Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking of Methods for Genomic Taxonomy

ABSTRACT One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is—that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
Audio Cover Song Identification using Convolutional Neural Network

In this paper, we propose a new approach to cover song identification using a CNN (convolutional neural network). Most previous studies extract the feature vectors that characterize the cover song relation from a pair of songs and used it to compute the (dis)similarity between the two songs. Based on the observation that there is a meaningful pattern between cover songs and that this can be learned, we have reformulated the cover song identification problem in a machine learning framework. To do this, we first build the CNN using as an input a cross-similarity matrix generated from a pair of songs. We then construct the data set composed of cover song pairs and non-cover song pairs, which are used as positive and negative training samples, respectively. The trained CNN outputs the probability of being in the cover song relation given a cross-similarity matrix generated from any two pieces of music and identifies the cover song by ranking on the probability. Experimental results show that the proposed algorithm achieves performance better than or comparable to the state-of-the-art.
CYP3A5 genotyping for assessing the efficacy of treatment with simvastatin and atorvastatin

In this work, we examined the impact of polymorphism in the cytochrome P450 (CYP) 3A5 gene, CYP3A5*1 (6986A > G, rs 776746), on the reduction in the lipid levels caused by simvastatin and atorvastatin. We studied 350 hyperlipidemic patients who received 10-40 mg of atorvastatin (n = 175) or simvastatin (n = 175) daily. Genotyping for CYP3A5 was done by PCR-RFLP analysis. Differences in the lipid profile before and after treatment were expressed as the % difference. The frequency of CYP3A5polymorphism was 13.4% for heterozygotes and 86.6% for homozygotes. Comparison of the responses to same dose of each drug showed that the highest % difference was associated with total cholesterol (TC) in subjects receiving atorvastatin 40 mg compared with simvastatin 40 mg (p = 0.048). However, comparison of the responses to equivalent doses of atorvastatin vs. simvastatin revealed no difference in the % change in any of the lipid parameters examined. In individuals with the same CYP3A5 genotype, a head to head comparison of the efficacy of the same dose of simvastatin vs. atorvastatin revealed an advantage for atorvastatin. For equivalent doses of atorvastatin vs. simvastatin there was no difference in the % change in any of the lipid parameters examined. Within the same genotype there was a significant difference in the % change related to the drug treatment.
Efficient indexing for big data in Hadoop MapReduce and main memory databases

In recent years, the database community has witnessed the advent and breakthrough of many new system designs like the famous Hadoop MapReduce or main memory databases like MonetDB, Hekaton, SAP Hana, and HyPer to solve the problems of “Big Data”. The system architectures in this generation of emerging systems often radically differ from traditional relational databases. For database research, this trend creates new challenges to design and optimize data structures for those novel architectures. Premier candidates for innovations are index structures, which are traditionally among the most crucial performance factors in databases. In this thesis, we focus on efficient indexing methods for Hadoop MapReduce and main memory databases. Our work consists of three independent parts that resulted from different research projects. In the first part, we introduce HAIL, a novel approach for efficient static and adaptive indexing in Hadoop MapReduce. We believe that efficient indexing becomes increasingly important in the context of very large data sets. HAIL combines very low index build times that are often even invisible for users, with significant runtime improvements for selective MapReduce jobs. We provide extensive experiments, and show that HAIL can improve job runtimes by up to 68x over Hadoop. In the second part of this thesis, we present an in-depth evaluation of the adaptive radix tree ART, a recent and very promising competitor in the domain of tree-indexes for main memory databases. ART was reported by its inventors to be significantly faster than previous tree indexes and even competitive to hash tables. However, the original evaluation of ART did not consider Judy Arrays, which is, to the best of our knowledge, the first data structure introducing adaptivity to radix trees. Furthermore, the hash table used in the comparison with ART was just a textbook implementation of chained hashing and not a more sophisticated state-of-the-art hash tables. We provide an extended analysis and experimental evaluation of ART, including a detailed comparison to Judy Arrays, hashing via quadratic probing, and three variants of Cuckoo hashing. Our results give a more differentiated look on ART. In particular, we present striking conceptual similarities between ART and Judy Arrays and show that well-engineered hash tables can beat the lookup throughput of adaptive radix trees by up 6x. In the third part, motivated by our previous results, we take a closer look at hashing methods in main memory databases. We identify seven key factors that influence hashing performance, evaluate their impact, and discuss the implications on hashing in modern databases. Our study indicates that choosing the right hashing method and configuration can make an order of magnitude difference in insert and lookup performance. We also provide a guideline for practitioners on when to use which hashing method.
Long‐Term Doppler Hemodynamics and Effective Orifice Areas of Edwards SAPIEN and Medtronic CoreValve Prostheses after TAVI

