Miracle-dz/UniFAR-FTUs huggingface dataset:
The HIV‐1 regulatory protein Nef has a specific function in viral expression in a murine macrophage cell line

Expression of reporter genes under the control of the HIV‐1 long terminal repeat (LTR) was up‐regulated in the murine macrophage cell line RAW264 by cotransfection of a plasmid coding for the viral regulatory protein Nef. To determine if a discrete section of the LTR was exclusively responsive to Nef, a series of promoters was produced by successive 5′ deletions from the LTR up to the boundary of the enhancer region. These truncated promoters were as active as the full‐length sequence in the RAW264 cells, but elimination of the direct repeats and one of the three Sp1 sites reduced promoter activity to minimal levels. Transcription driven by all constructs was equally susceptible to the trans‐activating effect of Nef and could be increased further by the addition of a Tat‐expressing plasmid to the cotransfection. Open reading frames of nef from NL4‐3, from HXB2, which has a premature stop, and a fully functional hybrid of the two under the control of the SRα artificial promoter (SV40 early promoter plus HTLV‐I R‐U5′) were able to trans‐activate the LTR in RAW264 cells to the same degree as HXB3 nef under the control of the cytomegalovirus (CMV) immediate‐early promoter. A frameshift mutation of Nef at the XhoI site at position 8475 did not abrogate trans‐activation of the LTR in macrophages. To further define the effective trans‐activation region of Nef, internal deletions were made. Changes downstream of the XhoI site at amino acid 35 resulted in little or no reduction in trans‐activation, whereas a deletion between the CMV promoter of the expression plasmid and the XhoI site largely abolished activity. Nef trans‐activation of the LTR may be restricted to macrophages. Parallel cotransfection experiments in COS‐1 simian fibroblast‐like cells showed repression of reporter expression by Nef. Results suggested that the section of nef responsible for trans‐activation of the LTR in macrophages differed slightly from that sufficient for trans‐repression in fibroblasts. Translation of the protein from the first translation start site (Met‐1) rather than from the second in‐frame ATG (Met‐20) appears to be necessary for the trans‐activating effect of Nef in RAW264 cells. Mutation of the initial ATG to ATA led to loss of trans‐activating activity. Expression of Nef also has a cytostatic/cytotoxic effect on RAW264 cells indicated by a reduced rate of establishment of stably transfected clones. The cytostatic effect of Nef was not relieved by internal deletions in the coding sequence. The effect required transcription of one of two regions of the nef gene. These observations suggest that effects of Nef on cell growth and LTR‐driven transcription in RAW264 cells are not related. Trans‐activation of the HIV‐1 LTR in the RAW264 cells by the regulatory protein Nef may be due to a novel protein‐promoter interaction. J. Leukoc. Biol. 56: 294–303; 1994.
Efficient Scheduling of Multi-User Multi-Antenna Systems

The capacity region of the Gaussian multi-antenna broadcast channel was characterized recently in [19]. It was shown that a scheme based on Dirty Paper Coding [2] achieves the full capacity region when the transmitter has perfect channel state information. However, this scheme potentially involves considerable amounts of feedback and complex algorithms for coding and user selection. This has led to a quest for practical transmission schemes and ways to reduce the amount of channel state information required. In particular, it has been shown that when the total number of users is large, the sum capacity can be closely approached by transmitting to a small subset of near-orthogonal users. In order to further quantify the latter observation, we study a Gaussian broadcast channel with two transmit antennas and K statistically identical, independent users each with a single receive antenna. We obtain an exact asymptotic characterization of the gap between the full sum capacity and the rate that can be achieved by transmitting to a suitably selected pair of users. Specifically, we consider various simple schemes for user-pair selection that take into account the channel norms as well as the relative orientation of the channel vectors. We conclude that a scheme that picks the strongest user and selects a second user to form the best pair, is asymptotically optimal, while also being attractive in terms of feedback and operational complexity.
Intracellular events regulating cross-presentation

