Miracle-dz/UniFAR-FTUs huggingface dataset:
DEEP—A tool for differential expression effector prediction

High-throughput methods for measuring transcript abundance, like SAGE or microarrays, are widely used for determining differences in gene expression between different tissue types, dignities (normal/malignant) or time points. Further analysis of such data frequently aims at the identification of gene interaction networks that form the causal basis for the observed properties of the systems under examination. To this end, it is usually not sufficient to rely on the measured gene expression levels alone; rather, additional biological knowledge has to be taken into account in order to generate useful hypotheses about the molecular mechanism leading to the realization of a certain phenotype. We present a method that combines gene expression data with biological expert knowledge on molecular interaction networks, as described by the TRANSPATH1 database on signal transduction, to predict additional—and not necessarily differentially expressed—genes or gene products which might participate in processes specific for either of the examined tissues or conditions. In a first step, significance values for over-expression in tissue/condition A or B are assigned to all genes in the expression data set. Genes with a significance value exceeding a certain threshold are used as starting points for the reconstruction of a graph with signaling components as nodes and signaling events as edges. In a subsequent graph traversal process, again starting from the previously identified differentially expressed genes, all encountered nodes ‘inherit’ all their starting nodes’ significance values. In a final step, the graph is visualized, the nodes being colored according to a weighted average of their inherited significance values. Each node's, or sub-network's, predominant color, ranging from green (significant for tissue/condition A) over yellow (not significant for either tissue/condition) to red (significant for tissue/condition B), thus gives an immediate visual clue on which molecules—differentially expressed or not—may play pivotal roles in the tissues or conditions under examination. The described method has been implemented in Java as a client/server application and a web interface called DEEP (Differential Expression Effector Prediction). The client, which features an easy-to-use graphical interface, can freely be downloaded from the following URL: http://deep.bioinf. med.uni-goettingen.de
GSFAP adaptive filtering using log arithmetic for resource-constrained embedded systems

Adaptive filters are widely used in many applications of digital signal processing. Digital communications and digital video broadcasting are just two examples. Traditionally, small embedded systems have employed the least computationally intensive filter adaptive algorithms, such as normalized least mean squares (NLMS). This article shows that FPGA devices are a highly suitable platform for more computationally intensive adaptive algorithms. We present an optimized core which implements GSFAP. GSFAP is an algorithm with far superior adaptation properties than NLMS, and with only slightly higher computational complexity. To further optimize resource requirements we use logarithmic arithmetic, rather than conventional floating point, within the custom core. Our design makes effective use of the pipelined logarithmic addition units, and takes advantage of the very low cost of logarithmic multiplication and division. The resulting GSFAP core can be clocked at more than 80MHz on a one million-gate Xilinx XC2V1000-4 device. The core can be used to implement adaptive filters of orders 20 to 1000 performing echo cancellation on speech signals at a sampling rate exceeding 50kHz. For comparison, we implemented a similar NLMS core and found that although it is slightly smaller than the GSFAP core and allows a higher signal sampling rate for the corresponding filter orders, the GSFAP core has adaptation properties that are much superior to NLMS, and that our core can provide very sophisticated adaptive filtering capabilities for resource-constrained embedded systems.
User adaptation in long-term, open-loop myoelectric training: implications for EMG pattern recognition in prosthesis control

Objective. Recent studies have reported that the classification performance of electromyographic (EMG) signals degrades over time without proper classification retraining. This problem is relevant for the applications of EMG pattern recognition in the control of active prostheses. Approach. In this study we investigated the changes in EMG classification performance over 11 consecutive days in eight able-bodied subjects and two amputees. Main results. It was observed that, when the classifier was trained on data from one day and tested on data from the following day, the classification error decreased exponentially but plateaued after four days for able-bodied subjects and six to nine days for amputees. The between-day performance became gradually closer to the corresponding within-day performance. Significance. These results indicate that the relative changes in EMG signal features over time become progressively smaller when the number of days during which the subjects perform the pre-defined motions are increased. The performance of the motor tasks is thus more consistent over time, resulting in more repeatable EMG patterns, even if the subjects do not have any external feedback on their performance. The learning curves for both able-bodied subjects and subjects with limb deficiencies could be modeled as an exponential function. These results provide important insights into the user adaptation characteristics during practical long-term myoelectric control applications, with implications for the design of an adaptive pattern recognition system.
Chronic pain and opioid use in US soldiers after combat deployment.

