Miracle-dz/UniFAR-FTUs huggingface dataset:
An ultrasensitive biological probe enhanced RT-IPCR assay for detecting benzo[a]pyrene in environmental samples based on the specific polyclonal antibody

Benzo[a]pyrene (BaP), a type of polycyclic aromatic hydrocarbon, is widely distributed in the environment. In this study, BaP immunogen and coating antigen were respectively prepared by different methods, and the specific antibody targeting the BaP analyte was obtained. Moreover, gold nanoparticles modified with the specific polyclonal antibody and thiol-capped DNA were prepared as biological probes. Based on the work above, an ultrasensitive biological probe enhanced real-time immuno-polymerase chain reaction (BP-rt-iPCR) assay was developed to detect BaP in several environmental samples. Under optimal conditions, the proposed method was used to detect BaP with a linearity ranging from 5 pg/l to 50 ng/l. The limit of detection was 1.63 pg/l. The recovery rates of the spiked samples ranged from 92.12% to 109.76% and the coefficients of variation were 7.53%-11.06%. This immunoassay was successfully used to detect BaP in environmental samples, and the BaP detection results were consistent with those obtained using high performance liquid chromatography, indicating that the BP-rt-iPCR method is accurate and reliable, and has great potential to detect trace amounts of BaP.
Temperature dependence of the ionization coefficients of InAlAs and AlGaAs digital alloys

Digital alloy In0.52Al0. 48As avalanche photodiodes exhibit lower excess noise than those fabricated from random alloys. This paper compares the temperature dependence, from 203 to 323 K, of the impact ionization characteristics of In0.52Al0. 48As and Al0.74Ga0. 26As digital and random alloys. These results provide insight into the low excess noise exhibited by some digital alloy materials, and these materials can even obtain lower excess noise at low temperature.
Robust Wireless Video Transmission Strategies for Video Communications

In this paper, novel video transmission architecture is proposed to meet the error robust requirement of wireless video communications. This architecture uses user-defined protocol to provide efficient bandwidth access from wireless link. By taking the time-varying wireless channel condition and video codec characteristics into account, first, we present an end-to-end transport architecture for video streaming over wireless network. Second, we adopt channel of Bernoulli channel model from application layers of 3G networks. And we propose a dynamically estimate the time-varying wireless network condition through estimate of throughout, RTT and merit of packet delay time. Third, we use H.264 as an experiment platform. A data partition scheme is also used to enhance error resilience performance. This architecture is also suitable for various motion compensation based standards like H.261, H.263 series, MPEG-1, MPEG-2, MPEG-4. The simulation results show our strategies can significantly improve the robustness of wireless video transmission.
Epigenetic mechanisms associated with addiction-related behavioural effects of nicotine and/or cocaine: implication of the endocannabinoid system

The addictive use of nicotine (NC) and cocaine (COC) continues to be a major public health problem, and their combined use has been reported, particularly during adolescence. In neural plasticity, commonly induced by NC and COC, as well as behavioural plasticity related to the use of these two drugs, the involvement of epigenetic mechanisms, in which the reversible regulation of gene expression occurs independently of the DNA sequence, has recently been reported. Furthermore, on the basis of intense interactions with the target neurotransmitter systems, the endocannabinoid (ECB) system has been considered pivotal for eliciting the effects of NC or COC. The combined use of marijuana with NC and/or COC has also been reported. This article presents the addiction-related behavioural effects of NC and/or COC, based on the common behavioural/neural plasticity and combined use of NC/COC, and reviews the interacting role of the ECB system. The epigenetic processes inseparable from the effects of NC and/or COC (i.e. DNA methylation, histone modifications and alterations in microRNAs) and the putative therapeutic involvement of the ECB system at the epigenetic level are also discussed.
The cancer care experiences of gay, lesbian and bisexual patients: A secondary analysis of data from the UK Cancer Patient Experience Survey

