Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Receptor Signaling Inhibits HIV-1 Replication in Macrophages through Multiple trans-Repression Mechanisms

ABSTRACT Sexually transmitted pathogens activate HIV-1 replication and inflammatory gene expression in macrophages through engagement of Toll-like receptors (TLRs). Ligand-activated nuclear receptor (NR) transcription factors, including glucocorticoid receptor (GR), peroxisome proliferator-activated receptor gamma (PPARγ), and liver X receptor (LXR), are potent inhibitors of TLR-induced inflammatory gene expression. We therefore hypothesized that ligand-activated NRs repress both basal and pathogen-enhanced HIV-1 replication in macrophages by directly repressing HIV-1 transcription and by ameliorating the local proinflammatory response to pathogens. We show that the TLR2 ligand PAM3CSK4 activated virus transcription in macrophages and that NR signaling repressed both basal and TLR-induced HIV-1 transcription. NR ligand treatment repressed HIV-1 expression when added concurrently with TLR ligands and in the presence of cycloheximide, demonstrating that they act independently of new cellular gene expression. We found that treatment with NR ligands inhibited the association of AP-1 and NF-κB subunits, as well as the coactivator CBP, with the long terminal repeat (LTR). We show for the first time that the nuclear corepressor NCoR is bound to HIV-1 LTR in unstimulated macrophages and is released from the LTR after TLR engagement. Treatment with PPARγ and LXR ligands, but not GR ligands, prevented this TLR-induced clearance of NCoR from the LTR. Our data demonstrate that both classical and nonclassical trans-repression mechanisms account for NR-mediated HIV-1 repression. Finally, NR ligand treatment inhibited the potent proinflammatory response induced by PAM3CSK4 that would otherwise activate HIV-1 expression in infected cells. Our findings provide a rationale for studying ligand-activated NRs as modulators of basal and inflammation-induced HIV-1 replication.
gamma/delta T cell-deficient mice have impaired mucosal immunoglobulin A responses

Mucosal tissues of mice are enriched in T cells that express the gamma/delta T cell receptor. Since the function of these cells remains unclear, we have compared mucosal immune responses in gamma/delta T cell receptor-deficient (TCRdelta-/-) mice versus control mice of the same genetic background. The frequency of intestinal immunoglobulin (Ig) A plasma cells as well as IgA levels in serum, bile, saliva, and fecal samples were markedly reduced in TCRdelta-/- mice. The TCRdelta-/- mice produced much lower levels of IgA antibodies when immunized orally with a vaccine of tetanus toxoid plus cholera toxin as adjuvant. Conversely, the antigen-specific IgM and IgG antibody responses were comparable to orally immunized control mice. Direct assessment of the cells forming antibodies against the tetanus toxoid and cholera toxin antigens indicated that significantly lower numbers of IgA antibody- producing cells were present in the intestinal lamina propria and Peyer's patches of TCRdelta-/- mice compared with the orally immunized control mice. The selective reduction of IgA responses to ingested antigens in the absence of gamma/delta T cells suggests a specialized role for gamma/delta cells in mucosal immunity.
Making the Transition From Standard Gynecologic Laparoscopy to Robotic Laparoscopy

Objectives: To determine the feasibility of using a simple procedure, a bilateral tubal ligation, as a transition procedure when adopting robotic laparoscopy for gynecologic surgery. Method: To obtain robotic credentialing and gain experience with the robotic system, the surgeons first went through robotic training, then 4 women desiring permanent sterilization had robotically assisted laparoscopic bilateral tubal ligations performed, using the Parkland method. Results: Total operating room time varied from 1 hour 25 minutes to 2 hours 31 minutes. Improvement in operating time for each surgeon was noted with each successive case. Best times in robotic cases were similar to those of standard laparoscopy. Conclusion: Robotically assisted laparoscopic tubal ligation using the Parkland method is a satisfactory procedure to provide transition for gynecologic surgeons and operating room personnel to gynecologic robotic surgery.
Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.
Birthdays of retinal amacrine cell subtypes are systematically related to their molecular identity and soma position