Chronic Pain and Opioid Use in US Soldiers After Combat Deployment Chronic pain affects a quarter of people seeking primary health care.1,2 Opioid medications are prescribed for chronic pain, but recently, rates of opioid use and misuse have ballooned, leading to significant numbers of overdose-related hospitalizations and deaths.3 The prevalence of chronic pain and opioid use assoc iated w ith deployment is not well known, despite large numbers of wounded service members. To our knowledge, this is the first study to assess chronic pain prevalence and opioid use in a non– treatment-seeking, active duty infantry population following deployment.
Impact of EV Battery Chargers on the Power Quality of Distribution Systems

A summary of the actual state of battery charger harmonics is presented. The effect of harmonic distortion on the distribution system, especially on distribution transformers, is analyzed. A program was developed that allows the consideration of the transformer life consumption as a function of the battery charger characteristics and charging algorithm. The program is considered to be a distribution planning and management tool. The proposed tool can be easily applied to determine the optimum charging time as a function of the existing load, ambient temperature, and time of day. From the study it can be deduced that a direct connect-and-charge scheme can be detrimental to the transformer life, especially under high temperature and large load. Calculations show the existence of a quadratic relationship between the transformer life consumption and the total harmonic distortion (THD) of the battery charger current. Furthermore, the current THD should be limited to 25 30% in order to have a reasonable transformer life expectancy.
An effective joint source-channel coding with unequal error protection using asymmetric turbo codes

In this paper, we firstly present a novel interleaver to improve the error correction performance of turbo codes. Secondly, we devise two types of asymmetric turbo codes to optimize the bit error rate of both water fall and error floor. Finally, we propose an efficient joint source-channel coding scheme based on unequal error protection technology using asymmetric turbo codes. The proposed scheme can adaptively adopt different coding strategies, different interleavers of turbo codes, various decoding algorithms and appropriate decoding iterative numbers in terms of the different significant levels of image data streams and the varying conditions of estimated channel state information. This scheme can also dynamically adjust the source and channel code rates according to the calculated peak signal to noise ratio of reconstructed images and the estimated channel states. The experimental results show that the proposed scheme can evidently increase the peak signal to noise ratio of the reconstructed images and improve the visual effect of the images but with no additional bandwidth, the scheme is more adaptive and feasible.
Evaluation of force delays on the operation of haptic sense by analytic hierarchy process

Virtual reality technology has been developing rapidly recently. Studies have been conducted on various fundamental techniques and applications. We experimented on the delay of a feedback force. Haptic media are very sensitive to network delays, jitter, and packet loss. The analytic hierarchy process is one method used to evaluate physical phenomena as perceived by humans, and was used in the present experiment. The results revealed that haptic media could be estimated from the delay time. In this study, we investigated the relationship between the delay time and haptic sensation. The effectiveness of our method was confirmed by conducting experiments on participants.
Cardiac myosin-binding protein-C is a critical mediator of diastolic function