Cross-presentation plays a fundamental role in the induction of CD8-T cell immunity. However, although more than three decades have passed since its discovery, surprisingly little is known about the exact mechanisms involved. Here we give an overview of the components involved at different stages of this process. First, antigens must be internalized into the cross-presenting cell. The involvement of different receptors, method of antigen uptake, and nature of the antigen can influence intracellular trafficking and access to the cross-presentation pathway. Once antigens access the endocytic system, different requirements for endosomal/phagosomal processing arise, such as proteolysis and reduction of disulfide bonds. The majority of cross-presented peptides are generated by proteasomal degradation. Therefore, antigens must cross a membrane barrier in a manner analogous to the fate of misfolded proteins in the endoplasmic reticulum (ER) that are retrotranslocated into the cytosol for degradation. Indeed, some components of the ER-associated degradation machinery have been implicated in cross-presentation. Further complicating the matter, endosomal and phagosomal compartments have been suggested as alternative sites to the ER for loading of peptides on major histocompatibility complex class I molecules. Finally, the antigen presenting cells involved, particularly dendritic cell subsets and their state of maturation, influence the efficiency of cross-presentation.
PS‐b‐P3HT Copolymers as P3HT/PCBM Interfacial Compatibilizers for High Efficiency Photovoltaics

A conducting diblock copolymer of PS-b-P3HT was added to serve as a compatibilizer in a P3HT/PCBM blend, which improved the power-conversion efficiency from 3.3% to 4.1% due to the enhanced crystallinity, morphology, interface interaction, and depth profile of PCBM.
Elements of Condom-Use Decision Making among South African Men Who Have Sex with Men

South African men who have sex with men (MSM) are at increased risk for HIV infection, and male condoms are fundamental to HIV prevention programs. We explored condom use experiences through in-depth interviews with 34 South African MSM from Cape Town and Port Elizabeth. For data analysis, we generated a codebook and used the constant comparison method. Condom use reinforcing elements included use of alternative sexual strategies, having a high level of self-worth that was linked to protective behaviors, and use of ready-made condom negotiation scripts. Elements inhibiting condom use included perceiving substantial declines in sexual pleasure/performance, experiences of condom failure (possibly related to petroleum-based lubricant), and being in trusted relationships. Our findings suggest nuanced HIV prevention approaches such as bolstering condom negotiation skills based on successful tactics already in use. Further research is needed to address how to mitigate perceptions and experiences that condoms negatively impact sexual pleasure and performance.
Designing seeds for similarity search in genomic DNA

Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements of genomes. To perform large comparisons e.ciently, BLAST [3, 2] and other widely used tools use seeded alignment, which compares only sequences that can be shown to share a common pattern or "seed" of matching bases. The literature suggests that the choice of seed substantially affects the sensitivity of seeded alignment, but designing and evaluating seeds is computationally challenging. This work addresses problems arising in seed design. We give the fastest known algorithm for evaluating the sensitivity of a seed in a Markov model of ungapped alignments, as well as theoretical results on which seeds are good choices. We also describe Mandala, a software tool for seed design, and show that it can be used to improve the sensitivity of alignment in practice.
Identification of Restricted Subsets of Mature microRNA Abnormally Expressed in Inactive Colonic Mucosa of Patients with Inflammatory Bowel Disease