The mammalian retina contains six major cell types, several of which are divided into multiple molecularly and morphologically distinct subtypes. To understand how subtype diversity arises during development, we focused on amacrine interneurons in the mouse retina; ∼30 amacrine subtypes have been identified in mammals. We used antibody markers to identify the two main amacrine subsets—GABAergic and glycinergic—and further subdivided these groups into smaller subsets based on expression of neurotransmitter and transcription factor markers. We then used bromodeoxyuridine (BrdU) labeling to see whether amacrine subsets are born (become postmitotic) at different times, as is the case for lamina‐specified subsets of cortical projection neurons. We found that GABAergic amacrines are generated on average 2–3 days before glycinergic amacrines. Moreover, subsets of GABAergic amacrines are born at distinct times. We also found a strong correlation between amacrine cell birthday and soma position in the mature retina, another point of similarity with cortical projection neurons. This relationship raised the possibility that amacrine subtype identity is determined by signals that uncommitted cells receive after they migrate to their destinations. However, cells labeled with BrdU in vivo, then dissociated and allowed to develop in vitro, acquired the amacrine subtype‐specific markers appropriate for their birthdays, supporting the idea that they become specified near the time and place of their birth. Together, our results suggest that the birthdays of amacrine cells independently specify their destinations and subtype identities. J. Comp. Neurol. 517:737–750, 2009. © 2009 Wiley‐Liss, Inc.
Omega-3 fatty acids and incident type 2 diabetes: the Singapore Chinese Health Study 1–4

Background: The role of omega-3 (n–3) fatty acids (FAs) in the development of type 2 diabetes is uncertain, especially with regard to any differential inﬂuence of a -linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Objective: The objective was to examine the association between total omega-3 FAs, marine omega-3 (EPA, DHA), nonmarine omega-3 (ALA), and omega-6 (n–6) FAs and omega-6:omega-3 ratio and risk of type 2 diabetes in a Chinese population in Singapore. Design: The analysis included 43,176 Chinese men and women free of chronic disease, aged 45–74 y, in the Singapore Chinese Health Study. Baseline data collection occurred between 1993 and 1998, with follow-up interviews between 1999 and 2004. Cox regression models were used to examine the associations between FA intakes at baseline and risk of developing diabetes. Results: Increased intakes of total omega-3 FAs were inversely associated with diabetes incidence [hazard ratio (HR) for the ﬁfth compared with the ﬁrst quintile: 0.78; 95% CI: 0.65, 0.94; P for trend = 0.02]. Omega-3 FAs from marine sources were not associated with diabetes risk, whereas nonmarine omega-3 FA intake was strongly associated (HR for the ﬁfth compared with the ﬁrst quintile: 0.79; 95% CI: 0.67, 0.93; P for trend = 0.004). Omega-6 and omega-6:omega-3 ratio were not associated with incidence of type 2 diabetes. Conclusion: Consumption of nonmarine sources (ALA) of omega-3 FAs is associated with a decreased risk of type 2 diabetes in Chinese
Epigallocatechin-3-gallate Inhibits LPS-Induced NF-κB and MAPK Signaling Pathways in Bone Marrow-Derived Macrophages