Diastolic dysfunction prominently contributes to heart failure with preserved ejection fraction (HFpEF). Owing partly to inadequate understanding, HFpEF does not have any effective treatments. Cardiac myosin-binding protein-C (cMyBP-C), a component of the thick filament of heart muscle that can modulate cross-bridge attachment/detachment cycling process by its phosphorylation status, appears to be involved in the diastolic dysfunction associated with HFpEF. In patients, cMyBP-C mutations are associated with diastolic dysfunction even in the absence of hypertrophy. cMyBP-C deletion mouse models recapitulate diastolic dysfunction despite in vitro evidence of uninhibited cross-bridge cycling. Reduced phosphorylation of cMyBP-C is also associated with diastolic dysfunction in patients. Mouse models of reduced cMyBP-C phosphorylation exhibit diastolic dysfunction while cMyBP-C phosphorylation mimetic mouse models show enhanced diastolic function. Thus, cMyBP-C phosphorylation mediates diastolic function. Experimental results of both cMyBP-C deletion and reduced cMyBP-C phosphorylation causing diastolic dysfunction suggest that cMyBP-C phosphorylation level modulates cross-bridge detachment rate in relation to ongoing attachment rate to mediate relaxation. Consequently, alteration in cMyBP-C regulation of cross-bridge detachment is a key mechanism that causes diastolic dysfunction. Regardless of the exact molecular mechanism, ample clinical and experimental data show that cMyBP-C is a critical mediator of diastolic function. Furthermore, targeting cMyBP-C phosphorylation holds potential as a future treatment for diastolic dysfunction.
Temporomandibular disorders, sleep bruxism, and primary headaches are mutually associated.

AIMS To investigate the association among temporomandibular disorders (TMD), sleep bruxism, and primary headaches, assessing the risk of occurrence of primary headaches in patients with or without painful TMD and sleep bruxism. METHODS The sample consisted of 301 individuals (253 women and 48 men) with ages varying from 18 to 76 years old (average age of 37.5 years). The Research Diagnostic Criteria for Temporomandibular Disorders were used to classify TMD. Sleep bruxism was diagnosed by clinical criteria proposed by the American Academy of Sleep Medicine, and primary headaches were diagnosed according to the International Classification of Headache Disorders-II. Data were analyzed by chi-square and odds ratio tests with a 95% confidence interval, and the significance level adopted was . 05. RESULTS An association was found among painful TMD, migraine, and tension-type headache (P < .01). The magnitude of association was higher for chronic migraine (odds ratio = 95.9; 95% confidence intervals = 12.51-734.64), followed by episodic migraine (7.0; 3.45-14.22) and episodic tension-type headache (3.7; 1.59-8.75). With regard to sleep bruxism, the association was significant only for chronic migraine (3.8; 1.83-7.84). When the sample was stratified by the presence of sleep bruxism and painful TMD, only the presence of sleep bruxism did not increase the risk for any type of headache. The presence of painful TMD without sleep bruxism significantly increased the risk in particular for chronic migraine (30.1; 3.58-252.81), followed by episodic migraine (3.7; 1.46-9.16). The association between painful TMD and sleep bruxism significantly increased the risk for chronic migraine (87.1; 10.79-702.18), followed by episodic migraine (6.7; 2.79-15.98) and episodic tension-type headache (3.8; 1.38-10.69). CONCLUSION The association of sleep bruxism and painful TMD greatly increased the risk for episodic migraine, episodic tension-type headache, and especially for chronic migraine.
The Essence of Three-Phase PFC Rectifier Systems—Part I

In the first part of this paper, three-phase power factor correction (PFC) rectifier topologies with sinusoidal input currents and controlled output voltage are derived from known single-phase PFC rectifier systems and/or passive three-phase diode rectifiers. The systems are classified into hybrid and fully active pulsewidth modulation boost-type or buck-type rectifiers, and their functionality and basic control concepts are briefly described. This facilitates the understanding of the operating principle of three-phase PFC rectifiers starting from single-phase systems, and organizes and completes the knowledge base with a new hybrid three-phase buck-type PFC rectifier topology denominated as Swiss Rectifier. Finally, core topics of future research on three-phase PFC rectifier systems are discussed, such as the analysis of novel hybrid buck-type PFC rectifier topologies, the direct input current control of buck-type systems, and the multi-objective optimization of PFC rectifier systems. The second part of this paper is dedicated to a comparative evaluation of four rectifier systems offering a high potential for industrial applications based on simple and demonstrative performance metrics concerning the semiconductor stresses, the loading and volume of the main passive components, the differential mode and common mode electromagnetic interference noise level, and ultimately the achievable converter efficiency and power density. The results are substantiated with selected examples of hardware prototypes that are optimized for efficiency and/or power density.
Influence of Systolic and Diastolic Blood Pressure on the Risk of Incident Atrial Fibrillation in Women

