Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning with sparsity: Structures, optimization and applications

The development of modern information technology has enabled collecting data of unprecedented size and complexity. Examples include web text data, microarray & proteomics, and data from scientific domains (e.g., meteorology). To learn from these high dimensional and complex data, traditional machine learning techniques often suffer from the curse of dimensionality and unaffordable computational cost. However, learning from large-scale high-dimensional data promises big payoffs in text mining, gene analysis, and numerous other consequential tasks. Recently developed sparse learning techniques provide us a suite of tools for understanding and exploring high dimensional data from many areas in science and engineering. By exploring sparsity, we can always learn a parsimonious and compact model which is more interpretable and computationally tractable at application time. When it is known that the underlying model is indeed sparse, sparse learning methods can provide us a more consistent model and much improved prediction performance. However, the existing methods are still insufficient for modeling complex or dynamic structures of the data, such as those evidenced in pathways of genomic data, gene regulatory network, and synonyms in text data. This thesis develops structured sparse learning methods along with scalable optimization algorithms to explore and predict high dimensional data with complex structures. In particular, we address three aspects of structured sparse learning: 1. Efficient and scalable optimization methods with fast convergence guarantees for a wide spectrum of high-dimensional learning tasks, including single or multi-task structured regression, canonical correlation analysis as well as online sparse learning. 2. Learning dynamic structures of different types of undirected graphical models, e.g., conditional Gaussian or conditional forest graphical models. 3. Demonstrating the usefulness of the proposed methods in various applications, e.g., computational genomics and spatial-temporal climatological data. In addition, we also design specialized sparse learning methods for text mining applications, including ranking and latent semantic analysis. In the last part of the thesis, we also present the future direction of the high-dimensional structured sparse learning from both computational and statistical aspects.
Mec 1 Is One of Multiple Kinases that Prime the Mcm 2-7 Helicase for Phosphorylation by Cdc 7

John C.W. Randell,1 Andy Fan,1,2,3 Clara Chan,1,2 Laura I. Francis,1,4 Ryan C. Heller,1 Kyriaki Galani,1 and Stephen P. Bell1,* 1Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 2These authors contributed equally to this work 3Present address: Department of Biomedical Engineering, Boston University, Boston MA 02215, USA 4Present address: Department of Biology, University of Massachusetts, Amherst MA 01003, USA *Correspondence: spbell@mit.edu DOI 10.1016/j.molcel. 2010.10. 017
Accuracy of the DriveABLE cognitive assessment to determine cognitive fitness to drive.

OBJECTIVE To evaluate the accuracy of the DriveABLE In-Office cognitive assessment in predicting cognitively impaired drivers' performance on the DriveABLE On-Road Evaluation (DORE). DESIGN Retrospective study comparing data from DriveABLE In-Office cognitive assessment outcomes with DORE outcomes. SETTING Nineteen of the locations in North America providing the DriveABLE assessment between the years 2007 and 2010. PARTICIPANTS Database records from 3662 patients (2639 men, mean age 74.1 years, range 18 to 99 years of age; 1023 women, mean age 73.5 years, range 18 to 94 years of age) with suspected or confirmed cognitive impairment. All patients were referred for DriveABLE evaluation and received both the In-Office cognitive assessment and, regardless of the In-Office test results, the DORE. This is a subset of the database because typically the DriveABLE In-Office cognitive assessment serves as the cognitive assessment and only those whose results are in the indeterminate range go on to complete the road test (ie, DORE). MAIN OUTCOME MEASURES Accuracy of the In-Office assessment for predicting the outcome of the DORE. RESULTS For the total sample, the error rate for predicting actual performance on the road test was 1.7% for pass predictions and 5.6% for fail predictions. Notably, these low error rates were consistent across the 4 years. On the basis of performance on the In-Office cognitive assessment, pass or fail decisions could have been made for more than half of the referrals, reducing the need to take dangerous drivers on the road and reducing the cost of the assessment process for patients and the system. CONCLUSION The accuracy of the DriveABLE In-Office cognitive assessment was evaluated in the context of normal clinical referral processes, with a large sample of referrals during a 4-year period and from multiple sites. The high and stable accuracy rates provide the evidence physicians need to be confident in using the recommendations from the DriveABLE cognitive evaluation to assist them in making evidence-based decisions about their patients' ability to continue driving.
Advanced Power Electronic Conversion and Control System for Universal and Flexible Power Management

