Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting the spectrum of TCR repertoire sharing with a data‐driven model of recombination

Despite the extreme diversity of T cell repertoires, many identical T cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as ‘public‘, have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here we show that even for large cohorts the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations we propose a public/private sequence classifier, ‘PUBLIC’ (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
Arabian Red Sea coastal soils as potential mineral dust sources

Abstract. Both Moderate Resolution Imaging Spectroradiometer (MODIS) and Spinning Enhanced Visible and InfraRed Imager (SEVIRI) satellite observations suggest that the narrow heterogeneous Red Sea coastal region is a frequent source of airborne dust that, because of its proximity, directly affects the Red Sea and coastal urban centers. The potential of soils to be suspended as airborne mineral dust depends largely on soil texture, moisture content and particle size distributions. Airborne dust inevitably carries the mineralogical and chemical signature of a parent soil. The existing soil databases are too coarse to resolve the small but important coastal region. The purpose of this study is to better characterize the mineralogical, chemical and physical properties of soils from the Arabian Red Sea coastal plain, which in turn will help to improve assessment of dust effects on the Red Sea, land environmental systems and urban centers. Thirteen surface soils from the hot-spot areas of windblown mineral dust along the Red Sea coastal plain were sampled for analysis. Analytical methods included optical microscopy, X-ray diffraction (XRD), inductively coupled plasma optical emission spectrometry (ICP-OES), ion chromatography (IC), scanning electron microscopy (SEM) and laser particle size analysis (LPSA). We found that the Red Sea coastal soils contain major components of quartz and feldspar, as well as lesser but variable amounts of amphibole, pyroxene, carbonate, clays and micas, with traces of gypsum, halite, chlorite, epidote and oxides. The range of minerals in the soil samples was ascribed to the variety of igneous and metamorphic provenance rocks of the Arabian Shield forming the escarpment to the east of the Red Sea coastal plain. The analysis revealed that the samples contain compounds of nitrogen, phosphorus and iron that are essential nutrients to marine life. The analytical results from this study will provide a valuable input into dust emission models used in climate, marine ecology and air quality studies.
Unsupervised Odometry and Depth Learning for Endoscopic Capsule Robots

In the last decade, many medical companies and research groups have tried to convert passive capsule endoscopes as an emerging and minimally invasive diagnostic technology into actively steerable endoscopic capsule robots which will provide more intuitive disease detection, targeted drug delivery and biopsy-like operations in the gastrointestinal(GI) tract. In this study, we introduce a fully unsupervised, realtime odometry and depth learner for monocular endoscopic capsule robots. We establish the supervision by warping view sequences and assigning the re-projection minimization to the loss function, which we adopt in multi-view pose estimation and single-view depth estimation network. Detailed quantitative and qualitative analyses of the proposed framework performed on non-rigidly deformable ex-vivo porcine stomach datasets proves the effectiveness of the method in terms of motion estimation and depth recovery.
An Adaptive Recursive Wavelet Based Algorithm for Real-Time Measurement of Power System Variables During Off-Nominal Frequency Conditions

An adaptive wavelet-based method of phasor and frequency estimations and its application for online monitoring, control, and protective equipment are presented in this paper. The method is recursive with a low computational burden, suited for real-time implementations, and does not need any preprocessing stages. It computes the frequency of the analyzing signal accurately during nominal and off-nominal frequency conditions. To reduce computational errors of the phase angle and amplitude estimations that occur during off-nominal frequency conditions, the proposed method adapts itself according to the frequency drift. The proposed recursive adaptive method along with three other approaches based on recursive wavelet transform, discrete Fourier transform (DFT), and recursive DFT is implemented and compared using MATLAB, considering dynamic and static conditions. The methods are also employed for real-time computation of the phasor and frequency of the recorded data of the South West Interconnected System (SWIS) in Western Australia, and their efficiencies are assessed and compared. In addition, a real 33.3 MVA, 132/23.3 kV transformer located in SWIS is modeled in the electromagnetic transients program (EMTP) software, and the recorded signals have been employed for performance evaluation of the above-mentioned methods. The method is also implemented on a computer-based system in the laboratory and its performance is appraised accordingly. Extensive MATLAB simulations, laboratory implementation, field data, and EMTP results show that the proposed adaptive method has better static and dynamic performances in comparison to the other approaches.
0.2 V 8T SRAM with improved bitline sensing using column-based data randomization

