Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

Breast cancer outcome can be predicted using models derived from gene expression data or clinical data. Only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. We rigorously compare three different integration strategies (early, intermediate, and late integration) as well as classifiers employing no integration (only one data type) using five classifiers of varying complexity. We perform our analysis on a set of 295 breast cancer samples, for which gene expression data and an extensive set of clinical parameters are available as well as four breast cancer datasets containing 521 samples that we used as independent validation.mOn the 295 samples, a nearest mean classifier employing a logical OR operation (late integration) on clinical and expression classifiers significantly outperforms all other classifiers. Moreover, regardless of the integration strategy, the nearest mean classifier achieves the best performance. All five classifiers achieve their best performance when integrating clinical and expression data. Repeating the experiments using the 521 samples from the four independent validation datasets also indicated a significant performance improvement when integrating clinical and gene expression data. Whether integration also improves performances on other datasets (e.g. other tumor types) has not been investigated, but seems worthwhile pursuing. Our work suggests that future models for predicting breast cancer outcome should exploit both data types by employing a late OR or intermediate integration strategy based on nearest mean classifiers.
αv integrins play an important role in myofibroblast differentiation

Transforming growth factor‐β1 is a potent mediator of the differentiation of fibroblasts into myofibroblasts, which is characterized by the appearance of the cytoskeletal protein α‐smooth muscle actin. The aim of this study was to investigate the role of integrin extracellular matrix receptors in transforming growth factor‐β1–induced myofibroblast differentiation. We show that blockade of the αv and/or β1 integrins prevents the transforming growth factor‐β1–induced myofibroblast differentiation, seen by the increased expression of α‐smooth muscle actin and enhanced collagen gel contraction in three human fibroblast cell lines (from the mouth, skin, and kidney). Further, blockade of αv specific integrins αvβ5 and αvβ3 suppressed myofibroblast differentiation in fibroblasts from the mouth and skin; however, in the kidney cells, the prevention of differentiation was seen only with blockade of αvβ5 integrin but not αvβ3. A possible reason for this result may be different degrees of responsiveness to transforming growth factor‐β1 treatment seen from different anatomical origins of the cell lines. These data indicate a novel role for αv integrins in the differentiation of human fibroblasts from the mouth, skin, and kidney into myofibroblasts and suggest that there is a common differentiation pathway.
Approximating Subdifferentials by Random Sampling of Gradients

Many interesting real functions on Euclidean space are differentiable almost everywhere. All Lipschitz functions have this property, but so, for example, does the spectral abscissa of a matrix a non-Lipschitz function. In practice, the gradient is often easy to compute. We investigate to what extent we can approximate the Clarke subdifferential of such a function at some point by calculating the convex hull of some gradients sampled at random nearby points.
Recent Adaptive Events in Human Brain Revealed by Meta-Analysis of Positively Selected Genes

Background and Objectives Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection. Methods and Results We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection. Conclusion Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.
High Isolation and Compact Diplexer Using the Hybrid Resonators

In this letter, a compact microstrip diplexer with very high output isolation is proposed. This diplexer consists of compact hybrid resonators, which are capable of introducing transmission zeros at desired frequencies and meanwhile suppressing signals below the resonant frequencies through tapping the feeding line close to the shorted vias. By designing the transmission zero of the lower-frequency channel in the higher passband, and utilizing the high lower-stopband suppression property of the higher-frequency channel, very high diplexer output isolation can be achieved. The proposed diplexer with center frequencies at 1.8 and 2.45 GHz, respectively, has demonstrated better than 55 dB output isolation and more than 55 dB suppressions in the stopbands. Furthermore, the diplexer occupies only a small area of 0. 13λ0 × 0. 2λ0.
Error probability of transparent optical networks with optical multiplexers/demultiplexers

This letter presents an accurate model for the evaluation of the error probability of transparent multiwavelength optical networks with cascaded optical multiplexers/demultiplexers (MUX/DMUXs). The error probability evaluation takes into account arbitrary pulse shapes, arbitrary optical MUX/DMUX and electronic lowpass filter transfer functions, intersymbol interference, and the accurate (non-Gaussian) noise probability density function at the output of the optically preamplified direct-detection receiver. As an example, the model is used to study the cascadability of arrayed waveguide grating routers in conjunction with nonreturn-to-zero pulses.
Pressure-drop studies of resistance components for integration into a SFM-based fluidic circuit

