Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals

Recently, thanks to the increasing throughput of new technologies, we have begun to explore the full extent of alternative pre–mRNA splicing (AS) in the human transcriptome. This is unveiling a vast layer of complexity in isoform-level expression differences between individuals. We used previously published splicing sensitive microarray data from lymphoblastoid cell lines to conduct an in-depth analysis on splicing efficiency of known and predicted exons. By combining publicly available AS annotation with a novel algorithm designed to search for AS, we show that many real AS events can be detected within the usually unexploited, speculative majority of the array and at significance levels much below standard multiple-testing thresholds, demonstrating that the extent of cis-regulated differential splicing between individuals is potentially far greater than previously reported. Specifically, many genes show subtle but significant genetically controlled differences in splice-site usage. PCR validation shows that 42 out of 58 (72%) candidate gene regions undergo detectable AS, amounting to the largest scale validation of isoform eQTLs to date. Targeted sequencing revealed a likely causative SNP in most validated cases. In all 17 incidences where a SNP affected a splice-site region, in silico splice-site strength modeling correctly predicted the direction of the micro-array and PCR results. In 13 other cases, we identified likely causative SNPs disrupting predicted splicing enhancers. Using Fst and REHH analysis, we uncovered significant evidence that 2 putative causative SNPs have undergone recent positive selection. We verified the effect of five SNPs using in vivo minigene assays. This study shows that splicing differences between individuals, including quantitative differences in isoform ratios, are frequent in human populations and that causative SNPs can be identified using in silico predictions. Several cases affected disease-relevant genes and it is likely some of these differences are involved in phenotypic diversity and susceptibility to complex diseases.
Heuristically Optimal Path Scanning ( HOPS ) for High Speed Multiphoton Circuit 1 Imaging

10 11 Population dynamics of patterned neuronal firing is fundamental to information 12 processing in the brain. Multiphoton microscopy in combination with calcium indicator 13 dyes allows circuit dynamics to be imaged with single neuron resolution. However, the 14 temporal resolution of fluorescent measures is constrained by the imaging frequency 15 imposed by standard raster scanning techniques. As a result, traditional raster scans 16 limit the ability to detect the relative timing of action potentials in the imaged neuronal 17 population. To maximize the speed of fluorescence measures from large populations of 18 neurons using a standard MPLSM setup we have developed Heuristically Optimal Path 19 Scanning (HOPS). HOPS optimizes the laser travel path length and thus the temporal 20 resolution of neuronal fluorescent measures using standard galvanometer scan mirrors. 21 Minimizing the scan path alone is insufficient for prolonged high speed imaging of 22 neuronal populations. Path stability and the SNR become increasingly important factors 23 as scan rates increase. HOPS addresses this by characterizing the scan mirror 24 galvanometers to achieve prolonged path stability. In addition, the neuronal dwell time is 25 optimized to sharpen the detection of action potentials while maximizing scan rate. The 26 combination of shortest path calculation and minimization of mirror positioning time 27 allows us to optically monitor a population of neurons in a field of view at high rates with 28 single spike resolution, ~125 Hz for 50 neurons and ~8.5 Hz for 1000 neurons. Our 29 approach introduces an accessible method for rapid imaging of large neuronal 30 populations using traditional multiphoton laser scanning microscopes – facilitating new 31 insights into neuronal circuit dynamics. 32 33 34
Robust result merging using sample-based score estimates

In federated information retrieval, a query is routed to multiple collections and a single answer list is constructed by combining the results. Such metasearch provides a mechanism for locating documents on the hidden Web and, by use of sampling, can proceed even when the collections are uncooperative. However, the similarity scores for documents returned from different collections are not comparable, and, in uncooperative environments, document scores are unlikely to be reported. We introduce a new merging method for uncooperative environments, in which similarity scores for the sampled documents held for each collection are used to estimate global scores for the documents returned per query. This method requires no assumptions about properties such as the retrieval models used. Using experiments on a wide range of collections, we show that in many cases our merging methods are significantly more effective than previous techniques.
Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.
Relationship Between Femur and Femoral Arteries for Identifying Risk Factors for Vascular Injury

