Miracle-dz/UniFAR-FTUs huggingface dataset:
Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments

Microarray technology allows simultaneous comparison of expression levels of thousands of genes under each condition. This paper concerns sample size calculation in the identification of differentially expressed genes between a control and a treated sample. In a typical experiment, only a fraction of genes (altered genes) is expected to be differentially expressed between two samples. Sample size determination depends on a number of factors including the specified significance level (alpha), the desired statistical power (1-beta), the fraction (eta) of truly altered genes out of the total g genes studied, and the effect sizes (Delta) for the altered genes. This paper proposes a method to calculate the number of arrays required to detect at least 100lambda % (where 0 < lambda < or = 1) of the truly altered genes under the model of an equal effect size for all altered genes. The required numbers of arrays are tabulated for various values of alpha, beta, Delta, eta, and lambda for the one-sample and two-sample t-tests for g = 10,000. Based on the proposed approach, to identify up to 90% of truly altered genes among the unknown number of truly altered genes, the estimated numbers of arrays needed appear to be manageable. For instance, when the standardized effect size is at least 2.0, the number of arrays needed is less than or equal to 14 for the two-sample t-test and is less than or equal to 10 for the one-sample t-test. As the cost per array declines, such array numbers become practical. The proposed method offers a simple, intuitive, and practical way to determine the number of arrays needed in microarray experiments in which the true correlation structure among the genes under investigation cannot be reasonably assumed. An example dataset is used to illustrate the use of the proposed approach to plan microarray experiments.
Effect of Subanesthetic Ketamine on Intrinsic Functional Brain Connectivity: A Placebo-controlled Functional Magnetic Resonance Imaging Study in Healthy Male Volunteers

Background:The influence of psychoactive drugs on the central nervous system has been investigated with positron emission tomography and task-related functional magnetic resonance imaging. However, it is not known how these drugs affect the intrinsic large-scale interactions of the brain (resting-state functional magnetic resonance imaging connectivity). In this study, the effect of low-dose S(+)-ketamine on intrinsic brain connectivity was investigated. Methods:Twelve healthy, male volunteers received a 2-h intravenous S(+)-ketamine infusion (first hour 20 mg/70 kg, second hour 40 mg/70 kg). Before, during, and after S(+)-ketamine administration, resting-state brain connectivity was measured. In addition, heat pain tests were performed between imaging sessions to determine ketamine-induced analgesia. A mixed-effects general linear model was used to determine drug and pain effects on resting-state brain connectivity. Results:Ketamine increased the connectivity most importantly in the cerebellum and visual cortex in relation to the medial visual network. A decrease in connectivity was observed in the auditory and somatosensory network in relation to regions responsible for pain sensing and the affective processing of pain, which included the amygdala, insula, and anterior cingulate cortex. Connectivity variations related to fluctuations in pain scores were observed in the anterior cingulate cortex, insula, orbitofrontal cortex, and the brainstem, regions involved in descending inhibition of pain. Conclusions:Changes in connectivity were observed in the areas that explain ketamine's pharmacodynamic profile with respect to analgesia and psychedelic and other side effects. In addition, pain and ketamine changed brain connectivity in areas involved in endogenous pain modulation.
DEMO: Polemical Video Annotation by Twitter

In this paper we present a method to enhance video metadata by using microposts generated through social interactions during live events. Our goal is to make visible the audience “polemical activity” (the exchange of arguments, counter-arguments and references) elicited by the talk, and use it as a tool to browse the video record. To achieve it, we design a new interface and service that makes a synthetic view of microposts interaction.
Cascade active learning for SAR image annotation

In this paper, a novel active learning approach and system incorporating multiple instance learning for SAR image mining and annotation is introduced. Based on a multiscale and hierarchial patch based image representation, a cascade classifier is learned at different levels. At each level of the hierarchy, a SVM classifier is trained based on active learning and the training sample propagation between different levels is achieved through Multiple Instance SVM (MI-SVM). Classification at the higher level is applied only to the positive patches obtained at the previous level, which can significantly reduce the burden of computation in the case of large data set. Performance has been evaluated through a large data set, which shows promising gain not only in accuracy but also in computation.
End-Expiratory Occlusion Test to Predict Fluid Responsiveness Is Not Suitable for Laparotomic Surgery.