Although initial hemodynamics of percutaneously implanted aortic bioprostheses compare favorably to surgically implanted valves, the durability of the flow characteristics remains unknown. As biological prostheses are at potential risk for early degeneration, the aim of our study was to compare Doppler hemodynamics and effective orifice area (EOA) directly after and at least 1 year after valve implantation.
Sub-mW $LC$ Dual-Input Injection-Locked Oscillator for Autonomous WBSNs

This paper presents a sub-mW, current-reused first-harmonic LC injection-locked oscillator (ILO) using in-phase dual-input injection technique. It can be used as a power oscillator in the injection-locked transmitter of wireless biomedical sensor nodes (WBSNs) integrated into a wireless body area network. A prototype chip, implemented in a standard 0.13-μm CMOS process occupying 200 × 380 μm, operates in the medical implantable communications service (MICS) band for medical implants. Measurement results show that the proposed ILO features a wide locking range of 800 MHz (150-950 MHz) at an input power of 0 dBm. More importantly, it has a high input sensitivity of -30 dBm to lock the 3-MHz bandwidth of the MICS band, while consuming only 660 μW at 1-V supply. This ultralow power consumption enables autonomous WBSNs.
MEASURING TINY MASS ACCRETION RATES ONTO YOUNG BROWN DWARFS

We present low-resolution Keck I/LRIS spectra spanning from 3200 to 9000 Å of nine young brown dwarfs and three low-mass stars in the TW Hya Association and in Upper Sco. The optical spectral types of the brown dwarfs range from M5.5 to M8.75, though two have near-IR spectral types of early L dwarfs. We report new accretion rates derived from excess Balmer continuum emission for the low-mass stars TW Hya and Hen 3-600A and the brown dwarfs 2MASS J12073347−3932540, UScoCTIO 128, SSSPM J1102−3431, USco J160606.29−233513.3, DENIS-P J160603.9−205644, and Oph J162225−240515B, and upper limits on accretion for the low-mass star Hen 3-600B and the brown dwarfs UScoCTIO 112, Oph J162225−240515A, and USco J160723.82−221102.0. For the six brown dwarfs in our sample that are faintest at short wavelengths, the accretion luminosity or upper limit is measurable only when the image is binned over large wavelength intervals. This method extends our sensitivity to accretion rate down to ∼10−13 M☉yr-1 for brown dwarfs. Since the ability to measure an accretion rate from excess Balmer continuum emission depends on the contrast between excess continuum emission and the underlying photosphere, for objects with earlier spectral types the upper limit on accretion rate is much higher. Absolute uncertainties in our accretion rate measurements of ∼3–5 include uncertainty in accretion models, brown dwarf masses, and distance. The accretion rate of 2 × 10−12 M☉ yr−1 onto 2MASS J12073347−3932540 is within 15% of two previous measurements, despite large changes in the Hα flux.
What you do is who you are: The role of task context in perceived social robot personality