Understanding the effects of population diversity on cancer-related experiences is a priority in oncology care. Previous research demonstrates inequalities arising from variation in age, gender and ethnicity. Inequalities and sexual orientation remain underexplored. Here, we report, for the first time in the UK, a quantitative secondary analysis of the 2013 UK National Cancer Patient Experience Survey which contains 70 questions on specific aspects of care, and six on overall care experiences. 68,737 individuals responded, of whom 0.8% identified as lesbian, gay or bisexual. Controlling for age, gender and concurrent mental health comorbidity, logistic regression models applying post-estimate probability Wald tests explored response differences between heterosexual, bisexual and lesbian/gay respondents. Significant differences were found for 16 questions relating to: (1) a lack of patient-centred care and involvement in decision-making, (2) a need for health professional training and revision of information resources to negate the effects of heteronormativity and (3) evidence of substantial social isolation through cancer. These findings suggest a pattern of inequality, with less positive cancer experiences reported by lesbian, gay and (especially) bisexual respondents. Poor patient-professional communication and heteronormativity in the healthcare setting potentially explain many of the differences found. Social isolation is problematic for this group and warrants further exploration.
Elevated AQP1 Expression Is Associated With Unfavorable Oncologic Outcome in Patients With Hilar Cholangiocarcinoma

Background: Hilar cholangiocarcinomas are malignant tumors with a poor prognosis. An early prediction of prognosis for patients may help us determine treatment strategies. Aquaporin 1 is a cell membrane channel involved in water transport, cell motility, and proliferation. Increasing evidences showed that aquaporin 1 played a role in tumor prognosis and diagnosis. The purpose of this study is to evaluate the role of aquaporin 1 in hilar cholangiocarcinoma. Methods: Here, we analyzed messenger RNA expression data of genes function as bile secretion in a data set of 169 samples using the R2 bioinformatic platform (http://r2.amc.nl). Quantitative polymerase chain reaction was performed to verify the gene expression in 17 hilar cholangiocarcinoma samples. Immunohistochemistry was also performed in a series of specimens from 62 hilar cholangiocarcinoma tissues, and its clinical significance was assessed by clinical correlation and Kaplan-Meier analyses. Results: All data were analyzed using the R2 web application, aquaporin 1 was selected for further analysis. The significant expression variation of aquaporin 1 among 17 cases with cholangiocarcinoma was also found using quantitative polymerase chain reaction. The expression level of aquaporin 1 protein significantly correlated with tumor-node-metastasis stage (P = .002) and overall survival time (P = .010). Higher aquaporin 1 expression indicated poor prognostic outcomes (P <.05, log-rank test). Multivariate analysis also showed strong aquaporin 1 protein expression was an independent adverse prognosticator in hilar cholangiocarcinoma (P = .002). Conclusion: This study highlighted the prognostic value of aquaporin 1 in hilar cholangiocarcinoma. Strong aquaporin 1 expression predicts poor survival, regardless of pathological features. Immunohistochemical detection of aquaporin 1, as a prognostic marker, may contribute to predicting clinical outcome for patients with hilar cholangiocarcinoma.
Treatment of Hepatitis C Infection in Renal Transplant Recipients: The Long Wait Is Over

The reported prevalence of chronic hepatitis C virus (HCV) infection in hemodialysis (HD) patients, at 2.6–22.9% in Western countries, is greater than that in the general population and is significantly correlated with the duration of HD (1). As a result, chronic HCV infection among kidney transplant (KT) recipients is not infrequent, and there is substantial evidence that HCV-infected KT recipients have worse survival after transplantation compared with HCV-negative KT recipients driven by higher rates of newonset diabetes after transplantation posttransplantation glomerulonephritis, malignancy, and hepatic failure (1,2). Thus, treatment of HCV infection post-KT with the goal of eliminating the risk of these complications is highly desirable but up until recently was difficult to achieve. HCV treatment in the era of interferon (IFN)containing regimens was fraught with poor tolerability, concern for IFN-induced acute allograft rejection, and, ultimately, very modest success in achieving viral eradication (1,2).
Structural Study of the C-Terminal Domain of Nonstructural Protein 1 from Japanese Encephalitis Virus