Background Ulcerative Colitis (UC) and Crohn's Disease (CD) are two chronic Inflammatory Bowel Diseases (IBD) affecting the intestinal mucosa. Current understanding of IBD pathogenesis points out the interplay of genetic events and environmental cues in the dysregulated immune response. We hypothesized that dysregulated microRNA (miRNA) expression may contribute to IBD pathogenesis. miRNAs are small, non-coding RNAs which prevent protein synthesis through translational suppression or mRNAs degradation, and regulate several physiological processes. Methodology/Findings Expression of mature miRNAs was studied by Q-PCR in inactive colonic mucosa of patients with UC (8), CD (8) and expressed relative to that observed in healthy controls (10). Only miRNAs with highly altered expression (>5 or <0.2 -fold relative to control) were considered when Q-PCR data were analyzed. Two subsets of 14 (UC) and 23 (CD) miRNAs with highly altered expression (5.2->100 -fold and 0.05–0.19 -fold for over- and under- expression, respectively; 0.001<p≤0.05) were identified in quiescent colonic mucosa, 8 being commonly dysregulated in non-inflamed UC and CD (mir-26a,-29a,-29b,-30c,-126*,-127-3p,-196a,-324-3p). Several miRNA genes with dysregulated expression co-localize with acknowledged IBD-susceptibility loci while others, (eg. clustered on 14q32.31), map on chromosomal regions not previously recognized as IBD-susceptibility loci. In addition, in silico clustering analysis identified 5 miRNAs (mir-26a,-29b,-126*,-127-3p,-324-3p) that share coordinated dysregulation of expression both in quiescent and in inflamed colonic mucosa of IBD patients. Six miRNAs displayed significantly distinct alteration of expression in non-inflamed colonic biopsies of UC and CD patients (mir-196b,-199a-3p,-199b-5p,-320a,-150,-223). Conclusions/Significance Our study supports miRNAs as crucial players in the onset and/or relapse of inflammation from quiescent mucosal tissues in IBD patients. It allows speculating a role for miRNAs as contributors to IBD susceptibility and suggests that some of the miRNA with altered expression in the quiescent mucosa of IBD patients may define miRNA signatures for UC and CD and help develop new diagnostic biomarkers.
Real Time Deformable Template Tracking

In this paper, I presenta systemfor real time deformable templatetracking that tracks line profiles within regions rather than regions or boundaries. There are two main contributionsof thiswork: therealisationthat tracking line profilesratherthanareascanbeeffectiveandefficient; the extensionof thesnakeminimisationalgorithmto allow tree structures. Theadvantagesof the approach are fourfold: sinceweare matching only a smallsetof lineswithin a regionthecomputationaload is greatlyreduced;deformable regionmatchingis inherentin themethod;sinceboundaries are not beingtracked,theproblemof backgroundclutter is reduced;trackingof articulatedstructuresis handlednatu-
Plant vacuole morphology and vacuolar trafficking

Plant vacuoles are essential organelles for plant growth and development, and have multiple functions. Vacuoles are highly dynamic and pleiomorphic, and their size varies depending on the cell type and growth conditions. Vacuoles compartmentalize different cellular components such as proteins, sugars, ions and other secondary metabolites and play critical roles in plants response to different biotic/abiotic signaling pathways. In this review, we will summarize the patterns of changes in vacuole morphology in certain cell types, our understanding of the mechanisms of plant vacuole biogenesis, and the role of SNAREs and Rab GTPases in vacuolar trafficking.
Nutrient Uptake Potential of Nonleguminous Species and Its Interaction with Soil Characteristics and Enzyme Activities in the Agro-ecosystem

The potential nutrient uptake abilities of a plant are essential for improving the yield and quality. Green manures can take up a huge amount of macronutrients from the soil. The mechanisms underlying the differences in nutrient uptake capacity among different nonlegume species remain unclear. The plot experiments were conducted to investigate the performance of nonlegume species including forage radish (Raphanus raphanistrum subsp. sativus), oil radish (Raphanus sativus var. Longipinnatus), February orchid (Orychophragmus violaceus L), and rapeseed (Baricca napus), while a ryegrass (Lolium perenne L.) species was used as a control. The study results showed that forage radish had the highest nutrient uptake (N and P), i.e., 322 and 101% in Hunan and 277 and 469% in the Sichuan site, respectively, compared with the control. While the greatest K uptake was found in forage radish, i.e., 123%, and February orchid, 243%, in the Hunan and Sichuan sites. Forage radish also presented higher phosphorus use efficiency in both experimental areas: Hunan by 301% and Sichuan by 633% compared to the control. Significant modifications were found in nutrient availability and enzyme activities after the cultivation of various species. The oil radish enhanced the β-glucosidase (BG) and leucine-aminopeptidase enzyme activities by 324 and 367%, respectively, while forage radish developed the highest phosphatase (Phase) and N-acetyl-glucosaminidase (NAG) activities compared to the ryegrass in Hunan. In the Sichuan site, the oil radish promotes enzyme activities such as Phase (126%), BG (19%), and NAG (17%), compared to the control. It is concluded that forage radish, oil radish, and February orchid can easily improve soil nutrient quality in green manuring practices and provide valuable nutrient management systems.
Approaching car detection via clustering of vertical-horizontal line scanning optical edge flow