8T SRAMs operating at sub-threshold supply voltages suffer from bit-line swing degradation when the data pattern of a column is dominated by `1' or `0'. Worst case scenarios happen when the accessed bit is different from the rest of the column. In this work, a simplified Linear Feedback Shift Register (LFSR) is used to shuffle input data so that distribution of “1” and “0” in each column is close to 50%. As a result, bit-line sensing margin is enhanced. In addition, a bitline boost biasing scheme is applied to further increase the bitline swing and the sensing window. A 16Kb test chips fabricated in a 65 nm CMOS technology demonstrates successful SRAM operation at 0.2 V, room temperate, having power consumption and access time of 0.7 μW and 2.5 μs, respectively.
The Cook‐Medley hostility scale: item content and ability to predict survival.

&NA; Previous studies have identified the MMPI‐based Cook and Medley hostility scale (Ho) as a predictor of health outcomes. To achieve a better understanding of the construct measured by this scale, Ho items were classified on an a priori basis. Six subsets were identified: Cynicism, Hostile Attributions, Hostile Affect, Aggressive Responding, Social Avoidance, and Other. Study 1 examined the correlations of these subsets with scales of the NEO Personality Inventory in two samples of undergraduates. Good convergent and discriminant validity were demonstrated, but there was some evidence that items in the Social Avoidance and Other categories reflect constructs other than hostility. Study 2 examined the ability of the Ho scale and the item subsets to predict the 1985 survival of 118 lawyers who had completed the MMPI in 1956 and 1957. As in previous studies, those with high scores had poorer survival (chi 2 = 6.37, p = 0.012). Unlike previous studies, the relation between Ho scores and survival was linear. Cynicism, Hostile Affect, and Aggressive Responding subsets were related to survival, whereas the other subsets were not. The sum of the three predictive subsets, with a chi 2 of 9.45 (p = 0.002), was a better predictor than the full Ho scale, suggesting that it may be possible to refine the scale and achieve an even more effective measure of those aspects of hostility that are deleterious to health.
Medicare Part D's Effects on Drug Utilization and Out‐of‐Pocket Costs: A Systematic Review

OBJECTIVE To update a past systematic review on whether Medicare Part D changed drug utilization and out-of-pocket (OOP) costs overall and within subpopulations, and to identify evidence gaps. DATA SOURCES/STUDY SETTING Published and gray literature from 2010 to 2015 meeting prespecified screening criteria, including having a comparison group, and utilization or OOP cost outcomes. STUDY DESIGN We conducted a systematic literature review with a quality assessment. DATA COLLECTION/EXTRACTION METHODS For each study, we extracted information on study design, data sources, analytic methods, outcomes, and limitations. Because outcome measures vary across studies, we did a qualitative synthesis rather than meta-analysis. PRINCIPAL FINDINGS Sixty-five studies met screening criteria. Overall, Medicare Part D enrollees have increased drug utilization and decreased OOP costs, but coverage gaps limit the program's impact. Beneficiaries whose insurance becomes more generous after enrollment had disproportionately increased drug utilization and decreased OOP costs. Outcomes among dual-eligibles were mixed. CONCLUSIONS There is strong evidence on how Medicare Part D and the donut hole coverage gap affect utilization and OOP costs, but weak evidence on how effects vary among dual-eligibles or across diseases. Findings suggest that the Affordable Care Act's provisions to expand coverage and reduce the donut hole should improve patient outcomes.
Power of an Adaptive Trial Design for Endovascular Stroke Studies: Simulations Using IMS (Interventional Management of Stroke) III Data