The future electricity network has to be able to manage energy coming from different grids as well as from renewable energy sources (RES) and other distributed generation (DG) systems. Advanced power electronic converters can provide the means to control power flow and ensure proper and secure operation of future networks. This paper presents analysis, design, and experimental validation of a back-to-back three-phase ac-dc-ac multilevel converter employed for universal and flexible power management (UNIFLEX-PM) of future electrical grids and its advanced control technique. The proposed system has been successfully tested for bidirectional power flow operation with different grid operating conditions such as voltage unbalance, frequency variation, harmonic distortion, and faults due to short circuits.
Prognostic Factors in Pancreatic Carcinoma: Serum LDH Levels Predict Survival in Metastatic Disease

In this study, our aim was to investigate the impact of various prognostic factors on survival in patients with pancreatic carcinoma. The group consisted of 127 cases with adenocarcinoma histologically. The patients had a median age of 58 years, and 81 (64%) were male. The median survival time of the whole group was 7 months, and the 4-year survival rate was 18%. The median survival duration of the patients without metastases was 8 months, and the survival rate at 1 year was 37.5% and 7.2% at 5 years. It was associated with improved survival compared with the cases with metastatic disease (p < 0.0001). In univariate analysis, decreased performance status (p = 0.0009) and unresectability of tumor (p < 0.0001) were associated with poor outcome. However, only surgery was found to be a statistically significant parameter in multivariate analysis (p = 0.002). The median survival duration of patients with metastases was 5 months, and the 1-year survival rate was 10%. Age younger than 60 years (p = 0.04), decreased serum hemoglobin levels (p = 0.04), and elevated lactic dehydrogenase (LDH) levels (p = 0.0001) were associated with a significantly shorter survival rate. In the Cox model, a high serum LDH level was the only independent unfavorable prognostic factor (p = 0.001). In conclusion, surgical intervention in the group without metastases and serum LDH levels in the group with metastases were the most important prognostic factors influencing survival. Pretreatment serum LDH determinations may provide a useful means of stratifying patient populations when comparing treatment programs for advanced pancreatic cancer.
Richard Havel , Howard Eder , and the evolution of lipoprotein analysis

In 1956, the JCI published a paper by Richard Havel, Howard Eder, and Joseph Bragdon on a method using an ultracentrifuge to physically separate plasma lipoproteins and chemical methods to analyze their lipid constituents. This paper has been much cited (7081 times as of this writing) in part because it represents a solid method that, with various modifications, has been applicable for the study of lipoproteins for almost half a century.
Cushing’s Disease: Subclinical Left Ventricular Systolic and Diastolic Dysfunction Revealed by Speckle Tracking Echocardiography and Tissue Doppler Imaging