Here, we describe a method that detects vehicle(s) approaching from behind to a commuting car in the lane in which both are travelling. This research contributes to the development of driver assistance systems by means of informing them about the approaching traffic from behind and warn the drivers in case they are drowsy or not alert and the driving conditions are hazardous. We use the image pairs extracted from a video clip obtained from a video camera mounted on the back side of the car. This allows detection of the moving objects from the video image pairs using optical flow. Objects which are determined as not cars or vehicles have been eliminated by edge extraction. In turn, this approach leads to lessen the operation processing cost. Then, Density Histogram of Cluster Rows (DHCR) and Density Histogram of Cluster Columns (DHCC) are generated for the purpose of classification of motion vectors (MVs). Consequently, approching vehicles and cars are detected by localizing the place of the motion vector clusters using Vertical Horizontal Line Scanning (VHLS) as experimental results demonstrate.
Towards a Practical Brain-Computer Interface

The use of a BCI in a practical application depends on the effective implementation of three adaptation levels. The BCI must adapt to the characteristic features of the user’s EEG, periodically adjust for reducing the impact of EEG variations, and engage the adaptive capabilities of the user’s brain through feedback. Implementing the adapting levels, requires the BCI to support several feature extraction methods, to use of flexible classifiers whose parameters can be dynamically updated according to an ”online” modality, and to provide sensible feedback to the user so that he can modulate his brain activity to make the BCI accomplish his intents.
Utilization possibilities of CO2 from cement industry in different products

LUT UNIVERSITY LUT School of Energy Systems Degree Programme in Environmental Technology Sustainability Science and Solutions Mariia Zhaurova Utilization possibilities of CO2 from cement industry in different products Master’s thesis 2018 112 pages, 14 figures, 12 tables, 4 appendices Examiners: Professor Risto Soukka Professor Jero Ahola Supervisor: Professor Risto Soukka
A Base Camp for Scaling AI

Modern statistical machine learning (SML) methods share a major limitation with the early approaches to AI: there is no scalable way to adapt them to new domains. Human learning solves this in part by leveraging a rich, shared, updateable world model. Such scalability requires modularity: updating part of the world model should not impact unrelated parts. We have argued that such modularity will require both "correctability" (so that errors can be corrected without introducing new errors) and "interpretability" (so that we can understand what components need correcting). To achieve this, one could attempt to adapt state of the art SML systems to be interpretable and correctable; or one could see how far the simplest possible interpretable, correctable learning methods can take us, and try to control the limitations of SML methods by applying them only where needed. Here we focus on the latter approach and we investigate two main ideas: "Teacher Assisted Learning", which leverages crowd sourcing to learn language; and "Factored Dialog Learning", which factors the process of application development into roles where the language competencies needed are isolated, enabling non-experts to quickly create new applications. We test these ideas in an "Automated Personal Assistant" (APA) setting, with two scenarios: that of detecting user intent from a user-APA dialog; and that of creating a class of event reminder applications, where a non-expert "teacher" can then create specific apps. For the intent detection task, we use a dataset of a thousand labeled utterances from user dialogs with Cortana, and we show that our approach matches state of the art SML methods, but in addition provides full transparency: the whole (editable) model can be summarized on one human-readable page. For the reminder app task, we ran small user studies to verify the efficacy of the approach.
Pharmacists on rounding teams reduce preventable adverse drug events in hospital general medicine units.