Background and Purpose— Adaptive trial designs that allow enrichment of the study population through subgroup selection can increase the chance of a positive trial when there is a differential treatment effect among patient subgroups. The goal of this study is to illustrate the potential benefit of adaptive subgroup selection in endovascular stroke studies. Methods— We simulated the performance of a trial design with adaptive subgroup selection and compared it with that of a traditional design. Outcome data were based on 90-day modified Rankin Scale scores, observed in IMS III (Interventional Management of Stroke III), among patients with a vessel occlusion on baseline computed tomographic angiography (n=382). Patients were categorized based on 2 methods: (1) according to location of the arterial occlusive lesion and onset-to-randomization time and (2) according to onset-to-randomization time alone. The power to demonstrate a treatment benefit was based on 10 000 trial simulations for each design. Results— The treatment effect was relatively homogeneous across categories when patients were categorized based on arterial occlusive lesion and time. Consequently, the adaptive design had similar power (47%) compared with the fixed trial design (45%). There was a differential treatment effect when patients were categorized based on time alone, resulting in greater power with the adaptive design (82%) than with the fixed design (57%). Conclusions— These simulations, based on real-world patient data, indicate that adaptive subgroup selection has merit in endovascular stroke trials as it substantially increases power when the treatment effect differs among subgroups in a predicted pattern.
20-Hydroxyeicosatetraenoic Acid as a Predictor of Neurological Deterioration in Acute Minor Ischemic Stroke

Background and Purpose— The relationship between high plasma 20-hydroxyeicosatetraenoic acid (20-HETE) levels and neurological deterioration (ND) has not been investigated in patients with acute minor ischemic stroke. Method— We conducted a prospective, multicenter observational study in patients with acute minor ischemic stroke. Plasma levels of 20-HETE were measured at admission in all patients. The primary end point of the study was ND within 10 days after admission. The degree of disability was assessed using modified Rankin scale at 3 months after admission. Results— A total of 322 patients were enrolled, of which 85 patients (26.4%) developed ND. Mean 20-HETE level was 1687±158 pmol/L. On multivariate analyses, high level (>1675 pmol/L) of 20-HETE was an independent predictor of ND (third and fourth quartiles). Neurological deterioration was associated with a higher risk of poor outcome (modified Rankin scale scores 3–6) at 3 months. Conclusions— ND is fairly common in acute minor ischemic stroke and is associated with poor prognosis. Elevated plasma level of 20-HETE may be a predictor for ND in acute minor ischemic stroke.
Induction of Eosinophilic Esophagitis by Sublingual Pollen Immunotherapy

Sublingual immunotherapy (SLIT) is increasingly investigated and utilized for the treatment of food and pollen allergies. Previous case reports suggested that eosinophilic esophagitis (EoE) might develop as a long-term complication in children after completion of oral immunotherapy. Here, we describe a 44-year-old female with a medical history of pollinosis who for the first time in her life developed complete manifestation of EoE (peak eosinophils 164/high power field) 4 weeks after initiation of SLIT using specific soluble allergens (hazelnut, birch, alder) according to previous specific serum IgE testing. After discontinuation of SLIT, EoE resolved completely within 4 weeks without any other medical intervention. During a follow-up of 12 months the patient remained free of any esophageal symptoms. This is the first case report demonstrating a close and therefore likely causative association between pollen SLIT and EoE in an adult patient.
Collaborative Repository for Cybersecurity Data and Threat Information

In this paper, we attempt to show how to build a collaborative repository for cybersecurity data and threat information by building on top of a privacy-aware storage system: Tamias. We set the following goals: allow data sharing with a very high level of control over the sharing scope, enhance collaboration of entities that may not know each other but deal with similar threats, and manage different levels of trust between each parties. These levels of trust will define how much information is shared with each entity.
Compatibility Challenges for High-ĸ Materials Integration into CMOS Technology

