Miracle-dz/UniFAR-FTUs huggingface dataset:
One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data

Even in the aggregate, genomic data can reveal sensitive information about individuals. We present a new model-based measure, PrivMAF, that provides provable privacy guarantees for aggregate data (namely minor allele frequencies) obtained from genomic studies. Unlike many previous measures that have been designed to measure the total privacy lost by all participants in a study, PrivMAF gives an individual privacy measure for each participant in the study, not just an average measure. These individual measures can then be combined to measure the worst case privacy loss in the study. Our measure also allows us to quantify the privacy gains achieved by perturbing the data, either by adding noise or binning. Our findings demonstrate that both perturbation approaches offer significant privacy gains. Moreover, we see that these privacy gains can be achieved while minimizing perturbation (and thus maximizing the utility) relative to stricter notions of privacy, such as differential privacy. We test PrivMAF using genotype data from the Welcome Trust Case Control Consortium, providing a more nuanced understanding of the privacy risks involved in an actual genome-wide association studies. Interestingly, our analysis demonstrates that the privacy implications of releasing MAFs from a study can differ greatly from individual to individual. An implementation of our method is available at http://privmaf.csail. mit.edu.
Network Summarization with Preserved Spectral Properties

Large-scale networks are widely used to represent object relationships in many real world applications. The occurrence of large-scale networks presents significant computational challenges to process, analyze, and extract information from such networks. Network summarization techniques are commonly used to reduce the computational load while attempting to maintain the basic structural properties of the original network. Previous works have primarily focused on some type of network partitioning strategies with application-dependent regularizations, most often resulting in strongly connected clusters. In this paper, we introduce a novel perspective regarding the network summarization problem based on concepts from spectral graph theory. We propose a new distance measurement to characterize the spectral differences between the original and coarsened networks. We rigorously justify the spectral distance with the interlacing theorem as well the results from the stochastic block model. We provide an efficient algorithm to generate the coarsened networks that maximally preserves the spectral properties of the original network. Our proposed network summarization framework allows the flexibility to generate a set of coarsened networks with significantly different structures preserved from different aspects of the original network, which distinguishes our work from others. We conduct extensive experimental tests on a variety of large-scale networks, both from real-world applications and the random graph model. We show that our proposed algorithms consistently perform better results in terms of the spectral measurements and running time compared to previous network summarization algorithms.
Replication Study: BET bromodomain inhibition as a therapeutic strategy to target c-Myc

In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Kandela et al., 2015) that described how we intended to replicate selected experiments from the paper "BET bromodomain inhibition as a therapeutic strategy to target c-Myc" (Delmore et al., 2011). Here we report the results of those experiments. We found that treatment of human multiple myeloma (MM) cells with the small-molecular inhibitor of BET bromodomains, (+)-JQ1, selectively downregulated MYC transcription, which is similar to what was reported in the original study (Figure 3B; Delmore et al., 2011). Efficacy of (+)-JQ1 was evaluated in an orthotopically xenografted model of MM. Overall survival was increased in (+)-JQ1 treated mice compared to vehicle control, similar to the original study (Figure 7E; Delmore et al., 2011). Tumor burden, as determined by bioluminescence, was decreased in (+)-JQ1 treated mice compared to vehicle control; however, while the effect was in the same direction as the original study (Figure 7C-D; Delmore et al., 2011), it was not statistically significant. The opportunity to detect a statistically significant difference was limited though, due to the higher rate of early death in the control group, and increased overall survival in (+)-JQ1 treated mice before the pre-specified tumor burden analysis endpoint. Additionally, we evaluated the (−)-JQ1 enantiomer that is structurally incapable of inhibiting BET bromodomains, which resulted in a minimal impact on MYC transcription, but did not result in a statistically significant difference in tumor burden or survival distributions compared to treatment with (+)-JQ1. Finally, we report meta-analyses for each result. DOI: http://dx.doi. org/10.7554/eLife.21253. 001
Effect of diet on fatty liver-hemorrhagic syndrome incidence in laying chickens.

Abstract Liver hemorrhages characteristic of those seen in Fatty Liver-Hemorrhagic Syndrome were not observed in livers having less than 4.0 g. lipid per liver or weighing less than 30 g. wet weight. However, liver size and lipid level per se were not the definitive causes of the hemorrhaging because birds without hemorrhages had liver weights and lipid values equal to or greater than those with hemorrhages. Incorporation of lipotropic vitamins (B12, E, choline, inositol) into the diet of laying chickens did not significantly (P > 0.01) reduce their liver lipid content. Increasing the dietary level of protein, vitamin B12, vitamin E, choline, inositol, selenium and/or cobalt did not prevent the occurrence of liver hemorrhages. Liver lipid was significantly (P > 0.01) reduced by feeding a low energy diet; and no liver hemorrhages were observed.
Oral Supplementation of Parturient Mothers with Vitamin D and Its Effect on 25OHD Status of Exclusively Breastfed Infants at 6 Months of Age: A Double-Blind Randomized Placebo Controlled Trial.