ABSTRACT Japanese encephalitis virus (JEV) is a mosquito-transmitted flavivirus that is closely related to other emerging viral pathogens, including dengue virus (DENV), West Nile virus (WNV), and Zika virus (ZIKV). JEV infection can result in meningitis and encephalitis, which in severe cases cause permanent brain damage and death. JEV occurs predominantly in rural areas throughout Southeast Asia, the Pacific Islands, and the Far East, causing around 68,000 cases of infection worldwide each year. In this report, we present a 2.1-Å-resolution crystal structure of the C-terminal β-ladder domain of JEV nonstructural protein 1 (NS1-C). The surface charge distribution of JEV NS1-C is similar to those of WNV and ZIKV but differs from that of DENV. Analysis of the JEV NS1-C structure, with in silico molecular dynamics simulation and experimental solution small-angle X-ray scattering, indicates extensive loop flexibility on the exterior of the protein. This, together with the surface charge distribution, indicates that flexibility influences the protein-protein interactions that govern pathogenicity. These factors also affect the interaction of NS1 with the 22NS1 monoclonal antibody, which is protective against West Nile virus infection. Liposome and heparin binding assays indicate that only the N-terminal region of NS1 mediates interaction with membranes and that sulfate binding sites common to NS1 structures are not glycosaminoglycan binding interfaces. This report highlights several differences between flavivirus NS1 proteins and contributes to our understanding of their structure-pathogenic function relationships. IMPORTANCE JEV is a major cause of viral encephalitis in Asia. Despite extensive vaccination, epidemics still occur. Nonstructural protein 1 (NS1) plays a role in viral replication, and, because it is secreted, it can exhibit a wide range of interactions with host proteins. NS1 sequence and protein folds are conserved within the Flavivirus genus, but variations in NS1 protein-protein interactions among viruses likely contribute to differences in pathogenesis. Here, we compared characteristics of the C-terminal β-ladder domain of NS1 between flaviviruses, including surface charge, loop flexibility, epitope cross-reactivity, membrane adherence, and glycosaminoglycan binding. These structural features are central to NS1 functionality and may provide insight into the development of diagnostic tests and therapeutics.
Internet-based peer support for Ménière's disease: a summary of web-based data collection, impact evaluation, and user evaluation

Abstract Objective: This paper presents a summary of web-based data collection, impact evaluation, and user evaluations of an Internet-based peer support program for Ménière’s disease (MD). Design: The program is written in html-form. The data are stored in a MySQL database and uses machine learning in the diagnosis of MD. The program works interactively with the user and assesses the participant’s disorder profile in various dimensions (i.e., symptoms, impact, personal traits, and positive attitude). The inference engine uses a database to compare the impact with 50 referents, and provides regular feedback to the user. Data were analysed using descriptive statistics and regression analysis. Study sample: The impact evaluation was based on 740 cases and the user evaluation on a sample of 75 cases of MD respectively. Results: The web-based system was useful in data collection and impact evaluation of people with MD. Among those with a recent onset of MD, 78% rated the program as useful or very useful, whereas those with chronic MD rated the program 55%. Conclusions: We suggest that a web-based data collection and impact evaluation for peer support can be helpful while formulating the rehabilitation goals of building the self-confidence needed for coping and increasing social participation.
Phosphatidylinositide 3-kinase (PI3K) and PI3K-related kinase (PIKK) activity contributes to radioresistance in thyroid carcinomas

