Spatial Fourier Transform for Blind Detection of Radio Observations of Rotating Radio Transients

In this thesis we propose a new blind algorithm, which we call Energy in Transformed Data (ETD), for the detection of isolated astrophysical pulses. Unlike the conventional algorithm, which requires de-dispersion, integration over frequency channels and matched filtering, the ETD algorithm detects pulses in a space reciprocal to the space of filterbank data. The ETD algorithm is implemented in three steps: (1) it applies the Spatial Fourier Transform (SFT) to filterbank data, (2) it evaluates the energy of signal in the transformed space, and (3) it compares the value of the total energy to a threshold. If the energy in transformed data exceeds the threshold, we claim that we detect a potential pulse.;To analyze the detection capabilities of the ETD algorithm, we applied it to data of ten different Rotating Radio Transients (RRATs). The performance of the algorithm was compared to the performance of two other algorithms, one of which is the conventional algorithm and the other one is an algorithm that performs matched filtering in the SFT domain. The performance of the ETD algorithm depends on the Signal-to-Noise ratio (SNR) of pulses. When the SNR threshold is set to a large value such as 8, the ETD algorithm can detect 80.5% of all pulses detected by the conventional algorithm. When the SNR threshold is set to 5, the ETD algorithm can detect only 40.4% detectable by the conventional algorithm.;The ability to detect broad and relatively weak astronomical pulses is a special feature of ETD. As we demonstrate it in this thesis, the energy of pulses with a broad pulse profile (broad compared to the time delay of the pulse arrival at the lower frequency of receiver) is concentrated around the origin in the SFT domain. This allows to easily detect broad pulses by ETD.;The main drawback of the ETD algorithm is in its inability to detect pulses which are relatively low in SNR value and have a narrow pulse profile. Analyzing the main advantages and disadvantages of ETD, we conclude that the algorithm can be used as a complementary method to the conventional algorithm, especially when the task is to detect broad pulses parameterized by a low SNR value. In addition to its use for current observations, we expect this method will be beneficial for detection of other types of isolated transients

Quantum Oscillations from Nontrivial States in Quasi-Two-Dimensional Dirac Semimetal ZrTe 5 Nanowires

Recently discovered Dirac semimetal ZrTe 5 bulk crystal, exhibits nontrivial conducting states in each individual layer, holding great potential for novel spintronic applications. Here, to reveal the transport properties of ZrTe 5 , we fabricated ZrTe 5 nanowires (NWs) devices, with much larger surface-to-volume ratio than bulk materials. Quantum oscillations induced by the two-dimensional (2D) nontrivial conducting states have been observed from these NWs and a finite Berry phase of ~π is obtained by the analysis of Landau-level fan diagram. More importantly, the absence of the Aharonov-Bohm (A-B) oscillations, along with the SdH oscillations, suggests that the electrons only conduct inside each layer. And the intralayer conducting is suppressed because of the weak connection between adjacent layers. Our results demonstrate that ZrTe 5 NWs can serve as a suitable quasi-2D Dirac semimetal with high mobility (~85000 cm 2 V −1 s −1 ) and large nontrivial conductance contribution (up to 8.68%)

Huntingtin toxicity in yeast model depends on polyglutamine aggregation mediated by a prion-like protein Rnq1

The cause of Huntington's disease is expansion of polyglutamine (polyQ) domain in huntingtin, which makes this protein both neurotoxic and aggregation prone. Here we developed the first yeast model, which establishes a direct link between aggregation of expanded polyQ domain and its cytotoxicity. Our data indicated that deficiencies in molecular chaperones Sis1 and Hsp104 inhibited seeding of polyQ aggregates, whereas ssa1, ssa2, and ydj1–151 mutations inhibited expansion of aggregates. The latter three mutants strongly suppressed the polyQ toxicity. Spontaneous mutants with suppressed aggregation appeared with high frequency, and in all of them the toxicity was relieved. Aggregation defects in these mutants and in sis1–85 were not complemented in the cross to the hsp104 mutant, demonstrating an unusual type of inheritance. Since Hsp104 is required for prion maintenance in yeast, this suggested a role for prions in polyQ aggregation and toxicity. We screened a set of deletions of nonessential genes coding for known prions and related proteins and found that deletion of the RNQ1 gene specifically suppressed aggregation and toxicity of polyQ. Curing of the prion form of Rnq1 from wild-type cells dramatically suppressed both aggregation and toxicity of polyQ. We concluded that aggregation of polyQ is critical for its toxicity and that Rnq1 in its prion conformation plays an essential role in polyQ aggregation leading to the toxicity

