 237±75 microm (117-489) p=0.000003. The mean preoperative CRV in the 1mm zone was 0.39±0.14 microL (0.19-0.74) and decreased postoperatively at the last control to 0.17±0.06 microL (0.09-0.36) p=0.000003. The mean preoperative CRT in the 6 mm zone was 407±105 microm (279-640) and decreased postoperatively at the last control to 282±40 µm (212-380) p=0.000004. The mean preoperative CRV in the 6 mm zone was 11.4±2.9 microL (7.85-17.93) and decreased postoperatively at the last control to 7.92±1.0 microL (5.62-10.97) p=0.000003. The 23 (79.3%) eyes showed improvement in BCVA ≥0.2 logMAR, 5 (17.2%) eyes improvement or stabilization of BCVA and 1(3.5%) eye deterioration. Preoperative BCVA was a positive factor for prognosis of BCVA at 12th month follow-up (b=0.42; p=0.006), while the negative factors were: previous panretinal photocoagulation (b=-0.24; p=0.04), presence of vitreomacular traction (b=-0.29; p=0.02) and preoperative CRT in the 1000 microm zone (b=-0.24; p=0.07). A greater visual acuity improvement occurred in eyes with worse baseline visual acuity (b=-1.01; p=0.00001). The presentation of vitreomacular traction (b=-0.38; p=0.02), previous panretinal photocoagulation (b=-0.31, p=0.04) and greater preoperative CRT in the 1000 µm zone (b=-0.31; p=0.07) were negative factors for visual improvement.


CONCLUSIONS
This combined treatment resulted in improvement or stabilization of BCVA and decrease of CRT and CRV. Larger comparative studies are necessary to establish the real impact of this therapeutic approach.
Emotion and moral judgment.

Research in psychology and cognitive science has consistently demonstrated the importance of emotion in a wide range of everyday judgments, including moral judgment. Most current accounts of moral judgment hold that emotion plays an important role, but the nature and extent of this role are still debated. We outline three increasingly strong claims about the role of emotion in moral judgment and assess the evidence for each. According to the first and least controversial claim, emotions follow from moral judgments, such that witnessing immorality can lead to negative emotions and witnessing moral virtue can lead to positive ones. According to the second claim, emotions amplify moral judgments, for instance, by making immoral acts seem even more immoral. Finally, on the last claim, emotions can actually moralize nonmoral behaviors-that is, they give nonmoral acts a moral status. Although this claim seems to be the most intriguing one theoretically, empirical support for it is still very limited. In this review, we discuss research findings that are in line with each of these views, we highlight recurring themes across these three categories of evidence, and we identify some open questions and areas for future research. WIREs Cogn Sci 2013, 4:169-178. doi: 10.1002/wcs.1216 For further resources related to this article, please visit the WIREs website.
A phase I trial of twice-weekly 17-allylamino-demethoxy-geldanamycin in patients with advanced cancer.

PURPOSE
To determine the maximum tolerated dose (MTD), dose-limiting toxicity, and pharmacokinetics of 17-allylamino-demethoxy-geldanamycin (17-AAG) administered on days 1, 4, 8, and 11 every 21 days and to examine the effect of 17-AAG on the levels of chaperone and client proteins.


EXPERIMENTAL DESIGN
A phase I dose escalating trial in patients with advanced solid tumors was done. Toxicity and tumor responses were evaluated by standard criteria. Pharmacokinetics were done and level of target proteins was measured at various points during cycle one.


RESULTS
Thirteen patients were enrolled in the study. MTD was defined as 220 mg/m2. Dose-limiting toxicities were as follows: dehydration, diarrhea, hyperglycemia, and liver toxicity. At the MTD, the mean clearance of 17-AAG was 18.7 L/h/m2. There was a significant decrease in integrin-linked kinase at 6 hours after infusion on day 1 but not at 25 hours in peripheral blood mononuclear cells. Treatment with 17-AAG on day 1 significantly increased pretreatment levels of heat shock protein (HSP) 70 on day 4, which is consistent with the induction of a stress response. In vitro induction of a stress response and up-regulation of HSP70 resulted in an increased resistance to HSP90-targeted therapy in A549 cells.


CONCLUSIONS
The MTD of 17-AAG on a twice-weekly schedule was 220 mg/m2. Treatment at this dose level resulted in significant changes of target proteins and also resulted in a prolonged increase in HSP70. This raises the possibility that HSP70 induction as part of the stress response may contribute to resistance to 17-AAG.
Inspiratory muscle training improves maximal inspiratory pressure and may assist weaning in older intubated patients: a randomised trial.