The design of swappable fluidic module (SFM) has the advantage that all components can be easily swapped. This paper reports a resistance component, which can be readily integrated into a SFM-based fluidic circuit for different applications. In this research, we designed and fabricated two basic modular fluidic components including channel and T-tube to transport the fluid with the pressure drops due to a continuous flow past a straight circular channel. From the electrohydraulic analogy, the hydraulic resistance for a uniform circular cross-section channel due to the viscous effect is therefore calculated and compared with the measured data. The measured results were reasonably close to the predictions with the maximum error within 9% in the measurements of pressure drop and hydraulic resistance.
Transformation method for problems involving perfect electromagnetic conductor (PEMC) structures

Perfect electric conductor (PEC) and perfect magnetic conductor (PMC) can be generalized to perfect electromagnetic conductor (PEMC), a medium where certain linear combinations of electromagnetic fields are required to vanish. In differential-form representation, the corresponding medium is characterized as the simplest possible medium. It is defined through a scalar admittance parameter, whose zero and infinite limits yield the PMC and PEC media, respectively. In this paper a duality transformation is found that has the property of transforming PEMC to PEC and an isotropic medium to itself. Thus, problems involving PEMC objects in air can be transformed to problems with PEC objects in air which can be solved through traditional techniques and then transformed back. Several simple examples are treated to demonstrate the principle. PEMC has the potential of having similar applications as PMC in antenna engineering and finding structures for its realization is a challenge.
Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application in Cross-Subspecies Amplification

We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. 454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The number of alleles detected at each locus ranged from four to 24 and the expected heterozygosity varied from 0.57 to 0.92. Cross-subspecies amplification for O. m. masou, O. m. ishikawae and O. m. subsp. was successful. These microsatellites can be utilized in studies of genetic structure, genetic diversity, and intra- and inter-subspecific hybridization, making a contribution to conservation and management of the Oncorhynchus masou complex.
Investigating impact of effective communication practices and project complexity on performance of international development projects

This study aims to explore and identify effective communication practices influencing performance of international development projects in Pakistan and also illustrates important project complexity elements which moderates the relationship between effective communication and project performance. After detailed literature review and conducting 9 expert interviews from project managers, project coordinators and communication coordinators working on international development projects, we identified 4 key communication practices which should be adopted by project professionals working on such projects. These practices involved (i) Quality of communication, (ii) Frequency of communication, (iii) Communication formality (iv) Communication bi-directionality. Task complexity is taken as moderator between communication and performance relationship. A survey was conducted to find the impact of communication practices and moderating impact of project complexity on project performance. Questionnaires were sent to 60 international organizations working on such projects. The results of the study showed that these practices have significant and positive impact on project performance; project complexity has a minimal impact on the communication and performance relationship. Recommendations were made on the basis of the results of the study.
Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

Chromatin in sperm is different from that in other cells, with most of the genome packaged by protamines not nucleosomes. Nucleosomes are, however, retained at some genomic sites, where they have the potential to transmit paternal epigenetic information. It is not understood how this retention is specified. Here we show that base composition is the major determinant of nucleosome retention in human sperm, predicting retention very well in both genic and non-genic regions of the genome. The retention of nucleosomes at GC-rich sequences with high intrinsic nucleosome affinity accounts for the previously reported retention at transcription start sites and at genes that regulate development. It also means that nucleosomes are retained at the start sites of most housekeeping genes. We also report a striking link between the retention of nucleosomes in sperm and the establishment of DNA methylation-free regions in the early embryo. Taken together, this suggests that paternal nucleosome transmission may facilitate robust gene regulation in the early embryo. We propose that chromatin organization in the male germline, rather than in somatic cells, is the major functional consequence of fine-scale base composition variation in the human genome. The selective pressure driving base composition evolution in mammals could, therefore, be the need to transmit paternal epigenetic information to the zygote.
Challenges for capacitor voltage balancing in a cascaded h-bridge StatCom utilising finite control set Model Predictive Control