BACKGROUND The end-expiratory occlusion test predicts fluid responsiveness in ventilated intensive care patients; however, its utility in the operating room is questioned. We assessed end-expiratory occlusion test in laparotomic surgery for predicting volume expansion. METHODS Forty-six patients were included in this study: stage 1 (n = 26) with an end-expiratory occlusion test of 15 seconds, followed by volume expansion, which consisted of 250 mL of colloid over 5 minutes and stage 2 (n = 20) with an end-expiratory occlusion test of 25 seconds followed by volume expansion. The last 10 patients had transdiaphragmatic pressures probed. Patients with an increase in cardiac index >15% after volume expansion were responders. Pulse pressure variation, stroke volume (SV) index, and cardiac index were analyzed. Receiver operating characteristic curves were established for changes in SV and pulse pressure induced by end-expiratory occlusion test and pulse pressure variation using the responders status for volume expansion as outcome. RESULTS A total of 44 (38%) volume expansions were deemed responders. After end-expiratory occlusion test of 15 seconds, no hemodynamic variables were significantly increased. After end-expiratory occlusion test of 25 seconds, SV index increased in responders (37.1 ± 8.8 mL/m after end-expiratory occlusion test of 25 seconds versus 35.7 ± 8.6 before; P < .0001). End-expiratory occlusion test could not discriminate responders from nonresponders. Only pulse pressure variation had significantly different area under the curve from that expected by chance (0.7 [0.57-0.81]; P = .002 for end-expiratory occlusion test of 15 seconds; and 0.78 [0.64-0.89]; P = .0001 for end-expiratory occlusion test of 25 seconds). After laparotomy, gastric pressure decreased significantly (4 [2.75-5] vs 2 [2-4] cm H2O; P = .0417); no difference was noticed in the transdiaphragmatic gradient. CONCLUSIONS End-expiratory occlusion test was not reliable to discriminate responders from nonresponders after volume expansion during laparotomic surgery.
Novel Extending Scheme for the Construction of Rate-Compatible IRA-Like Codes

In this paper, a novel extending algorithm is proposed for the construction of rate compatible (RC) irregular repeat accumulate like (IRA-like) codes. Based on the structure characters of IRA-like codes, we propose an extending algorithm with uniform check node degree distribution and strong dependency in parity check matrix. Lower rate codes constructed through this method are efficiently encodable and well performed. Starting from initial code rate 8/16, the designed extending algorithm combining with existing puncturing algorithm realizes a series of RC IRA-like codes with rate R = 8/24, 8/23. 8/9. Simulation results show that the constructed RC IRA-like codes outperform those of similar algorithms from 0.04dB to 0.4 dB.
A Novel Native Store-operated Calcium Channel Encoded by Orai3

Store-operated calcium (Ca2+) entry (SOCE) mediated by STIM/Orai proteins is a ubiquitous pathway that controls many important cell functions including proliferation and migration. STIM proteins are Ca2+ sensors in the endoplasmic reticulum and Orai proteins are channels expressed at the plasma membrane. The fall in endoplasmic reticulum Ca2+ causes translocation of STIM1 to subplasmalemmal puncta where they activate Orai1 channels that mediate the highly Ca2+-selective Ca2+ release-activated Ca2+ current (ICRAC). Whereas Orai1 has been clearly shown to encode SOCE channels in many cell types, the role of Orai2 and Orai3 in native SOCE pathways remains elusive. Here we analyzed SOCE in ten breast cell lines picked in an unbiased way. We used a combination of Ca2+ imaging, pharmacology, patch clamp electrophysiology, and molecular knockdown to show that native SOCE and ICRAC in estrogen receptor-positive (ER+) breast cancer cell lines are mediated by STIM1/2 and Orai3 while estrogen receptor-negative (ER−) breast cancer cells use the canonical STIM1/Orai1 pathway. The ER+ breast cancer cells represent the first example where the native SOCE pathway and ICRAC are mediated by Orai3. Future studies implicating Orai3 in ER+ breast cancer progression might establish Orai3 as a selective target in therapy of ER+ breast tumors.
Differential Effects of a Tier Two Behavior Intervention Based on Function of Problem Behavior