BACKGROUND Exclusively breastfed infants are at increased risk of vitamin D deficiency and many lactating mothers have been found deficient in 25OHD stores. OBJECTIVE To compare serum vitamin D levels in exclusively breastfed infants at 6 months of age with or without oral supplementation of 600,000 IU of vitamin D3 to mothers in early postpartum period. METHODS Exclusively breastfeeding term parturient mothers were randomized 24-48 hours following delivery to receive either 600,000 IU of vitamin D3 (Cholecalciferol) over 10 days in a dose of 60,000 IU/day or placebo. 25OHD levels were measured by Radio Immuno Assay method at recruitment and after 6 months in all mothers and their infants. Urinary calcium and creatinine ratio was measured to monitor adverse effects of vitamin D3 in both mothers and infants at 14 weeks and 6 months of age. X-ray of both wrists in anteroposterior view and serum alkaline phosphatase of infants were done in both groups at 6 months of age to look for evidence of rickets. RESULTS Maternal profile was similar in intervention (A) and control (B) groups. Mothers' serum 25OHD levels at recruitment were also similar being 16.2 ± 9.3 ng/mL in group A and 14.1 ± 7.1 ng/mL in group B. After 6 months, 25OHD levels were 40.3 ± 21.6 and 22.9 ± 20.1 ng/mL in group A and group B mothers (p ≤ 0.00), respectively. The serum 25OHD levels in cord blood were 9.9 ± 5.7 and 8.9 ± 5.1 ng/mL, respectively, in infants born to mothers in intervention and control groups (p = 0.433). At 6 months of age, the serum 25OHD levels significantly (p < 0.00) raised to 29.1 ± 14.6 ng/mL in infants of group A compared to those of group B (15.7 ± 17.7 ng/mL). Four infants developed radiological rickets at 6 months of age, two infants each in intervention group and study group. As against 10 infants in the control group (16.94%), no infant in the study group had biochemical rickets. Urinary calcium and creatinine ratio in mothers and infants at 14 weeks and 6 months of age in both intervention and study group was within normal limits, indicating there was no adverse effects of oral administration of 600,000 IU of vitamin D3. CONCLUSION Serum 25OHD levels of exclusively breastfed infants significantly rise at 6 months of age when their mothers are orally supplemented with 60,000 IU of vitamin D3 daily for 10 days in the early postpartum period in comparison to infants of vitamin D3 unsupplemented mothers.
Influence of Cl~- concentration on the initial corrosion behavior of 2A12 aluminum alloy

The initial corrosion laws and electrochemical behaviors of 2A12 aluminum alloy were investigated by using alternate immersion test,scanning electron microscopy(SEM)as well as electrochemical impedance spectroscopy(EIS). The results showed that obvious pitting phenomena were observed for all the specimens in various Cl-containing solutions after 48 h alternate immersion.With the increase of Cl-concentration,the initiation and development of pitting corrosion were promoted and more corrosion products formed.At a lower Cl-concentration,the corrosion process was mainly controlled by charge transfer resistance;with increasing Cl-concentration,the electrochemical characteristic transferred to the mixed control of charge transfer resistance and Warburg resistance.
Inversion response to optimize lumped‐element circuits for metamaterial

Enhancing electromagnetic research on prior light bend mechanisms is a significant issue for composite material phenomena, and one that is not available in nature. The unit cell of metamaterial can be revised, such that it is significantly smaller than the free space of the wavelength. It is essential to extend the appropriate retrieval process to measure electrical and magnetic responses to the backward wave propagation and dispersion diagram characteristics. In this paper, we propose a retrieval process inversion response between known and unknown parameters of the lumped unit‐cell circuits that optimizes the best fit parameters. By utilizing the optimization of particle swarm techniques, we provide appropriate values of periodic unit cells of CRLH transmission line circuits that matched with the microstrip implementation model. The group velocity of the wave is indicated in the parallel direction, whereas the phase velocity is in the anti‐parallel direction. The dispersion diagram displayed a specifically left‐handed and right‐handed medium, and a tiny band gap appeared in the attenuation medium. The constitutive parameters of dielectric permittivity, permeability, and refractive index were obtained from the periodic composite transmission line circuits.
WEPIR 2018: Workshop on Evaluation of Personalisation in Information Retrieval