People tend to unconsciously attribute personality traits to all kinds of technology including robots. But what personality do they want robots to have? Previous research has found support for two contradicting theories: similarity attraction and complementary attraction. The similarity attraction theory implies that people prefer a robot with a similar personality to their own (e.g., an extroverted person prefers an extroverted robot). According to the complementary attraction theory, people prefer a robot's personality opposite to their own (e.g., extroverted people prefer an introverted robot). In contrast to both theories, we argue that what is considered an appropriate personality for a robot depends on the task context. In a 2×2 between-groups experiment (N=45), we found trends that indicated similarity attraction for extrovert participants when the robot was a tour guide and complementary attraction for introverted participants when the robot was a cleaner. These trends show that preferences for robot personalities may indeed depend on the context of the robot's role and the stereotype perceptions people hold for certain jobs. Robot behaviors likely need to be adapted not in complimentary or similarity to the users' personality but to the users' expectations about what kind of personality and behaviors are consistent with such a task or role.
Neural Substrates of Motor and Non-Motor Symptoms in Parkinson’s Disease: A Resting fMRI Study

Background Recently, non-motor symptoms of Parkinson’s disease (PD) have been considered crucial factors in determining a patient’s quality of life and have been proposed as the predominant features of the premotor phase. Researchers have investigated the relationship between non-motor symptoms and the motor laterality; however, this relationship remains disputed. This study investigated the neural connectivity correlates of non-motor and motor symptoms of PD with respect to motor laterality. Methods Eight-seven patients with PD were recruited and classified into left-more-affected PD (n = 44) and right-more affected PD (n = 37) based on their MDS-UPDRS (Movement Disorder Society-sponsored revision of the Unified Parkinson’s Disease Rating Scale) motor examination scores. The patients underwent MRI scanning, which included resting fMRI. Brain regions were labeled as ipsilateral and contralateral to the more-affected body side. Correlation analysis between the functional connectivity across brain regions and the scores of various symptoms was performed to identify the neural connectivity correlates of each symptom. Results The resting functional connectivity centered on the ipsilateral inferior orbito-frontal area was negatively correlated with the severity of non-motor symptoms, and the connectivity of the contralateral inferior parietal area was positively correlated with the severity of motor symptoms (p < 0.001, |r| > 0.3). Conclusions These results suggest that the inferior orbito-frontal area may play a crucial role in non-motor dysfunctions, and that the connectivity information may be utilized as a neuroimaging biomarker for the early diagnosis of PD.
A cost-effectiveness evaluation comparing originator follitropin alfa to the biosimilar for the treatment of infertility

Objectives To perform a cost-effectiveness evaluation comparing the originator follitropin alfa (Gonal-f®) to the biosimilar (Bemfola®) in the Italian and Spanish contexts, with an assessment of the German and UK backgrounds. Methods Starting from the study by Rettenbacher et al, a cost-effectiveness model was developed in the Italian and Spanish contexts. Clinical data on subjects, doses of gonadotropin, pregnancies, live-born children, and ovarian hyperstimulation syndrome were used to feed the model. Costs related to drugs, hospitalizations, specialist visits, and examinations were retrieved from Italian and Spanish tariffs. Gonadotropin acquisition costs for Germany and the UK were also taken into account to expand the economical assessment to the other countries. The evaluation was done based on the National Health Service perspective. Sensitivity analyses, both univariate and probabilistic, as long as scenario analyses, tested the robustness of the model. Results Originator follicle-stimulating hormone (FSH) costs were €3,663 and €6,387 in Italy and Spain, respectively, whereas biosimilar FSH costs were €3,483 and €6,342. The efficacy was found to be 0.52 for the originator and 0.47 for the biosimilar. The average cost per live birth was estimated to be €7,044 and €12,283 for the originator FSH and €7,411 and €13,494 for the biosimilar for Italy and Spain, respectively. Furthermore, the originator FSH generated an incremental cost-effectiveness ratio of €3,600 for Italy and €900 for Spain compared to the biosimilar. Sensitivity analyses confirmed the results of the base case model. Conclusion This analysis indicated that the originator FSH is a cost-efficient treatment strategy for Italian and Spanish health services compared to the biosimilar and it would be worthwhile extending this evaluation to other countries.
Holographic pseudo-Goldstone boson

