Miracle-dz/UniFAR-FTUs huggingface dataset:
Observation of Photon Noise by a Parallel-Series Array of Cold-Electron Bolometers

The quasioptical qualification of cold-electron bolometers (CEB) operated in the cross-slot antenna at 350GHz, are presented. The photon noise observation by a parallel/series array of CEBs is demonstrated for power loads of the order of 1 pW. The experimental results have been fitted to theoretical model with two heat-balance equations for the absorber and for superconducting electrodes. The measured noise has been decomposed into several terms with the help of theory. It is demonstrated that the photon noise exceeds any other noise components at some voltage range, that allows us to conclude that the bolometers see the photon noise. A shape of the noise dependence on the bolometer voltage originates from the photonic component according to the theory. In the additional experiment on heating of the sample holder the photonic component is almost absent and the total noise is lower, proving the presence of the photon noise in the first experiment.
A database for degraded Arabic historical manuscripts

Data base is important as it help conducting research more effectively. This paper proposes a database for degraded Arabic historical manuscripts dating to the Islamic and ancient Arabic eras. The documents in the database exhibit different types of degradation such as smears, uneven illumination, contrast variation, blur, deteriorated paper, bleed-through, faded ink or faint characters, and thin or weak text. There are three documents for each type of degradation, and there is a ground truth image of each document for use in later performance measurements and verification. This database aims to facilitate a range of image processing experiments on Arabic degraded documents
The Anopheles gambiae 2La chromosome inversion is associated with susceptibility to Plasmodium falciparum in Africa

Chromosome inversions suppress genetic recombination and establish co-adapted gene complexes, or supergenes. The 2La inversion is a widespread polymorphism in the Anopheles gambiae species complex, the major African mosquito vectors of human malaria. Here we show that alleles of the 2La inversion are associated with natural malaria infection levels in wild-captured vectors from West and East Africa. Mosquitoes carrying the more-susceptible allele (2L+a) are also behaviorally less likely to be found inside houses. Vector control tools that target indoor-resting mosquitoes, such as bednets and insecticides, are currently the cornerstone of malaria control in Africa. Populations with high levels of the 2L+a allele may form reservoirs of persistent outdoor malaria transmission requiring novel measures for surveillance and control. The 2La inversion is a major and previously unappreciated component of the natural malaria transmission system in Africa, influencing both malaria susceptibility and vector behavior. DOI: http://dx.doi. org/10.7554/eLife.25813. 001
Docosahexaenoic Acid-Derived Neuroprotectin D1 Induces Neuronal Survival via Secretase- and PPARγ-Mediated Mechanisms in Alzheimer's Disease Models

Neuroprotectin D1 (NPD1) is a stereoselective mediator derived from the omega-3 essential fatty acid docosahexaenoic acid (DHA) with potent inflammatory resolving and neuroprotective bioactivity. NPD1 reduces Aβ42 peptide release from aging human brain cells and is severely depleted in Alzheimer's disease (AD) brain. Here we further characterize the mechanism of NPD1's neurogenic actions using 3xTg-AD mouse models and human neuronal-glial (HNG) cells in primary culture, either challenged with Aβ42 oligomeric peptide, or transfected with beta amyloid precursor protein (βAPP)sw (Swedish double mutation APP695sw, K595N-M596L). We also show that NPD1 downregulates Aβ42-triggered expression of the pro-inflammatory enzyme cyclooxygenase-2 (COX-2) and of B-94 (a TNF-α-inducible pro-inflammatory element) and apoptosis in HNG cells. Moreover, NPD1 suppresses Aβ42 peptide shedding by down-regulating β-secretase-1 (BACE1) while activating the α-secretase ADAM10 and up-regulating sAPPα, thus shifting the cleavage of βAPP holoenzyme from an amyloidogenic into the non-amyloidogenic pathway. Use of the thiazolidinedione peroxisome proliferator-activated receptor gamma (PPARγ) agonist rosiglitazone, the irreversible PPARγ antagonist GW9662, and overexpressing PPARγ suggests that the NPD1-mediated down-regulation of BACE1 and Aβ42 peptide release is PPARγ-dependent. In conclusion, NPD1 bioactivity potently down regulates inflammatory signaling, amyloidogenic APP cleavage and apoptosis, underscoring the potential of this lipid mediator to rescue human brain cells in early stages of neurodegenerations.
The Effect of TNF-α on Regulatory T Cell Function in Graft-versus-Host Disease