The purpose of the WEPIR 2018 workshop is to bring together researchers from different backgrounds, interested in advancing the evaluation of personalisation in information retrieval. The workshop focus is on the development of a common understanding of the challenges, requirements and practical limitations of meaningful evaluation of personalisation in information retrieval. The planned outcome of the workshop is the proposal of methodologies to support evaluation of personalised information retrieval from both the perspectives of the user experience in interactive search settings, and of user models for personalised information retrieval and their algorithmic incorporation in the search process.
Catheter-related Bloodstream Infection due to Lodderomyces elongisporus in a Patient with Lung Cancer

Dear Editor, Lodderomyces elongisporus was first described as a cause of bloodstream infections in 2008 [1]. We present a case of L. elongisporus fungemia in a patient with lung cancer who had a central venous catheter. A 56-year-old female presented at the emergency department of Asan Medical Center (Seoul, Korea) complaining of dyspnea. She had undergone a left lung lobectomy because of non-small cell lung cancer and had been treated with high-dose dexamethasone and cord decompression surgery for spinal cord metastasis two months ago; she was then treated with meropenem and teicoplanin for one week, owing to methicillin-resistant Staphylococcus aureus bacteremia. She was subsequently transferred to a secondary care hospital, in which a peripherally inserted central catheter had been placed for chemotherapy with docetaxel and antimicrobials. This study was performed retrospectively and was exempt from the requirements of informed consent and ethical approval. Initial vital signs revealed a spiking fever up to 40°C. Abnormal laboratory findings included a peripheral leukocyte count of 19.9×10/L, platelets at 69×10/L, C-reactive protein at 1,937.2 nmol/L, lactate dehydrogenase at 6.13 μkat/L, prothrombin time of 14.2 seconds, activated partial thromboplastin time of 42.8 seconds, and D-dimer at 72.3 nmol/L. Chest computed tomography showed pleural effusion with multiple lung nodules and an edematous gall bladder. Three sets of Bactec blood culture (Beckton-Dickenson, Sparks, MD, USA) collected at admission grew a single morphotype of yeast in aerobic vials only. Detection times were 25.7 hours for catheter-drawn blood and 28.6 and 31.1 hours in two peripheral blood sets. Microscopic evaluation of this yeast showed blastoconidia and branching pseudohyphae similar to those in Candida parapsilosis (Fig. 1). CHROMagar Candida medium (Komed, Sungnam, Korea) revealed a turquoise-blue colony, which differed from the green colonies of Candida albicans and blue colonies of Candida tropicalis (Fig. 1). The Vitek 2 YST ID (bioMérieux, Durham, NC) and API 20C AUX (bioMérieux) system identified it as C. parapsilosis. However, Bruker Biotyper MALDI-TOF (Brucker Daltonics, Breman, Germany) analysis indicated a likely identification of L. elongisporus (score value=1.79), followed by C. parapsilosis (score value=1.12). Sequence analysis of an internal transcribed spacer (ITS) region of ribosomal DNA demonstrated 100% homology with L. elongisporus and 97% homology with C. parapsilosis. By antifungal susceptibility testing using ATB Fungus 3 (bio-
Test point insertion in hybrid test compression/LBIST architectures

Logic built-in self-test (LBIST), originally introduced for board, system, and in-field tests, is now being increasingly used with on-chip test compression. This hybrid approach allows LBIST to become a complementary solution for in-system test, where high quality, low power, low silicon area, and most importantly short test application time are key factors affecting ICs that are targeted for safety-critical and automotive systems. Test points are common in BIST-ready designs where they play a key role in reducing both test application time given a test coverage goal and the overall silicon overhead so that one can get a desired coverage with the minimal number of patterns. Unfortunately, these test points are typically dysfunctional when enabled in an ATPG-based test compression mode. Similarly, test points used to reduce ATPG-based test pattern counts cannot guarantee desired random testability. Incompatibility of both types of test points has motivated research presented in this paper. We present a novel hybrid test point technology designed to both reduce deterministic pattern counts and improve fault detection likelihood by means of the same minimal set of test points. Experimental results obtained for large industrial designs illustrate feasibility of the proposed hybrid test points and are reported herein.
Design of a CMOS multi‐rate adaptive continuous‐time equalizer based on power spectrum estimation

An adaptive continuous‐time equalizer for reliable short‐haul high‐speed serial communications is described in this paper. The adaptive equalizer uses the spectrum‐balancing technique to adapt its response to changes in the bandwidth, amplitude, and bit rate of the input signal. In this way, it is able to compensate the frequency response of a 1‐mm diameter step‐index plastic optical fiber, for lengths up to 50 m, and bit rates ranging from 400 Mb/s to 2.5 Gb/s. Experimental results are shown to demonstrate its feasibility. Copyright © 2017 John Wiley & Sons, Ltd.
Dual skew codes from annihilators: Transpose Hamming ring extensions