QUESTIONS
Does inspiratory muscle training improve maximal inspiratory pressure in intubated older people? Does it improve breathing pattern and time to wean from mechanical ventilation?


DESIGN
Randomised trial with concealed allocation and intention-to-treat analysis.


PARTICIPANTS
41 elderly, intubated adults who had been mechanically ventilated for at least 48 hr in an intensive care unit.


INTERVENTION
The experimental group received usual care plus inspiratory muscle training using a threshold device, with an initial load of 30% of their maximal inspiratory pressure, increased by 10% (absolute) daily. Training was administered for 5 min, twice a day, 7 days a week from the commencement of weaning until extubation. The control group received usual care only.


OUTCOME MEASURES
The primary outcome was the change in maximal inspiratory pressure during the weaning period. Secondary outcomes were the weaning time (ie, from commencement of pressure support ventilation to successful extubation), and the index of Tobin (ie, respiratory rate divided by tidal volume during a 1-min spontaneous breathing trial).


RESULTS
Maximal inspiratory pressure increased significantly more in the experimental group than in the control group (MD 7.6 cmH(2)0, 95% CI 5.8 to 9.4). The index of Tobin decreased significantly more in the experimental group than in the control group (MD 8.3 br/min/L, 95% CI 2.9 to 13.7). In those who did not die or receive a tracheostomy, time to weaning was significantly shorter in the experimental group than in the control group (MD 1.7 days, 95% CI 0.4 to 3.0).


CONCLUSIONS
In intubated older people, inspiratory muscle training improves maximal inspiratory pressure and the index of Tobin, with a reduced weaning time in some patients.


TRIAL REGISTRATION
NCT00922493.
Swarm Intelligence: Foundations, Perspectives and Applications

This chapter introduces some of the theoretical foundations of swarm intelligence. We focus on the design and implementation of the Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO) algorithms for various types of function optimization problems, real world applications and data mining. Results are analyzed, discussed and their potentials are illustrated.
A model for assessing the impact of e-learning systems on employees' satisfaction

In a knowledge and information society, e-learning has built on the extensive use of advanced information and communication technologies to deliver learning and instruction. In addition, employees who need the training do not have to gather in a place at the same time, and thus it is not necessary for them to travel far away for attending training courses. Furthermore, the flexibility allows employees who perform different jobs or tasks for training courses according to their own scheduling. Since many studies have discussed learning and training of employees and most of them are focused on the learning emotion, learning style, educational content, and technology, there is limited research exploring the relationship between the e-learning and employee’s satisfaction. Therefore, this study aims to explore how to enhance employee’s satisfaction by means of e-learning systems, and what kinds of training or teaching activities are effective to increase their learning satisfaction. We provide a model and framework for assessing the impact of e-learning on employee’s satisfaction which improve learning and teaching outcomes. Findings from the study confirmed the validity of the proposed model for e-learning satisfaction assessment. In addition, the results showed that the four variables technology, educational content, motivation, and attitude significantly influenced employee’s learning satisfaction. 2015 Elsevier Ltd. All rights reserved.
Received Signal Strength Database Interpolation by Kriging for a Wi-Fi Indoor Positioning System

The main approach for a Wi-Fi indoor positioning system is based on the received signal strength (RSS) measurements, and the fingerprinting method is utilized to determine the user position by matching the RSS values with the pre-surveyed RSS database. To build a RSS fingerprint database is essential for an RSS based indoor positioning system, and building such a RSS fingerprint database requires lots of time and effort. As the range of the indoor environment becomes larger, labor is increased. To provide better indoor positioning services and to reduce the labor required for the establishment of the positioning system at the same time, an indoor positioning system with an appropriate spatial interpolation method is needed. In addition, the advantage of the RSS approach is that the signal strength decays as the transmission distance increases, and this signal propagation characteristic is applied to an interpolated database with the Kriging algorithm in this paper. Using the distribution of reference points (RPs) at measured points, the signal propagation model of the Wi-Fi access point (AP) in the building can be built and expressed as a function. The function, as the spatial structure of the environment, can create the RSS database quickly in different indoor environments. Thus, in this paper, a Wi-Fi indoor positioning system based on the Kriging fingerprinting method is developed. As shown in the experiment results, with a 72.2% probability, the error of the extended RSS database with Kriging is less than 3 dBm compared to the surveyed RSS database. Importantly, the positioning error of the developed Wi-Fi indoor positioning system with Kriging is reduced by 17.9% in average than that without Kriging.
Analysis of switched reluctance motor drive under fault conditions