Model Predictive Control (MPC) can provide performance benefits over established schemes in power electronic converter control. However, the implementation of the scheme changes the characteristics of the voltage and current control systems relative to established control methods and different approaches for control are required. This paper considers the implication of the speed of the stack voltage balancing scheme on the regulation of the capacitor voltages in a 5 level cascaded h-bridge StatCom. A dead-beat scheme with phase shifted carrier pulse width modulation (PSC-PWM) and a finite control set model predictive control (FCS-MPC) scheme are compared with simulation results.
CLNS 04/1877 hep-ph/0405196 STATUS OF ψ ′ ′ DECAYS TO CHARMLESS FINAL STATES 1

The ψ′′ ≡ ψ(3770) particle is the lowest-mass charmonium resonance above DD̄ threshold. It is produced through virtual photons in e+e− collisions, and can serve as a well-defined source of charmed particle pairs [1] in the same way that the Υ(4S) state, lying just above BB̄ threshold, is a good source of nonstrange B mesons. While discovered a number of years ago [2], the ψ′′ is now being exploited through high-intensity studies under way at the CLEO Detector at Cornell [3] and at the BES Detector in China [4]. The couplings of the ψ′′ to charmless states are of interest for a number of reasons. (1) ψ′′ production and decays are sensitive to the mixing between S and D waves in its wave function. It is predominantly a cc̄(1D1) state, 4 but contains important contributions from mixing with the 2S1 level (of which ψ ′ = ψ(3686) contains the major share) as well as with possible other S1 levels and DD̄ continuum states [5, 6]. This mixing can affect not only ψ′′ modes, but also ψ′ modes, suppressing some of them while leading to contributions in ψ′′ decays [7] which may be hard to see in those decays as a result of interference effects [8, 9, 10, 11]. (2) New measurements of the cross section σ(e+e− → ψ′′ → DD̄) ≡ σ(DD̄) have recently been reported by the BES [4] and CLEO [12] Collaborations. The CLEO measurement employs a “double-tag” method pioneered by the Mark III group in a previous study [13]. Although the values appear higher than that of Mark III, σ(DD̄)
Trend-Aware Video Caching Through Online Learning

This paper presents Trend-Caching, a novel cache replacement method that optimizes cache performance according to the trends of video content. Trend-Caching explicitly learns the popularity trend of video content and uses it to determine which video it should store and which it should evict from the cache. Popularity is learned in an online fashion and requires no training phase, hence it is more responsive to continuously changing trends of videos. We prove that the learning regret of Trend-Caching (i.e., the gap between the hit rate achieved by Trend-Caching and that by the optimal caching policy with hindsight) is sublinear in the number of video requests, thereby guaranteeing both fast convergence and asymptotically optimal cache hit rate. We further validate the effectiveness of Trend-Caching by applying it to a movie.douban. com dataset that contains over 38 million requests. Our results show significant cache hit rate lift compared to existing algorithms, and the improvements can exceed 40% when the cache capacity is limited. Furthermore, Trend-Caching has low complexity.
FOREST HEIGHT MAPPING BASED ON LIDAR AND SAR DATA

Researches have shown that 3D vegetation structure exerts a strong influence on radiation transmission and changes radiation and energy balance at the land surface. Vegetation spatial structure including plant height, biomass, vertical and horizontal heterogeneity, is an important factor influencing the exchanges of matter and energy between the landscape and atmosphere, and the biodiversity of ecosystems. Boreal Forest is one of the largest ecosystems on the Earth, and it plays an important part in environment and economy. Estimation of boreal forest canopy height is an extremely urgent research because it is essential for understanding ecosystems changing by human activities and climate change. Lidar with capabilities of recording the time-varying return signals provide the vegetation height, ground surface height, and the vertical distribution of vegetated surfaces intercepted by laser pulses. On the other side, radars have the capability responding to the amount of water in forest canopy, as well as its spatial structure. Data from these sensors contain information relevant to different aspects of the biophysical properties of the vegetation canopy.
Hybridization in Genetic Algorithm with Hill Climbing to Optimize the Knapsack Problem

Genetic Algorithm (GA) is used to solve optimization problems. Knapsack is an optimization problem. To solve the knapsack problem we used two algorithms and their results were compared. To solve the knapsack problem we use genetic algorithm operators as selection, crossover, and mutation after that we perform the hybridization of GA and the results of both algorithms were compared. Memetic algorithm is combination of genetic algorithm and hill climbing on the Knapsack problem to obtain the more optimized result.
The effect of a multisensory exercise program on engagement, behavior, and selected physiological indexes in persons with dementia