Anaplastic (ATC) and certain follicular thyroid-carcinomas (FTCs) are radioresistant. The Phosphatidylinositide 3-kinase (PI3K) pathway is commonly hyperactivated in thyroid-carcinomas. PI3K can modify the PI3K-related kinases (PIKKs) in response to radiation: How PIKKs interact with PI3K and contribute to radioresistance in thyroid-carcinomas is unknown. Further uncertainties exist in how these interactions function under the radioresistant hypoxic microenvironment. Under normoxia/anoxia, ATC (8505c) and FTC (FTC-133) cells were irradiated, with PI3K-inhibition (via GDC-0941 and PTEN-reconstitution into PTEN-null FTC-133s) and effects on PIKK-activation, DNA-damage, clonogenic-survival and cell cycle, assessed. FTC-xenografts were treated with 5 × 2 Gy, ± 50 mg/kg GDC-0941 (twice-daily; orally) for 14 days and PIKK-activation and tumour-growth assessed. PIKK-expression was additionally assessed in 12 human papillary thyroid-carcinomas, 13 FTCs and 12 ATCs. GDC-0941 inhibited radiation-induced activation of Ataxia-telangiectasia mutated (ATM), ATM-and Rad3-related (ATR) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Inhibition of ATM and DNA-PKcs was PI3K-dependent, since activation was reduced in PTEN-reconstituted FTC-133s. Inhibition of PIKK-activation was greater under anoxia: Consequently, whilst DNA-damage was increased and prolonged under both normoxia and anoxia, PI3K-inhibition only reduced clonogenic-survival under anoxia. GDC-0941 abrogated radiation-induced cell cycle arrest, an effect most likely linked to the marked inhibition of ATR-activation. Importantly, GDC-0941 inhibited radiation-induced PIKK-activation in FTC-xenografts leading to a significant increase in time taken for tumours to triple in size: 26.5 ± 5 days (radiation-alone) versus 31.5 ± 5 days (dual-treatment). PIKKs were highly expressed across human thyroid-carcinoma classifications, with ATM scoring consistently lower. Interestingly, some loss of ATM and DNA-PKcs was observed. These data provide new insight into the mechanisms of hypoxia-associated radioresistance in thyroid-carcinoma.
In-DRAM Data Initialization

Initializing memory with zero data is essential for safe memory management. However, initializing a large memory area slows down the system significantly. The most likely cause for initialization to slow down the system is the limited DRAM initialization method. At present, the only way to initialize DRAM area is to execute multiple WRITE commands. However, the WRITE command slows the initialization because of its small granularity and data bus occupancy. In this brief, we propose an efficient in-DRAM initialization method inspired by the internal structure and operation of DRAM. The proposed method, called row reset, uses a DRAM row buffer to zero out a single DRAM row at a time. Row Reset allows for parallel initialization on multiple DRAM banks without using off-chip data transfer, thus reducing initialization time by up to 63 times. Row reset is a practical approach, because it can be implemented with existing circuitry in DRAM without additional area overhead.
Homer1 Scaffold Proteins Govern Ca2+ Dynamics in Normal and Reactive Astrocytes

Abstract In astrocytes, the intracellular calcium (Ca2+) signaling mediated by activation of metabotropic glutamate receptor 5 (mGlu5) is crucially involved in the modulation of many aspects of brain physiology, including gliotransmission. Here, we find that the mGlu5‐mediated Ca2+ signaling leading to release of glutamate is governed by mGlu5 interaction with Homer1 scaffolding proteins. We show that the long splice variants Homer1b/c are expressed in astrocytic processes, where they cluster with mGlu5 at sites displaying intense local Ca2+ activity. We show that the structural and functional significance of the Homer1b/c‐mGlu5 interaction is to relocate endoplasmic reticulum (ER) to the proximity of the plasma membrane and to optimize Ca2+ signaling and glutamate release. We also show that in reactive astrocytes the short dominant‐negative splice variant Homer1a is upregulated. Homer1a, by precluding the mGlu5‐ER interaction decreases the intensity of Ca2+ signaling thus limiting the intensity and the duration of glutamate release by astrocytes. Hindering upregulation of Homer1a with a local injection of short interfering RNA in vivo restores mGlu5‐mediated Ca2+ signaling and glutamate release and sensitizes astrocytes to apoptosis. We propose that Homer1a may represent one of the cellular mechanisms by which inflammatory astrocytic reactions are beneficial for limiting brain injury.
Importance of Proactive Treatment of Depression in Lewy Body Dementias: The Impact on Hippocampal Neurogenesis and Cognition in a Post-Mortem Study