Objective Novel echocardiographic techniques, such as speckle tracking echocardiography (STE) and tissue Doppler imaging, are sensitive tools for assessing left ventricular (LV) performance. LV global longitudinal strain (GLS), assessed by STE, is a sensitive marker of myocardial systolic function. Cardiovascular complications in patients with Cushing’s disease (CD) determine a higher mortality than that in an age- and gender-matched population. Cardiac systolic dysfunction may be detected in early stages by STE. Thus, the aim of this study was to investigate the usefulness of STE in detecting subclinical LV dysfunction in three groups of patients: CD group, arterial hypertension group (AHG), and healthy volunteers (HV). Methods Echocardiographic assessments of LV systolic and diastolic function were performed in 171 subjects (CD: 22, AHG: 114, HV: 35) with no symptoms of heart failure. A statistical comparison included separate analyses for men and women. Results CD patients showed good blood pressure (BP) control (below 140/90 mmHg in 82% of cases). However, in comparison AHG and HV groups they exhibited: (1) significantly lower LV contractility expressed by GLS (CD group: −17.7%, AHG group: −19.2%, HV: −20.0%; p = 0.004) and (2) higher prevalence of LV diastolic dysfunction (45.0, 14.2, 0.0%, respectively; p < 0.00001). Men with CD showed significantly more pronounced LV diastolic dysfunction. Cortisol excess in women was related to impaired LV systolic function. Conclusion CD, even with well-controlled BP, is associated with LV dysfunction which depends individually on sex. These hemodynamic alterations can be detected by modern non-invasive diagnostic tools and may become potential therapeutic objectives.
A Fully Integrated Fail-safe Stimulator Output Stage Dedicated to FES Stimulation

There is a great demand to reduce the volume of implantable multi-channel stimulators for functional electrical stimulation applications. Miniaturization is currently limited by the size of the large off-chip blocking capacitors that are required for safety. This paper describes a fail-safe stimulator output stage circuit utilizing the principle of high-frequency current-switching, which allows the blocking capacitors to be integrated on-chip. The proposed circuit is based on the bridge rectifier circuit, hence fully utilizing the bidirectional current through the blocking capacitor. The approach has been verified by post-layout simulations in a 1 mum CMOS SOI technology.
In vivo application of an inhibitory RNA aptamer against T7 RNA polymerase

Synthetic biology involves the design of complex articial biological systems with exploitable features for human benet through an ecological and sustainable way. Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. Using in vitro transcription assays, we rst demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks. As a step to quickly assess the feasibility of aptamer functions in vivo, a cell-free expression system was used as a breadboard to emulate the in vivo conditions of E. coli. We tested the aptamer and its three sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. In vivo expression of aptamer and its variants demonstrated control over GFP expression driven by T7 RNA polymerase with dierent response curves, indicating its ability to serve as building blocks for both logic circuits and transcriptional cascades. This work elucidates the potential of RNA-based regulators for implementing dierent \biocodes" for cell programming and for improved controllability thanks to the fast production and degradation time scales of RNA molecules.
Alternative periplasmic copper‐resistance mechanisms in Gram negative bacteria

Bacteria have evolved different systems to tightly control both cytosolic and envelope copper concentration to fulfil their requirements and at the same time, avoid copper toxicity. We have previously demonstrated that, as in Escherichia coli, the Salmonella cue system protects the cytosol from copper excess. On the other hand, and even though Salmonella lacks the CusCFBA periplasmic copper efflux system, it can support higher copper concentrations than E. coli under anaerobic conditions. Here we show that the Salmonella cue regulon is also responsible for the control of copper toxicity in anaerobiosis. We establish that resistance in this condition requires a novel CueR‐controlled gene named cueP. A ΔcueP mutant is highly susceptible to copper in the absence of oxygen, but shows a faint phenotype in aerobic conditions unless other copper‐resistance genes are also deleted, resembling the E. coli CusCFBA behaviour. Species that contain a cueP homologue under CueR regulation have no functional CusR/CusS‐dependent Cus‐coding operon. Conversely, species that carry a CusR/CusS‐regulated cus operon have no cueP homologues. Even more, we show that the CueR‐controlled cueP expression increases copper resistance of a Δcus E. coli. We posit that CueP can functionally replace the Cus complex for periplasmic copper resistance, in particular under anaerobic conditions.
Large eddy simulation of heated pulsed jets in high speed turbulent crossflow

CH4/air), 1.0 (air/air) and 1.5 (CO2/air). The simulations show that the lower density jet develops faster than a higher density. This results in more jet spread for the lower density jet. Further, the existence of ‘side jets’ has been observed in this case. A variable density scaling law has been developed and used to predict jet penetration in the far eld.
Application of the Prony’s method for induction machine stator fault diagnosis