Background/Aims Epigallocatechin-3-gallate (EGCG), the primary catechin in green tea, has anti-inflammatory and anti-oxidative properties. The aim of the current study was to characterize the impact of EGCG on lipopolysaccharide (LPS)-induced innate signaling in bone marrow-derived macrophages (BMMs) isolated from ICR mice. Methods The effect of EGCG on LPS-induced pro-inflammatory gene expression and nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling was examined using reverse transcription-polymerase chain reaction, Western blotting, immunofluorescence, and the electrophoretic mobility shift assay. Results EGCG inhibited accumulation of LPS-induced IL-12p40, IL-6, MCP-1, ICAM-1, and VCAM-1 mRNA in BMMs. EGCG blocked LPS-induced IκBα degradation and RelA nuclear translocation. EGCG blocked the DNA-binding activity of NF-κB. LPS-induced phosphorylation of ERK1/2, JNK, and p38 was inhibited by EGCG. U0126 (an inhibitor of MEK-1/2) suppressed the LPS-induced IL-12p40, IL-6, MCP-1, ICAM-1, and VCAM-1 mRNA accumulation in BMMs. Conclusions These results indicate that EGCG may prevent LPS-induced pro-inflammatory gene expression through blocking NF-κB and MAPK signaling pathways in BMMs.
Comp-denoiser adapted to coronary X-ray images

Compression of coronary angiographic images has been shown to be difficult as compared to other medical imaging modalities. Some of the factors partially responsible for this is the presence of complex detail structures that are only apparent by subtle changes in the contrast and altered by significant amount of noise. Simultaneous compression and denoising is required when images are altered by additive noise. In our work we developed a wavelet based comp-denoiser adapted to coronary X-ray images. The proposed approach consists on integrating an inter-scale dependant thresholding function, using Bayesian estimation theory, with WTCQ coding algorithm. Experimental results show that despite its simplicity and computational efficiency, our method yields a higher compression performance with a superior image quality. It also outperforms the state of the art of compression based denoisers in terms of distortion.
Learning outcomes and tutoring in problem based-learning: how do undergraduate medical students perceive them?

OBJECTIVES To explore opinions of undergraduate medical students regarding learning outcomes of the instructional strategy of Problem Based Learning (PBL). In addition their views were sought about the role of tutors and qualities of effective tutors. METHOD This was a cross-sectional, questionnaire based study which was conducted in two colleges of Medicine, Central region, Saudi Arabia during the period of 1st of April to 30(th) June 2012. RESULTS One hundred seventy four undergraduate medical students participated in this study. Seventy percent of participants have indicated that PBL strategy contributed to the development of their knowledge, presentation skills, team work abilities, and accepting criticism from other colleagues. Regarding the tutors' role in PBL tutorials, majority of the participants (75%) indicated that this role is essential, nevertheless, only 58% of students indicated that this role is clear and well identified. Sixty three percent of participants preferred a member role in the PBL tutorials and 80 percent of participants preferred both content and process expert tutors in the PBL tutorials. Significant statistical difference was noted between the views of students and their schools, gender, and study phase. CONCLUSION Majority of the participants believed that PBL had a positive impact on the development of their cognitive, personal and teamwork skills. The view of the students in this study and the available evidence suggest that tutor should have both qualities; content and process expertise, in order to have the best outcomes from the PBL tutorials.
Orchestrating the nucleases involved in DNA interstrand cross-link (ICL) repair

DNA interstrand cross-links (ICLs) pose a significant threat to genomic and cellular integrity by blocking essential cellular processes, including replication and transcription. In mammalian cells, much ICL repair occurs in association with DNA replication during S phase, following the stalling of a replication fork at the block caused by an ICL lesion. Here, we review recent work showing that the XPF-ERCC1 endonuclease and the hSNM1A exonuclease act in the same pathway, together with SLX4, to initiate ICL repair, with the MUS81-EME1 fork incision activity becoming important in the absence of the XPF-SNM1A-SLX4-dependent pathway. Another nuclease, the Fanconi anemia-associated nuclease (FAN1), has recently been implicated in the repair of ICLs, and we discuss the possible ways in which the activities of different nucleases at the ICL-stalled replication fork may be coordinated. In relation to this, we briefly speculate on the possible role of SLX4, which contains XPF and MUS81- interacting domains, in the coordination of ICL repair nucleases.
Similarity Queries on Structured Data in Structured Overlays