Background— The influence of systolic and diastolic blood pressure (BP) on incident atrial fibrillation (AF) is not well studied among initially healthy, middle-aged women. Methods and Results— A total of 34 221 women participating in the Women's Health Study were prospectively followed up for incident AF. The risk of AF across categories of systolic and diastolic BP was compared by use of Cox proportional-hazards models. During 12.4 years of follow-up, 644 incident AF events occurred. Using BP measurements at baseline, we discovered that the long-term risk of AF was significantly increased across categories of systolic and diastolic BP. Multivariable-adjusted hazard ratios for systolic BP categories (<120, 120 to 129, 130 to 139, 140 to 159, and ≥160 mm Hg) were 1.0, 1.00 (95% CI, 0.78 to 1.28), 1.28 (95% CI, 1.00 to 1.63), 1.56 (95% CI, 1.22 to 2.01), and 2.74 (95% CI, 1.77 to 4.22) (P for trend <0.0001). Adjusted hazard ratios across baseline diastolic BP categories (<65, 65 to 74, 75 to 84, 85 to 89, 90 to 94, and ≥95 mm Hg) were 1.0, 1.17 (95% CI, 0.81 to 1.69), 1.18 (95% CI, 0.84 to 1.65), 1.53 (95% CI, 1.05 to 2.23), 1.35 (95% CI, 0.82 to 2.22), and 2.15 (95% CI, 1.21 to 3.84) (P for trend=0.004). When BP changes over time were accounted for in updated models, multivariable-adjusted hazard ratios were 1.0, 1.14 (95% CI, 0.89 to 1.46), 1.37 (95% CI, 1.07 to 1.76), 1.71 (95% CI, 1.33 to 2.21), and 2.21 (95% CI, 1.45 to 3.36) (P for trend <0.0001) for systolic BP categories and 1.0, 1.12 (95% CI, 0.82 to 1.52), 1.13 (95% CI, 0.83 to 1.52), 1.30 (95% CI, 0.89 to 1.88), 1.50 (95% CI, 1.01 to 1.88), and 1.54 (95% CI, 0.75 to 3.14) (P for trend=0.026) for diastolic BP categories. Conclusions— In this large cohort of initially healthy women, BP was strongly associated with incident AF, and systolic BP was a better predictor than diastolic BP. Systolic BP levels within the nonhypertensive range were independently associated with incident AF even after BP changes over time were taken into account.
Choosing the Best Child Assessment Instrument for a Specific Context: A Methodology for Engaging Local Experts Applied in Chile

Objective: Chile is considering expanding its system for early childhood development to include 5- to 7-year olds, but it has no consensus about how to identify at-risk children. This study facilitated a process for incorporating local priorities and best practices to choose a child assessment instrument. Methods: Using the priority-setting method of the Child Health and Nutrition Research Initiative (CHNRI), 21 Chilean experts defined and weighted ideal assessment instrument characteristics; 130 instruments were scored according to how closely they matched experts' ideal definitions. Instruments were ranked by score under different inclusion criteria. Results: Experts weighted instrument quality highest (95 on 1–100 scale), followed by administration site (87), domains assessed (82), cost (80), administrator (76), Spanish version (75), time (75), and prior use in Chile (53). Experts agreed that an ideal instrument (1) would reliably assess language, socioemotional well-being, mental health, and parenting abilities, (2) could be administered at schools or home, and (3) could be administered by teachers or parents. No single instrument matched all Chilean priorities. Three instruments met 11 of 13 priorities (age; quality; administration at school, home, or waiting rooms; assess language and socioemotional domains; administered by teachers, parents, or psychologists; time ⩽30 minutes). Including mental health or parenting abilities ranked instruments whose composite scores were 35% lower. Conclusion: Decisions about how to assess children at developmental risk should be informed by local context. The CHNRI method provided a useful process that made explicit mutually exclusive priorities, quantified trade-offs of different assessment strategies, and identified 3 of the instruments that best met local needs and priorities.
Viral Oncogene–Induced DNA Damage Response Is Activated in Kaposi Sarcoma Tumorigenesis