FoxP3+ regulatory T cells (Tregs) are a subset of CD4+ T cells that can suppress proliferation and effector functions of T cells, B cells, NK cells, and antigen-presenting cells. Treg deficiency causes dramatic immunologic disease in both animal models and humans. As they are capable to suppress the function and the proliferation of conventional CD4+ and CD8+ T cells, Treg-based cell therapies are under evaluation for the treatment of various autoimmune diseases and are currently employed to prevent graft-versus-host disease (GvHD) in clinical trials of hematopoietic stem cell transplantation. Even though tumor necrosis factor-α (TNF-α) is well known for its pro-inflammatory role, recent studies show that it promotes Treg activation and suppressive function. In the present review, we discuss the role of TNF-α in Treg function and the possible implications on the actual treatments for immune-mediated diseases, with a particular attention to GvHD.
Task Shifting Routine Inpatient Pediatric HIV Testing Improves Program Outcomes in Urban Malawi: A Retrospective Observational Study

Background This study evaluated two models of routine HIV testing of hospitalized children in a high HIV-prevalence resource-constrained African setting. Both models incorporated “task shifting,” or the allocation of tasks to the least-costly, capable health worker. Methods and Findings Two models were piloted for three months each within the pediatric department of a referral hospital in Lilongwe, Malawi between January 1 and June 30, 2008. Model 1 utilized lay counselors for HIV testing instead of nurses and clinicians. Model 2 further shifted program flow and advocacy responsibilities from counselors to volunteer parents of HIV-infected children, called “patient escorts. ” A retrospective review of data from 6318 hospitalized children offered HIV testing between January-December 2008 was conducted. The pilot quarters of Model 1 and Model 2 were compared, with Model 2 selected to continue after the pilot period. There was a 2-fold increase in patients offered HIV testing with Model 2 compared with Model 1 (43.1% vs 19.9%, p<0.001). Furthermore, patients in Model 2 were younger (17.3 vs 26.7 months, p<0.001) and tested sooner after admission (1.77 vs 2.44 days, p<0.001). There were no differences in test acceptance or enrollment rates into HIV care, and the program trends continued 6 months after the pilot period. Overall, 10244 HIV antibody tests (4779 maternal; 5465 child) and 453 DNA-PCR tests were completed, with 97.8% accepting testing. 19.6% of all mothers (n = 1112) and 8.5% of all children (n = 525) were HIV-infected. Furthermore, 6.5% of children were HIV-exposed (n = 405). Cumulatively, 72.9% (n = 678) of eligible children were evaluated in the hospital by a HIV-trained clinician, and 68.3% (n = 387) successfully enrolled into outpatient HIV care. Conclusions/Significance The strategy presented here, task shifting from lay counselors alone to lay counselors and patient escorts, greatly improved program outcomes while only marginally increasing operational costs. The wider implementation of this strategy could accelerate pediatric HIV care access in high-prevalence settings.
Early versus Delayed Decompression for Traumatic Cervical Spinal Cord Injury: Results of the Surgical Timing in Acute Spinal Cord Injury Study (STASCIS)

Background There is convincing preclinical evidence that early decompression in the setting of spinal cord injury (SCI) improves neurologic outcomes. However, the effect of early surgical decompression in patients with acute SCI remains uncertain. Our objective was to evaluate the relative effectiveness of early (<24 hours after injury) versus late (≥24 hours after injury) decompressive surgery after traumatic cervical SCI. Methods We performed a multicenter, international, prospective cohort study (Surgical Timing in Acute Spinal Cord Injury Study: STASCIS) in adults aged 16–80 with cervical SCI. Enrolment occurred between 2002 and 2009 at 6 North American centers. The primary outcome was ordinal change in ASIA Impairment Scale (AIS) grade at 6 months follow-up. Secondary outcomes included assessments of complications rates and mortality. Findings A total of 313 patients with acute cervical SCI were enrolled. Of these, 182 underwent early surgery, at a mean of 14.2(±5.4) hours, with the remaining 131 having late surgery, at a mean of 48.3(±29.3) hours. Of the 222 patients with follow-up available at 6 months post injury, 19.8% of patients undergoing early surgery showed a ≥2 grade improvement in AIS compared to 8.8% in the late decompression group (OR = 2.57, 95% CI:1.11,5.97). In the multivariate analysis, adjusted for preoperative neurological status and steroid administration, the odds of at least a 2 grade AIS improvement were 2.8 times higher amongst those who underwent early surgery as compared to those who underwent late surgery (OR = 2.83, 95% CI:1.10,7.28). During the 30 day post injury period, there was 1 mortality in both of the surgical groups. Complications occurred in 24.2% of early surgery patients and 30.5% of late surgery patients (p = 0.21). Conclusion Decompression prior to 24 hours after SCI can be performed safely and is associated with improved neurologic outcome, defined as at least a 2 grade AIS improvement at 6 months follow-up.
Emotion Co-referencing - Emotional Expression, Holder, and Topic