Pseudo-Goldstone bosons in 4D strongly coupled theories have a dual description in terms of 5D gauge theories in warped backgrounds. We introduce systematic methods of computing the pseudo-Goldstone potential for an arbitrary warp factor in 5D. When applied to electroweak symmetry breaking, our approach clarifies the relation of physical observables to geometrical quantities in five dimensions.
Dust Lanes Causing Structure in the Extended Narrow-Line Region of Early-Type Seyfert Galaxies

We construct near-infrared to visible broadband NICMOS/WFPC color maps for four early-type Seyfert galaxies with S-shaped or one-sided ionization cones. We find that dust lanes are near or connected to many of the features seen in the [O III] and Hα + [N II] line emission maps. This suggests that much of the structure of line emission in these ionization cones is determined by the distribution of ambient dense galactic gas. Spiral arms, dust lanes caused by bars, or gaseous warps provide dense gas, which when illuminated by a conical beam of ultraviolet photons can result in the complicated line emission morphologies observed.
Sharing schistosomes: the elephant schistosome Bivitellobilharzia nairi also infects the greater one-horned rhinoceros (Rhinoceros unicornis) in Chitwan National Park, Nepal

Abstract Because the digenetic trematode fauna of Nepal is poorly known, we began to search for schistosomes in and around Chitwan National Park (CNP) of southern Nepal. Both domestic and wild Indian elephants (Elephus maximus) are present, and we found one of two dung samples from wild elephants and 1 of 22 (4.5%) dung samples from domestic elephants to be positive for schistosome eggs. The morphology of the eggs and both cox1 and 28S sequences derived from the eggs/miracidia were consistent with Bivitellobilharzia nairi, reported here for the first time from Nepal. Also, 7 of 14 faecal samples from the Asian or greater one-horned rhinoceros (Rhinoceros unicornis) contained viable eggs indistinguishable from those of B. nairi. This identification was confirmed by comparison with both cox1 and 28S sequences from B. nairi eggs/miracidia derived from Nepalese and Sri Lankan elephants. This represents the first sequence-verified identification of a schistosome from any species of rhinoceros, and the first verified occurrence of a representative of Bivitellobilharzia (a genus of ‘elephant schistosomes’) in mammals other than elephants. Our work suggests that elephants and rhinos share B. nairi in CNP, even though these two members of the ‘charismatic megafauna’ belong to unrelated mammalian families. Their shared life style of extensive contact with freshwater habitats likely plays a role, although the snail intermediate host and mode of definitive host infection for B. nairi have yet to be documented. This report also supports Bivitellobilharzia as a monophyletic group and its status as a distinct genus within Schistosomatidae.
Clinical correlates of plantar pressure among diabetic veterans.

OBJECTIVE To assess the relationship between diabetes characteristics, medical history, foot deformity, sensory neuropathy, and plantar foot pressure. RESEARCH DESIGN AND METHODS There were 517 subjects from a cohort of diabetic veterans enrolled in a prospective study of risk factors for foot complications who contributed 1,017 limbs for study. We interviewed subjects to collect data on demographics, diabetes characteristics, and medical history. A research nurse practitioner performed a directed physical exam of the lower extremities, assessing foot deformities and including quantitative sensory testing with a 5.07 monofilament. In-shoe foot-pressure measurements were obtained with F-scan insoles on subjects wearing their own footwear while walking 10 m at their usual pace. RESULTS In univariate analyses, significant associations were seen between at least one measure of plantar pressure and body mass, sex, race, age, insulin use, certain foot deformities, plantar callus, and sensory neuropathy. Diabetes duration, HbA1c, and history of foot ulcer or amputation were unrelated to plantar pressure. In multiple regression analyses, body mass measured as log (weight), insulin use, white race, male sex, plantar callus, and diabetes duration were significantly related to certain pressures. Foot deformities were related primarily to forefoot pressures. With high pressure at two or more sites defined as the outcome, only body mass remained statistically significant as a predictor of this outcome in a backwards elimination logistic regression model. CONCLUSIONS High in-shoe plantar pressure in diabetic subjects can be predicted in part from readily available clinical characteristics. The mechanisms by which these characteristics may be related to plantar pressure require further study.
Stars Need Benefits: An Experiment on Network Formation