Background This study aimed to identify risk factors for vascular injury in proximal femoral fracture through identifying frequency and distances between femur and femoral arteries with computed tomography angiography and 3-dimensional reconstruction. Material/Methods In a series of 400 participants, based on measurement results regarding the distribution of femoral arteries in the medial femur, the femoral portion covering that part was divided into levels A–E. The center region, margin region, and risky area in the medial femur were defined. The frequency of femoral arteries and interested shortest distance between the outer femur and superficial, deep, and perforating femoral arteries (SFAs, DFAs, and PFAs) in the center region, margin region, and risky area at each level were recorded. Results There were 173 males and 227 females (average age: 63.61±19.18 years) in this study. The starting point and end point for femoral arteries in the medial femur were from 22.55±4.23% to 54.56±8.39% of the whole femur. The femoral arteries in the medial femur mainly were distributed at levels B (88.2%), C (65.9%), and D (40.6%). The femoral arteries in center regions in the risky area, most of which were DFAs and PFAs, were mainly concentrated at levels B (26.93%) and C (11.81%). Conclusions The mid-shaft level was the most risky level, and the DFAs and PFAs were easier to injure than the SFAs when performing internal fixation of proximal femoral fracture. We recommended that great attention be paid to drill and screw insertion around the mid-shaft level for prevention of iatrogenic vascular injury.
Bridging Morpho-Syntactic Gap between Source and Target Sentences for English-Korean Statistical Machine Translation

Often, Statistical Machine Translation (SMT) between English and Korean suffers from null alignment. Previous studies have attempted to resolve this problem by removing unnecessary function words, or by reordering source sentences. However, the removal of function words can cause a serious loss in information. In this paper, we present a possible method of bridging the morpho-syntactic gap for English-Korean SMT. In particular, the proposed method tries to transform a source sentence by inserting pseudo words, and by reordering the sentence in such a way that both sentences have a similar length and word order. The proposed method achieves 2.4 increase in BLEU score over baseline phrase-based system.
A Unified Framework of Management Earnings Forecasts:

Prior research characterizes management earnings forecasts (MEFs) as voluntary corporate disclosures designed to increase transparency (i.e., reduce information asymmetry between managers and investors, satisfy analysts‟ demand for information, lower a firm‟s cost of capital, reduce a firm‟s litigation risk) or allow managers to trade opportunistically in their firm‟s stock based on their inside information. We offer and test a unified framework of management guidance that incorporates these two reasons along with an additional, and often overlooked rationale for managers to issue MEFs under rule 10b-5 of the Securities Acts managers have an affirmative duty to disclose material information or abstain from trading in their firm‟s securities. An empirical model combining all three rationales for managers to issue forecasts reveals that the typical variables of interest in MEF studies exhibit different explanatory power depending on which of the three underlying rationales is most likely driving the manager‟s decision to issue guidance. The finding that managers‟ 10b-5 disclose or abstain incentives affect the issuance of MEFs has implications for the sample selection and research design choices of future MEF research. It also suggests that prior studies ignoring this explanation for managers‟ issuance of MEFs suffer from identification problems as well as from the effects of correlated omitted variables, both of which serve to undermine the inferences drawn in such studies. Current draft: October 20, 2010 We gratefully acknowledge the financial support provided by the Simon School at the University of Rochester and comments from Bill Cready, Shane Heitzman, Chris Noe, Stan Markov, Sanjog Misra, Joanna Wu and seminar participants at University of Pittsburgh, Syracuse University, and The University of Texas at Dallas.
A new ensemble learning with support vector machines

Cascade of classifiers can, in general, improve the performance of any given classifier. In this paper, we present a new cascade classifier constructed with the support vector machine (SVM) classifiers where a set of SVMs is learned repeatedly with the bounded support vectors of the previous SVM. A binary decision tree is formed using the learned classifiers to take the decision of a new example. Experimental results show that the proposed method can improve the generalization performance over a single SVM
Secrecy wireless information and power transfer with transmit antenna selection in MISO systems

Simultaneous wireless information and power transfer (SWIPT) has recently drawn significant attention, however, due to the broadcast nature of wireless channels, guaranteeing the security of SWIPT system is an important research area. In this paper, we propose and analyze a low feedback overhead and low signal processing cost scheme, that using transmit antenna selection (TAS) to enhance physical layer security, in a MISO SWIPT system. We formulate the power splitting ratio algorithm design as an optimization problem, which maximizes the secrecy rate of the valid receiver under transmit power and energy harvesting constraints. Through solving this problem, secrecy rate-energy function was derived. The results show that as the increasing of transmit number, the larger Rs-E region can be achieved.
Mental Function and Cerebral Cartography: Functional Localization in fMRI Research