The present approach aims to identify the emotional expression, holder, topic, and their co-reference from Bengali blog sentences. Two techniques are employed, one is a rule-based baseline system and the other is a supervised system that consists of different syntactic, semantic, rhetorical, and overlapping features. Different error cases have been resolved using rule-based post processing techniques. The evaluative vectors containing emotional expressions, holders, and topics are prepared from annotated blog posts as well as from system generated output. The evaluation metric, Krippendorff's α, achieves agreement scores of 0.53 and 0.67 for the baseline and supervised co-reference classification systems, respectively.
Reliability and Validity of the Dutch Version of the Brief Infant-Toddler Social and Emotional Assessment (BITSEA)

Background The Brief Infant-Toddler Social and Emotional Assessment (BITSEA) is a relatively new and short (42-item) questionnaire that measures psychosocial problems in toddlers and consists of a Problem and a Competence scale. In this study the reliability and validity of the Dutch version of the BITSEA were examined for the whole group and for gender and ethnicity subgroups. Methods Parents of 7140 two-year-old children were invited in the study, of which 3170 (44.4%) parents completed the BITSEA. For evaluation of the score distribution, the presence of floor/ceiling effects was determined. The internal consistency (Cronbach's alpha) was evaluated and in subsamples the test-retest, parent-childcare provider interrater reliability and concurrent validity with regard to the Child Behavioral Checklist (CBCL). Discriminative validity was evaluated by comparing scores of parents that worry and parents that do not worry about their child's development. Results The BITSEA showed no floor or ceiling effects. Psychometric properties of the BITSEA Problem and Competence scale were respectively: Cronbach's alphas were 0.76 and 0.63. Test-retest correlations were 0.75 and 0.61. Interrater reliability correlations were 0.30 and 0.17. Concurrent validity was as hypothesised. The BITSEA was able to discriminate between parents that worry about their child and parents that do not worry. The psychometric properties of the BITSEA were comparable across gender and ethnic background. Conclusion The results in this large-scale study of a diverse sample support the reliability and validity of the BITSEA Problem scale. The BITSEA Competence scale needs further study. The performance of the BITSEA appears to be similar in subgroups by gender and ethnic background.
Distributed spectrum trading via dynamic matching with evolving preferences

Spectrum trading benefits both primary users (PUs) and secondary users (SUs), while centralized spectrum trading designs need designated spectrum trader, incur extra control cost, and may miss lots of instantaneous spectrum trading opportunities. In this paper, a novel distributed frequency reuse based opportunistic spectrum trading (D-FRONT) scheme is proposed to further improve spectrum utilization, provide more accessing opportunities for SUs, and increase the revenues of PUs. Conflict graph is employed to characterize the SUs' co-channel and radio interferences. Based on the interference relationship, we formulate a centralized PUs' revenue maximization problem under multiple wireless transmission constraints. Due to the NP-hardness to solve the problem and no-existence of centralized trading entity, we develop the D-FRONT algorithms based on dynamic matching with evolving preferences. Through extensive simulations, we show that the proposed D-FRONT algorithm out-performs other distributed spectrum trading algorithms without considering spectrum reuse, yields results close to the centralized optimal one, and is effective in increasing PUs' revenue and improving spectrum utilization.
The Design, Deployment, and Analysis of SignetLab: A Sensor Network Testbed and Interactive Management Tool