The paper presents a comprehensive analysis of a switched reluctance motor (SRM) drive system under different realistic fault conditions. A simple modeling and simulation technique is used to investigate the fault tolerant behavior of SRMs, based on current and position dependent nonlinear flux linkage, which is found to be more appropriate compared to other methods reported in literature. Typical cases considered are: open circuit faults on windings, converter device short or open circuit, and reduced DC link voltage caused by rectifier faults and single phasing of input supply. Pre-fault condition is taken to be the steady state operation under no load or full load torque at rated speed. The performance indices under fault conditions are speed ripple, torque ripple, steady state error in speed, starting and reversal time. The response of speed, current and torque under pre-fault and pod-fault conditions are compared to illustrate the fault tolerant capabilities of the SRM drive under dynamic operating conditions.
Aripiprazole monotherapy for maintenance therapy in bipolar I disorder: a 100-week, double-blind study versus placebo.

OBJECTIVE
A 26-week, double-blind, placebo-controlled relapse prevention study of aripiprazole was designed a priori with a prospective, 74-week, double-blind, placebo-controlled extension phase. Efficacy and tolerability of aripiprazole for relapse prevention in bipolar I disorder was, therefore, evaluated for 100 weeks.


METHOD
Patients with DSM-IV bipolar I disorder, recent manic or mixed episode, received open-label aripiprazole 15 or 30 mg/day (started at 30 mg/day) for 6 to 18 weeks. Patients achieving stabilization (Young Mania Rating Scale score <or= 10 and Montgomery-Asberg Depression Rating Scale score <or= 13 for 6 consecutive weeks) entered the double-blind phase, at which point they were randomly assigned to double-blind treatment with aripiprazole or placebo for 26 weeks. The primary endpoint was time to relapse for any mood episode. Patients who completed the 26-week stabilization continued in a double-blind fashion with aripipra-zole or placebo for an additional 74 weeks and were monitored for relapse, efficacy, and tolerability. The study was conducted from March 2000 to June 2003.


RESULTS
In total, 161 patients met the stabilization criteria and were randomly assigned to aripiprazole (N = 78) or placebo (N = 83). At 100 weeks, time to relapse was significantly longer with aripiprazole (N = 7) than placebo (N = 5; hazard ratio = 0.53 [p = .011; 95% CI = 0.32 to 0.87]); however, a further 24 patients had discontinued due to study closure. Aripiprazole was superior to placebo in delaying time to manic relapse (p = .005; hazard ratio = 0.35 [95% CI = 0.16 to 0.75]); however, no significant differences were observed in time to depressive relapse (p = .602; hazard ratio = 0.81 [95% CI = 0.36 to 1.81]). The adverse events reported during 100 weeks of treatment with aripiprazole versus placebo (>or= 5% incidence and twice placebo rate) were tremor, akathisia, dry mouth, hypertension, weight gain, vaginitis, abnormal thinking, pharyngitis, and flu syndrome. Mean weight change from baseline to 100 weeks (last observation carried forward) was +0.4 +/- 0.8 kg with aripiprazole and -1.9 +/- 0.8 kg with placebo.


CONCLUSIONS
Over a 100-week treatment period, aripiprazole monotherapy was effective for relapse prevention in patients who were initially stabilized on aripiprazole for 6 consecutive weeks, and it maintained a good safety and tolerability profile.


CLINICAL TRIALS REGISTRATION
ClinicalTrials.gov identifier NCT00036348.
E V ects of L-arginine on lower limb vasodilator reserve and exercise capacity in patients with chronic heart failure

Objective—To determine whether the reactive hyperaemic response of the lower limb increases with improved exercise capacity after acute supplementation with L-arginine, the precursor of nitric oxide, in patients with chronic heart failure. Methods—19 patients with chronic heart failure were enrolled in the study. Rest calf blood flow and femoral occlusion induced calf blood flow changes were measured by venous occlusion plethysmography before and after intravenous infusion of 10% L-arginine solution (5 ml/kg for 30 minutes) or placebo. Postexercise calf blood flow was also measured after the experimental infusion. During both postinfusion periods, several exercise capacity indices were determined by a symptom limited cardiopulmonary exercise test using a bicycle ergometer. Results—Baseline calf blood flow, systemic blood pressure, and heart rate showed no significant changes in either of the two experimental conditions. However, the occlusion induced blood flow response was significantly enhanced by L-arginine infusion (mean (SEM) peak flow, 19.6 (1.5) v 28.9 (3.1) ml/min/dl calf tissue; p < 0.01), but not by placebo (peak flow, 19.1 (1.4) v 20.9 (1.8) ml/min/dl calf tissue; NS). Calf blood flow response after exercise was also higher after L-arginine infusion than after placebo (peak flow, 4.8 (0.4) v 6.0 (0.8) ml/min/dl calf tissue; p < 0.05). L-arginine infusion had no significant eVect compared with placebo on exercise capacity indices such as peak oxygen uptake (17.1 (1.0) v 15.8 (1.1) ml/min/kg; NS), anaerobic threshold (10.5 (0.6) v 10.4 (0.7) ml/min/kg; NS), and exercise time (296 (23) v 283 (22) s; NS). Conclusions—Acute supplementation with the nitric oxide precursor L-arginine increased lower limb reactive hyperaemia but did not lead to any significant improvement in exercise capacity in patients with chronic heart failure. (Heart 1999;81:512–517)
Femtosecond Laser-Induced Nanowelding: Fundamentals and Applications