This dissertation advances a novel philosophical account of the relationship between brain mapping and cognitive theorizing in functional magnetic resonance imaging (fMRI) research. I argue that testing hypotheses about human cognition and behavior with fMRI critically depends on bridging assumptions about how cognitive functions map onto the brain. I demonstrate that in light of recent theoretical (e.g., network thinking) and methodological (e.g., resting state fMRI) advancements, these bridging assumptions are often problematic. I conclude that at this stage of scientific development, fMRI research should focus on articulating and testing new bridging assumptions rather than testing psychological theories.
Rapid Endocytosis Does Not Recycle Vesicles within the Readily Releasable Pool

Endocytosis is essential in maintaining exocytosis at secretory cells. Rapid endocytosis with a time course less than a few seconds is widely observed at nerve terminals and non-neuronal secretory cells. It is generally assumed that rapid endocytosis recycles vesicles within the readily releasable pool (RRP) via a kiss-and-run mechanism that involves rapid opening and closure of a fusion pore at the release site. The present work suggests that both rapid (τ less than ∼2 s) and slow (τ = ∼10–20 s) endocytosis do not recycle vesicles to the RRP but to a recycling pool at least a few times larger than the RRP at a nerve terminal, the calyx of Held in rat brainstem. Challenging the long-held view that rapid endocytosis offers a rapid, local vesicle recycling within the RRP, our finding calls for reconsideration of the function and the underlying mechanism of rapid endocytosis. We suggest that rapid endocytosis provides the nerve terminal the ability to recycle vesicles rapidly via the recycling pool and to maintain the normal morphology of the nerve terminal, including the release site, by rapidly clearing the fused vesicle membrane from the release site during intense firing.
Aliasing-free implementation of discrete-time glottal source models and their applications to speech synthesis and F0 extractor evaluation

A closed-form representation of anti-aliased L-F model is derived for a LPF function family based on cosine series. The Matlab based implementation of the derived form provides virtually aliasing-free source signal, which is applicable to speech synthesis and F0 extractor evaluation. This aliasing-free representation is also suitable for testing perceptual effects of wave shape parameters in the L-F model, since possible artifacts caused by spurious component are completely removed. A post processing procedure for fine tuning spectral shape is also introduced. An interactive tool for investigating speech production model parameters is designed using this Matlab implementation and will be made freely available.
Unlicensed Spectrum Usage Method for Cellular Communication Systems

Cellular systems operate on ISM band with the co-existence of wide-deployed WLAN is a promising solution to offload the crowded cellular band, where cellular device acting as virtual a WLAN station contends for WLAN channel resource via applying the same IEEE 802.11 Distributed Coordination Function(DCF) as WLAN rivals is a straightforward way. However, the conventional mechanism cannot fully utilize the spectrum resource, we propose an adaptive probability access (APA) method which could adjust the channel access probability of cellular system by maximizing the proportional fairness throughput of both systems. This method can adjust the cellular access probability step by step to ensure that both cellular and WLAN work near the optimum operating spot. Simulation results show that the proposed APA method improves both the proportional fairness and total throughput.
A New Pseudo-automatic Outer Lip Contour Extraction Approach Based on RGB Components

Detection and tracking of the lip contour is an important issue in speech reading. While there are solutions for lip tracking once a good contour initialization in the first frame is available, the problem of finding such a good initialization is not yet solved automatically, but done manually. Solutions based on edge detection and tracking have failed when applied on real world mouth images. In this paper we propose a solution to the lip contour detection that minimizes the user interaction. A minimal number of points to be manually marked on the mouth image are required initially as reference points. The method is based on the examination of values of the RGB components of the outer surface of the region enclosed by the outer lip contour. The paper also includes the limitations of the other existing approaches.
The liquidity effects of remittances and conditional cash transfers on credit demand: Evidence from a randomized experiment in Nicaragua

