Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance evaluation of seed based random (SBR) Interleaver in Rayleigh fading channel

In this paper, the performance of SBR Interleaver [1] is evaluated in Rayleigh fading channel. Our proposed Interleaver showed to have near optimal properties of spread and dispersion [1]. These properties assure to have higher probability to distribute burst of errors into single error optimally. The results are carried out with coded and uncoded data in Rayleigh and AWGN channel with proposed Interleaver. Our method shows superior performance as compared to random Interleaver. Result shows that there is 2db improvement at BER 10-4 and more than 2db improvement at BER 10-5. Results are discussed in detail in performance evaluation section.
Multiplex In-cell Reverse Transcription-Polymerase Chain Reaction for the Simultaneous Detection of p210 and p190 BCR-ABL mRNAs in Chronic Myeloid Leukemia and Philadelphia-Positive Acute Lymphoblastic Leukemia Cell Lines

Abstract We designed a novel multiplex in-cell reverse transcription- polymerase chain reaction method for the simultaneous detection and differentiation of p190 and p210 BCR-ABL mRNAs within single cells from the human chronic myeloid leukemia and Philadelphia positive acute lymphoblastic leukemia. Human K562 chronic myeloid leukemia and SUP B-15 Ph+ acute lymphoblastic leukemia cell lines were used as positive controls for p210 and p190 BCR-ABL mRNAs, respectively. HL60 cell line was used as a negative control. After the leukemia cells were fixed and permeabilized, without extracting nucleic acids, the mRNAs were reverse transcribed to cDNAs, and the cDNAs were amplified by multiplex polymerase chain reaction with fluorescent primers specific for p190 and p210 BCR-ABL mRNAs. After transfer onto glass slides by cytospin, the amplified cells were detected by fluorescence microscopy. Fluorescence microscopy after propidium iodide or 4′,6-diamidino-2-phenylindone counterstaining showed that the positive K562 cells exhibited a yellow-green fluorescent cytoplasm around a red nucleus, and that the positive SUP B-15 cells exhibited an orange cytoplasm around a blue nucleus. Only the red or blue nucleus was visible in respective negative HL60 cells. The specificity of amplification was confirmed by the absence of a signal when control experiments were performed either with RNase digestion of mRNA or without reverse transcriptase/Taq polymerase. We conclude that the multiplex in-cell reverse transcription-polymerase chain reaction method is capable of simultaneously detecting and differentiating the p210 and p190 BCR-ABL mRNAs of chronic myeloid leukemia and Philadelphia-positive acute lymphoblastic leukemia cells, and that it may be useful in quantitatively monitoring the minimal residual disease during therapy.
Tinjauan Perspektif Ekonomi dan Nonekonomi Perempuan Bali yang Bekerja di Sektor Publik: Studi Konflik Peran

Abstract: The purpose of this study is to examine: (1) the influence of culture on the economy and work environment, (2) the influence of the social economy, (3) the influence of economic and noneconomic (cultural, work environmental, and social) on role conflict, (4 ) behavior of Balinese women in resolving conflicts. Total respondents were 216 people. Data were analyzed by PLS method (Partial Least Square) and descriptive qualitative. The research results showed that Balinese women’s role conflict significantly influenced by cultural and work environment variables. Culture also has significant effect on the economy and work environment variables. Economy variables has significant effect on social variable. While the economic and social variables are not shown to increase role conflict, Balinese women who workin public sector experience behavioral changes Keywords: balinese women, conflict, work, public sector
Importance-Driven Composition of Multiple Rendering Styles

We introduce a non-uniform composition that integrates multiple rendering styles in a picture driven by an importance map. This map, either issued from saliency estimation or designed by a user, is introduced both in the creation of the multiple styles and in the final composition. Our approach accommodates a variety of stylization techniques, such as color desaturation, line drawing, blurring, edge-preserving smoothing and enhancement. We illustrate the versatility of the proposed approach and the variety of rendering styles on different applications such as images, videos, 3D scenes and even mixed reality. We also demonstrate that such an approach may help in directing user attention.
De novo identification of replication-timing domains in the human genome by deep learning

Abstract Motivation: The de novo identification of the initiation and termination zones—regions that replicate earlier or later than their upstream and downstream neighbours, respectively—remains a key challenge in DNA replication. Results: Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model–HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the ‘replication-domain’ model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Availability and implementation: Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM. The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. Contact: shuwj@bmi.ac. cn or boxc@bmi.ac. cn Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting Attribute Dependencies from Query Feedback