It is often found that networked public goods are provided in networks with a core-periphery structure. In such networks, a minority invests in the good and forms the core, while the majority free rides and forms the periphery. Galeotti and Goyal (2010) show that these types of networks may result as a consequence of strategic interaction. In this paper, we investigate the provision of networked public goods in a controlled laboratory experiment. In our 2x2 design, we examine the effects of group size and the presence of (social) benefits for incoming links. We find that group size does not affect the rate of convergence to stable networks, but that social benefits are highly important. The introduction of social benefits leads to more convergence to equilibrium networks and more stable and efficient outcomes. Moreover, the presence of social benefits in large groups leads to the formation of superstars: star networks which are more efficient than Nash stars.
The Sealed-bid Abstraction in Online Auctions Commentary: Bidders' Experience and Learning in Online Auctions: Issues and Implications Commentary: Do Bids Equal Values on Ebay? Rejoinder: Causes and Implications of Some Bidders Not Conforming to the Sealed-bid Abstraction Estimating Cannibalization 

Editorial: It’s Never Good-bye to Marketing Science Eric T. Bradlow 963 The Sealed-Bid Abstraction in Online Auctions Robert Zeithammer and Christopher Adams 964 Commentary: Bidders’ Experience and Learning in Online Auctions: Issues and Implications Kannan Srinivasan and Xin Wang 988 Commentary: Do Bids Equal Values on eBay? Ali Hortaçsu and Eric R. Nielsen 994 Rejoinder: Causes and Implications of Some Bidders Not Conforming to the Sealed-Bid Abstraction Robert Zeithammer and Christopher Adams 998 Online Demand Under Limited Consumer Search Jun B. Kim, Paulo Albuquerque, and Bart J. Bronnenberg 1001 Estimating Cannibalization Rates for Pioneering Innovations Harald J. van Heerde, Shuba Srinivasan, and Marnik G. Dekimpe 1024 The Economics of Buyer Uncertainty: Advance Selling vs. Probabilistic Selling Scott Fay and Jinhong Xie 1040 Optimal Reverse-Pricing Mechanisms Martin Spann, Robert Zeithammer, and Gerald Häubl 1058 Optimal Reverse Channel Structure for Consumer Product Returns Jeffrey D. Shulman, Anne T. Coughlan, and R. Canan Savaskan 1071 Customer-Base Analysis in a Discrete-Time Noncontractual Setting Peter S. Fader, Bruce G. S. Hardie, and Jen Shang 1086 The Seeds of Dissolution: Discrepancy and Incoherence in Buyer–Supplier Exchange Qiong Wang, Ujwal Kayande, and Sandy Jap 1109 The Effects of Information Transparency on Suppliers, Manufacturers, and Consumers in Online Markets Zach Zhizhong Zhou and Kevin Xiaoguo Zhu 1125 Converting Pirates Without Cannibalizing Purchasers: The Impact of Digital Distribution on Physical Sales and Internet Piracy Brett Danaher, Samita Dhanasobhon, Michael D. Smith, and Rahul Telang 1138 Search and Choice in Online Consumer Auctions Ernan Haruvy and Peter T. L. Popkowski Leszczyc 1152 Statement from the Editor Regarding “New Perspectives on Customer ‘Death’ Using a Generalization of the Pareto/NBD Model” Steven M. Shugan 1165 Focus on Authors 1166