The purpose of this study was to investigate the effectiveness of a tier two daily behavior card intervention and differential effects based on function of problem behavior. The participants were 36 elementary school students nominated for additional intervention beyond universal School-Wide Positive Behavior Support. Measures included standardized behavior rating scales and rate of office discipline referrals before and after 8 weeks of intervention. A multivariate analysis of variance was used, and results showed statistically significant differences in response to intervention based on teacher-identified function of problem behavior. Results are discussed in terms of considering function of behavior in selecting tier two interventions and implementing a three-tier response to intervention model.
The Escherichia coli Cell Division Protein FtsW Is Required To Recruit Its Cognate Transpeptidase, FtsI (PBP3), to the Division Site

ABSTRACT The bacterial cell division protein FtsW has been suggested to perform two functions: stabilize the FtsZ cytokinetic ring, and facilitate septal peptidoglycan synthesis by the transpeptidase FtsI (penicillin-binding protein 3). We show here that depleting Escherichia coli cells of FtsW had little effect on the abundance of FtsZ rings but abrogated recruitment of FtsI to potential division sites. Analysis of FtsW localization confirmed and extended these results; septal localization of FtsW required FtsZ, FtsA, FtsQ, and FtsL but not FtsI. Thus, FtsW is a late recruit to the division site and is essential for subsequent recruitment of its cognate transpeptidase FtsI but not for stabilization of FtsZ rings. We suggest that a primary function of FtsW homologues—which are found in almost all bacteria and appear to work in conjunction with dedicated transpeptidases involved in division, elongation, or sporulation—is to recruit their cognate transpeptidases to the correct subcellular location.
Immunohistochemical Maspin Expression in Transitional Cell Carcinoma of the Bladder

Purpose: Evaluation of Maspin marker in TCC of urine bladder, its grade, and stage, and to compare Maspin expression in normal transitional cell epithelium and TCC in patients admitted to Modarres Hospital from 2009 to 2012. Materials & Methods: Paraffin blocks of bladder tissue, from total number of 76 patients with TCC, and normal epithelium were included. Slides were prepared, and stained by Immunohistochemical staining method for Maspin marker, and assessed by two independent pathologists. Results: Maspin marker expression had been reduced in bladder tissue with TCC, which corresponded to the grade and stage. Normal urothelial mucosa was strongly Maspin-positive, while the intensity of staining in TCC was reduced as both the grade and stage were increased. Conclusion: Maspin expression, by Immunohistochemistry method, is reduced in TCCs of the urinary bladder. There was a meaningful reverse relationship between the intensity of Maspin expression and tumor stage. It can be suggested that evaluation of the Maspin marker can be helpful as a prognostic factor and to determine the low and high grade TCC in difficult cases.
Implied volatility functions: empirical tests

Black and Scholes (1973) implied volatilities tend to be systematically related to the option's exercise price and time to expiration. Derman and Kani (1994), Dupire (1994), and Rubinstein (1994) attribute this behavior to the fact that the Black/Scholes constant volatility assumption is violated in practice. These authors hypothesize that the volatility of the underlying asset's return is a deterministic function of the asset price and time and develop the deterministic volatility function (DVF) option valuation model, which has the potential of fitting the observed cross-section of option prices exactly. Using a sample of S and P 500 index options during the period June 1988 through December 1993, we evaluate the economic significance of the implied deterministic volatility function by examining the predictive and hedging performance of the DVF option valuation model.
Dual-plan bandwidth smoothing for layer-encoded video