A multisensory exercise approach that evokes the stimulation and use of various senses, such as combining physical and cognitive stimuli, can assist in the management of persons with Alzheimer's disease (AD). The objective of this study was to evaluate the outcomes of a multisensory exercise program on cognitive function (engagement), behavior (mood), and physiological indices (blood pressure, resting heart rate, and weight) in 13 nursing home residents diagnosed with moderate to severe AD. A one-group pretest/post-test, quasi-experimental design was used. The program combined a variety of sensory stimulations, integrating storytelling and imaging strategies. Results showed an improvement in resting heart rate, overall mood, and in engagement of physical activity. The findings suggest that a multisensory exercise approach can be beneficial for individuals with AD.
An Area-Efficient and Tunable Bandwidth- Extension Technique for a Wideband CMOS Amplifier Handling 50+ Gb/s Signaling

This paper reports an area-efficient and tunable bandwidth (BW)-extension technique for a wideband CMOS amplifier to handle very high rate (50+ Gb/s) signaling while keeping a low jitter penalty. We identify its architectural advantages by correlating the performances with the frequency domain (magnitude and group delay (GD) responses) and time domain (impulse and step responses) and comparing them with the existing solutions. Specifically, our technique enables a flexible ac characteristic by introducing a tunable grounded active inductor in the bridged-shunt peaking topology, offering: 1) a high BW enhancement ratio (BWER = <inline-formula> <tex-math notation="LaTeX">$2.65\times$ </tex-math></inline-formula>); 2) BW-power scalability with small in-band gain variation; and 3) fine tunability of the passband gain without affecting the BW, GD, and power. The experimental prototype is a 65-nm CMOS four-stage differential amplifier occupying just 0.0077 mm<sup>2</sup>. It delivers a 15-dB gain over a 43-GHz BW with 45-mW power consumption. Small in-band gain variation (0.58 dB) and ripple (1.53 dB) are concurrently achieved with low in-band GD variation (17 to 35.3 ps) and ripple (18.3 ps). The achieved figure of merit of 5.48 [(dc Gain <inline-formula> <tex-math notation="LaTeX">$\times$ </tex-math></inline-formula> BW)/Power] compares favorably with the prior art.
Activity-centered design for temporal data management

With our interviews, we found that professors need to organize and use fine-grained information from diverse sources and formats in their everyday tasks, such as taking a meeting, hosting a project and etc. Although there is a bunch of computer applications and devices which can help them easily manage all these cross-media information, professors are still often confused about reviewing their old information as time goes on. In this paper, we present activity-centered learning design, a meaningful structure for task information, to assist professors with their present and future teaching tasks. We also illustrate a prototype of the Activity construct from the end-user's perspective.
Correlation between biochemical indicators of blood lipid with cerebral vascular diseases.

OBJECTIVE The objective of this study was to investigate correlation of the changes in serum levels of cholesterol (chol), lipoprotein (a) (Lpa) and homocysteine (HCY) with incident cerebral infarction and cerebral hemorrhage. METHODS Data on a total of 418 patients (318 cerebral infarction events and 100 cerebral hemorrhage cases) were analyzed in this study. Serum chol and HCY levels were tested by means of GPO-PAP. Serum Lpa levels were measured using latex agglutination turbidimetry. RESULTS Patients with cerebral infarction showed significantly higher serum Lpa levels and anomaly ratio than those with cerebral hemorrhage (P<0.05), while no significant changes were identified for chol and HCY (P>0.05). Analyses by age indicated substantially increased Lpa concentration among cerebral infarction patients>60 years of age (P<0.05). No statistical significance was observed in other analyses carried out in the study. CONCLUSION These results demonstrate that Lpa concentration is clearly correlated with cerebral infarction incidence. Lpa may act as an independent risk factor and could be used as a biomarker for this disease.
Characterizing the process of reaching consensus for social systems

A novel way of characterizing the process of reaching consensus for a social system is given. The foundation of the characterization is based on the theorem which states that the sufficient and necessary condition for a system to reach the state of consensus is the occurrence of communicators, defined as the units of the system that can directly communicate with all the others simultaneously. A model is proposed to illustrate the characterization explicitly. The existence of communicators provides an efficient way for unifying two systems that a state of consensus is guaranteed after the mergence.