Real-world datasets exhibit a complex dependency structure among the data attributes. Learning this structure is a key task in automatic statistics configuration for query optimizers, as well as in data mining, metadata discovery, and system management. In this paper, we provide a new method for discovering dependent attribute pairs based on query feedback. Our approach avoids the problem of searching through a combinatorially large space of candidate attribute pairs, automatically focusing system resources on those pairs of demonstrable interest to users. Unlike previous methods, our technique combines all of the pertinent feedback for a specified pair of attributes in a principled and robust manner, while being simple and fast enough to be incorporated into current commercial products. The method is similar in spirit to the CORDS algorithm, which proactively collects frequencies of data values and computes a chi-squared statistic from the resulting contingency table. In the reactive query-feedback setting, many entries of the contingency table are missing, and a key contribution of this paper is a variant of classical chi-squared theory that handles this situation. Because we typically discover a large number of dependent attribute pairs, we provide novel methods for ranking the pairs based on degree of dependency. Such ranking information, e.g., enables a database system to avoid exceeding the space budget for the system catalog by storing only the currently most important multivariate statistics. Experiments indicate that our dependency rankings are stable even in the presence of relatively few feedback records.
Immersion infection of germ-free zebrafish with Listeria monocytogenes induces transient expression of innate immune response genes

Zebrafish, Denio rerio, can be an alternative to other classic animal models for human infectious diseases to examine the processes of microbial infections and host–pathogen interactions in vivo because of their small body dimension but large clutch size. We established germ-free zebrafish infection models of Listeria monocytogenes through different routes of infection: oral immersion and injection via yolk sac, brain ventricle and blood island. Immersion of zebrafish larva even with 1010 CFU/mL L. monocytogenes EGDe strain in egg water was unable to cause mortality, but GFP-expressing bacteria in the gut lumen can be observed in frozen sections. Several selected maker genes of the innate immune system, including cyp1a, irg1l, il1b, and mmp9, were significantly induced by oral immersion not only with strain EGDe, but also with strain M7 and L. innocua, though to a lesser degree (P < 0.01). Such induction appears to be transient with peak at 48 h post-infection, but returned to basal level at 72 h post-infection. Of the three injection routes, mortality after infection by yolk sac was 80% in early stage of infection. Few eggs can survive and hatch. Injection into zebrafish embryos via brain ventricle or blood island led to progressive lethal infection. L. mocytogenes EGDe showed steady replication in the fish embryos and was far more pathogenic than strain M7, which is consistent with findings in the murine model. We conclude that zebrafish can serve as susceptible and microscopically visible infection models for L. monocytogenes via different routes and can be applied to further studies on the interactions between bacterial virulence factors and host immune responses.
Vehicle Traffic Simulation CIS 400 / 401-Senior Project Final Report

Abstract: Computer graphics has recently become steadily more applicable for use in technological devices and entertainment. Along with that development, virtual crowd simulations have become increasingly popular and necessary to successfully create realistic movies, video games, and training simulations. An important component of designing a realistic population simulator is to incorporate automobiles, traffic, road networks, and the associated rules which allow those vehicles to properly interact with pedestrians and other vehicles. Many traffic simulators currently exist independently of a crowd simulator with human agents. The goal of this project is to design a traffic simulation system that can be incorporated into an existing crowd simulation system, full scale 3D model city, and road network. Currently the crowd simulator does not include vehicles, and is therefore not entirely realistic. By including a traffic simulation the environment will gain another level of detail and realism. Computer graphics has recently become steadily more applicable for use in technological devices and entertainment. Along with that development, virtual crowd simulations have become increasingly popular and necessary to successfully create realistic movies, video games, and training simulations. An important component of designing a realistic population simulator is to incorporate automobiles, traffic, road networks, and the associated rules which allow those vehicles to properly interact with pedestrians and other vehicles. Many traffic simulators currently exist independently of a crowd simulator with human agents. The goal of this project is to design a traffic simulation system that can be incorporated into an existing crowd simulation system, full scale 3D model city, and road network. Currently the crowd simulator does not include vehicles, and is therefore not entirely realistic. By including a traffic simulation the environment will gain another level of detail and realism.
Hippocampal sclerosis and TDP‐43 pathology in aging and Alzheimer disease

To investigate the association of hippocampal sclerosis (HS) with TAR‐DNA binding protein of 43kDa (TDP‐43) and other common age‐related pathologies, dementia, probable Alzheimer disease (AD), mild cognitive impairment (MCI), and cognitive domains in community‐dwelling older subjects.
A comprehensive study of polymorphisms in the ABCB1, ABCC2, ABCG2, NR1I2 genes and lymphoma risk

