Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical Scoring Functions for Affinity Prediction of Protein‐ligand Complexes

The ability to rapidly assess the quality of a protein‐ligand complex in terms of its affinity is of fundamental importance for various methods of computer‐aided drug design. While simple filtering or matching critieria may be sufficient in fast docking methods or at early stages of virtual screening, estimates of the actual free energy of binding are needed whenever refined docking solutions, ligand rankings or support for the optimization of hit compounds are required. If rigorous free energy calculations based on molecular simulations are impractical, such affinity estimates are provided by scoring functions. The class of empirical scoring functions aims to provide them via a regression‐based approach. Using experimental structures and affinity data of protein‐ligand complexes and descriptors suitable to capture the essential features of the interaction, these functions are trained with classical linear regression techniques or machine‐learning methods. The latter have led to considerable improvements in terms of prediction accuracy for large generic data sets. Nevertheless, many limitations are not yet resolved and pose significant challenges for future developments.
Clinical Implications of Myocardial Pre-And Postconditioning : Who is the Better Player ?

Brief cycles of ischemia followed by reperfusion before prolonged ischemia is referred to as ischemic preconditioning (IPC), while brief periods of ischemia and reperfusion applied after pronged ischemia and at the onset of reperfusion denote ischemic postconditioning (IPOS). IPC and IPOS have been designated as two cardioprotective phenomenon against myocardial ischemia-reperfusion (I/R) injury by certain mechanisms like activation of prosurvival kinases, activation of eNOS (endothelial nitric oxide synthase) and release of NO. Recently, IPC and IPOS have been widely used in the clinical practice affording variable degrees of protection. The present review article deals with the mechanisms involved in IPC and IPOS mediated cardioprotection. Additionally, the clinical applications of myocardial pre-and postconditioning in patients with high prevalence of ischemic heart disease have been critically discussed. Introduction Ischemic heart disease (IHD) represents one of the major burdens on healthcare systems today [1] . Ischemia/reperfusion (I/R) injury is a major contributory factor to cardiac dysfunction that can be defined as the damage to cardiac tissue when blood supply is restored after a prolonged period of ischemia [2-3] . Ischemic preconditioning (IPC) and postconditioning (IPOS) represent two such interventions that are noted to afford cardioprotection. Brief episodes of ischemia and reperfusion applied before prolonged ischemia and reperfusion represents IPC [4] , whereas brief episodes of ischemia and reperfusion applied after pronged ischemia and just at the onset of reperfusion represents IPOS [5] . These two anti-jeopardized phenomenons are the most potent and reproducible methods of rescuing cardiac tissue from undergoing irreversible *Corresponding Author
Relation between smoking and risk of dementia and Alzheimer disease

Background and Objective: Previous studies relating smoking with the risk of dementia have been inconsistent and limited in their validity by short follow-up times, large intervals between baseline and follow-up assessments, and unspecific determination of dementia diagnosis. We re-assessed after longer follow-up time in the large population-based cohort of the Rotterdam Study whether smoking habits and pack-years of smoking are associated with the risk of dementia, Alzheimer disease (AD), and vascular dementia (VaD). Methods: Prospective population-based cohort study in 6,868 participants, 55 years or older and free of dementia at baseline. First, Cox proportional hazard models were used to relate smoking status at baseline with the risks of incident dementia, VaD, and AD, using never smokers as the reference category in all analyses. Then Cox proportional hazard models were used to relate pack-years of smoking with the risks of incident dementia, VaD, and AD. To explore the impact of the APOEε4 allele, sex, and age on the association between smoking status and dementia, we repeated all analyses stratifying, in separate models, by APOEε4 genotype, sex, and median of age. Results: After a mean follow-up time of 7.1 years, current smoking at baseline was associated with an increased risk of dementia (HR 1.47, 95% CI 1.18 to 1.86) and AD (HR 1.56, 95% CI 1.21 to 2.02). This increase in disease risk was restricted to persons without the APOEε4 allele. There was no association between current smoking and risk of VaD, and there was no association between past smoking and risk of dementia, AD, or VaD. Conclusion: Current smoking increases the risk of dementia. This effect is more pronounced in persons without the APOEε4 allele than APOEε4 carriers.
A novel high-sensitivity butterfly gyroscope driven by horizontal driving force

Sensitivity is an important index of the performance of micro-machined gyroscope, and enhancing sensitivity is an effective way to improve the performance of gyroscope. In this paper, a new type of vibration structure to enhance the sensitivity of butterfly micro-machined gyroscope was proposed. By using dry etching processing, the vibration structure can obtain a rectangle vibration beam rather than the traditional one which can change its driving method from vertical force to horizontal force. The horizontal driving amplitude and initial capacitive gap of traditional butterfly micro-machined gyroscope are subjected to its vertical driving method, which, to a great extent, limits its sensitivity. But the proposed structure driven by horizontal force can not only increase the driving amplitude, but also reduce the initial capacitance gap, so as to enhance the sensitivity of butterfly micro-machined gyroscope.
Chemogenetic inhibition reveals midline thalamic nuclei and thalamo‐accumbens projections mediate cocaine‐seeking in rats