Socioeconomic inequalities in human papillomavirus knowledge and vaccine uptake: evidence from a cross-sectional study in China

ObjectiveProviding the human papillomavirus (HPV) vaccine is effective to eliminate the disparity in HPV-related cancers. It is unknown regarding inequality in the distribution of HPV vaccination in China since the vaccine was licensed and approved for use in 2016. This study aimed to examine socioeconomic inequalities in HPV-related knowledge and vaccination and identified factors associated with such inequalities.MethodsSelf-administered questionnaires measuring HPV-related knowledge and vaccine uptake were completed by 1,306 women through online survey platform. HPV knowledge was assessed using a 12-item question stem that covered the hazards of HPV infection, HPV vaccine dosage, benefits, and protection. Cluster analysis by combining monthly household income, educational level, and employment status was used to identify socioeconomic status (SES) class. The concentration index (CI) was employed as a measure of socioeconomic inequalities in HPV-related knowledge and vaccination. Linear regression and logistic regression were established to decompose the contributions of associated factors to the observed inequalities.ResultsThe CI for HPV-related knowledge and vaccine uptake was 0.0442 and 0.1485, respectively, indicating the higher knowledge and vaccination rate were concentrated in groups with high SES. Education and household income made the largest contribution to these inequalities. Age, residency and cervical cancer screening were also important contributors of observed inequalities.ConclusionSocioeconomic inequalities in HPV-related knowledge and vaccination uptake are evident in China. Interventions to diffuse HPV-related information for disadvantaged groups are helpful to reduce these inequalities. Providing low or no-cost HPV vaccination and ensuring accessibility of vaccines in rural areas are also considered to be beneficial

Interface magnetic and electrical properties of CoFeB /InAs heterostructures

Amorphous magnetic CoFeB ultrathin films have been synthesized on the narrow band gap semiconductor InAs(100) surface, and the nature of the interface magnetic anisotropy and electrical contact has been studied. Angle-dependent hysteresis loops reveal that the films have an in-plane uniaxial magnetic anisotropy (UMA) with the easy axis along the InAs [0-11] crystal direction. The UMA was found to be dependent on the annealing temperatures of the substrates, which indicates the significant role of the Fe, Co-As bonding at the interface related to the surface condition of the InAs(100). I-V measurements show an ohmic contact interface between the CoFeB films and the InAs substrates, which is not affected by the surface condition of the InAs (100)

Functional Polymorphisms of CTLA4 Associated with Aggressive Periodontitis in the Chinese Han Population

Background/Aims: CTLA4 has been identified functioning as a protein receptor which functions as an immune checkpoint, downregulating the immune system. Susceptibility to aggressive periodontitis (AgP) is influenced by gene polymorphisms related to the immune response. In this study, we focused on SNPs in the 3’-UTR of CTLA4 among Chinese AgP patients, and investigated any further relationships between the SNPs and miRNAs. Methods: This case–control study included 120 AgP patients and 150 healthy controls. Genotyping was used to detect allele distribution. Cell transfection and the dual luciferase reporter assay were performed to investigate the potential functions of SNPs located in the 3’UTR of CTLA4. Results: The data show that patients with a history of smoking were more susceptible compared to controls, exhibiting deeper probing depth, greater attachment loss and more sites of bleeding on probing. The results of genotyping analysis revealed that individuals with the GA and AA genotypes, and with the A carrier had a decreased risk (P = 0.015, P = 0.03). Furthermore, patients with the G allele might be regulated by miR-105, which caused a down-regulation of CTLA4. The carriers of the GG genotype exhibited the worst results of attachment loss and bleeding on probing. Conclusion: These findings show that rs56102377 in the 3’-UTR of CTLA4 may act as a protective factor by disrupting the regulatory role of miR-105 in CTLA4 expression. Thus, our study highlighted a potential role of these polymorphisms as genetic susceptibility biomarkers of periodontitis in Chinese Han populations