Owing to their role in controlling the efflux of toxic compounds, transporters are central players in the process of detoxification and elimination of xenobiotics, which in turn is related to cancer risk. Among these transporters, ATP‐binding cassette B1/multidrug resistance 1 (ABCB1/MDR1), ABCC2/multidrug resistance protein 2 (MRP2) and ABCG2/breast cancer resistance protein (BCRP) affect susceptibility to many hematopoietic malignancies. The maintenance of regulated expression of these transporters is governed through the activation of intracellular “xenosensors” like the nuclear receptor 1I2/pregnane X receptor (NR1I2/PXR). SNPs in genes encoding these regulators have also been implicated in the risk of several cancers. Using a tagging approach, we tested the hypothesis that common polymorphisms in the transporter genes ABCB1, ABCC2, ABCG2 and the regulator gene NR1I2 could be implicated in lymphoma risk. We selected 68 SNPs in the four genes, and we genotyped them in 1,481 lymphoma cases and 1,491 controls of the European case–control study (EpiLymph) using the Illumina GoldenGate™ assay technology. Carriers of the SNP rs6857600 minor allele in ABCG2 was associated with a decrease in risk of B‐cell lymphoma (B‐NHL) overall (p < 0.001). Furthermore, a decreased risk of chronic lymphocytic leukemia (CLL) was associated with the ABCG2 rs2231142 variant (p = 0.0004), which could be replicated in an independent population. These results suggest a role for this gene in B‐NHL susceptibility, especially for CLL.
Retrieving Medical Records with "sennamed": NEC Labs America at TREC 2012 Medical Record Track

Abstract : In this notebook, we describe the automatic retrieval runs from NEC Laboratories America (NECLA) for the Text REtrieval Conference (TREC) 2012 Medical Records track. Our approach is based on a combination of UMLS medical concept detection and a set of simple retrieval models. Our best run, sennamed2, has achieved the best inferred average precision (infAP) score on 5 of the 47 test topics, and obtained a higher score than the median of all submission runs on 27 other topics. Overall, sennamed2 ranks at the second place amongst all the 82 automatic runs submitted for this track, and obtains the third place amongst both automatic and manual submissions.
Minimization of length and curvature on planar curves

In this paper we consider the problem of reconstructing a curve that is partially hidden or corrupted by minimizing the functional ¿¿(1+K2)ds, depending both on length and curvature K. We fix starting and ending points as well as initial and final directions. For this functional, we find non-existence of minimizers on various functional spaces in which the problem is naturally formulated. In this case, minimizing sequences of trajectories can converge to curves with angles. We instead prove existence of minimizers for the "time-reparameterized" functional ¿¿¿¿(t)¿¿(1+K¿ 2)dt for all boundary conditions if initial and final directions are considered regardless to orientation.
The Use of Functional Electrical Stimulation on the Upper Limb and Interscapular Muscles of Patients with Stroke for the Improvement of Reaching Movements: A Feasibility Study

Introduction Reaching movements in stroke patients are characterized by decreased amplitudes at the shoulder and elbow joints and greater displacements of the trunk, compared to healthy subjects. The importance of an appropriate and specific contraction of the interscapular and upper limb (UL) muscles is crucial to achieving proper reaching movements. Functional electrical stimulation (FES) is used to activate the paretic muscles using short-duration electrical pulses. Objective To evaluate whether the application of FES in the UL and interscapular muscles of stroke patients with motor impairments of the UL modifies patients’ reaching patterns, measured using instrumental movement analysis systems. Design A cross-sectional study was carried out. Setting The VICON Motion System® was used to conduct motion analysis. Participants Twenty-one patients with chronic stroke. Intervention The Compex® electric stimulator was used to provide muscle stimulation during two conditions: a placebo condition and a FES condition. Main outcome measures We analyzed the joint kinematics (trunk, shoulder, and elbow) from the starting position until the affected hand reached the glass. Results Participants receiving FES carried out the movement with less trunk flexion, while shoulder flexion elbow extension was increased, compared to placebo conditions. Conclusion The application of FES to the UL and interscapular muscles of stroke patients with motor impairment of the UL has improved reaching movements.
Designing a Testing Framework for Transfer Learning Algorithms (Application Paper)

Most works covering the topic of transfer learning propose an algorithm to solve a given domain adaptation problem, then test the algorithm using real-world datasets. A test with a real-world dataset represents a single transfer learning test condition, which partially measures an algorithm's performance. Previous research has placed little emphasis on developing a comprehensive and uniform test for transfer learning algorithms. With this in mind, a test framework is proposed, comprising of distortion profiles which define a comprehensive test suite. The unique contribution of this paper is the definition of a test framework that measures a more complete profile of a transfer learning algorithm's capability, facilitating the identification of relative poor and good performance areas. As a proof of concept, the test framework is used to test a homogeneous transfer learning algorithm. The test framework will be the basis for a number of future applications.
Heterogeneous distance functions for prototype rules : influence of parameters on probability estimation