Kaposi sarcoma is a tumor consisting of Kaposi sarcoma herpesvirus (KSHV)–infected tumor cells that express endothelial cell (EC) markers and viral genes like v-cyclin, vFLIP, and LANA. Despite a strong link between KSHV infection and certain neoplasms, de novo virus infection of human primary cells does not readily lead to cellular transformation. We have studied the consequences of expression of v-cyclin in primary and immortalized human dermal microvascular ECs. We show that v-cyclin, which is a homolog of cellular D-type cyclins, induces replicative stress in ECs, which leads to senescence and activation of the DNA damage response. We find that antiproliferative checkpoints are activated upon KSHV infection of ECs, and in early-stage but not late-stage lesions of clinical Kaposi sarcoma specimens. These are some of the first results suggesting that DNA damage checkpoint response also functions as an anticancer barrier in virally induced cancers.
The capacity region of a class of three-receiver broadcast channels with degraded message sets

Korner and Marton established the capacity region for the two-receiver broadcast channel with degraded message sets. Recent results and conjectures suggest that a straightforward extension of the Korner-Marton region to more than two receivers is optimal. This paper shows that this is not the case. We establish the capacity region for a class of three-receiver broadcast channels with two-degraded message sets and show that it can be strictly larger than the straightforward extension of the Korner-Marton region. The idea is to split the private message into two parts, superimpose one part onto the ldquocloud centerrdquo representing the common message, and superimpose the second part onto the resulting ldquosatellite codeword.rdquo One of the receivers finds the common message directly by decoding the ldquocloud center,rdquo a second receiver finds it indirectly by decoding a satellite codeword, and a third receiver finds it by jointly decoding the transmitted codeword. This idea is then used to establish new inner and outer bounds on the capacity region of the general three-receiver broadcast channel with two and three degraded message sets. We show that these bounds are tight for some nontrivial cases. The results suggest that finding the capacity region of the three-receiver broadcast channel with degraded message sets is at least as hard finding as the capacity region of the general two-receiver broadcast channel with common and private message.
A Critique of “Fine Particulate Air Pollution and Total Mortality Among Elderly Californians, 1973–2002” by James E. Enstrom

In view of the societal importance of the health effects of fine particulates, new studies on the subject are very important. In a previous issue of Inhalation Toxicology, Dr. Enstrom presents findings from a long-term follow-up of the ACS I cohort in California, suggesting that there was a slight effect of fine particulate matter (PM) on total mortality over the first 10 yr of follow-up (1973–1982), but none thereafter (1983– 2002) (Enstrom, 2005). A few issues are worth raising as they may help in fuller understanding of the findings. One is the very long follow-up period. Baseline data on this cohort were obtained in 1959, and only data on smoking were reassessed in 1972. This means that for the later follow-up period (1983–2002), adjustment was based on data obtained 24–43 yr before death for all other variables except smoking, and 11–30 yr for smoking. It is likely that significant changes in smoking as well as diet and other risk factors have occurred over this period, which may have obscured any relationship with air pollution. The data show that smoking especially declined dramatically, and without detailed insight as to when this happened over time in the cohort, inaccuracies in assessment of smoking can easily obscure relationships with less important exposures such as air pollution. Adjustment for exposure to environmental tobacco smoke was absent in this study. Another issue is exposure assessment. PM2.5 was assigned on the basis of data from just a few monitoring sites and on the basis of sometimes very few measurements: Of 15 monitoring sites in 11 counties, 8 provided less than 100 daily measurements. No discussion was provided as to representativeness of sites; it is surprising that Kern County, for instance, with measurements from Chester Avenue in Bakersfield, ranked higher