Traditional bandwidth smoothing techniques can be naturally supported by the renegotiated constant bit rate (RCBR) service model, but renegotiation failure in RCBR may cause buffer underflow and interrupt the playback of video. To address this concern, a novel dual-plan bandwidth smoothing (DBS) scheme is proposed in this paper by taking advantage of the SNR scalability of layer-encoded video. Upon renegotiation failure, the proposed scheme can adaptively discard certain enhancement layers to guarantee continuous video playback at the original frame rate. Experiments are carried out to demonstrate the validity of the proposed scheme. The impacts of renegotiation interval, granularity of enhancement layers, and playback buffer size on resulted video quality are also studied. From the simulation results, it is shown that the performance of the RCBR-based DBS scheme can be improved by 1) reducing the minimum time gap of renegotiation interval; 2) employing multilayer video encoding with finer granularity; and/or 3) increasing the playback buffer size.
Design rationale: Researching under uncertainty

Abstract Rationale research in software development is a challenging area because although there is no shortage of advocates for its value, there is also no shortage of reasons for why rationale is unlikely to be captured in practice. Despite more than 30 years of research there still remains much uncertainty: how useful are the potential benefits and how insurmountable are the barriers? Will the value of the rationale (design and otherwise) justify the cost of collecting it? Although there have been numerous rationale research projects, many, if not most, received little or no empirical evaluation. There also have not been many studies examining what the needs are of the practitioners who would be supported by the rationale. This article discusses the “doom and gloom” predictions of rationale's failure, provides a survey of evaluations of rationale systems, and discusses what we hope is a brighter outlook for rationale research in the future. There are development standards and synergistic research areas that may help with rationale research and its acceptance in the software community with which we should be working. This article also presents the results of a pilot survey of software developers who were asked how they would envision using rationale and what they believe the most important barriers are. Although some results were as expected, there were also some surprises. Research on technology transfer indicates that, among other things, to transition successfully from research into practice we need to understand the need that is being met and demonstrate the value of our approach. Until we have determined how our work is needed by the people we are trying to help we will remain researching under uncertainty.
Low power scheduling method using multiple supply voltages

In this paper, we propose a method to solve the multiple supply voltage scheduling problem which is to assign the operational nodes of a control/data flow graph to a voltage level to minimize the average power consumption within a given computation time. Different from the previous researches focused on the operational nodes in the critical path and utilized the slack time to change the voltage of other nodes, our method can deal with all nodes without considering whether the node is in the critical path or not, and the benefit is that the voltage assignment of each node becomes more flexible. The proposed method consists of two phases, the scheduling phase and the adjusting phase, and considers both the power (delay) of the computational components and the power (delay) of the level shifters. Experimental result shows that using three voltages on a number of standard benchmarks, an average power saving of 34.23% can be obtained if the delay overhead is set as 0, and 48.07% can be obtained if the total delay is set as 1.6 times of the original delay
The effectiveness of a short form of the Household Food Security Scale.

OBJECTIVES On the basis of an 18-item Household Food Security Scale, a short form was developed to assess financially based food insecurity and hunger in surveys of households with and without children. METHODS To maximize the probability that households would be correctly classified with respect to food insecurity and hunger, 6 items from the full scale were selected on the basis of April 1995 Current Population Survey data. RESULTS The short form classified 97.7% of households correctly and underestimated the prevalence of overall food insecurity and of hunger by 0.3 percentage points. CONCLUSIONS The short form of the Household Food Security Scale is a brief but potentially useful tool for national surveys and some state/local applications.
An alternative design flow for receiver performance optimization through a trade-off between RF and ADC

The lack of a systematic design strategy that can monitor the relation between RF blocks and ADC is one of the main obstacles for achieving overall system optimization. This paper presents an alternative design flow based on the translation of ADC parameters into the RF domain. This design flow indicates four variables that can be used for the trade-off between RF and ADC blocks. Associating these key variables to power consumption enables the trade-off between the block performance and system power consumption. The demonstrated capability of this method is illustrated by comparing two scenarios, related to the IEEE 802.11a standard.
Diagnostic and surgical therapeutic features of extrahepatic bile duct carcinoma without jaundice.