In addition to meeting the formidable challenges of replacing the nearly perfect SiO_2 dielectric, a new dielectric ideally needs to replace SiO_2 with minimal rearrangement of the complementary metal oxide semiconductor (CMOS) process flow. In this article, we outline the essential materials-integration issues that arise out of the technical requirements for minimizing changes to future process technologies. These include interfacial layer formation, film microstructure, deposition technologies, and electrical performance challenges such as trapped charge and the mobility degradation associated with any replacement material. Integration of the high- ĸ materials currently under consideration presents a significant challenge for materials scientists and engineers in industry and academia.
Cardiac Troponin Release is Associated with Biomarkers of Inflammation and Ventricular Dilatation During Critical Illness

Introduction: Troponin release is common during critical illness. We hypothesized that there was an association between cardiac troponin T (cTnT) and biomarkers of systemic inflammation and ventricular dilatation. Methods: In an observational prospective cohort study, we enrolled consecutive adult patients admitted for noncardiac reasons to the intensive care unit (ICU) in two tertiary care centers. We measured cTnT, C-reactive protein (CRP), interleukin-6 (IL-6), procalcitonin (PCT), and N-terminal pro brain natriuretic peptide (NT-proBNP) daily in the first week, and on alternate days in the second week. Using a peak cTnT cutoff ≥15 ng/L and concomitant changes on electrocardiogram, patients were categorized as “definite myocardial infarction (MI),” “possible MI,” “cTnT rise only,” or “no cTnT rise. ” Within each group, associations between CRP, IL-6, PCT, NT-proBNP, and cTnT were investigated using mixed effect models. Results: One hundred seventy-two patients were included in the analysis of whom 84% had a cTnT rise ≥15 ng/L. Twenty-one patients (12%) had a definite MI, 51 (30%) had a possible MI, and 73 (42%) had a cTnT rise only. At the time of peak cTnT, 71% of patients were septic and 67% were on vasopressors. Multivariable analysis showed a significant association between cTnT and IL-6 in all patients with a cTnT rise independent of age, gender, renal function, and cardiovascular risk factors. In patients without a definite MI, cTnT levels were significantly associated with PCT and NT-proBNP values. In patients without elevated cTnT levels, there was no associated NT-proBNP rise. Conclusions: In ICU patients admitted for non-cardiac reasons, serial cTnT levels were independently associated with markers of systemic inflammation and NT-proBNP.
Electronic Structure and Transport Properties of Doped Lead Chalcogenides from First Principles

The structural and electronic properties of lead chalcogenides PbX (X=S, Se, and Te) are investigated by first-principles calculations based on the range-separated hybrid functionals and semilocal generalized gradient approximation. It is found that an accurate band structure description requires the hybrid functional with the spin-orbit coupling included. Using this approach, the band structure of lead telluride and doped lead selenide are calculated, and its influences on the transport properties are discussed.
Sub-wavelength Lithography and Variability Aware SRAM Characterization

With shrinking of minimum feature size of advanced technology nodes, the impact of litho process variations on the resulting electrical parameters of printed circuits dramatically increases. Litho process variations correspond to random changes in the actual optical conditions (dose and focus) which develop at every mask exposure, hence from die to die. In this way the litho process variations act as a global variability component affecting all devices on a particular die in the same way. In contrast to this, the intrinsic variability of the devices and interconnects originating mostly from local Random Dopant Fluctuations (RDF) and Line Edge Roughness (LER) has a purely spatially uncorrelated component. Yet, it is not clear which of the two limits scaling down variability sensitive circuits such as SRAM beyond 45 nm. This paper presents a tool flow to perform SRAM wide statistical analysis subject to combinations of global litho and local variability components. The tool flow is illustrated in 45 nm industry grade SRAM vehicle. Selected case studies show how this tool flow successfully captures non-trivial statistical interactions between the SRAM cell and the periphery, otherwise less visible when using statistical electrical simulations of the critical path alone.
Deciphering the modulatory role of oxytocin in human altruism