Structured P2P systems based on distributed hash tables are a popular choice for building large-scaled data management systems. Generally, they only support exact match queries, but data heterogeneities often demand for more complex query types, particularly similarity queries. In this work, we suggest a vertical data organization, which allows for efficient processing of similarity queries on instance as well as on schema level, and we introduce corresponding physical similarity operators. Our novel approach is shown to be suitable in conjunction with P-Grid, as an example of robust, large-scaled and self-organizing P2P systems.
Association of EGFR mutation or ALK rearrangement with expression of DNA repair and synthesis genes in never‐smoker women with pulmonary adenocarcinoma

Epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) rearrangement may predict the outcome of targeted drug therapy and also are associated with the efficacy of chemotherapy in patients with nonsmall cell lung cancer (NSCLC). The authors of this report investigated the relation of EGFR mutation or ALK rearrangement status and the expression of DNA repair or synthesis genes, including excision repair cross‐complementing 1 (ERCC1), ribonucleotide reductase subunit M1 (RRM1), thymidylate synthetase (TS), and breast cancer‐early onset (BRCA1), as a potential explanation for these observations.
Lateral Control Assistance for Car Drivers: A Comparison of Motor Priming and Warning Systems

Objective: This paper's first objective is to determine whether motor priming assistance (consisting of directional steering wheel vibrations) can be of some benefit compared with more traditional auditory (lateralized sound) or vibratory (symmetric steering wheel oscillation) warning devices. We hypothesize that warning devices favor driving situation diagnosis, whereas motor priming can improve the initiation of action even further. Another objective is to assess the possible benefits of using multimodal information by combining auditory warning with simple steering wheel vibration or motor priming. Background: Within the context of active safety devices, the experiment dealt with moderately intrusive driving assistance devices that intervene when a certain level of risk in terms of lane departure is reached. Method: An analysis of the steering behavior of 20 participants following episodes of visual occlusion was carried out. Five warning and motor priming devices were compared. Results: All tested devices improved the drivers' steering performance, although their effects were modulated by the drivers' risk assessment. However, performance improvements were found to be greater with a motor priming device. No additional performance enhancement was observed when auditory warning was added to steering wheel vibration or motor priming devices. Conclusion: This study confirms the hypothesis that the direct intervention of motor priming at the action level is more effective than a simple warning, which intervenes upstream in situation diagnosis. Multimodal information did not seem to improve driver performance. Application: This study proposes a new kind of lateral control assistance, which acts at a sensorimotor level, in contrast with traditional warning devices.
Hemorrhagic and Ischemic Strokes Compared: Stroke Severity, Mortality, and Risk Factors

Background and Purpose— Stroke patients with hemorrhagic (HS) and ischemic strokes were compared with regard to stroke severity, mortality, and cardiovascular risk factors. Methods— A registry started in 2001, with the aim of registering all hospitalized stroke patients in Denmark, now holds information for 39 484 patients. The patients underwent an evaluation including stroke severity (Scandinavian Stroke Scale), CT, and cardiovascular risk factors. They were followed-up from admission until death or censoring in 2007. Independent predictors of death were identified by means of a survival model based on 25 123 individuals with a complete data set. Results— Of the patients 3993 (10.1%) had HS. Stroke severity was almost linearly related to the probability of having HS (2% in patients with the mildest stroke and 30% in those with the most severe strokes). Factors favoring ischemic strokes vs HS were diabetes, atrial fibrillation, previous myocardial infarction, previous stroke, and intermittent arterial claudication. Smoking and alcohol consumption favored HS, whereas age, sex, and hypertension did not herald stroke type. Compared with ischemic strokes, HS was associated with an overall higher mortality risk (HR, 1.564; 95% CI, 1.441–1.696). The increased risk was, however, time-dependent; initially, risk was 4-fold, after 1 week it was 2.5-fold, and after 3 weeks it was 1.5-fold. After 3 months stroke type did not correlate to mortality. Conclusion— Strokes are generally more severe in patients with HS. Within the first 3 months after stroke, HS is associated with a considerable increase of mortality, which is specifically associated with the hemorrhagic nature of the lesion.
Juvenile Hormone Is Required to Couple Imaginal Disc Formation with Nutrition in Insects