The emergence of small, inexpensive, network-capable sensing devices led to a great deal of research on the design and implementation of sensor networks. A critical step in taking protocols from theory to actual deployment is comprehensive testing on physical sensor networks. Sensor network testbeds provide one way to facilitate such testing without requiring the deployment of a specialized sensor network for each protocol. However, for such testbeds to be useful, they must not overwhelm researchers with maintenance tasks and high learning curves. Previous work in testbed design has primarily focused on creating interfaces to maximize their usage by convenient scheduling of jobs and output access. In this work, we present two contributions to sensor network testbed design. The first is a unique management tool that allows users to program, interact with, and receive data from nodes in the network, filling a gap in current testbed management solutions. The second is the design, deployment, and analysis of the SignetLab testbed. The analysis of the testbed and its results provide quantitative measurements of the impact of physical deployment on signal propagation characteristics. Additionally, we present two case studies where researchers have used the testbed and discuss the user experiences and lessons learned.
Reducing the Power Consumption of Fault Tolerant Registers Through Hybrid Protection

Soft errors produced by radiation events can cause malfunctions in modern day electronics. To preserve the system functionality, its elements must be protected against the effects of these events. Two of the possible techniques usually employed to implement fault tolerant registers are triple modular redundancy (TMR) and single error correcting (SEC) codes. However, the use of these techniques increases circuit area, timing, and power consumption to different extents. In this paper, we study the influence of each of these approaches on the circuit when they are implemented in application-specific integrated circuits and, based on the results, present some guidelines to choose between both of them depending on the design requirements. Additionally, we present a new low power fault tolerant technique destined for registers in which a subset of bits have a lower switching activity than the rest. This approach is based on the idea of combining TMR and SEC codes within a register to implement a hybrid protection that can exploit the strengths of each of the techniques. Our results show that the use of this technique achieves both power and area savings with respect to TMR in most cases, whereas it achieves large power savings with respect to SEC codes at the cost of increasing the area overhead.
Efficacy of adalimumab in patients with Crohn's disease and failure to infliximab therapy: a clinical series.

BACKGROUND adalimumab, a human anti-TNF, is an effective induction and maintenance therapy for patients with moderate to severe Crohn's disease. It seems to be effective in patients with resistance to infliximab, too, though the experience is more limited. AIM to evaluate the efficacy of adalimumab, in patients with Crohn's disease (CD) and failure to previous treatment with infliximab. METHODS twenty-five patients with CD and failure to previous treatment with infliximab were enrolled; they were treated with 160/80 (24 patients) and 80/40 (1 patient) induction doses. We analyze clinical response to treatment with adalimumab by the Crohn's disease Activity Index (CDAI) and plasma concentration of C-reactive protein (CRP), steroid sparing and complete fistula closure at week 48. RESULTS eighteen out of twenty-five patients (72%) achieved clinical remission (CDAI score < 150) at week 24 and 15/25 (60%) patients at week 48. There was a statistically significant difference(p < 0.01) in CRP serum levels from 21 to 8 mg/dl at week 48.Nine out of fifteen patients (60%) treated with corticosteroids were able to discontinue steroids. Three out of eleven patients (27%) with fistulizing Crohn's disease had complete fistula closure after the treatment. Seventy two percent of the patients (18/25) needed to increase adalimumab to weekly dose, in order to maintain clinical response. Five out of twenty-five patients (20%) had adverse events; two of them (8%) with serious adverse events (tuberculous meningitis and abdominal abscess) that forced the withdrawal of treatment. CONCLUSIONS according to these data, adalimumab provides a clinical and analytical improvement in patients with CD and failure to previous therapy with infliximab.
Noncanonical regulation of insulin-mediated ERK activation by phosphoinositide 3-kinase γ

Classically, Class IB phosphoinositide 3-kinase (PI3Kγ) plays a role in ERK activation following G-protein–coupled receptor (GPCR) activation. Here we show that PI3Kγ noncanonically regulates ERK phosphorylation in a kinase-independent mechanism, irrespective of the upstream signals. PI3Kγ sequesters PP2A, allowing sustained ERK function.
Single-cell RNA-sequencing: The future of genome biology is now

ABSTRACT Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis.
Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

Background The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed ‘-omics’ techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. Methodology The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. Conclusions We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.
Electronic properties of DNA Written presentation for seminar II course

This seminar shortly reviews basic properties of DNA molecule in the beginning in order to understand the foundations of electronic conduction. It describes why and how DNA conducts charge carriers. I shall develop a simple model to show how π–π coupling influences the complex DNA conduction behavior. Two conduction mechanisms will be explained on rather empirical level. I will also try to find the background for such a variety of amazingly different experimental outcomes. A short review of experiment is covered at the end of the seminar.