Abstract Unlike any other species, humans frequently engage in altruistic behaviors by which they increase another individual’s welfare even if this implies personal costs. The psychological motives underlying altruistic behaviors remain diverse, ranging from the ability to reciprocate trust and cooperation to bonding and empathizing with family members or even genetically unrelated others. This article explores the neuroendocrine architecture of altruism by emphasizing the crucial role of the evolutionarily highly conserved peptide hormone oxytocin as a modulator of cooperative behaviors including empathy-driven altruism. However, accumulating evidence suggests that oxytocin does not invariably facilitate cooperation but also produces protective or even defensive-aggressive responses in specific social contexts. In addition, we highlight the relevance of message frames as critical determinants of whether the peptide promotes altruism toward prosocial ends.
Robust synthesis for master-slave synchronization of Lur'e systems

In this paper a method for robust synthesis of full static-state error feedback and dynamic-output error feedback for master-slave synchronization of Lur'e systems is presented. Parameter mismatch between the systems is considered in the synchronization schemes. Sufficient conditions for uniform synchronization with a bound on the synchronization error are derived, based on a quadratic Lyapunov function. The matrix inequalities from the case without parameter mismatch between the Lur'e systems remain preserved, but an additional robustness criterion must be taken into account. The robustness criterion is based on an uncertainty relation between the synchronization error bound and the parameter mismatch. The robust synthesis method is illustrated on Chua's circuit with the double scroll. One observes that it is possible to synchronize the master-slave systems up to a relatively small error bound, even in the case of different qualitative behavior between the master and the uncontrolled slave system, such as limit cycles and stable equilibria.
An optimized pipelined architecture of SHA-256 hash function

Real time applications of digital communication systems are rapidly increasing. Due to this there is a huge demand for high level of security. In cryptographic algorithms, SHA-256 has become an integral part in many applications. A hardware implementation of the SHA-256 hash algorithm is physically separate from the main processor and hence, it has more security and higher performance than the software implementation. An execution of a hash algorithm on FPGAs is convenient, as it is flexible and easily upgradable. However, implementation of this algorithm on hardware has been challenging, due to the demand of high processing speed. In this paper, an optimized pipelined architecture of SHA-256 hash function has been implemented in hardware HDL Verilog language and synthesized in Xilinx Virtex-4 FPGA. The compressor and expander block of hash function are modified. Carry skip adder is also used to improve the performance of the architecture. The obtained result shows a significant improvement in the performance of the proposed SHA-256 algorithm and it is compared with existing various architectures. Its maximum clock frequency is 170.75 MHz, throughput of 1344.98 Mbps and an improved efficiency of 2.2 Mbps/ slice.
Non-intrusive program tracing and debugging of deployed embedded systems through side-channel analysis

One of the hardest aspects of embedded software development is that of debugging, especially when faulty behavior is observed at the production or deployment stage. Non-intrusive observation of the system's behavior is often insufficient to infer the cause of the problem and identify and fix the bug. In this work, we present a novel approach for non-intrusive program tracing aimed at assisting developers in the task of debugging embedded systems at deployment or production stage, where standard debugging tools are usually no longer available. The technique is rooted in cryptography, in particular the area of side-channel attacks. Our proposed technique expands the scope of these cryptographic techniques so that we recover the sequence of operations from power consumption observations (power traces). To this end, we use digital signal processing techniques (in particular, spectral analysis) combined with pattern recognition techniques to determine blocks of source code being executed given the observed power trace. One of the important highlights of our contribution is the fact that the system works on a standard PC, capturing the power traces through the recording input of the sound card. Experimental results are presented and confirm that the approach is viable.