In starved larvae of the tobacco hornworm moth Manduca sexta, larval and imaginal tissues stop growing, the former because they lack nutrient-dependent signals but the latter because of suppression by juvenile hormone. Without juvenile hormone, imaginal discs form and grow despite severe starvation. This hormone inhibits the intrinsic signaling needed for disc morphogenesis and does so independently of ecdysteroid action. Starvation and juvenile hormone treatments allowed the separation of intrinsic and nutrient-dependent aspects of disc growth and showed that both aspects must occur during the early phases of disc morphogenesis to ensure normal growth leading to typical-sized adults.
Drug- or Alcohol-Facilitated, Incapacitated, and Forcible Rape in Relationship to Mental Health Among a National Sample of Women

Rape is a well-established risk factor for mental health disorders such as posttraumatic stress disorder (PTSD) and depression. However, most studies have focused on forcible rape tactics and have not distinguished these from tactics that involve drug or alcohol intoxication. The authors’ aim was to examine correlates of PTSD and depression in a community sample of women, with particular emphasis on evaluating the unique effects of lifetime exposure to three specific rape tactics. A nationally representative sample of 3,001 noninstitutionalized, civilian, English- or Spanish-speaking women (aged 18-86 years) participated in a structured telephone interview by use of Computer-Assisted Telephone Interviewing (CATI) technology. Multivariable models showed that history of drug or alcohol-facilitated rape tactics (OR = 1.87, p < .05) and history of forcible rape tactics (OR = 3.46, p < .001) were associated with PTSD. History of forcible rape was associated with depression (OR = 3.65, p < .001). Forcible rape tactics were associated with a number of factors that may have contributed to their stronger association with mental health outcomes, including force, injury, lower income, revictimization history, and labeling the event as rape. The results underscore the importance of using a behaviorally specific assessment of rape history, as rape tactic and multiple rape history differentially predicted psychopathology outcomes. The association between drug- or alcohol-facilitated rape tactics and PTSD suggests that these are important rape tactics to include in assessments and future studies.
Cardiac repolarization analysis using the surface electrocardiogram

Sudden cardiac death (SCD) is a challenging health problem in the western world. Analysis of cardiac repolarization from the electrocardiogram (ECG) provides valuable information for stratifying patients according to their risk of suffering from arrhythmic events that could end in SCD, as well as for assessing efficacy of antiarrhythmic therapies. In this paper, we start by exploring the cellular basis of ECG repolarization waveforms under both normal and pathological conditions. We then describe basic preprocessing steps that need to be accomplished on the ECG signal before extracting repolarization indices. A comprehensive review of techniques aimed to characterize spatial or temporal repolarization dispersion is provided, together with a summary of their usefulness for clinical risk stratification. Techniques that describe spatial dispersion of repolarization are based on either differences in repolarization duration or T-wave loop morphology. Techniques that evaluate temporal dispersion of repolarization include the analysis of QT interval adaptation to heart rate changes, QT interval and T-wave variability, and T-wave alternans.
Stability Analysis via Fuzzy Weighting-Dependent Approach for Nonlinear Time-Delay Systems

This paper is concerned with the asymptotic stability for Takagi-Sugeno (T-S) fuzzy systems with interval timevarying delay. By constructing an appropriate type of fuzzy weighting-dependent Lyapunov functional and adopting the free-weighting matrix method, a new delay-dependent stability criterion is derived in terms of linear matrix inequalities(LMIs). Due to the reservation of some useful terms in the derivative of Lyapunov functional and the introduction of some relaxation matrices into the proposed Lyapunovfunctional, the results obtained in this paper may improve the existing ones. The last numerical examples are given to demonstrate the effectiveness of the design procedure.