In this paper a framework to study the dual of skew cyclic codes is proposed. The transposed Hamming ring extensions are based in the existence of an anti-isomorphism of algebras between skew polynomial rings. Our construction is applied to left ideal convolutional codes, skew constacyclic codes and skew Reed-Solomon code, showing that the dual of these codes belong to the same class.
Adipose-Derived Mesenchymal Stem Cells for the Treatment of Articular Cartilage: A Systematic Review on Preclinical and Clinical Evidence

Among the current therapeutic approaches for the regeneration of damaged articular cartilage, none has yet proven to offer results comparable to those of native hyaline cartilage. Recently, it has been claimed that the use of mesenchymal stem cells (MSCs) provides greater regenerative potential than differentiated cells, such as chondrocytes. Among the different kinds of MSCs available, adipose-derived mesenchymal stem cells (ADSCs) are emerging due to their abundancy and easiness to harvest. However, their mechanism of action and potential for cartilage regeneration are still under investigation, and many other aspects still need to be clarified. The aim of this systematic review is to give an overview of in vivo studies dealing with ADSCs, by summarizing the main evidence for the treatment of cartilage disease of the knee.
Dual Memory Neural Computer for Asynchronous Two-view Sequential Learning

One of the core tasks in multi-view learning is to capture relations among views. For sequential data, the relations not only span across views, but also extend throughout the view length to form long-term intra-view and inter-view interactions. In this paper, we present a new memory augmented neural network that aims to model these complex interactions between two asynchronous sequential views. Our model uses two encoders for reading from and writing to two external memories for encoding input views. The intra-view interactions and the long-term dependencies are captured by the use of memories during this encoding process. There are two modes of memory accessing in our system: late-fusion and early-fusion, corresponding to late and early inter-view interactions. In the late-fusion mode, the two memories are separated, containing only view-specific contents. In the early-fusion mode, the two memories share the same addressing space, allowing cross-memory accessing. In both cases, the knowledge from the memories will be combined by a decoder to make predictions over the output space. The resulting dual memory neural computer is demonstrated on a comprehensive set of experiments, including a synthetic task of summing two sequences and the tasks of drug prescription and disease progression in healthcare. The results demonstrate competitive performance over both traditional algorithms and deep learning methods designed for multi-view problems.
Securing OFDM-based wireless links using temporal artificial-noise injection

We investigate the physical layer security of wireless single-input single-output orthogonal-division multiplexing (OFDM) when a transmitter, which we refer to as Alice, sends her information to a receiver, which we refer to as Bob, in the presence of an eavesdropping node, Eve. To prevent information leakage, Alice sends an artificial-noise (AN) signal superimposed over her information signal. We investigate the impact of the channel delay spread, OFDM cyclic prefix, information/AN power allocation, and information and AN precoders design on the achievable average secrecy rate. We consider the two cases of known and unknown channel state information (CSI) at Alice. Furthermore, we compare both cases of per-sub-channel processing and joint sub-channels processing at Eve's receiver. Our numerical results show the gains of AN injection in terms of average secrecy rate for different OFDM operating conditions. Moreover, based on our new insights, we demonstrate that the AN-aided scheme is effective and achieves almost the same average secrecy rate as the full-CSI case without the need for Eve's instantaneous CSI at Alice.
Robust estimation via robust gradient estimation

We provide a new computationally efficient class of estimators for risk minimization. We show that these estimators are robust for general statistical models, under varied robustness settings, including in the classical Huber ε‐contamination model, and in heavy‐tailed settings. Our workhorse is a novel robust variant of gradient descent, and we provide conditions under which our gradient descent variant provides accurate estimators in a general convex risk minimization problem. We provide specific consequences of our theory for linear regression and logistic regression and for canonical parameter estimation in an exponential family. These results provide some of the first computationally tractable and provably robust estimators for these canonical statistical models. Finally, we study the empirical performance of our proposed methods on synthetic and real data sets, and we find that our methods convincingly outperform a variety of baselines.
Recent advances in proteomic applications for schistosomiasis research: potential clinical impact

ABSTRACT Introduction: Schistosomiasis is a neglected tropical disease affecting hundreds of millions of people worldwide. Recent advances in the field of proteomics and the development of new and highly sensitive mass spectrometers and quantitative techniques have provided new tools for advancing the molecular biology, cell biology, diagnosis and vaccine development for public health threats such as schistosomiasis. Areas covered: In this review we describe the latest advances in research that utilizes proteomics-based tools to address some of the key challenges to developing effective interventions against schistosomiasis. We also provide information about the potential of extracellular vesicles to advance the fight against this devastating disease. Expert commentary: Different proteins are already being tested as vaccines against schistosomiasis with promising results. The re-analysis of the Schistosoma spp. proteomes using new and more sensitive mass spectrometers as well as better separation approaches will help identify more vaccine targets in a rational and informed manner. In addition, the recent development of new proteome microarrays will facilitate characterisation of novel markers of infection as well as new vaccine and diagnostic candidate antigens.