Objective: To examine the impact of selective serotonin reuptake inhibitors (SSRIs) and depression on neurogenesis and cognition in dementia with Lewy bodies (DLB) and Parkinson disease dementia (PDD). Methods: Late-stage progenitor cells were quantified in the subgranular zone (SGZ) of the hippocampal dentate gyrus of DLB/PDD patients (n = 41) and controls without dementia (n = 15) and compared between treatment groups (unmedicated, SSRIs, acetyl cholinesterase inhibitors [AChEIs], combined SSRIs and AChEIs). Results: DLB/PDD patients had more doublecortin-positive cells in the SGZ compared to controls. The doublecortin-positive cell count was higher in the SGZ of patients treated with SSRIs and correlated to higher cognitive scores. Conclusion: SSRI treatment was associated with increased hippocampal neurogenesis and preservation of cognition in DLB/PDD patients.
Chinese Word Sense Induction based on Hierarchical Clustering Algorithm

Word Sense induction seeks to automatically identify word senses of polysemous words encountered in a corpus.Unsupervised word sense induction can be viewed as a clustering problem.In this paper,we used the Hierarchical Clustering Algorithm as the classifier for word sense induction.Experiments show the system can achieve 72% F-score about train-corpus and 65% F-score about test-corpus.
Active dispersal in loggerhead sea turtles (Caretta caretta) during the ‘lost years’

Highly migratory marine species can travel long distances and across entire ocean basins to reach foraging and breeding grounds, yet gaps persist in our knowledge of oceanic dispersal and habitat use. This is especially true for sea turtles, whose complex life history and lengthy pelagic stage present unique conservation challenges. Few studies have explored how these young at-sea turtles navigate their environment, but advancements in satellite technology and numerical models have shown that active and passive movements are used in relation to open ocean features. Here, we provide the first study, to the best of our knowledge, to simultaneously combine a high-resolution physical forcing ocean circulation model with long-term multi-year tracking data of young, trans-oceanic North Pacific loggerhead sea turtles during their ‘lost years’ at sea. From 2010 to 2014, we compare simulated trajectories of passive transport with empirical data of 1–3 year old turtles released off Japan (29.7–37.5 straight carapace length cm). After several years, the at-sea distribution of simulated current-driven trajectories significantly differed from that of the observed turtle tracks. These results underscore current theories on active dispersal by young oceanic-stage sea turtles and give further weight to hypotheses of juvenile foraging strategies for this species. Such information can also provide critical geographical information for spatially explicit conservation approaches to this endangered population.
DD-αAMG on QPACE 3

We describe our experience porting the Regensburg implementation of the DD-αAMG solver from QPACE 2 to QPACE 3. We first review how the code was ported from the first generation Intel Xeon Phi processor (Knights Corner) to its successor (Knights Landing). We then describe the modifications in the communication library necessitated by the switch from InfiniBand to Omni-Path. Finally, we present the performance of the code on a single processor as well as the scaling on many nodes, where in both cases the speedup factor is close to the theoretical expectations.
Integrating multi-source big data to infer building functions

ABSTRACT Information about the functions of urban buildings is helpful not only for developing a better understanding of how cities work, but also for establishing a basis for policy makers to evaluate and improve the effectiveness of urban planning. Despite these advantages, however, and perhaps simply due to a lack of available data, few academic studies to date have succeeded in integrating multi-source ‘big data’ to examine urban land use at the building level. Responding to this deficiency, this study integrated multi-source big data (WeChat users’ real-time location records, taxi GPS trajectories data, Points of Interest (POI) data, and building footprint data from high-resolution Quickbird images), and applied the proposed density-based method to infer the functions of urban buildings in Tianhe District, Guangzhou, China. The results of the study conformed to an overall detection rate of 72.22%. When results were verified against ground-truth investigation data, the accuracy rate remained above 65%. Two important conclusions can be drawn from our analysis: 1.The use of WeChat data delivers better inference results than those obtained using taxi data when used to identify residential buildings, offices, and urban villages. Conversely, shopping centers, hotels, and hospitals, were more easily identified using taxi data. 2. The use of integrated multi-source big data is more effective than single-source big data in revealing the relation between human dynamics and urban complexes at the building scale.