Drug addiction is a chronic disease that is shaped by alterations in neuronal function within the cortical–basal ganglia‐thalamic circuit. However, our understanding of how this circuit regulates drug‐seeking remains incomplete, and relapse rates remain high. The midline thalamic nuclei are an integral component of the cortical–basal ganglia‐thalamic circuit and are poised to mediate addiction behaviors, including relapse. It is surprising that little research has examined the contribution of midline thalamic nuclei and their efferent projections in relapse. To address this, we expressed inhibitory, Gi/o‐coupled DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) in a subset of the midline thalamic nuclei or in midline thalamic nuclei neurons projecting to either the nucleus accumbens or the amygdala. We examined the effect of transiently decreasing activity of these neuronal populations on cue‐induced and cocaine‐primed reinstatement of cocaine‐seeking. Reducing activity of midline thalamic nuclei neurons attenuated both cue‐induced and cocaine‐primed reinstatement, but had no effect on cue‐induced reinstatement of sucrose‐seeking or locomotor activity. Interestingly, attenuating activity of efferent projections from the anterior portion of midline thalamic nuclei to the nucleus accumbens blocked cocaine‐primed reinstatement but enhanced cue‐induced reinstatement. Decreasing activity of efferent projections from either the posterior midline thalamic nuclei to the nucleus accumbens or the midline thalamic nuclei to amygdala had no effect. These results reveal a novel contribution of subsets of midline thalamic nuclei neurons in drug‐seeking behaviors and suggest that modulation of midline thalamic nuclei activity may be a promising therapeutic target for preventing relapse.
Seasonal and sex differences in responsiveness to adrenocorticotropic hormone contribute to stress response plasticity in red-sided garter snakes (Thamnophis sirtalis parietalis)

ABSTRACT As in many vertebrates, hormonal responses to stress vary seasonally in red-sided garter snakes (Thamnophis sirtalis parietalis). For example, males generally exhibit reduced glucocorticoid responses to a standard stressor during the spring mating season. We asked whether variation in adrenal sensitivity to adrenocorticotropic hormone (ACTH) explains why glucocorticoid responses to capture stress vary with sex, season and body condition in red-sided garter snakes. We measured glucocorticoids at 0, 1 and 4 h after injection with ACTH (0.1 IU g−1 body mass) or vehicle in males and females during the spring mating season and autumn pre-hibernation period. Because elevated glucocorticoids can influence sex steroids, we also examined androgen and estradiol responses to ACTH. ACTH treatment increased glucocorticoids in both sexes and seasons. Spring-collected males had a smaller integrated glucocorticoid response to ACTH than autumn-collected males. The integrated glucocorticoid response to ACTH differed with sex during the spring, with males having a smaller glucocorticoid response than females. Although integrated glucocorticoid responses to ACTH did not vary with body condition, we observed an interaction among season, sex and body condition. In males, ACTH treatment did not alter androgen levels in either season, but androgen levels decreased during the sampling period. Similar to previous studies, plasma estradiol was low or undetectable during the spring and autumn, and therefore any effect of ACTH treatment on estradiol could not be determined. These data provide support for a mechanism that partly explains how the hypothalamus–pituitary–adrenal (HPA) axis integrates information about season, sex and body condition: namely, variation in adrenal responsiveness to ACTH. Summary: The adrenal glucocorticoid response to ACTH varies with season and sex in garter snakes; decreased responsiveness to ACTH partly explains reduced stress sensitivity in males during the spring breeding season.
Fast Power Allocation Algorithms for Adaptive MIMO Systems.

Recent research results have shown that the MIMO wireless communication architecture is a promising approach to achieve high bandwidth efficiencies. MIMO wireless channels can be simply defined as a link for which both the transmitting and receiving ends are equipped with multiple antenna elements. Adaptive modulation and power allocation could be used to further improve the performance of MIMO systems. This thesis focuses on developing a fast and high performance power allocation algorithm. Three power allocation algorithms are proposed in this thesis and their performances are compared in various system sizes and transceiver architectures. Among the three algorithms proposed in this thesis, the fast algorithm may be considered as the best power allocation algorithm since the performance of the fast algorithm is almost as good as the fullsearch (optimal) algorithm and the mean processing time is considerably less than the fullsearch algorithm. The fast algorithm achieves about 97.6% agreement with the optimal throughput on average. In addition, the time taken to find the power scaling factors using the fullsearch algorithm is about 2300 times longer than the processing time of the fast algorithm in a 6 × 6 system when the SNR is 20dB. As an extension to the power allocation process, excess power allocation methods are introduced. Excess power is the unused power during the power allocation process. The power allocation algorithm allocates power to each received SNR to maximize the throughput of the system whereas the excess
A low-noise voltage-controlled ring oscillator in 28-nm FDSOI technology