Fundamentals of femtosecond laser pulse and nanoparticles are analyzed by a two-temperature model. Ultrafast surface melting, surface nanoengineering and shock wave impact are evident in the surface of graphite by femtosecond irradiation. The interaction between femtosecond laser pulses and Au/Ag nanoparticles has been investigated. Two effects are identified at different intensities: photofragmentation at rather high intensity (~10 W/cm), nanojoining at low intensity (~10W/cm). Photofragmentation forms a large number of tiny nanoparticles with an average size of tens of nanometers. Control over irradiation conditions at intensities near 10 W/cm results in nanojoining of most of the nanoparticles. This nanojoining is obtained in both liquid solution and in solid state thin films assembled from nanoparticles. Nanojoining mechanism is further studied by joining Ag nanoparticles encapsulated by a polymer shell. Nonthermal melting is investigated. Nanojoined Au nanoparticles are expected to have numerous applications, such as probes for surface enhance Raman spectroscopy.
The convergence insufficiency treatment trial: design, methods, and baseline data.

OBJECTIVE
This report describes the design and methodology of the Convergence Insufficiency Treatment Trial (CITT), the first large-scale, placebo-controlled, randomized clinical trial evaluating treatments for convergence insufficiency (CI) in children. We also report the clinical and demographic characteristics of patients.


METHODS
We prospectively randomized children 9 to 17 years of age to one of four treatment groups: 1) home-based pencil push-ups, 2) home-based computer vergence/accommodative therapy and pencil push-ups, 3) office-based vergence/accommodative therapy with home reinforcement, 4) office-based placebo therapy. Outcome data on the Convergence Insufficiency Symptom Survey (CISS) score (primary outcome), near point of convergence (NPC), and positive fusional vergence were collected after 12 weeks of active treatment and again at 6 and 12 months posttreatment.


RESULTS
The CITT enrolled 221 children with symptomatic CI with a mean age of 12.0 years (SD = +2.3). The clinical profile of the cohort at baseline was 9Delta exophoria at near (+/- 4.4) and 2Delta exophoria (+/-2.8) at distance, CISS score = 30 (+/-9.0), NPC = 14 cm (+/- 7.5), and near positive fusional vergence break = 13 Delta (+/- 4.6). There were no statistically significant nor clinically relevant differences between treatment groups with respect to baseline characteristics (p > 0.05).


CONCLUSION
Hallmark features of the study design include formal definitions of conditions and outcomes, standardized diagnostic and treatment protocols, a placebo treatment arm, masked outcome examinations, and the CISS score outcome measure. The baseline data reported herein define the clinical profile of those enrolled into the CITT.
Evaluation of Ad Hoc Networks in Disaster Scenarios

Ad hoc networks have been proved to be suitable for disaster scenarios since any infrastructure need to be deployed in order to establish a wireless network. Routing protocols play an important role in the performance of mobile ad hoc networks. Routing protocols are responsible for deciding how the information is going to move through the network. Although one paramount parameter of ad hoc networks is the mobility of nodes, little effort has been made to evaluate the performance of mobile ad hoc networks under mobility models which model the movements of rescue teams during evacuating operations. The objective of this paper is to evaluate real case disaster scenarios in terms of performance using several well-known routing protocols metrics.
The sums of the reciprocals of Fibonacci polynomials and Lucas polynomials

* Correspondence: sky.wzgfff@163. com Department of Mathematics, Northwest University, Xi’an, Shaanxi, P.R. China Abstract In this article, we consider infinite sums derived from the reciprocals of the Fibonacci polynomials and Lucas polynomials, and infinite sums derived from the reciprocals of the square of the Fibonacci polynomials and Lucas polynomials. Then applying the floor function to these sums, we obtain several new equalities involving the Fibonacci polynomials and Lucas polynomials. Mathematics Subject Classification (2010): Primary, 11B39.