AIM To analyze the diagnostic and therapeutic features of extrahepatic bile duct carcinoma (EBDC) without jaundice. METHODS Between 1985 and 1999, 101 patients underwent surgery for EBDC in Xiangya Hospital. These patients were divided into two groups: 84 jaundiced patients and 17 non-jaundiced patients according to preoperative serum total bilirubin levels. The clinical manifestations, laboratory findings, location, pathology and surgical resectability of the tumors were compared between the two groups. RESULTS The laboratory parameters such as hemoglobin, serum albumin ALB, AKP, gamma-GT, and sonography appearance were similar between the two groups, and there was no significant difference in tumor location, pathological type and resectability. However, the number of non-jaundiced patients associated with chololithiasis was significantly greater than that of jaundiced patients (P = 0.008). CONCLUSION The presence of jaundice is not a reliable criterion for the prediction of the resectability and the extent of tumor progression in extrahepatic bile duct carcinoma. Decreased levels of blood hemoglobin and serum albumin, elevated levels of AKP and gamma-GT, and /or abnormal sonography may be suggestive. Biopsy of a stenotic or thickened bile duct is strongly recommended for a correct diagnosis before the appearance of jaundice.
Two layers obstacle avoidance algorithm for Autonomous Underwater Vehicle

Autonomous Underwater Vehicles (AUVs) operate in unknown underwater environments and take decisions based on sensor readings, without any link with a human operator. It is critical for the AUVs to be able to avoid submerged obstacles such as cliffs, wrecks and floating mines to improve vehicle survivability. In this study obstacle avoidance algorithm that combining pre-planning and reactive techniques is presented. The approach uses forward looking sonar with image processing for obstacle detection. So it can be used as a logic sensor. The proposed algorithms are focused on horizontal plane obstacle detection and avoidance.
Immersive Virtual Undersea World

This paper proposes a virtual undersea world for users based on the real world. As the sensor technology in which one can feel things as if they were in the real world owing to the development of equipment techniques like HMD and data gloves was introduced, real-time interactions with a virtual world is made possible. Based on this, this study generated images in the direction of the user experiencing the virtual world, and used the wireless HMD in a real world designed in a 1‐to‐1 size to the virtual world to support free exploration in the virtual world. Also, it enhanced the user’s sense of experience at the virtual undersea world by generating images with control of virtual fish in accordance with the user’s hand movements.
Calibration Risk for Exotic Options

For academic modelers, the major objective is typically to derive a valuation equation for a derivative instrument, while computing Greek letter risks is only a secondary consideration. For users of models in the real world, however, the market provides the correct value and the parameters of the theoretical pricing model are calibrated to match the market, in order to generate risk assessment and risk management strategies consistent with the way the market is currently pricing the security. But calibration can be done in a number of ways. Do we want parameters that minimize the overall discrepancy between model values and market prices in dollars, or in percent? Alternatively, should we focus on the crucial but unobservable volatility parameter and minimize aggregate differences between the implied volatility from the model and Black-Scholes implied volatility, either in volatility points or in percentages? This might make sense because the latter are often used in setting option price quotes in the market. In this paper, the authors examine what impact this choice has on the results of model calibration, taking as examples the Heston stochastic volatility model and the Bates model, which allows price jumps as well. They find considerable difference among parameters estimated by using absolute price differences versus one of the other techniques. The paper demonstrates that the choice of calibration method can have a substantial impact on pricing of exotic option contracts and on model risk. One result is that calibration based on absolute price discrepancies produces quite different parameter estimates than the other three methods.