This paper presents a 1V low phase noise ring based voltage-controlled-oscillator (VCO) for ultra-wide band (UWB) applications. The circuit is implemented in a 28-nm FDSOI technology. The VCO delay cell structure is characterized by a 3.75 mW power consumption and benefits from a new voltage control through the transistor body bias in order to achieve high performance with a wide tuning range. In the frequency range from 29 to 49 GHz, the lowest phase noise result is −132 dBc/Hz at 1 MHz frequency offset while operating at 49 GHz. These measurements lead to an excellent Figure of Merit (FoM) of −220 dBc/Hz.
Priority-based virtual machine load balancing in a scientific federated cloud

Cloud computing offers utility oriented services to users. It also reduces the maintenance cost of the infrastructure as well as initial investment cost for users or startup companies. Due to the effectiveness of these services, many companies or institutes are trying to adopt this technology for offloading scientific or industrial applications. Virtualization in cloud computing is used to build virtual infrastructure which is managed by a load balancer. Efficient design of the load balancer can reduce over or under provisioning. Load balancer contains virtual machine allocation technique which performs an important role with respect to power consumption of the data center. In this paper, we propose a system architecture and the virtual machine allocation algorithm for the load balancer in a scientific federated cloud. We have tested the proposed approach in a scientific federated cloud. Experimental results show that the proposed algorithm not only increases the utilization of resources but also reduces the energy consumption.
A Novel SSR Mitigation Method Based on GCSC in DFIG with Series Connected Compensator

This paper presents a novel study for SSR mitigating in the wind power systems based on DFIG using GCSC (Gate controlled series capacitor). The GCSC is composed of three pairs of anti-parallel GTO Thyristors (Gate Turn- off) connected in parallel with a fixed capacitor. The GCSC is applied to reduce inrush current in capacitor compensator during the transient operation by executing a proper firing angle control of thyristor gates. In order to realize SSR oscillation when the transient operation occurred, the DFIG turbine is connected through the shaft turbine model. The simulation results shown that the GCSC device is suitable and reasonable for suppressing SSR caused by torsional interaction (TI) and torque amplification (TA) and also damping the subsynchronous oscillation as well. The transient simulations have been carried out using PSCAD/EMTDC program to demonstrate the capability of the GCSC device in mitigating SSR.
A general sampling theory for nonideal acquisition devices

The authors first describe the general class of approximation spaces generated by translation of a function /spl psi/(x), and provide a full characterization of their basis functions. They then present a general sampling theorem for computing the approximation of signals in these subspaces based on a simple consistency principle. The theory puts no restrictions on the system input which can be an arbitrary finite energy signal; bandlimitedness is not required. In contrast to previous approaches, this formulation allows for an independent specification of the sampling (analysis) and approximation (synthesis) spaces. In particular, when both spaces are identical, the theorem provides a simple procedure for obtaining the least squares approximation of a signal. They discuss the properties of this new sampling procedure and present some examples of applications involving bandlimited, and polynomial spline signal representations. They also define a spectral coherence function that measures the "similarity" between the sampling and approximation spaces, and derive a relative performance bound for the comparison with the least squares solution. >
Very Large Scale Bundle Adjustment by Global Camera Consensus Runze

The increasing scale of Structure-from-Motion is fundamentally limited by the conventional optimization framework for the all-in-one global bundle adjustment. In this paper, we propose a distributed approach to coping with this global bundle adjustment for very large scale Structurefrom-Motion computation. First, we derive the distributed formulation from the classical optimization algorithm ADMM, Alternating Direction Method of Multipliers, based on the global camera consensus. Then, we analyze the conditions under which the convergence of this distributed optimization would be guaranteed. In particular, we adopt over-relaxation and self-adaption schemes to improve the convergence rate. After that, we propose to split the large scale camera-point visibility graph in order to reduce the communication overheads of the distributed computing. The experiments on both public large scale SfM data-sets and our very large scale aerial photo sets demonstrate that the proposed distributed method clearly outperforms the state-of-the-art method in efficiency and accuracy.
Population attributable risk for breast cancer: diet, nutrition, and physical exercise.