The fundamental positive and negative sequence components of the voltage and current are always characters in induction machine stator fault diagnosis. This paper presents the application of the Pronypsilas method for deriving these components from the measured data. It is known that the Pronypsilas method is sensitive to noise and takes a long computation time by increasing of the length of the data. In order to enhance its performance, pretreatments, including frame transformation, frequency shifting and decimation, are employed before using the Pronypsilas method. Finally, the fundamental sequence components, figured out by using the Pronypsilas method, are put into a neural network to calculate the indicator for diagnosis. The proposed technique is verified by applying to diagnose the stator fault in a three-phase induction motor.
A Nonvolatile, Low-Power, and Highly Reliable MRAM Block for Advanced Microarchitectures

Following the scale down of complementary metal-oxide semiconductor (CMOS) technology, radiation-induced soft errors have become a concerning issue in CMOS circuit design. Today’s integrated circuits suffer from single event double node upset (SEDU) that takes place when an energetic particle strike affects two adjacent nodes. In this letter, a magnetic random access memory block capable of tolerating SEDUs is proposed and evaluated. The proposed circuit utilizes a hybrid design of magnetic and CMOS-based technology that considerably reduces the static power, improves the performance, and offers the advantage of nonvolatility. Simulation results validated that the proposed circuit is fully single event upset and also SEDU immune beside the other advantages offered.
Liver growth in the embryo and during liver regeneration in zebrafish requires the cell cycle regulator, uhrf1

In contrast to the deregulated hepatocellular division that is a feature of many hepatic diseases and malignancies, physiologic liver growth during embryonic development and after partial hepatectomy (PH) in adults is characterized by tightly controlled cell proliferation. We used forward genetic screening in zebrafish to test the hypothesis that a similar genetic program governs physiologic liver growth during hepatogenesis and regeneration after PH. We identified the uhrf1 gene, a cell cycle regulator and transcriptional activator of top2a expression, as required for hepatic outgrowth and embryonic survival. By developing a methodology to perform PH on adult zebrafish, we found that liver regeneration inuhrf1+/− adult animals is impaired.uhrf1 transcript levels dramatically increase after PH in both mice, and zebrafish and top2a is not up-regulated in uhrf1+/− livers after PH. This indicates that uhrf1 is required for physiologic liver growth in both embryos and adults and illustrates that zebrafish livers regenerate.
Range of Motion, Postural Alignment, and LESS Score Differences of Those With and Without Excessive Medial Knee Displacement

Objective:To determine range of motion (ROM), postural alignment, and dynamic motion differences between those with and without medial knee displacement (MKD) during the overhead squat (OHS). We hypothesized those with MKD would have restricted ROM, differing postural alignment, and poorer quality dynamic motion than those without MKD. Design:Observational. Setting:University Research Laboratory. Participants:Ninety-seven healthy recreationally active college-aged individuals. Independent Variables:Groups were determined by the presence (MKD group) or absence (control group) of MKD during an OHS. Main Outcome Measures:Range of motion measures were active and passive ankle dorsiflexion with the knee straight and bent, hip internal and external rotation, and hip abduction. Postural alignment measures were Q angle, navicular drop, and genu recurvatum. Quality of dynamic motion was measured using total Landing Error Scoring System (LESS) score. Results:The MKD group had significantly less active (P = 0.017) and passive (P = 0.045) ankle dorsiflexion with the knee straight, as well as significantly increased Q angle (P = 0.004) and decreased navicular drop (P = 0.009). There were no significant differences in total LESS score or the other outcome measures. Conclusions:There is select ROM, such as ankle dorsiflexion, and postural measures clinicians can screen for that may be related to increased MKD and theoretically elevated risk of injury.
The effect of different degrees of subdiaphragmatic aortic constriction on heart weight and blood pressure of normal and hypophysectomized rats.