BACKGROUND Previous studies found that medication errors result from lack of sufficient information during the prescribing step. Therefore, it is proposed that having a pharmacist available when patients are evaluated during the rounding process may reduce the likelihood of preventable adverse drug events (ADEs). The objectives of this study were to evaluate the impact of having a pharmacist participate with a physician rounding team on preventable ADEs in general medicine units and to document pharmacist interventions made during the rounding process. METHODS A single-blind, standard care-controlled study design was used to compare patients receiving care from a rounding team including a pharmacist with patients receiving standard care (no pharmacist on rounding team). Patients admitted to and discharged from the same general medicine unit were included in the study. The main outcome measure of this study was preventable ADEs. Patient records were randomly selected and evaluated by a blinded process involving independent senior pharmacist specialists and a senior staff physician. Interventions made by the pharmacists in the treatment group were documented. RESULTS The rate of preventable ADEs was reduced by 78%, from 26.5 per 1000 hospital days to 5.7 per 1000 hospital days. There were 150 documented interventions recommended during the rounding process, 147 of which were accepted by the team. The most common interventions were (1) dosing-related changes and (2) recommendations to add a drug to therapy. CONCLUSION Pharmacist participation with the medical rounding team on a general medicine unit contributes to a significant reduction in preventable ADEs.
Clinical research on therapeutic effect of virtual reality technology on Broca Aphasia patients

Objective: To explore the therapeutic effect of virtual reality technology on speech function of Broca Aphasia patients after stroke. Method: Eighteen patients with stroke were enrolled in the Rehabilitation Medicine Department, the Third Affiliated Hospital of Sun Yat-sen University from December 2016 to August 2017. The patients were divided into observation group and control group by random number table. Both groups were trained in speech function. The observation group received regular speech training for 20 minutes per day, Virtual Reality (VR) training for 20 minutes per day; the control group was given conventional speech training 40 minutes per day but the same training content with the observation group. And both groups of patients were treated for 5 days per week lasting for 4 weeks. CRRCAE was used to evaluate the language ability before and after treatment. The Boston Diagnostic Aphasia Examination, BDAE was used to assess the severity of aphasia. Bucco-facial-apraxia and speech apraxia Methods were used to assess the patient's state of bucco facial function and speech function. Result: There was no significant difference (P > 0.5) between the situations of two groups in general data, bucco-facial-apraxia and speech apraxia. Before treatment, the difference in CRRCAE and BDAE between the two groups is also not so big(P > 0.05). After 4 weeks of treatment, the severity of aphasia was improved in both groups (P < 0.05). Except computing ability, listening comprehension, repetition, expression, readout, reading, transcription, depiction and dictation were all improved (P < 0.01). And in noun repetition(P = 0.03), sentence repetition (P = 0.01), noun expression(P < 0.01), verb expression (P = 0.02), sentence expression (P < 0.01), comic expression (P = 0.01), enumeration (P = 0.03), verb readout(P = 0.04), verb reading(P < 0.01), sentence reading (P = 0.04), noun transcription (P = 0.02), sentence transcription (P = 0.048), verb depiction (P = 0.01) and so on, language ability of the observation group is significantly better than the control group. Conclusion: Virtual reality technology combined with speech function training can improve the language ability of patients with Broca Aphasia, and its improvement is better than the simple speech function training.
Selective laser sintering of patch antennas on FR4

The paper investigates the fabrication of microwave components using selective laser sintering (SLS) on FR4. This technique has exciting potential for the metallization of low-temperature substrates. The effects of the laser process parameters on the DC conductivity are examined. These results are applied to produce a patch antenna which is compared to simulation and an identical patch antenna fabricated by traditional manufacturing methods. The antenna was demonstrated to match both the simulation and the antenna fabricated by traditional milling. While the conductivity is not as high as that produced by traditional screen printing techniques, this process allows for patterning on substrates that cannot survive the high sintering temperatures of traditional thick film processing.