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.published_or_final_versio

IL-17 and TNF-β: Predictive biomarkers for transition to psychosis in ultra-high risk individuals

BackgroundDysregulation of immunity, such as levels of inflammatory factors, has been regarded as a sign of schizophrenia. Changes in cytokine levels are not only described in the early onset of disease, but also observed in ultra-high risk (UHR) individuals. This study aimed to investigate the potential of cytokines as biomarkers for psychotic disorders and in individuals at UHR of developing a psychotic disorder in the future.MethodsThe Luminex liquid chip technology was used to detect the concentrations of Interferon-gamma (INF-γ), Interleukin (IL)-2, Interleukin (IL)-4, Interleukin (IL)-6, Interleukin (IL)-17, Interleukin-1beta (IL-1β), and Tumor Necrosis Factor-beta (TNF-β) in the plasma of all subjects. Meanwhile, the plasma level of Tumor Necrosis Factor-Alpha (TNF-α) was measured with the enzyme-linked immunosorbent assay (ELISA) kits. Then, the levels of these cytokines were compared among patients with Drug-naïve first-episode schizophrenia (FES; n = 40), UHR population (UHR; n = 49), and healthy controls (HCs; n = 30). Baseline cytokine levels were compared among UHR individuals who later transitioned (UHR-T; n = 14), those who did not transition (UHR-NT; n = 35), and HCs (n = 30).ResultsOur analysis results showed that IL-1β levels were significantly higher in UHR group than HC group (p = 0.015). Meanwhile, TNF-α concentration was significantly increased in FES group compared with HC group (p = 0.027). IL-17 (p = 0.04) and TNF-β (p = 0.008) levels were significantly higher in UHR-T group compared with UHR-NT group.ConclusionIn conclusion, our findings suggest that the immuno-inflammatory activation level is increased in the early stage of psychosis before psychotic conversion and the Drug-naïve FES. IL-1β and TNF-α are the representatives of the specific biomarkers for UHR and FES, respectively. IL-17 and TNF-β may be the potential selective predictive biomarkers for future transition in UHR individuals

High-resolution myelin-water fraction and quantitative relaxation mapping using 3D ViSTa-MR fingerprinting

Purpose: This study aims to develop a high-resolution whole-brain multi-parametric quantitative MRI approach for simultaneous mapping of myelin-water fraction (MWF), T1, T2, and proton-density (PD), all within a clinically feasible scan time. Methods: We developed 3D ViSTa-MRF, which combined Visualization of Short Transverse relaxation time component (ViSTa) technique with MR Fingerprinting (MRF), to achieve high-fidelity whole-brain MWF and T1/T2/PD mapping on a clinical 3T scanner. To achieve fast acquisition and memory-efficient reconstruction, the ViSTa-MRF sequence leverages an optimized 3D tiny-golden-angle-shuffling spiral-projection acquisition and joint spatial-temporal subspace reconstruction with optimized preconditioning algorithm. With the proposed ViSTa-MRF approach, high-fidelity direct MWF mapping was achieved without a need for multi-compartment fitting that could introduce bias and/or noise from additional assumptions or priors. Results: The in-vivo results demonstrate the effectiveness of the proposed acquisition and reconstruction framework to provide fast multi-parametric mapping with high SNR and good quality. The in-vivo results of 1mm- and 0.66mm-iso datasets indicate that the MWF values measured by the proposed method are consistent with standard ViSTa results that are 30x slower with lower SNR. Furthermore, we applied the proposed method to enable 5-minute whole-brain 1mm-iso assessment of MWF and T1/T2/PD mappings for infant brain development and for post-mortem brain samples. Conclusions: In this work, we have developed a 3D ViSTa-MRF technique that enables the acquisition of whole-brain MWF, quantitative T1, T2, and PD maps at 1mm and 0.66mm isotropic resolution in 5 and 15 minutes, respectively. This advancement allows for quantitative investigations of myelination changes in the brain.Comment: 38 pages, 12 figures and 1 tabl