An interesting and little explored way to understand data is based on prototype rules (P-rules). The goal of this approach is to find optimal similarity (or distance) functions and position of prototypes to which unknown vectors are compared. In real applications similarity functions frequently involve different types of attributes, such as continuous, discrete, binary or nominal. Heterogeneous distance functions that may handle such diverse information are usually based on probability distance measure, such as the Value Difference Metrics (VDM). For continuous attributes calculation of probabilities requires estimations of probability density functions. This process requires careful selection of several parameters that may have important impact on the overall classification accuracy. In this paper various heterogeneous distance function based on VDM measure are presented, among them some new heterogeneous distance functions based on different types of probability estimation. Results of many numerical experiments with such distance functions are presented on artificial and real datasets, and quite simple P-rules for several heterogeneous databases extracted.
Relationship between Oral Flow Patterns, Nasal Obstruction, and Respiratory Events during Sleep.

STUDY OBJECTIVES Sleep breathing patterns are altered by nasal obstruction and respiratory events. This study aimed to describe the relationships between specific sleep oral flow (OF) patterns, nasal airway obstruction, and respiratory events. METHODS Nasal flow and OF were measured simultaneously by polysomnography in 85 adults during sleep. OF was measured 2 cm in front of the lips using a pressure sensor. RESULTS OF could be classified into three patterns: postrespiratory event OF (postevent OF), during-respiratory event OF (during-event OF), and spontaneous arousal-related OF (SpAr-related OF). Postevent OFs begin at the end of airflow reduction, are preceded by respiratory arousal, and are accompanied by postapneic hyperventilation; during-event OFs occur during nasal flow reduction; and SpAr-related OFs to OF begin during stable breathing, and are preceded by spontaneous arousal but are rarely accompanied by apnea/hypopnea. Multivariate regression showed that nasal obstruction was predictive of SpAr-related OF. The relative frequency of SpAr-related OF events was negatively correlated with the apnea-hypopnea index. The fraction of SpAr-related OF duration relative to total OF duration was significantly greater in patients with nasal obstruction than in those without. CONCLUSION SpAr-related OF was associated with nasal obstruction, but not respiratory events. This pattern thus functions as a "nasal obstruction bypass", mainly in normal subjects and patients with mild sleep disordered breathing (SDB). By contrast, the other two types were related to respiratory events and were typical patterns seen in patients with moderate and severe SDB.
The cell cycle restricts activation-induced cytidine deaminase activity to early G1

Activation-induced cytidine deaminase (AID) converts cytosine into uracil to initiate somatic hypermutation (SHM) and class switch recombination (CSR) of antibody genes. In addition, this enzyme produces DNA lesions at off-target sites that lead to mutations and chromosome translocations. However, AID is mostly cytoplasmic, and how and exactly when it accesses nuclear DNA remains enigmatic. Here, we show that AID is transiently in spatial contact with genomic DNA from the time the nuclear membrane breaks down in prometaphase until early G1, when it is actively exported into the cytoplasm. Consistent with this observation, the immunoglobulin (Igh) gene deamination as measured by uracil accumulation occurs primarily in early G1 after chromosomes decondense. Altering the timing of cell cycle–regulated AID nuclear residence increases DNA damage at off-target sites. Thus, the cell cycle–controlled breakdown and reassembly of the nuclear membrane and the restoration of transcription after mitosis constitute an essential time window for AID-induced deamination, and provide a novel DNA damage mechanism restricted to early G1.
Phosphorylation of S776 and 14-3-3 Binding Modulate Ataxin-1 Interaction with Splicing Factors

Ataxin-1 (Atx1), a member of the polyglutamine (polyQ) expanded protein family, is responsible for spinocerebellar ataxia type 1. Requirements for developing the disease are polyQ expansion, nuclear localization and phosphorylation of S776. Using a combination of bioinformatics, cell and structural biology approaches, we have identified a UHM ligand motif (ULM), present in proteins associated with splicing, in the C-terminus of Atx1 and shown that Atx1 interacts with and influences the function of the splicing factor U2AF65 via this motif. ULM comprises S776 of Atx1 and overlaps with a nuclear localization signal and a 14-3-3 binding motif. We demonstrate that phosphorylation of S776 provides the molecular switch which discriminates between 14-3-3 and components of the spliceosome. We also show that an S776D Atx1 mutant previously designed to mimic phosphorylation is unsuitable for this aim because of the different chemical properties of the two groups. Our results indicate that Atx1 is part of a complex network of interactions with splicing factors and suggest that development of the pathology is the consequence of a competition of aggregation with native interactions. Studies of the interactions formed by non-expanded Atx1 thus provide valuable hints for understanding both the function of the non-pathologic protein and the causes of the disease.