BACKGROUND The percentages of breast cancer cases in a given population attributable to specific risk factors (i.e., the population-attributable risks) can be calculated; determination of such risks associated with potentially modifiable risks factors, such as diet (e.g., levels of consumption of fruits, vegetables, vitamins, etc.), alcohol consumption, exercise, and body weight, are necessary to focus prevention strategies. METHODS With the use of data from a case-control study conducted in Italy from June 1991 through April 1994 on 2569 breast cancer case subjects and 2588 control subjects, we calculated multivariate odds ratios and population-attributable risks for breast cancer in relation to dietary beta-carotene and vitamin E intake, alcohol consumption, physical activity, and, for postmenopausal women, body mass index. RESULTS Among all subjects, the following attributable risks for the indicated risk factors were observed: 10.7% (95% confidence interval [CI] = 4.4%-17.0%) for high alcohol intake (i.e., >20 g/day), 15.0% (95% CI = 7.4%-22.9%) for low beta-carotene intake (i.e., <3366 microg/day), 8.6% (95% CI = -0.4%-17.5%) for low vitamin E intake (i.e., <8.5 mg/day), and 11.6% (95% CI = -0.1%-23.3%) for low levels of physical activity. The risks associated with alcohol and beta-carotene intake were larger among premenopausal women, and the risk associated with physical activity was larger among postmenopausal women. Being overweight accounted for 10.2 % (95% CI = 0.2%-20.2%) of breast cancer cases in postmenopausal women. Beta-carotene plus alcohol accounted for 28.1% (95% CI = 16.8-39.4) of the cases. Beta-carotene and physical activity accounted for 32% (95% CI = 14.3-49.8), and these three factors together accounted for 33% (95% CI = 19.9-46.1) of the breast cancer cases in the overall dataset. CONCLUSION Exposure to a few selected and potentially modifiable risk indicators explained about one third of the cases of breast cancer in this Italian population, indicating the theoretical scope for prevention of the disease.
Optimal Weight Design Approach for the Geometrically-Constrained Matching of Satellite Stereo Images

This study presents an optimal weighting approach for combined image matching of high-resolution satellite stereo images (HRSI). When the rational polynomial coefficients (RPCs) for a pair of stereo images are available, some geometric constraints can be combined in image matching equations. Combining least squares image matching (LSM) equations with geometric constraints equations necessitates determining the appropriate weights for different types of observations. The common terms between the two sets of equations are the image coordinates of the corresponding points in the search image. Considering the fact that the RPCs of a stereo pair are produced in compliance with the coplanarity condition, geometric constraints are expected to play an important role in the image matching process. In this study, in order to control the impacts of the imposed constraint, optimal weights for observations were assigned through equalizing their average redundancy numbers. For a detailed assessment of the proposed approach, a pair of CARTOSAT-1 sub-images, along with their precise RPCs, were used. On top of obtaining different matching results, the dimension of the error ellipses of the intersection points in the object space were compared. It was shown through analysis that the geometric mean of the semi-minor and semi-major axis by our method was reduced 0.17 times relative to the unit weighting approach.
An Effective History-based Background Extraction System

Problem statement: In many visions-based surveillance systems, the first step is accomplished by detecting moving objects resulted from subtraction of the current captured frame from the extracted background. So, the results of these systems mainly depend on the accuracy of the background image. Approach: In this study, a proposed background extraction system is presented to model the background using a simple method, to initialize the model, to extract the moving objects and to construct the final background. Our model saves the history of each pixel separately. It uses the saved information to extract the background using a probability-based method. It updates the history of the pixel consequently and according to the value of that pixel in the current captured image. Results: Results of the experiments certify that not only the quality of the final extracted background is the best between four recently re-implemented methods, but also the time consumption of the extraction is acceptable. Conclusion: Since History-based methods use temporal information extracted from the several previous frames, they are less sensitive to noise and sudden changes for extracting the background image.
Improving a design methodology of synthesizable VHDL with formal verification

In this paper we present a synthesizable VHDL design methodology that includes exhaustive verification of properties. The work was developed in a company environment with the goal of increasing reliability of products and reduce time of verification procedure. In this methodology the properties are represented using VHDL oriented patterns based on the OVL library and applied, with the VHDL code, into a verification environment (based on open source tools) that returns the results. Counterexamples are generated for properties that failed and returned as VHDL testbench, allowing the user to identify the faulty behavior with simulation. The methodology is illustrated with a simple memory controller application.
Testing for floating gates defects in CMOS circuits

This paper studies the detectability of MOS floating gate transistor faults considering classical static voltage, dynamic voltage and static current strategies. The behavior of the defect depends on two classes of parameters: the predictable and unpredictable parameters. A floating gate fault can induce abnormal logic values, additional delays, or increased power supply current. Consequently, classical test strategies can only detect floating gate faults for a given range of the unpredictable parameter. Here, a new test scheme is proposed, which allows a considerable current to flow in the stable state making the circuit with a floating gate I/sub DDQ/ testable. It is shown that a combination of voltage and current testing can ensure 100% detection of the floating gate defects, i.e., regardless of the unpredictable parameters. Analysis with increasing initial charge on the floating gate transistor shows how the detectability intervals become smaller for the voltage testing strategies and increase for the static current strategy.