The aortae of groups of normal and hypophysectomized rats were constricted with rings of five different sizes (0.93, 0.83, 0. 74, 0.71, and 0.63 mm. diameter). In normal rats constriction caused an increase in heart weight and blood pressure which was the greater the narrower the constriction. If constriction exceeded 0.74 mm. , cardiac hypertrophy reached extremely high values, while the blood pressure was lower than in groups with less constriction. The blood pressure response to Adrenalin or Infundin increased in proportion to the degree of constriction down to 0.74 mm. ; greater constriction reduced the response. In hypophysectomized rats no degree of aortic constriction produced hypertension or cardiac hypertrophy, yet the increase in blood pressure after Adrenalin or Infundin was as great as in the normal intact rats.
Telling Your Secrets without Page Faults: Stealthy Page Table-Based Attacks on Enclaved Execution

Protected module architectures, such as Intel SGX, enable strong trusted computing guarantees for hardware-enforced enclaves on top a potentially malicious operating system. However, such enclaved execution environments are known to be vulnerable to a powerful class of controlled-channel attacks. Recent research convincingly demonstrated that adversarial system software can extract sensitive data from enclaved applications by carefully revoking access rights on enclave pages, and recording the associated page faults. As a response, a number of state-of-the-art defense techniques has been proposed that suppress page faults during enclave execution. This paper shows, however, that page table-based threats go beyond page faults. We demonstrate that an untrusted operating system can observe enclave page accesses without resorting to page faults, by exploiting other side-effects of the address translation process. We contribute two novel attack vectors that infer enclaved memory accesses from page table attributes, as well as from the caching behavior of unprotected page table memory. We demonstrate the effectiveness of our attacks by recovering EdDSA session keys with little to no noise from the popular Libgcrypt cryptographic software suite.
Advanced Applications of Polarisation / Depolarisation Current Analysis on Power Transformers

One case study in this paper shows how to identify wet insulation system in an on-load tap changer (OLTC) by polarisation / depolarisation current (PDC) analysis. It emphasizes the importance of filling a new transformer with good oil having very low conductivity. The other two case studies on transformers without oil (before oil refilling) demonstrate how aging type of solid insulation can be identified by the PDC technique.
Comparison of direct immunofluorescence, modified acid-fast staining, and enzyme immunoassay techniques for detection of Cryptosporidium spp in naturally exposed kittens.

OBJECTIVE To evaluate a modified Ziehl-Neelsen acid-fast staining technique (mZN), a direct immunofluorescence detection procedure (DIF), and 3 commercial enzyme immunoassays (EIAs) for detection of Cryptosporidium oocysts in fecal specimens from kittens. DESIGN Prospective study. SAMPLE POPULATION 416 fecal specimens collected from 104 randomly selected domestic shorthair kittens (8 to 16 weeks of age) that were naturally exposed to Cryptosporidium spp. PROCEDURE Fresh fecal specimens were collected once daily for 4 consecutive days and processed immediately. Sensitivities of mZN, DIF, and 3 commercial EIAs (EIA-1, EIA-2, and EIA-3) were estimated and compared. RESULTS EIA-2 had the highest sensitivity on day 1 (89%), followed by EIA-1 (80%), and mZN (72%). EIA-3 had the lowest sensitivity on day 1 (15%). EIA-2, EIA-1, and mZN had similar sensitivities after 2 consecutive fecal examinations (approx 90%). Determination of specificities was compromised by the small number of cats that had negative results for all tests (n = 3). CONCLUSIONS AND CLINICAL RELEVANCE Results suggest that EIA-2 and EIA-1 had the highest sensitivities when only a single fecal specimen was examined; however, mZN and EIA-1 had similar sensitivities when 2 consecutive fecal specimens were examined. The higher costs of EIA-2 and EIA-1 may be offset by the tests' high sensitivity, simplicity of use, and ease of interpretation and by savings in technician time.