Understanding the way the poor manage their liquid assets is necessary for the successful implementation of many social and economic development programs. Some examples are Conditional Cash Transfer (CCT) programs that aim to improve child education and health or microfinance programs that aim to provide financial tools for the poor so that they take advantage of existent investment opportunities. This paper explores how poor agrarian households in Northern Nicaragua make use of different liquidity sources available to them by analyzing data from a randomized field experiment. Specifically, it studies how a rise in income through access to remittances and direct subsidies such as CCTs change these households' use of another liquidity source, namely credit, through income and substitution effects. Results show that, on average, CCTs do not change the households' decision to request a loan and this is attributed to the restrictions on time and income allocation that these transfers are subject to. Remittances on the other hand are seen to increase the likelihood of requesting a loan as their use is much less restricted allowing households to re-optimize time and income allocations such that they take advantage of the implicitly cheaper credit to get closer to their optimal liquidity level. When analyzing only the subgroup of households that had access to remittances it is seen that those households that receive CCTs are less likely to request a loan than those that do not. That is households with relatively higher income that receive additional liquidity through CCTs tend to substitute away from credit as they find it optimal to avoid its cost.
Partially Separated Page Tables for Efficient Operating System Assisted Hierarchical Memory Management on Heterogeneous Architectures

Heterogeneous architectures, where a multicore processor is accompanied with a large number of simpler, but more power-efficient CPU cores optimized for parallel workloads, are receiving a lot of attention recently. At present, these co-processors, such as the Intel Xeon Phi product family, come with limited on-board memory, which requires partitioning computational problems manually into pieces that can fit into the device's RAM, as well as efficiently overlapping computation and communication. In this paper we propose an application transparent, operating system (OS)assisted hierarchical memory management system, where the OS orchestrates data movement between the host and the device and updates the process virtual memory address space accordingly. We identify the main scalability issues of frequent address space changes, such as the increasing price of TLB invalidations with the growing number of CPU cores, and propose partially separated page tables with address-range CPU masks to overcome the problem. With partially separated page tables each core maintains its own set of mappings of the computation area, enabling the OS to perform address space updates in a scalable manner, and involve a particular CPU core in TLB invalidation only if it is absolutely necessary. Furthermore, we propose dedicated data movement cores in order to efficiently overlap computation and communication. We provide experimental results on stencil computation, a common HPCkernel, and show that OS assisted memory management has the potential for scalable transparent data movement.
Signal Detection in Antenna-Hopping Space-Division Multiple-Access Systems With Space-Shift Keying Modulation

To take the advantages of the M-ary space-shift keying (MSSK) modulation invented recently, a MSSK fast antenna-hopping space-division multiple-access (MSSK FAH-SDMA) scheme is proposed and studied in this paper. In addition to supporting multiple-access, the FAH is introduced also to achieve transmit diversity by sending every MSSK symbol over several time-slots under the control of a FAH pattern (address). Associated with the MSSK FAH-SDMA, a range of linear and nonlinear detection schemes are studied. Specifically, the linear detection schemes considered include the matched-filtering single-user detector (MF-SUD), zero-forcing multiuser detector (ZF-MUD) and minimum mean-square error (MMSE)-MUD, while the nonlinear detection schemes addressed include the maximum likelihood (ML)-MUD and the receiver multiuser diversity aided multi-stage MMSE (RMD/MS-MMSE) MUD. The single-user pairwise error probability (SU-PEP) and bit error rate (BER) union-bound of the single-user MSSK FAH-SDMA systems employing ML detection are analyzed in detail. Based on the SU-PEP, the minimum transmit diversity order of the MSSK FAH-SDMA systems is specified. For the MSSK FAH-SDMA systems with linear detection, we study two types of MSSK demodulation schemes, which are referred to as the intrauser detections (IUDs), named as the maximum likelihood (ML)-IUD and direct (D)-IUD. For the MSSK FAH-SDMA systems employing the RMD/MS-MMSE MUD, two types of reliability measurement (RM) schemes are proposed, which are the maximum a-posteriori (MAP)-RM and ratio test (RT)-RM. Finally, the BER performance of the MSSK FAH-SDMA systems with various combinations of the proposed techniques is studied, when assuming that the channels from any transmit antennas to any receive antennas experience independent and identically distributed (i.i.d.) Rayleigh fading.